@article {pmid42291329, year = {2026}, author = {Zeng, Y and Jiang, Y and Huang, Y and Yin, S and Yang, Z and Zhang, F}, title = {The dialogue between breast cancer and microorganisms.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1738739}, pmid = {42291329}, issn = {2235-2988}, mesh = {Humans ; *Breast Neoplasms/microbiology/pathology/therapy ; Female ; Tumor Microenvironment ; *Microbiota ; Animals ; Dysbiosis ; Cell Transformation, Neoplastic ; Estrogens/metabolism ; }, abstract = {Breast cancer is a complex pathological process involving multiple factors and stages, characterized by pronounced molecular and phenotypic heterogeneity. Its global incidence and mortality rates have shown a continuous upward trend. With the advancement of microbiome research, microbial communities have been recognized as key determinants influencing host health and disease states. Increasing evidence suggests a close association between breast tissue-resident and systemic microbiota and the initiation and progression of breast cancer. Specifically, microorganisms may be associated with abnormal proliferation and malignant transformation of mammary epithelial cells through diverse mechanisms, including the modulation of estrogen metabolism, production of bioactive metabolites, induction of chronic inflammation, and remodeling of the tumor microenvironment. In addition, certain microbes may directly interact with host cells, potentially inducing DNA damage and contributing to the transition from normal to malignant phenotypes. This review systematically summarizes the origins and compositional characteristics of the breast microbiota, with a particular focus on current evidence regarding its roles in breast cancer initiation, progression, metastasis, therapeutic response, and prognosis. Currently, the majority of evidence originates from cross-sectional studies and in vitro/in vivo model, to better evaluate the current evidence, the limitations of different research designs and the levels of evidence are summarized in Table 1, aiming to provide new theoretical insights and research perspectives for microbiota-based strategies in breast cancer diagnosis and therapy.}, }
@article {pmid42291330, year = {2026}, author = {Arishi, RA and Cheema, AS and McEachran, JL and Gridneva, Z and Vlaskovsky, P and Norrish, I and Bilston-John, SH and Zhou, X and Lai, CT and Payne, MS and Geddes, DT and Stinson, LF}, title = {Concentrations of selected human milk components influence the infant oral microbiome to a greater degree than estimated intakes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1765736}, pmid = {42291330}, issn = {2235-2988}, mesh = {Humans ; *Milk, Human/chemistry ; Infant ; *Microbiota ; Female ; *Mouth/microbiology ; Breast Feeding ; Lactose/analysis ; RNA, Ribosomal, 16S/genetics ; Australia ; Male ; Micronutrients/analysis ; Adult ; }, abstract = {BACKGROUND: Human milk is characterised by its complex composition, consisting of nutrient and bioactive components that play a crucial role in infant health. Although the infant oral cavity is directly exposed to these components during breastfeeding, their effects on the developing oral microbiome remains underexplored. This study aimed to assess associations between the concentrations and daily estimated intakes of human milk components (including minerals, lactose, and antimicrobial proteins) and the oral microbiome of exclusively breastfed infants.<br><br>METHODS: We profiled infant oral samples collected at 3 months of age using full-length 16S rRNA gene sequencing, alongside paired analyses of human milk components from 45 mother-infant dyads in the Western Australian BLOSOM cohort. Concentrations of milk lactose, antimicrobial proteins (AMPs), and micronutrients (16 components in total) were measured, and their daily estimated intakes were calculated based on 24-hour milk intake.<br><br>RESULTS: The composition of the infant oral microbiome was significantly associated with a number of AMPs and micronutrients, with concentration exerting a far stronger effect than estimated intakes. Lactose, the major sugar in human milk, was not associated with any feature of the infant oral microbiome. Both concentrations and estimated intakes of lactoferrin (P&#xa0;=&#xa0;0.032 and P&#xa0;=&#xa0;0.005, respectively), as well as estimated intakes of sodium and iodine (P&#xa0;=&#xa0;0.041 and 0.022, respectively) were negatively associated with infant oral Shannon diversity. While some associations were consistent when both estimated intakes and concentrations were analysed, some appeared only in one analysis, suggesting differing mechanisms of action.<br><br>CONCLUSION: These findings underscore the influence of human milk composition on the developing oral microbiome during early life, highlighting that local, concentration-driven mechanisms are the primary drivers of these effects.}, }
@article {pmid42291363, year = {2026}, author = {Trachu, N and Sensorn, I and Khiewngam, K and Monnamo, N and Chantratita, W and Sirachainan, E and Reungwetwattana, T and Oranratnachai, S}, title = {Gut microbiome in advanced non-small cell lung cancer: effect of chemotherapy and impact on efficacy.}, journal = {Translational lung cancer research}, volume = {15}, number = {5}, pages = {127}, pmid = {42291363}, issn = {2218-6751}, abstract = {BACKGROUND: While evidence linking the gut microbiome (GM) to cancer immunotherapy is growing, data regarding its role in chemotherapy remains limited. This study aims to investigate the effect of chemotherapy on GM composition and its potential as a predictive biomarker for treatment outcomes in advanced non-small cell lung cancer (NSCLC).<br><br>METHODS: Advanced NSCLC patients treated with chemotherapy at Ramathibodi Hospital were prospectively enrolled. Clinical data and stool samples were collected at three time points: baseline, post-evaluation, and at progression of disease (PD). Fecal bacterial DNA was extracted, followed by PacBio Sequel II sequencing and comprehensive bioinformatic analysis. Clinical data were summarized using descriptive statistics. Progression-free survival (PFS) and overall survival (OS) were estimated by the Kaplan-Meier method, and predictive factors were identified using Cox-regression analysis.<br><br>RESULTS: This study analyzed 54 stool samples from 27 NSCLC patients treated with platinum-doublet chemotherapy. The median PFS and OS were 5.3 months [95% confidence interval (CI): 2.4-8.4] and 13.8 months (95% CI: 5.2-not reached), respectively. Post-chemotherapy changes (n=20 paired samples) showed a significant decrease in microbial richness, as evidenced by reduced abundance-based coverage estimator (ACE) (P=0.02) and Chao1 (P=0.03) alpha diversity indices. Taxonomically, the relative abundance of Enterobacter was significantly decreased post-chemotherapy (P=0.03). Regarding treatment response (n=26 evaluable patients; 13 PD, 13 clinical benefit), baseline alpha diversity was not predictive of outcome. However, the relative abundance of Akkermansia was notably higher in the clinical benefit group, approaching statistical significance (P=0.07).<br><br>CONCLUSIONS: Chemotherapy significantly reduced GM by decreasing species richness (as measured by the ACE and Chao1 index), while species diversity (as measured by the Shannon and Simpson index) remained unchanged. Therefore, confirming the definitive role of the GM as a predictive biomarker in chemotherapy-treated NSCLC patients necessitates further investigation in a larger, more robustly powered cohort.}, }
@article {pmid42291470, year = {2026}, author = {Agzamova, SA and Babadjanova, FR}, title = {Gut Microbiome and Short-Chain Fatty Acid Alterations After Cardiopulmonary Bypass are Associated with Nutritional and Functional Impairment in Young Children with Congenital Heart Defects.}, journal = {Clinical and experimental gastroenterology}, volume = {19}, number = {}, pages = {600414}, pmid = {42291470}, issn = {1178-7023}, abstract = {BACKGROUND: Cardiac surgery with cardiopulmonary bypass (CPB) in young children is associated with systemic stress, gastrointestinal dysfunction, and impaired nutritional recovery. The role of gut microbiome disruption and short-chain fatty acid (SCFA) metabolism in these processes remains insufficiently studied.<br><br>OBJECTIVE: To evaluate changes in gut microbiome composition, SCFA profiles, and nutritional status in children aged 0-3 years after CPB, and to assess their association with postoperative feeding intolerance and impaired growth.<br><br>METHODS: This prospective observational study included 20 children undergoing cardiac surgery with CPB. Stool samples were collected preoperatively and during the early postoperative period. Microbiota composition was assessed using culture-based microbiological methods, and fecal SCFA concentrations were measured by gas chromatography. Clinical, anthropometric, and laboratory parameters were assessed, and their associations with CPB characteristics and microbiome alterations were analyzed.<br><br>RESULTS: The postoperative period was characterized by significant intestinal dysbiosis, including reduced abundance of beneficial bacteria (Bifidobacterium, Lactobacillus, Bacteroides) and decreased SCFA-producing taxa. Fecal butyrate and propionate levels were significantly reduced. These changes were associated with increased intestinal inflammation, feeding intolerance, impaired nutrient absorption, and insufficient weight gain. The severity of dysbiosis correlated with CPB duration.<br><br>CONCLUSION: CPB in early childhood is associated with disruption of gut microbiota and reduced SCFA production, which are linked to postoperative feeding intolerance and impaired nutritional recovery. Targeted monitoring and modulation of the gut microbiome may improve clinical outcomes in pediatric cardiac surgery patients.}, }
@article {pmid42291758, year = {2026}, author = {Zhang, S and Shoaie, S and Carpenter, GH}, title = {Suprathreshold non-volatile flavour perception is associated with multiple species rather than any single species via bacterial metabolism.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2686537}, pmid = {42291758}, issn = {2000-2297}, abstract = {BACKGROUND: The microbiome is the characteristic microbial community inhabiting a well-defined habitat with distinct physicochemical properties. During eating, food is masticated and mixed with saliva to form a bolus; non-volatile flavour molecules are released into the saliva and delivered to receptors on the tongue. Throughout this process, the oral microbiome is in direct contact with non-volatile flavour molecules. In this cross-sectional study, we hypothesised that the oral microbiome interacts with non-volatile flavour molecules to modulate suprathreshold taste perception.<br><br>MATERIALS AND METHODS: Fifty-three participants were included, with suprathreshold sensory data, salivary microbiome data (including both taxonomic and functional profiles), and salivary metabolome data. Associations were explored using fixed-effects linear-regression models and unsupervised clustering.<br><br>RESULTS: Suprathreshold non-volatile flavour perception was associated with the salivary microbiome via multispecies interactions rather than single-species effects. Taurine (an amino acid and confirmed bacterial metabolite) and ethanolamine (a phospholipid-related metabolite and confirmed bacterial metabolite) showed the greatest number of associations with suprathreshold taste perception in this study (6 of 8 sensory solution each).<br><br>CONCLUSION: This study suggested that suprathreshold taste perception was associated with inferred microbial metabolic pathways via multispecies interactions. Because inferred microbial metabolic pathways are encoded by multiple bacteria, they may better capture multispecies contributions than species-level taxonomic profiles.}, }
@article {pmid42291953, year = {2026}, author = {Finlayson, CR and Hansen, NM and Stewart, S and Smith, M}, title = {Aetiology and Management of Acute Septic Arthritis and Prosthetic Joint Infection Presentations to Orthopaedics: An Evaluation of Tertiary Centre Performance.}, journal = {Cureus}, volume = {18}, number = {5}, pages = {e108830}, pmid = {42291953}, issn = {2168-8184}, abstract = {Background Septic arthritis (SA) and prosthetic joint infection (PJI) are common emergency referrals to orthopaedics in the United Kingdom. These infections carry a significant risk of harm due to chondrolysis and arthropathy and are a potential source of sepsis, requiring prompt assessment, investigation, and treatment. A joint aspirate is routinely sent for microscopy, culture , and sensitivities to aid treatment. In suspected PJI, this must be taken under sterile conditions to reduce the risk of iatrogenic PJI. Empirical antibiotics should then commence per the British National Formulary (BNF) or local policy. Due to the risks of delayed or ineffective treatment, evaluating local practice may identify areas to optimise treatment delivery and efficacy. Aims This study will evaluate the incidence of SA and PJI within a tertiary orthopaedic centre over 12 months. The culprit organisms and sensitivities, delivery of timely and appropriate antibiotics, serum infection markers, length of stay (LOS), and mortality will be reviewed. Methods Admissions to the orthopaedic unit between November 2023 and October 2024 were screened using the ICD-10 codes for pyogenic arthritis, prosthesis infection, or infection following a procedure. Further review confirmed cases of SA or PJI, excluding unsuitable admissions. Each patient's electronic record was examined for demographics, serum infection markers, LOS, 30-day mortality, relevant imaging, time to aspirate relative to admission, culture results, and timing and type of antibiotics initiated. Antibiotics used were compared to sensitivities and BNF recommendations to determine efficacy. Results A total of 27 admissions with SA and 24 of PJI were seen, accounting for 51 (1.9%) of 2,670 total admissions, relative to a mean annual arthroplasty incidence of 1,204 across the health board. The median age of PJI patients was 72 years, significantly higher than the median SA patient age of 52 years (p<0.01). Median LOS was also higher in PJI patients at 13.5 days compared to nine days in SA (p=0.036). Most infections were hip and knee joints at nine (33.3%) cases in SA, and 11 (45.8%) total knee replacements in PJI cohorts. Staphylococcus aureus was the most prevalent organism in each group; however, 11 (40.7%) of the SA aspirate cultures were negative. The median aspiration time, relative to admission, was 5.6 and 10.2 hours in SA and PJI, respectively. The median time to initiate antibiotics was 7.1 and 17.9 hours in SA and PJI, respectively. The majority of admissions received appropriate antibiotics at 20 (74.1%) of SA and 17 (70.8%) of PJI patients. Culture results confirmed sensitivity to recommended antibiotics in 14 (51.8%) of SA and 18 (75%) of PJI cases. The most initiated antibiotic overall was flucloxacillin. There was no significant difference in infection markers. Conclusion This study finds that PJI patients were typically older, with a greater LOS and comorbidity. Large joint infections, such as hips and knees, were the commonest presentation. The majority of each cohort was appropriately treated per the BNF, with S. aureus being the commonest cause. Factors such as prehospital antibiotics may reduce the bacterial yield of aspirations. Both groups show prolonged time taken to aspirate and treat, in which quality improvement interventions may reduce. Other centres may benefit from similar evaluations of the infective microbiome and the speed and efficacy of septic joint treatment.}, }
@article {pmid42292075, year = {2026}, author = {Beattie McAliley, R and Hooper, L and Hoss, K and Vigerust, DJ}, title = {Test, Treat, Repopulate™ method reduces red complex bacteria and stabilizes the oral microbiome.}, journal = {Frontiers in dental medicine}, volume = {7}, number = {}, pages = {1839034}, pmid = {42292075}, issn = {2673-4915}, abstract = {Despite advances in dental hygiene and clinical interventions, preventable conditions such as tooth decay and gum disease remain widespread public health concerns. Recent research implicates complex, polymicrobial interactions as central drivers of disease pathogenesis, which often limits the effectiveness of traditional therapeutic approaches. Here, researchers evaluate the effectiveness of the Test, Treat, Repopulate method, a multi-phase oral health protocol combining scaling and root planing, targeted antibiotic therapy, use of a pH-balanced, prebiotic containing toothpaste and rinse, and daily oral probiotic use on the health of the oral microbiome. Retrospective analysis of RT-qPCR salivary diagnostic data from 38 de-identified U.S. patients, collected before and after treatment during routine care, demonstrated significant and sustained reductions in key oral pathogens following the combined treatment approach. Seven bacterial species were significantly reduced post-treatment, including Treponema denticola, Tannerella forsythia, Prevotella intermedia, Campylobacter rectus, Fusobacterium nucleatum, Fusobacterium nucleatum subsp. animalis, and Streptococcus mutans. Additional pathogens, including Aggregatibacter actinomycetemcomitans and Porphyromonas gingivalis, were also reduced. The protocol had minimal impact on the fungal species Candida albicans, highlighting an area for potential optimization. Additionally, four viral targets were assessed pre- and post-protocol, making this one of the first studies to evaluate a dental intervention's effects on oral viruses. Comparison of the cohort with 35,570 pre-treatment salivary diagnostic tests across the United States shows that baseline pathogen distributions reflect national patterns, supporting the generalizability of the protocol. A structured protocol for patients with elevated red complex bacteria is detailed, providing clinicians with a data-driven, reproducible framework for precision oral healthcare. These findings underscore the potential for microbiome-focused interventions to achieve measurable, lasting improvements in oral health across diverse populations.}, }
@article {pmid42292333, year = {2026}, author = {Reynolds, A and Glenn, E and Lavoie, B and Ishaq, SL and Li, Y}, title = {Plant-derived bioactives, the gut-brain axis, and neurodegenerative diseases: mechanistic roles of diet-microbiota interactions.}, journal = {Frontiers in neuroscience}, volume = {20}, number = {}, pages = {1815972}, pmid = {42292333}, issn = {1662-4548}, abstract = {Diet is increasingly recognized as a potential upstream modulator of the gut-brain axis (GBA) through its effects on the microbiome, microbial metabolites, and host immune and endocrine responses. The GBA is a complex, bidirectional network connecting the gastrointestinal tract and central nervous system, with diet influencing microbial community structure and metabolic output. Plant-based diets, such as Mediterranean and MIND, have been associated with increased production of anti-inflammatory microbial metabolites and improved barrier function, while high calorie/low nutrient diets are often linked to increased immune activation and barrier dysfunction. However, while microbial metabolites, especially short-chain fatty acids, indoles, bile acids, and isothiocyanates, have been proposed as mediators of neuroprotective effects, their role in neurodegenerative diseases remains an area of active investigation, with evidence largely derived from preclinical and associative human studies. Cruciferous vegetables, especially broccoli sprouts, are an emerging focus of research for their bioactive compound sulforaphane, which activates Nrf2-centered cytoprotective pathways. Animal and early human studies suggest sulforaphane can improve cognitive and behavioral outcomes, though larger clinical trials are needed. Personalized, microbiota-targeted dietary interventions may offer scalable strategies for managing neuroinflammatory and neurodegenerative conditions, and we emphasize the need for integrated research across diet, microbiome, and brain health.}, }
@article {pmid42292359, year = {2026}, author = {Zhang, Y and Qin, Y and Cheng, Z}, title = {Innate immune regulation of adaptive immunity: mechanisms, implications, and bias.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1847470}, pmid = {42292359}, issn = {1664-3224}, mesh = {Humans ; *Immunity, Innate ; *Adaptive Immunity ; Animals ; Signal Transduction ; Hypersensitivity/immunology ; Trained Immunity ; Epigenesis, Genetic ; Immune Tolerance ; }, abstract = {Innate immunity is not merely an early defensive system but a key regulator of adaptive immune fate. Through pattern-recognition receptor signaling, antigen presentation, cytokine production, and metabolic-epigenetic reprogramming, innate immune responses shape the strength, duration, and direction of T- and B-cell immunity. This review summarizes how innate immune regulation of adaptive immunity contributes to immune dysregulation in infection, autoimmunity, and allergic disease. We focus on three major mechanisms: remodeling of antigen presentation and costimulation, reshaping of cytokine microenvironments that guide T helper cell polarization, and metabolic-epigenetic programming associated with trained immunity or immune tolerance. We further propose that disease outcomes can be interpreted through three regulatory dimensions of innate immune signaling: insufficient signal strength promotes defective pathogen control and weak adaptive priming; persistent or excessive activation sustains autoimmune inflammation and loss of tolerance; and type 2-biased epithelial-innate signaling drives allergic inflammation through the alarmin-ILC2-Th2-IgE axis. By integrating molecular signaling, innate immune cell crosstalk, metabolic regulation, and epigenetic remodeling, this review provides a concise framework for understanding how innate immune imbalance shapes adaptive immune dysfunction and highlights therapeutic opportunities targeting interferon pathways, inflammasomes, epithelial alarmins, metabolic programs, and microbiome-related immune regulation.}, }
@article {pmid42292378, year = {2026}, author = {Gargaro, M and Fallarino, F and Zelante, T}, title = {Editorial: Host-microbe immunometabolic chat: a new era of organismal communication.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1882702}, doi = {10.3389/fimmu.2026.1882702}, pmid = {42292378}, issn = {1664-3224}, }
@article {pmid42292405, year = {2026}, author = {Xiao, J and Duan, L and Yang, J and Deng, Y and Pang, S and Wang, H and Yin, X and Wang, H and Qiu, Y and Li, X and Gong, Y and Li, H}, title = {The landscape of cellular immune alteration in systemic lupus erythematosus.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1755310}, pmid = {42292405}, issn = {1664-3224}, mesh = {Humans ; *Lupus Erythematosus, Systemic/immunology/metabolism/therapy ; Animals ; *Immunity, Cellular ; Dysbiosis/immunology ; Gastrointestinal Microbiome/immunology ; Autoantibodies/immunology ; }, abstract = {Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by multi-organ inflammation and profound immune dysregulation. Aberrant interactions among adaptive and innate immune cells-including T cells, B cells, dendritic cells, macrophages, neutrophils, and natural killer cells-disrupt immune tolerance and perpetuate chronic inflammation. This review provides a comprehensive overview of the dysfunctional cellular immune landscape in SLE, focusing on the pathogenic crosstalk among immune cell subsets and its contribution to disease progression. We highlight the imbalance of T cell subsets (Th1, Th17, Tfh, Treg), B cell hyperactivation, and impaired regulatory cell function. Furthermore, we discuss how excessive NETosis, type I interferon signaling, and impaired apoptotic clearance amplify autoantibody production and immune complex-mediated injury. Emerging evidence positions gut microbiome dysbiosis as a critical environmental driver of immune dysregulation in SLE, characterized by depletion of beneficial butyrate-producing commensals and enrichment of pro-inflammatory taxa. This dysbiosis contributes to disease pathogenesis through gut barrier dysfunction, molecular mimicry, and short-chain fatty acid deficiency. Finally, we examine potential therapeutic strategies, including immune checkpoint modulation, metabolic interventions, and novel cellular therapies, aimed at restoring immune equilibrium in SLE.}, }
@article {pmid42292406, year = {2026}, author = {Sun, B and Wang, T}, title = {The microbiota-metabolite-immune axis in colorectal cancer: mechanistic insights and emerging clinical applications.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1768792}, pmid = {42292406}, issn = {1664-3224}, mesh = {Humans ; *Colorectal Neoplasms/immunology/metabolism/microbiology/etiology ; *Gastrointestinal Microbiome/immunology ; Animals ; Tumor Microenvironment/immunology ; Dysbiosis/immunology ; Signal Transduction ; }, abstract = {Colorectal cancer (CRC) results from a complex interplay of host genetics, environmental factors, and gut microbiota. Increasing evidence suggests that intestinal microorganisms significantly affect the initiation and progression of CRC through metabolic and immunological reprogramming. Dysbiosis, defined as an imbalance between beneficial and harmful microbial species, leads to chronic inflammation, genotoxic stress, and disruption of epithelial homeostasis. Microbial metabolites, such as short-chain fatty acids, secondary bile acids, and tryptophan derivatives, function as signaling molecules that influence epithelial proliferation, apoptosis, and immune cell activity. These metabolites regulate essential oncogenic and inflammatory pathways, including Wnt/β-catenin, NF-κB, and STAT3, and alter the tumor microenvironment by affecting regulatory T cells (Tregs), Th17 cells, macrophages, and myeloid-derived suppressor cells. Specific bacteria, such as Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, and colibactin-producing Escherichia coli, illustrate how particular microbes can promote tumorigenesis through metabolite-mediated signaling and immune modulation. This review summarizes recent advances in understanding how gut microbiota and their metabolites contribute to colorectal carcinogenesis by influencing inflammatory signaling, epithelial homeostasis, and tumor immune responses. These mechanistic insights highlight the microbiota-metabolite-immune axis as a crucial driver of CRC initiation and progression. The increasing recognition that microbial alterations occur alongside early neoplastic changes and affect tumor behavior emphasizes their translational potential. Although further validation in large, well-controlled clinical settings is necessary, microbiome- and metabolite-based markers could enhance current strategies for the early detection, risk assessment, and therapeutic guidance of CRC. Ultimately, deepening our understanding of the intricate interactions between intestinal microbes, host metabolism, and immune regulation will facilitate the development of microbiome-informed approaches for CRC monitoring and intervention in the future.}, }
@article {pmid42292417, year = {2026}, author = {Wang, Y and Dong, C and Xiao, Y}, title = {Polystyrene nanoplastics promotes inflammation and aging in young mice through the oral-gut microbiome axis.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1806158}, pmid = {42292417}, issn = {1664-3224}, mesh = {Animals ; *Polystyrenes/toxicity/adverse effects ; *Aging/drug effects/immunology ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Inflammation/chemically induced/metabolism ; Cytokines/metabolism ; Mice, Inbred C57BL ; Male ; *Microplastics ; *Nanoparticles/toxicity ; *Mouth/microbiology ; Inflammation Mediators/metabolism ; Dysbiosis/chemically induced ; Cellular Senescence/drug effects ; }, abstract = {With the escalating global pollution of nanoplastics, their impacts on organismal health have become a focal concern. The oral-gut microbiota axis plays a pivotal role in host health regulation, yet how nanoplastics influence this axis and drive inflammation and aging in young organisms remain undefined. This study aimed to investigate whether polystyrene nanoplastics (PS-NPs) promote inflammation and aging in young mice by disrupting the oral-gut microbiota axis. Therefore, we established a free-feeding model with 1000 μg/L PS-NPs using 8-week-old C57BL/6 mice. We quantified tissue inflammatory cytokines and cellular senescence markers to assess PS-NPs-induced inflammatory and aging effects, while 16S rRNA sequencing was employed to characterize oral and gut microbiota structural changes. We found that PS-NPs exposure significantly increased the expression levels of cellular senescence markers p21[Cip1/Waf] and p16[Ink4a] in lung and liver. Meanwhile, PS-NPs promoted the release of inflammatory cytokines such as IL-1β, IL-6 and TNF-α, by modulating the p38 MAPK pathway. In addition, PS-NPs also decreased the expression levels of antioxidant genes. Furthermore, 16S rRNA sequencing analysis revealed that PS-NPs exposure caused dysbiosis in oral and intestinal microbiota, manifested as significant alterations in microbial diversity and community structure. Our work provided mechanistic insights into nanoplastic toxicity and theoretical basis for developing preventive strategies.}, }
@article {pmid42292476, year = {2026}, author = {Zhou, Y and Li, Z and Chu, Y and Zhou, Z and Zhang, T and Yi, N and Sun, W and Yan, J and Yan, Z and Zhu, A}, title = {Reframing precision nutrition in irritable bowel syndrome: a mechanism-informed conceptual framework for responder prediction and clinical translation.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1809221}, pmid = {42292476}, issn = {1664-3224}, mesh = {Humans ; *Irritable Bowel Syndrome/diet therapy/microbiology/metabolism ; *Gastrointestinal Microbiome ; FODMAP Diet ; *Precision Medicine/methods ; Multiomics ; Translational Research, Biomedical ; }, abstract = {BACKGROUND: The low-Fermentable Oligosaccharides, Disaccharides, Monosaccharides and Polyols (FODMAP) diet is widely used for irritable bowel syndrome (IBS), but response varies markedly across patients. This heterogeneity has shifted the field from testing average efficacy toward forecasting individual benefit and translating microbiome science into practical precision-nutrition tools.<br><br>METHODS: We present a conceptual analysis grounded in evidence mapping from human IBS studies that paired dietary interventions (primarily low-FODMAP pathways) with baseline microbiome and/or multi-omics measurements. Findings are organized within a "microbiome-to-model" roadmap that specifies responder endpoints, candidate data layers (taxa, functions, metabolites and volatile signatures), modeling choices, and the validation and implementation requirements needed for clinical decision support.<br><br>RESULTS: Three recurring signals emerge across cohorts. Baseline microbial ecology can stratify response, but taxonomic features alone often fail to transport across studies. Functional readouts, including metabolites and volatile signatures, are closer to symptom mechanisms and can improve interpretability; however, clinical deployment is still limited by endpoint heterogeneity, imperfect exposure and adherence measurement, batch effects, and insufficient external validation and calibration.<br><br>CONCLUSION: IBS is well suited for microbiome-informed responder prediction, provided that models are developed with deployment in mind. Progress will depend on validation-first study designs, harmonized responder endpoints and adherence capture, robust multi-omics pipelines, and biologically interpretable decision rules that can be prospectively tested and monitored for temporal instability in real-world care.}, }
@article {pmid42292489, year = {2026}, author = {Zhang, L and Gu, Y and Deng, R and Ouyang, Y}, title = {Dual role of IL-17A in COPD: amplifier of inflammatory cascades and mediator of airway remodeling and alveolar destruction.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1828172}, pmid = {42292489}, issn = {1664-3224}, mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/immunology/pathology/metabolism/drug therapy ; *Interleukin-17/metabolism/immunology ; *Airway Remodeling/immunology ; Animals ; Signal Transduction ; Inflammation/immunology ; *Pulmonary Alveoli/pathology/immunology ; }, abstract = {Corticosteroid resistance remains a central challenge in managing chronic obstructive pulmonary disease (COPD). This refractory phenotype is primarily driven by persistent, neutrophil-dominated airway inflammation. Interleukin-17A (IL-17A) bridges innate and adaptive immunity and helps sustain this refractory inflammation, although it operates within a redundant cytokine network and its pathogenic contribution is clearest in a defined molecular subset of patients. Following an overview of upstream drivers including lung-gut microbiome dysbiosis and Th17/Treg immune imbalance, the downstream effector network of IL-17A is analyzed. In sustaining inflammation, IL-17A stabilizes pro-inflammatory transcripts via ACT1-mediated post-transcriptional regulation and produces a self-amplifying positive feedback loop with neutrophil extracellular traps (NETs). In tissue remodeling, IL-17A induces alveolar epithelial ferroptosis via the ACT1-TRAF6-p38 MAPK cascade to drive emphysema. It also mediates irreversible structural alterations in the airway and alveolar parenchyma by inhibiting fibroblast autophagy through the PI3K/AKT/mTOR pathway and inducing epithelial mucus hypersecretion. Given the lack of significant clinical benefit from early non-selective IL-17A blockade in unselected populations, precision intervention strategies guided by clinical endotypes are evaluated. Optimizing next-generation targeted therapies in COPD necessitates biomarker-driven patient stratification, coupled with upstream signal interception and the restoration of systemic immune homeostasis. Together, these strategies support a shift from symptomatic management toward endotype-specific disease modification.}, }
@article {pmid42292620, year = {2026}, author = {Zhou, Q and Lai, C and Zhang, M and Li, R and Li, K and He, W}, title = {Pediatric health: mechanistic insights into inflammatory diseases and emerging therapeutic pathway-targeted approaches.}, journal = {Translational pediatrics}, volume = {15}, number = {5}, pages = {195}, pmid = {42292620}, issn = {2224-4344}, abstract = {Pediatric inflammatory diseases, including juvenile idiopathic arthritis, pediatric inflammatory bowel disease, asthma, Kawasaki disease, and multisystem inflammatory syndrome in children, are an increasing global health concern. These conditions arise from dysregulated immune responses shaped by genetic susceptibility, environmental exposures, and the distinctive features of the developing pediatric immune system. This review presents a mechanism-centered overview of pediatric inflammation, emphasizing immune ontogeny, innate and adaptive immune dysregulation, cytokine signaling, inflammasome activation, oxidative stress, and the gut-immune axis. It also highlights emerging pathway-targeted therapies, including cytokine blockade, JAK inhibitors, microbiome-based interventions, and gene-editing strategies, with attention to their relevance for pediatric precision medicine. Early, mechanism-based intervention during critical developmental windows may improve long-term outcomes and reduce the lifetime burden of inflammatory disease. Overall, this review provides a concise, pediatric-focused perspective on how developmental immunology and targeted therapeutics can inform more precise and effective management of childhood inflammatory disorders.}, }
@article {pmid42292737, year = {2026}, author = {Qiu, C and Guo, C and Xue, X and Feng, P and Zhang, Q and Li, Y and Liu, S and Li, Y and Bukhari, I and Ren, F and Zhang, Y and Zheng, P and Mi, Y}, title = {Exposure to calcium stearyl lactylate induces hepatointestinal toxicity and gut microbiota dysbiosis in mice.}, journal = {Current research in toxicology}, volume = {10}, number = {}, pages = {100301}, pmid = {42292737}, issn = {2666-027X}, abstract = {Calcium stearyl lactylate (CSL) is a widely used food emulsifier, particularly in pasta products. In this study, we investigated the potential toxicological effects of CSL exposure on organ health and gut microbiota in mice. Over a 12-week period, mice were administered CSL at 50, 500, and 5000 mg/kg·bw. Our study found that CSL exposure induced liver and colon inflammation, significantly elevating hepatic injury markers (ALT and AST). In parallel, key intestinal functional markers (CXCL-1, CXCL-2, IL-1β, TNF-α, ZO-1, and Occludin) were markedly altered, indicating compromised gut barrier integrity. 16S rRNA sequencing revealed that CSL administration disrupted gut microbial diversity, characterized by decreased beneficial bacteria (e.g., Bifidobacterium and Lactobacillus) and increased potentially harmful genera, including Anaerotruncus, Desulfovibrio, and Helicobacter. These findings indicate that long-term CSL intake can induce hepatointestinal damage and provoke significant dysbiosis of the gut microbiome.}, }
@article {pmid42292847, year = {2026}, author = {You, Q and Jin, M and Zhou, B and Huang, C and Lin, Z and Hu, J and Xue, J and Chen, X and Xiao, Y and Li, R and Zong, Y and Wu, M and Zhang, T and Liu, H}, title = {Gut microbiome components predict response to neoadjuvant short-course radiotherapy followed by camrelizumab and chemotherapy in locally advanced rectal cancer (UNION): a prospective study.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1829108}, pmid = {42292847}, issn = {1663-9812}, abstract = {BACKGROUND: Although the gut microbiome shapes responses to anti-tumor immunotherapy and chemotherapy, its predictive value for neoadjuvant short-course radiotherapy (SCRT) followed by camrelizumab (CAM) and CAPOX in patients with locally advanced rectal cancer (LARC) has not been defined. This exploratory study aimed to evaluate whether the gut microbiome is associated with response to neoadjuvant SCRT followed by CAM and CAPOX.<br><br>METHODS: We obtained a total of 77 fecal samples from 36 patients with LARC, including 17 assigned to the long-course chemoradiotherapy (LCRT) group and 19 to the SCRT group. Samples were collected at three time points: baseline, after radiotherapy, and after chemoimmunotherapy. DNA was extracted, followed by metagenomic sequencing to profile microbiota dynamics during neoadjuvant treatment.<br><br>RESULTS: In this pilot analysis, we observed significant differences in the gut microbiota between the SCRT and LCRT treatment cohorts. Specifically, Bifidobacterium and Dorea were significantly enriched following completion of SCRT sequential CAM and CAPOX therapy. Further analysis revealed that the relative abundances of these two genera changed significantly only before and after the SCRT regimen, with no notable changes observed in the LCRT group. Preliminary ROC analysis suggested potential utility of these taxa for predicting treatment response, though validation in larger cohorts is needed.<br><br>CONCLUSION: The gut microbiome offers potential biomarkers that may stratify response to SCRT followed by CAM and CAPOX, representing a promising exploratory finding with potential clinical relevance.<br><br>CLINICAL TRIAL REGISTRATION: https://clinicaltrials.gov/, identifier NCT04928807.}, }
@article {pmid42292951, year = {2026}, author = {Li, M and Hao, L and Shi, X and Wang, J and Li, H and Wang, Y and Khambalkar, P and Sun, X and Rima, S and Guo, X and Fang, X and Ma, L}, title = {Solanaceous vegetables and Fusarium oxysporum interactions: pathogen genomics, pathogenesis, host resistance, and emerging microbiome-driven disease management.}, journal = {Horticulture research}, volume = {13}, number = {6}, pages = {uhag074}, pmid = {42292951}, issn = {2662-6810}, abstract = {Solanaceous vegetables are continuously threatened by Fusarium wilt disease, which is mainly caused by Fusarium oxysporum (Fo), a fungal species complex comprising many devastating soil-borne pathogens, resulting in severe yield losses worldwide. Over the past decade, significant and numerous advances have been made in dissecting the molecular and genomic basis underlying the interaction between solanaceous vegetables and Fo, particularly owing to the emergence of the tomato-Fo pathosystem as a powerful model system for studying the molecular basis of resistance and susceptibility in solanaceous vegetables against vascular wilt pathogens. In this review, we summarize recent advances driven by improvements in genome sequencing and assembly of Fo infecting solanaceous vegetables, the virulence strategies and diverse arsenals employed by Fo to modulate and suppress host immunity, as well as the identification and functional characterization of race-specific resistance genes in solanaceous vegetables and their corresponding Fo determinants. We address the potential downstream signaling pathways involved in activating solanaceous vegetable immunity against Fo. In addition, we explore emerging insights into microbiome-based strategies for disease control, emphasizing the potential use of beneficial and synthetic microbes in the sustainable management of Fusarium wilt in tomato. Collectively, this review provides an integrated perspective on pathogen genomics, pathogenesis, host resistance, and microbiome-driven control of Fusarium wilt in tomato, offering promising avenues for developing durable and broad-spectrum resistance against various Fo strains in solanaceous vegetables.}, }
@article {pmid42293013, year = {2026}, author = {Suo, Y and Zhang, X and Li, L and Si, X and Xu, F and Wang, X and Cheng, P and Li, Q and Yan, M}, title = {Impact of wheat straw incorporation and fertilizer reduction on peanut yield and soil functions.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1828860}, pmid = {42293013}, issn = {1664-462X}, abstract = {INTRODUCTION: Balancing crop productivity with sustainable soil management is a critical challenge in modern agriculture.<br><br>METHODS: We conducted a three-year randomized complete block field experiment (2022-2024) to evaluate the integrated effects of wheat straw incorporation regimes and fertilizer reduction on the plant-soil-microbe nexus in peanut (Arachis hypogaea L.) production. Six treatments were compared: no straw return (CT), conventional straw incorporation (SI), deep straw incorporation with a decomposition accelerator (SD), deep incorporation with accelerator and a 25% fertilizer reduction (SDR), surface mulching (SM), and SM with a 25% fertilizer reduction (SMR).<br><br>RESULTS: Relative to CT, deep straw incorporation (SD and SDR) significantly increased the three-year mean peanut yield by 12-25%. Notably, the SDR regime maintained final yields, plant nutrient uptake, and soil aggregate stability statistically equivalent to the fully fertilized SD treatment (P > 0.05), successfully substituting for a 25% reduction in mineral inputs. Mechanistically, deep straw incorporation actively reshaped the rhizosphere microenvironment. Deep straw incorporation actively reshaped the rhizosphere microenvironment, enriching beneficial functional microbial taxa including Bacillus, Sphingomonas, and Trichoderma, which subsequently elevated the activities of carbon, nitrogen, and phosphorus-cycling extracellular hydrolases and oxidative enzymes by 1.4- to 2.6-fold. This microbially mediated acceleration of nutrient cycling enhanced soil organic carbon, microbial biomass carbon, and available nutrient pools, thereby improving soil nutrient availability and peanut production capacity.<br><br>DISCUSSION: Our findings demonstrate that deep straw incorporation with targeted microbial decomposition accelerators, combined with a 25% reduction in mineral fertilizer, provides a practical, low-input strategy to sustain high peanut yields, optimize root-zone functions, and advance climate-smart agricultural systems.}, }
@article {pmid42293143, year = {2026}, author = {Kocaadam-Bozkurt, B and Aslan, S and Bozkurt, O and Bodur, M and Agagündüz, D and Budán, F}, title = {Gerobiotics and neuroprotection: effects on the gut-brain axis in age-related neurodegenerative diseases.}, journal = {Frontiers in aging neuroscience}, volume = {18}, number = {}, pages = {1814234}, pmid = {42293143}, issn = {1663-4365}, abstract = {As the global population ages, effective strategies to attenuate or prevent neurodegenerative processes are becoming increasingly important. Gerobiotics, an emerging class of probiotic strains and their derived postbiotics, are considered promising geroprotective agents because of their potential to target fundamental mechanisms of aging, modulate the gut-brain axis, and attenuate age-related cognitive and functional decline. This review aims to synthesize existing evidence from preclinical and clinical studies on the neuroprotective effects of gerobiotics, with particular emphasis on ageing-related changes in gut microbiota composition, systemic inflammation, and the pathophysiology of neurodegenerative diseases. Preclinical animal studies show that gerobiotics ameliorate memory impairment, preserve synaptic integrity, and attenuate neuroinflammation. Furthermore, clinical results suggest improvements in cognitive performance, mood regulation, and gastrointestinal function, particularly in the early stages of neurodegenerative disorders and among individuals with mild cognitive impairment. The microbiota-gut-brain axis has emerged as a relevant therapeutic target, with gerobiotic supplementation representing a multidimensional approach to support healthy cognitive ageing and counteract neurodegenerative processes. The underlying mechanisms, manifested mostly through modulation of microbial metabolites, include the restoration of intestinal and blood-brain barrier integrity, the reduction of neuroinflammation, the enhancement of neurotrophic factors, and the modulation of immunological pathways. Although current evidence is promising, heterogeneity in probiotic strains, dosages, and study designs indicates the need for further rigorous investigation. Further well-designed, large-scale clinical studies are required to establish efficacy, optimize intervention protocols, and support the translation of gerobiotics into evidence-based clinical practice for the prevention and management of age-related neurodegenerative diseases.}, }
@article {pmid42293159, year = {2026}, author = {Ike, I and Teymouri, F and Crook, C and Guzman, S and Hazeltine, M and Castillo, D and Li, D and Brar, G}, title = {The interplay between bile acid metabolism and gut microbiome in biliary tract cancers.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1774429}, pmid = {42293159}, issn = {2813-4338}, abstract = {The gut microbiota and bile acids (BAs) exist in a tightly regulated, bidirectional relationship that influences host metabolism, immune function, and disease. Primary BAs synthesized in the liver are chemically transformed by intestinal microbes into a diverse pool of secondary BAs, which exert antimicrobial effects and activate host signaling pathways including Farnesoid X Receptor (FXR), Takeda G protein-coupled receptor 5 (TGR5), and sphingosine-1-phosphate receptor 2 (S1PR2). These pathways regulate BA homeostasis, epithelial barrier integrity, inflammation, and carcinogenesis. Disruption of this BA-microbiome axis has been implicated in biliary tract cancers (BTCs), a group of aggressive malignancies with rising global incidence and limited therapeutic options. Secondary BAs and BA receptor signaling contribute to tumor initiation and progression through NF-κB activation, oxidative stress, and altered cell survival, whereas reduced FXR signaling and obstructed enterohepatic circulation further promote inflammatory dysregulation. Emerging evidence demonstrates that microbial dysbiosis and altered BA metabolism are associated with distinct BTC microbial profiles, enriched in taxa such as Fusobacterium, Salmonella, Prevotella, and Actinomyces, alongside depletion of commensals including Lactobacillus. These taxa influence inflammatory signaling, BA transformation, and epithelial injury, contributing to carcinogenesis. Microbiome-BA interactions also shape anti-tumor immunity and responses to immune checkpoint inhibitors (ICIs). Specific microbial signatures-particularly enrichment of Lachnospiraceae, Erysipelotrichaceae, Bacteroidetes, and Alistipes-correlate with enhanced immune activation and improved clinical outcomes in hepatobiliary cancers. Modulation of gut microbiota through antibiotics, probiotics, or fecal microbiota transplantation can influence BA composition, immune surveillance, and therapeutic efficacy. Collectively, these data highlight the central role of the BA-microbiome axis in BTC pathogenesis and treatment response. Microbial and BA metabolite profiling represent promising avenues for biomarker development, while targeted manipulation of BA signaling and microbial ecology offers potential therapeutic strategies to improve BTC outcomes.}, }
@article {pmid42293160, year = {2026}, author = {Han, Y and Zhang, H and Zhang, J}, title = {Altered early-life gut microbiota in offspring of pregnancies complicated by CHD-associated pulmonary hypertension.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1785707}, pmid = {42293160}, issn = {2813-4338}, abstract = {BACKGROUND: Pulmonary arterial hypertension is a progressive disease involving the pulmonary vasculature and is defined as a mean pulmonary arterial pressure (mPAP) >20 mmHg at rest. Pulmonary arterial hypertension during pregnancy is associated with increased maternal mortality and adverse fetal outcomes. The present study aimed to investigate differences in the initial meconium microbiota between neonates born to mothers with congenital heart disease-associated pulmonary arterial hypertension (CHD-PAH) and those born to mothers with congenital heart disease (CHD) alone, thereby elucidating the potential influence of pulmonary arterial hypertension on the establishment of the early-life gut microbiome.<br><br>METHODS: We collected first-pass meconium samples from neonates in the pulmonary hypertension group (PH group, n = 23) and the control group without pulmonary hypertension (NC group, n = 17) and characterized microbial profiles using 16S rRNA sequencing.<br><br>RESULTS: The PH group showed lower alpha diversity, with reduced Shannon and observed features indices (both P < 0.05), whereas Bray-Curtis beta diversity showed substantial overlap between groups. At the phylum level, the overall gut microbial structure was broadly comparable between the PH and NC groups, with no statistically significant differences in the relative abundance of dominant taxa. At the genus level, the mean relative abundance of Streptococcus was significantly lower in the PH group than in the NC group (0.20% vs. 2.09%, P = 0.0072). Predicted functional profiling suggested potential differences in dominant metabolic pathways between groups, including enrichment of ubiquinone biosynthesis and aromatic amino acid/chorismate biosynthesis pathways in the PH group.<br><br>CONCLUSION: Collectively, these findings extend current evidence on PAH-related alterations in early-life microbial ecosystems and provide a plausible microbiome-based basis for investigating the biological mechanisms underlying adverse maternal-fetal outcomes associated with pulmonary arterial hypertension.}, }
@article {pmid42293161, year = {2026}, author = {Nunez, H and Straub, TJ and Imam, N and Goad, D and Mueller, NT and Mars, RAT and Sew Hoy, C and Paullin, T and Sukhum, KV}, title = {Age-specific early-life gut microbiome associations with eczema and food allergies during early immune development.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1804117}, pmid = {42293161}, issn = {2813-4338}, abstract = {INTRODUCTION: Eczema and food allergy commonly emerge during infancy and are linked to changes in the gut microbiome, yet it remains unclear when microbiome differences associated with allergic disease first appear during development.<br><br>METHODS: We analyzed age-stratified shotgun metagenomic data from 97 children aged 4-36 months, including physician-confirmed cases of eczema or food allergy and non-allergic controls, excluding recent antibiotic or probiotic exposure. Microbial taxa, functional pathways, and composite microbiome metrics were evaluated across three developmental stages: early infancy (4-6 months), mid-infancy (6-12 months), and toddlerhood (12-36 months).<br><br>RESULTS: Differences between allergic and non-allergic children were minimal before 6 months of age but became more apparent during mid-infancy and persisted into toddlerhood. Allergic conditions were associated with reduced abundance of fiber-fermenting and butyrate-producing taxa, enrichment of facultative and inflammation-associated microbes, lower microbiome maturation scores, and shifts in metabolic and inflammatory functional capacity.<br><br>DISCUSSION: These findings suggest that gut microbiome divergence associated with allergic disease becomes more apparent during mid-infancy, highlighting a developmentally relevant period for understanding early immune disruption. The results support further longitudinal and interventional studies aimed at clarifying whether earlier microbiome-targeted strategies may help modify progression along the atopic march.}, }
@article {pmid42293186, year = {2026}, author = {Chen, K and Jin, S and Nie, Y and He, N and Chen, H and Yuan, J and Li, X and Liong, MT}, title = {Efficacy of Bifidobacterium lactis BLa80 in preventing early childhood eczema and respiratory infections via gut microbiome and immune modulation.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1727191}, pmid = {42293186}, issn = {2296-861X}, abstract = {BACKGROUND: Early childhood is a critical period for immune development, with eczema and respiratory infections representing common health challenges. This study investigated the efficacy of Bifidobacterium animalis subsp. lactis BLa80 in reducing these conditions potentially through gut microbiome modulation.<br><br>METHODS: In a randomized, double-blind, placebo-controlled trial, 360 formula-fed infants and children aged below 3 years old with elevated allergy risk received daily B. lactis BLa80 (5 &#xd7; 10[9] CFU) or placebo for 180 days. Primary outcomes included eczema incidence and symptom burden, with secondary outcomes assessing respiratory infections, gastrointestinal symptoms, gut microbiota composition (16S rRNA sequencing), functional pathways (KEGG analysis), and fecal immune markers (ELISA).<br><br>RESULTS: The probiotic group demonstrated significantly reduced eczema incidence (27.6% vs. 69.5%, RR: 0.398, p < 0.001) and upper respiratory tract infections (19.4% vs. 42.5%, RR: 0.457, p < 0.001). Significant reductions were observed in symptom burden, including nasal congestion, vomiting, milk aspiration, and irritability. Microbiota profiling showed enrichment of beneficial taxa (Akkermansia, Fusicatenibacter) with enhanced metabolic pathways including tryptophan metabolism, vitamin biosynthesis, and xenobiotic degradation. Immunological profiling showed maintained human beta-defensin-2 (p = 0.005), increased secretory IgA (p < 0.001), and reduced calprotectin (p < 0.001).<br><br>CONCLUSIONS: B. lactis BLa80 supplementation effectively reduces eczema and respiratory infections associated with gut microbiome remodeling that may enhance barrier function, immune regulation, and metabolic capacity, supporting its use as a preventive nutritional strategy in early childhood.<br><br>CLINICAL TRIAL REGISTRATION: ChiCTR2300074956.}, }
@article {pmid42293192, year = {2026}, author = {Shahbazi, S and Aminzadeh, S and Taati Moghadam, M and Rajabi, S and Vaziri, SS and Rostamian, M}, title = {Ramadan intermittent fasting and the gut microbiome: modulation of diversity and implications for metabolic health.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1767573}, pmid = {42293192}, issn = {2296-861X}, abstract = {Ramadan fasting (RF), a culturally embedded form of time-restricted eating, involves daily abstinence from food and drink from dawn to sunset and provides a real-world human model to examine the potential impact of intermittent fasting on the gut microbiome and metabolic health. This review synthesizes evidence from human studies, predominantly observational in design, to evaluate the associations between RF, microbial composition and diversity, and metabolic outcomes. Current evidence suggests that RF may be associated with changes in gut microbial richness and community structure, including reported increases in taxa such as Akkermansia muciniphila, Faecalibacterium prausnitzii, Roseburia, and Bacteroides, many of which are linked to short-chain fatty acid (SCFA) production and intestinal barrier function. However, findings across studies are not entirely consistent, particularly with respect to microbial taxa abundance and SCFA levels. Observational studies also report concurrent changes in anthropometric and metabolic parameters, including body weight, lipid profiles, glycemic markers, and inflammatory indices, although these associations may be influenced by confounding factors such as dietary composition, lifestyle changes, and weight loss during Ramadan. Proposed mechanisms include alterations in feeding-fasting rhythms and microbiota-related pathways such as bile acid metabolism and gut barrier function; however, these mechanisms are largely inferred from related experimental models and should be considered hypothesis-generating in the context of RF. Therefore, while RF represents a relevant ecological model for studying time-restricted eating in humans, the current evidence remains limited by small sample sizes, interindividual variability, and methodological heterogeneity. Further well-controlled, longitudinal, and multi-omics studies are required to clarify causal relationships and determine the extent to which RF-associated microbial changes contribute to metabolic health.}, }
@article {pmid42293200, year = {2026}, author = {Shi, Y and Zhu, S and Chen, Z and Chao, K and Huang, Z and Gao, X}, title = {Gastrointestinal dysfunction score for mortality prediction in intensive care unit patients with pre-existing digestive system disease: a prospective observational study.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1831897}, pmid = {42293200}, issn = {2296-861X}, abstract = {BACKGROUND: Gastrointestinal (GI) dysfunction has been increasingly recognized as a common and clinically important problem in patients in the Intensive Care Unit (ICU). GI dysfunction may affect nutrition, immune function, and microbiome homeostasis, which has been associated with adverse outcomes in ICU patients. However, conventional organ failure scores such as the Sequential Organ Failure Assessment (SOFA) score do not adequately account for GI dysfunction, particularly in patients with pre-existing digestive system disease.<br><br>OBJECTIVE: This study aimed to evaluate the performance of the Gastrointestinal Dysfunction Score (GIDS) in adult ICU patients with pre-existing digestive system disease and to examine whether integrating GIDS with SOFA improves discrimination for 28-day mortality compared to SOFA alone.<br><br>METHODS: This single-center, prospective observational study included adult patients admitted to the ICU, excluding pregnancy, ICU readmission, cessation of active treatment, loss to follow-up and death within 24 h of ICU admission. Patients were stratified into GI and non-GI cohorts based on the presence of pre-existing digestive system disease at ICU admission. GIDS, SOFA and acute gastrointestinal irnjury (AGI) gades were recorded daily for the first ICU week. We compared baseline clinical characteristics and 28-day mortality between cohorts and evaluated whether adding GIDS to SOFA improved discrimination.<br><br>RESULTS: A total of 486 patients were included, with 359 in the GI cohort. Using the score of the first day in ICU, GIDS (AUC = 0.701) outperformed AGI (AUC = 0.614). When combined with SOFA, GIDS+SOFA had the highest AUC of 0.764, compared with SOFA alone (AUC = 0.739). In the GI cohort, GIDS+SOFA also demonstrated superior discrimination (AUC = 0.754) compared to SOFA alone (AUC = 0.723).<br><br>CONCLUSION: GIDS provides a meaningful stratification of 28-day mortality risk, especially in patients with pre-existing digestive system disease. Adding GIDS to SOFA modestly improved discrimination for 28-day mortality and warrants external validation. These findings support further validation and potential incorporation of GIDS into clinical practice.}, }
@article {pmid42293219, year = {2026}, author = {Abu Dheir, N and Radwan, H and Hasan, H and Papandreou, D and Zeb, F and Abdelrahim, DN and Abdelaziz, MA and Abdoh, NN and Mohamad, MN and Al Dhaheri, AS and Stojanovska, L and Cheikh Ismail, L}, title = {Breastfeeding and prevention of childhood obesity: a narrative review of behavioral, hormonal, and microbiome programming.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1800487}, pmid = {42293219}, issn = {2296-861X}, abstract = {Childhood obesity has emerged as a major public health concern worldwide, with increasing prevalence in high-income countries. Growing evidence suggests that early-life nutrition, particularly breastfeeding, plays a critical role in reducing obesity that shaping long-term metabolic health. This narrative review highlight association between breastfeeding duration, exclusivity, and childhood obesity risk, synthesizing current evidence while exploring potential biological and behavioral mechanisms. Most studies report that breastfeeding, particularly when exclusive and sustained for longer durations, is associated with a reduced risk of childhood overweight and obesity. Evidence consistently shows that breastfed infants exhibit healthier growth trajectories, lower rates of rapid weight gain, and reduced adiposity compared to formula-fed infants. Several studies also identify plausible biological mechanisms, including appetite regulation, favorable insulin responses, and the influence of bioactive components in human milk, such as leptin, adiponectin, ghrelin, insulin-like growth factors (IGFs) and gut microbiome modulating factors. Nonetheless, some studies show weak or non-significant associations, often attributable to methodological differences, inconsistent breastfeeding practices, or inadequate adjustment for confounders such as maternal BMI and socioeconomic status. Current literature indicates that breastfeeding may serve as a protective factor against childhood obesity, highlighting its relevance in early-life nutrition and long-term health outcomes. This review underscores that promoting exclusive breastfeeding for at least 6 months should be a cornerstone of public health strategies to prevent childhood obesity.}, }
@article {pmid42293411, year = {2025}, author = {Liu, M and Gong, J and Liu, Y and Yu, J and Hu, Z and Liu, Z}, title = {Multi-omics reveals circadian regulation of bone homeostasis by gut microbiota metabolites: mechanisms and chronotherapeutic implications.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1719445}, pmid = {42293411}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Multiomics ; Animals ; *Homeostasis ; *Circadian Rhythm ; *Bone and Bones/metabolism/physiology ; Bone Remodeling ; Metabolomics ; Fatty Acids, Volatile/metabolism ; Osteogenesis ; }, abstract = {The gut-bone axis plays a pivotal role in skeletal health, yet the integration of multi-omics approaches to elucidate circadian metabolite-bone interactions remains limited. This review synthesizes evidence from metagenomics, metabolomics, and germ-free models to uncover how microbiota-derived metabolites-including short-chain fatty acids (SCFAs), bile acids, tryptophan derivatives, and gaseous molecules-orchestrate bone remodeling in osteoporosis, osteoarthritis, and bone malignancies. Many studies demonstrate that SCFAs inhibit osteoclastogenesis via GPR43/HDAC signaling and promote osteoblast metabolic reprogramming, while bile acids enhance osteogenesis through FXR/Wnt/β-catenin activation. Tryptophan metabolites repair intestinal barrier integrity and modulate osteoimmunity via the AhR pathway. Single-cell omics reveal circadian oscillations of metabolite receptors (e.g., GPR43, FXR) in bone stromal cells, linking microbial diurnal rhythms to epigenetic regulation of bone turnover. We propose a novel "metabolite-immune-bone triad" model, highlighting microbiome-driven immunometabolic reprogramming as a central regulator of skeletal homeostasis. These insights advance precision microbial therapeutics and chrono-nutritional strategies, bridging multi-omics discoveries with clinical applications for bone disorders.}, }
@article {pmid42293516, year = {2026}, author = {Zou, Y and Liu, L and Chen, H and Luo, Z and Zhu, Z and Li, Z and Lin, B and Zhuang, Z and Li, W and Yang, Q and Yang, X and Zhou, H and Luo, M and Dai, D}, title = {Study protocol for a randomized controlled trial of fecal microbiota transplantation via different routes in children with moderate-to-severe autism spectrum disorder.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1829532}, pmid = {42293516}, issn = {1664-302X}, abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) shows promise for autism spectrum disorder (ASD) by modulating the gut-brain axis, but the optimal delivery route remains unknown. Our previous single-arm study suggested efficacy of nasojejunal FMT in children with moderate-to-severe ASD, yet could not exclude placebo effects or compare routes. This randomized controlled trial aims to determine the most effective and tolerable FMT administration route.<br><br>METHODS: This single-center, randomized, triple-blind, double-dummy, placebo-controlled, three-arm parallel-group trial will enroll 75 children (aged 3-16 years) with moderate-to-severe ASD [Childhood Autism Rating Scale, Second Edition (CARS-2) &#x2265;36]. Participants are randomized 1:1:1 to: (1) FMT via nasojejunal tube + sham colonoscopy (FMT-NJT); (2) active FMT via colonoscopy with transendoscopic enteral tube placement (first session) + two subsequent infusions via the indwelling tube + sham nasojejunal intubation (FMT-C); (3) placebo via both routes (sham procedures). Three FMT/placebo sessions (5 mL/kg, max 100 mL) are administered over 5 days. Primary outcome is change in CARS-2 score from baseline to Week 24. Secondary outcomes include changes in Social Responsiveness Scale, Autism Behavior Checklist, Gastrointestinal Symptom Rating Scale, Short Sensory Profile, Children's Sleep Habits Questionnaire, gut metagenomic profiles (baseline, Weeks 2,6,12,24,48), and adverse events.<br><br>RESULTS: This is a study protocol; no results are available.<br><br>CONCLUSIONS: This first head-to-head comparison of FMT routes in pediatric ASD will provide high-level evidence to guide treatment standardization, directly addressing the translational gap identified in our preliminary work.}, }
@article {pmid42293528, year = {2026}, author = {Seth, N and Bansal, M and Mazumdar, S and Mazumdar-Leighton, S and Lakhanpaul, S and Vats, S and Arafat, Y and Babu, CR}, title = {Functional diversity in bacterial communities of an integrated constructed wetland used for in situ bioremediation of sewage.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1803785}, pmid = {42293528}, issn = {1664-302X}, abstract = {Constructed wetlands (CWs) offer effective, economical, environment-friendly and energy-efficient solution to growing challenges of increasing sewage and wastewater loads in urban areas. Although microbial communities form an integral component of constructed wetlands for sewage treatment, functional processes and their dynamics during sewage bioremediation in constructed wetlands remain largely uncharacterized. Moreover, the association of specific bacterial taxa with remediation of different sewage and water quality parameters remains largely unclear. This study explored the functional diversity likely associated with microbial communities of a constructed wetland system used for in situ remediation of 1 MLD (Million Liters per Day) sewage without external energy input since 2014. Different bacterial functional groups in the sludge from a stabilization pond and from rhizospheric sediments of the integrated constructed wetland were predicted using a 16S rRNA gene metagenomic sequencing dataset. Correlation analysis, multivariate statistics and a co-occurrence network were used to assess the bacterial groups associated with changes in water quality as it flows through different components of the integrated CW and highlight association patterns predicting major exchanges which might be operating in the microbial communities. While stabilization pond microbiome was dominated by bacterial groups such as Firmicutes, Desulfobacterota and Methylomirabilota known to be involved in carbon fermentation, sulphate reduction and methanogenesis, the rhizospheric sediments showed prevalence of bacteria associated with nitrogen reduction including Nitrospirota and Planctomycetota contributing to improved sewage quality parameters. Such results indicated complex microbial interactions involving bacteria from diverse functional groups sustaining bioremediation in the CW. The identification of primary bacterial taxa along with their putative functions can help in designing strategies to improve sustainable, nature-based wastewater treatment by CW systems.}, }
@article {pmid42293540, year = {2026}, author = {Velaz Martín, M and Rießland, H and Rabe, KS and Niemeyer, CM}, title = {Primer choice shapes microbial community interpretation across habitats and informs short-term structured enrichment in environmental and applied systems.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1838890}, pmid = {42293540}, issn = {1664-302X}, abstract = {Microbial communities play central roles in ecosystem functioning across natural and engineered environments, yet their accurate characterization remains challenging due to methodological biases in amplicon sequencing. Primer choice can strongly influence taxonomic resolution, diversity estimates, and ecological interpretation. Here, we systematically compared primer performance across multiple ribosomal marker genes (16S, 18S, 28S rRNA, and ITS) and contrasting habitats, including soil, wastewater, and a photobioreactor-derived suspension. Amplicon-based profiles were benchmarked against shotgun metagenomic data. Primer choice significantly affected community composition, diversity metrics, and concordance with metagenomic profiles across all habitats and markers. Although 16S rRNA gene primers targeting the V3 region showed the highest agreement, no primer set fully reconstructed community structure. Applying the best-performing primer to a structured soil enrichment system using MESIF chips revealed rapid divergence from native soil and convergence toward less diverse communities, consistently favoring copiotrophic, surface-associated taxa while characteristic soil taxa declined. Across the 21-day incubation period, MESIF-associated communities diverged strongly from native soil, whereas medium-specific differences were comparatively smaller. This suggests that early enrichment was dominated by colonization of the structured matrix, while longer incubations and functional analyses will be needed to resolve substrate-specific selection. Overall, our findings highlight primer selection as a critical factor in microbial community analysis and show that combining optimized amplicon sequencing with structured cultivation enables reproducible enrichment, improved community monitoring, and targeted recovery of functionally relevant microorganisms. These insights are relevant for environmental monitoring, wastewater treatment, biotechnology, and controlled environment agriculture.}, }
@article {pmid42293542, year = {2026}, author = {Liu, L and Liu, J and He, J and Xing, Y and Zhang, D and Zhang, X and Ma, C and Xu, M and Li, R and Peng, M and Mei, S}, title = {Multi-kingdom gut microbiota analysis identifies bacterial-viral association in multiple myeloma.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1798330}, pmid = {42293542}, issn = {1664-302X}, abstract = {INTRODUCTION: Alterations in the gut microbiome are closely associated with the progression of multiple myeloma (MM). Previous research has predominantly focused on the bacterial components of the microbiota; however, the virome, a significant component of the microbiota, also plays a critical role, with bacteriophages influencing bacterial community composition and evolution.<br><br>METHODS: This study utilized shotgun metagenomic sequencing of fecal samples to explore the interaction between the gut microbiota and MM development. Fecal samples from 28 MM patients and 20 healthy controls were analyzed to evaluate microbial diversity. Taxonomic profiling of both bacterial and viral communities was performed using the Kraken2 classifier.<br><br>RESULTS: Our analysis confirmed microbial dysbiosis in MM patients and revealed concomitant changes in both bacterial and viral communities. At the phylum level, this study identified a significant increase in the relative abundance of Pseudomonadota (from 1.63 to 8.88%, p&#x202f;<&#x202f;0.001) and a decrease in Bacillota in MM patients compared to controls. Furthermore, several viral taxa were notably enriched in the MM cohort, including the phylum Heunggongvirae (linear discriminant analysis [LDA] = 4.74, p&#x202f;= 0.00003), phylum Uroviricota, and genus Punavirus (specifically Punavirus RCS47). Functional analysis demonstrated shifts in microbial metabolic pathways associated with MM, including a reduced capacity for amino acid and secondary bile acid biosynthesis and an enrichment of pathways associated with biofilm formation and cationic antimicrobial peptide (CAMP) resistance.<br><br>DISCUSSION: This multi-kingdom metagenomic analysis reveals distinct bacterial and viral signatures associated with MM, enhancing our understanding of gut microbial dysbiosis in the disease. These findings lay the groundwork for future mechanistic investigations and highlight the importance of validating these results in larger, independent cohorts.}, }
@article {pmid42293547, year = {2026}, author = {Wei, X and Tian, N and Mei, W and Li, J and Liu, M and Zhou, H and Yang, Z and Yang, C and Hu, Y}, title = {Progress in understanding the infection mechanisms, soil microecological imbalance, and integrated control strategies of tobacco black shank.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1856708}, pmid = {42293547}, issn = {1664-302X}, abstract = {Tobacco black shank (TBS), caused by the oomycete pathogen Phytophthora nicotianae, is a destructive soilborne disease that seriously threatens tobacco production worldwide. This review summarizes recent progress in the infection biology of P. nicotianae, the disturbance of rhizosphere microbial communities under disease pressure, and integrated strategies for disease management. Current evidence indicates that TBS development is not only associated with direct pathogen infection, but also with rhizosphere microecological imbalance, including the decline of beneficial microbes, enrichment of opportunistic pathogens, reduced microbial diversity, and weakened soil suppressiveness. These changes may further promote pathogen persistence and disease recurrence. Based on this understanding, effective management should combine crop rotation, biological control, rational chemical intervention, resistant cultivars, and reductive soil disinfestation to suppress pathogen pressure while restoring soil microbial balance. Future research should further integrate multi-omics analysis, microbiome-based regulation, and intelligent monitoring to support early warning and precision control. This review provides an integrated perspective on pathogen-host-soil microbiome interactions and offers a theoretical basis for sustainable management of tobacco black shank.}, }
@article {pmid42293552, year = {2026}, author = {Aldriwesh, MG and Bin Shuraym, H and Asiri, NY and Asiri, WY and Abukhalid, NF and Alasiri, A and Alghoribi, MF}, title = {Microbiome and One Health in GCC countries: current status, research gaps, and future directions.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1821688}, pmid = {42293552}, issn = {1664-302X}, abstract = {BACKGROUND: Microbiome science has emerged as a central component of the One Health framework, linking human, animal, and environmental health. Although global microbiome research has expanded rapidly, a comprehensive evaluation of microbiome research development and integration across the Gulf Cooperation Council (GCC) countries remains lacking. This systematic review aimed to characterize microbiome research in the GCC countries, identify major research gaps, and evaluate alignment with One Health principles while proposing a strategic framework to support coordinated regional development.<br><br>METHODS: This systematic review followed PRISMA 2020 guidelines. A structured search of PubMed, ScienceDirect, Google Scholar, and EBSCO databases identified microbiome-related studies published up to January 31, 2025. Eligible studies included original research conducted in the GCC countries (Saudi Arabia, Qatar, Kuwait, United Arab Emirates, Oman, and Bahrain) investigating human, animal, or environmental microbiomes. Findings were synthesized descriptively to assess study distribution, research design, analytical methodologies, and thematic focus.<br><br>RESULTS: A total of 110 studies met the inclusion criteria. Human microbiome studies accounted for 49% of publications, followed by environmental microbiome studies (40%) and animal microbiome studies (11%). Research output increased substantially after 2020 but remained uneven among the GCC countries, with Saudi Arabia contributing 44% of publications, whereas Bahrain and Oman together accounted for fewer than 7%. Most studies were observational and primarily used 16S rRNA gene sequencing on Illumina platforms. Human studies focused mainly on gut and oral microbiomes and frequently investigated metabolic disorders such as obesity and diabetes. Animal microbiome research was limited and largely centered on camels, with minimal investigation of livestock relevant to food security. Environmental studies predominantly examined soil and desert environments. No included study simultaneously investigated human, animal, and environmental microbiomes within an integrated One Health study design.<br><br>CONCLUSION: Microbiome research in the GCC countries is growing but remains uneven and largely disconnected across human, animal, and environmental studies, with limited adoption of One Health approaches. A coordinated regional strategy integrating governance, infrastructure, funding, and workforce development is needed to advance translational microbiome research and strengthen the GCC's contribution to global health, food security, and environmental sustainability.}, }
@article {pmid42293560, year = {2026}, author = {Tenea, GN and Jarrín-V, P and Reyes, P}, title = {Metagenomic insights into postbiotic-mediated modulation of strawberry surface microbiome and metabolic activity.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1841388}, pmid = {42293560}, issn = {1664-302X}, abstract = {INTRODUCTION: The increasing demand for sustainable alternatives to chemical disinfectants in postharvest fruit handling has incentivized exploration into microbiome-based interventions. We evaluated the impact of lactic acid bacteria (LAB)-derived postbiotic formulations (FF1, FF2, FF3) and a commercial disinfectant (CD) on the microbial community structure of the strawberry fruit surface.<br><br>METHODS: Taxonomic and functional changes in the microbial communities were evaluated using shotgun metagenomic sequencing, enabling comprehensive profiling of microbial composition and functional potential through gene family abundance, EggNOG functional categories, KEGG pathways, and MetaCyc metabolic reconstruction. The tested formulations consisted of a precipitated peptide-protein extract (PP) from Weissella cibaria UTNGt21O (FF2), used as the antimicrobial agent, and an exopolysaccharide (EPS) from W. confusa UTNCys2-2 (FF3), serving as a biopolymer carrier, applied in combination (FF1: PPGt21O + EPSCys2-2) or individually.<br><br>RESULTS: Our integrated analysis revealed that the highly suppressive formulation, FF1, outperformed the CD by fundamentally restructuring the microbial landscape. Taxonomically, FF1 notably reduced the abundance of key opportunistic spoilage or hazardous organisms. Rather than acting as an indiscriminate biocide, FF1 functioned as a targeted ecological disruptor. Functional profiling (eggNOG, KEGG, and MetaCyc) suggested potential shifts in functional capacity, including a reduced relative abundance of genes associated with translation machinery, cellular membrane expansion (stearate biosynthesis), and host lipid degradation (fatty acid &#x3b2;-oxidation). In parallel, the FF1-treated microbiome showed a higher relative abundance of genes linked to stress-response functions, including heat shock proteins and cell wall-related processes such as peptidoglycan maturation. In contrast, less restrictive formulations (FF2 and FF3) permitted the proliferation of opportunists such as Pseudomonas spp. and Xanthomonas fragariae, accompanied by active energy-consuming and tissue-degrading metabolic signatures.<br><br>CONCLUSION: These findings suggest possible underlying mechanisms of LAB-derived postbiotics, demonstrating that FF1 forces the surface microbiome into a metabolically restricted, non-degradative survival state, potentially contributing to the preservation of postharvest strawberry quality.}, }
@article {pmid42293567, year = {2026}, author = {Vougiouklaki, D and Prountzou, E and Siatelis, A and Ladias, K and Papaparaskevas, M and Tsakali, E and Polanska, M and Van Impe, JFM and Houhoula, D}, title = {Decoding the seminal microbial fingerprint and semen quality: insights from the first Greek pilot study.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1829292}, pmid = {42293567}, issn = {1664-302X}, abstract = {BACKGROUND: Recent evidence suggests that human semen harbors a complex microbiome that may influence semen quality and male fertility. However, comprehensive characterization of bacterial and fungal communities in semen remains limited, particularly using long-read sequencing technologies.<br><br>METHODS: In this pilot study, 80 semen samples from 80 men were analyzed and classified based on conventional semen-analysis findings into normozoospermic (n&#x202f;=&#x202f;48) and abnormal (n&#x202f;=&#x202f;32) groups. The abnormal group included men with asthenozoospermia and oligoasthenozoospermia. Microbial profiling was conducted using full-length 16S rRNA gene and internal transcribed spacer (ITS) sequencing on the Oxford Nanopore MinION platform.<br><br>RESULTS: Phylum-level analysis revealed distinct microbial profiles between groups. Normozoospermic samples were dominated by Bacillota (64.13%), followed by Actinomycetota (14.61%) and Pseudomonadota (12.95%). In contrast, abnormal samples showed reduced Bacillota abundance (2.32%) and enrichment of Campylobacteriota (10.82%). At the genus level, normozoospermic samples were characterized by predominance of Enterococcus, Cutibacterium, Streptococcus, Finegoldia, and Staphylococcus, whereas abnormal samples showed increased abundance of Campylobacter, Stenotrophomonas, and Agrobacterium. Species-level profiling identified Enterococcus faecalis as the dominant species in normozoospermic samples (41.3%), while Campylobacter ureolyticus predominated in abnormal samples (49.6%). ITS sequencing did not detect fungal DNA in any semen sample, whereas all fungal controls amplified successfully, confirming methodological reliability.<br><br>CONCLUSION: Our findings demonstrate significant differences in seminal microbiome composition between normozoospermic and abnormal semen samples parameters. Alterations at the phylum, genus, and species levels were associated with impaired semen parameters, suggesting a potential link between microbial dysbiosis and male reproductive health. Furthermore, the absence of detectable fungal communities indicates that fungi may be rare or absent in human semen under physiological conditions. This study provides novel insights into the bacterial and fungal landscape of the seminal microbiome using long-read sequencing technology.}, }
@article {pmid42293685, year = {2026}, author = {Shen, Y and Lu, SM and Yang, L and Li, Y and Zhang, Y and Liang, LG}, title = {Engineered bacteria in disease diagnosis and therapy: A synthetic biology perspective.}, journal = {Synthetic and systems biotechnology}, volume = {14}, number = {}, pages = {459-470}, pmid = {42293685}, issn = {2405-805X}, abstract = {Synthetic biology is an interdisciplinary field that integrates knowledge and techniques from modern biology and many other disciplines to design and construct novel biological systems or to modify existing life forms. Its core technologies include gene editing (e.g., CRISPR/Cas9), DNA assembly, in vivo directed evolution, and integration with artificial intelligence. The development of these technologies has greatly advanced the application of synthetic biology in medicine. In disease diagnosis, engineered bacteria have shown considerable promise. They can be designed to sense disease-specific signals and produce detectable reporter outputs, thereby establishing new paradigms for early diagnosis and real-time disease monitoring. For example, bacteria engineered via synthetic biology have been developed as "living sensors" to detect disease biomarkers. In therapeutic applications, synthetic biology offers a fresh perspective on using microorganisms to treat diseases. Researchers can design and construct microorganisms with tailored functions for targeted drug delivery, immunotherapy, and microbiome modulation. These applications not only improve the precision and efficacy of treatments but also offer innovative solutions to overcome the limitations of conventional therapeutic approaches. However, despite their considerable potential, the clinical translation of engineered bacteria still faces numerous challenges, such as ensuring stable in vivo colonization, controlling immunogenicity, standardizing large-scale production, and establishing robust regulatory and ethical frameworks. This review summarizes engineering strategies aimed at enhancing the safety and efficacy of bacterial therapies, with the goal of optimizing bacterial functions and expanding their potential in diagnostics and precision medicine.}, }
@article {pmid42293984, year = {2026}, author = {Li, Y and Huang, M and Mao, Z and Liu, C and Qu, W and Ni, J and Xu, W and Li, A and Bao, J and Han, D and Yu, F and Shen, Y and Wang, Y and Chen, W and Zheng, S}, title = {Ventilation-Associated Differences in Lower Airway Microbial Signatures and Peripheral Blood Transcriptome Among Critically Ill COVID-19 Patients.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {586598}, pmid = {42293984}, issn = {1178-6973}, abstract = {BACKGROUND: Invasive mechanical ventilation (IMV) is a critical intervention for severe respiratory failure and has been widely used in the clinical management of COVID-19 patients. The relationship between such microbiota changes and the host transcriptome in IMV patients remains poorly documented.<br><br>METHODS: We prospectively enrolled 69 critically ill COVID-19 patients, among whom 41 received IMV. Correlation analyses were conducted to investigate the relationship between the lung microbiome and host immune status in IMV COVID-19 patients.<br><br>RESULTS: Compared to the Non-mechanical ventilation (NMV) group, patients in the IMV group exhibited significantly reduced alpha diversity, while no significant difference was observed in beta diversity. The abundance of Streptococcus genus was significantly higher in the NMV group, primarily dominated by Streptococcus oralis and Streptococcus mitis. Transcriptomic enrichment analysis revealed significant upregulation of inflammation-related pathways in the IMV group, including "positive regulation of inflammatory response" and "cellular response to interleukin-1". The decreased relative abundance of Streptococcus genus in the IMV group showed significant correlations with upregulation of genes including CXCL8, PLAU, SELENOK, SDC4, RPL17, RPS23, TOMM7, and PLK3. These upregulated genes promoted the recruitment of immune cells to inflammatory sites through activation of pathways including chemotaxis, leukocyte migration, and leukocyte cell-cell adhesion, ultimately triggering a robust innate immune response.<br><br>CONCLUSION: IMV COVID-19 ARDS patients demonstrated significantly reduced pulmonary microbial diversity, with a marked decrease in the abundance of Streptococcus-primarily Streptococcus oralis and Streptococcus mitis. Transcriptomic profiling further revealed substantial upregulation of inflammatory pathways in IMV patients, including "positive regulation of inflammatory response".}, }
@article {pmid42294020, year = {2026}, author = {Lamberti, L and Rusiñol, C and Guisande, A and Peñalba, F and Irastorza, M and Konik, F and Parada, A and Iglesias, C and Mendive, P and Riera, N and Garrido, G}, title = {Clinical and sociodemographic characterization of a sibling-matched cohort of children with autism Spectrum disorder in Uruguay.}, journal = {Frontiers in child and adolescent psychiatry}, volume = {5}, number = {}, pages = {1835921}, pmid = {42294020}, issn = {2813-4540}, abstract = {This study characterized clinical, sociodemographic, psychiatric, and gastrointestinal variables in 55 families, comparing children with Autism Spectrum Disorder (ASD) to neurotypical siblings. Primary objectives were to delineate sociodemographic profiles and systemic barriers, establish a clinical-nutritional baseline for Uruguayan children, and generate metadata for future microbiome research. We conducted a cross-sectional, case-control study including children aged 4-10 years and sibling controls. Professionals collected data via clinical interviews. Findings indicate a higher male prevalence in the ASD group. Mothers predominantly participated in caregiving and interviews. In the ASD group, 60% of pregnancies had complications, including 12 twin pregnancies. No significant differences were found regarding parental age, delivery method, prematurity, or birth anthropometry. Head circumference at birth did not associate with regression or severity. All children with ASD showed sensory particularities; 94.3% reported gastrointestinal symptoms. We observed a 20-month diagnostic gap and 65% regression rates between 12 and 36 months. These data highlight the need for improved early detection and provide essential local evidence for the Uruguayan ASD population. This interdisciplinary approach bridges clinical practice and research, advancing contextualized care in Uruguay.}, }
@article {pmid42294507, year = {2026}, author = {Kristiana, H and Kartawijaya, M and Tuentifiany, L and Hartanti, AW and Tjandrawinata, RR}, title = {Acute and sub-chronic oral toxicity evaluation and gut microbiota modulation of indigenous Lactobacillus helveticus strains from Indonesia in rats.}, journal = {Toxicology reports}, volume = {16}, number = {}, pages = {102286}, pmid = {42294507}, issn = {2214-7500}, abstract = {Probiotics are widely used to support gastrointestinal health, but their safety must be evaluated on a strain-specific basis. Lactobacillus helveticus DLBSA201 and DLBSA202 are indigenous strains with previously demonstrated probiotic potential in vitro. However, their in vivo safety profile has not been fully assessed. This study aimed to evaluate the acute and sub-chronic oral toxicity of these strains and their effects on selected gut microbial parameters in Wistar rats. In the acute toxicity study, rats received a single oral dose of L. helveticus DLBSA201 or DLBSA202 at 2.5 × 10[10], 2.5 × 10[11], or 5 × 10[11] CFU/rat. In the sub-chronic study, rats were orally administered a 1:1 mixture of both strains daily for 90 days at doses of 1 × 10[9], 1 × 10[10], or 1 × 10[11] CFU/rat/day. Clinical observations, hematological and biochemical parameters, histopathology, bacterial translocation, bacterial enzyme activity, and fecal microbiological analyses were evaluated. No mortality or treatment-related adverse effects were observed, and the LD50 of both strains was estimated to be greater than 5 × 10[11] CFU/rat. No significant treatment-related toxicological abnormalities were detected in the sub-chronic study, with a NOAEL of 1 × 10[11] CFU/rat/day. Probiotic administration was also associated with reduced harmful bacterial enzyme activity and altered selected fecal bacterial populations. In conclusion, L. helveticus DLBSA201 and DLBSA202 were well tolerated in Wistar rats at the tested dose range and study duration, and warrant further investigation using comprehensive microbiome and clinical approaches.}, }
@article {pmid42294611, year = {2026}, author = {Cui, Y and Li, L and Wu, S and Zhang, X and Wang, L and Yang, H and Yan, Z}, title = {Salivary Proteome-Microbiome Profiling in Burning Mouth Syndrome Might Highlight Mucin-Related Host-Microbe Features.}, journal = {Journal of oral rehabilitation}, volume = {}, number = {}, pages = {}, doi = {10.1111/joor.70242}, pmid = {42294611}, issn = {1365-2842}, support = {82170967//National Natural Science Foundation of China/ ; }, abstract = {OBJECTIVE: This pilot study was designed to analyze salivary proteomic and microbiome profile in burning mouth syndrome (BMS) and to explore the potential role of salivary mucins in barrier-related host-microbe interactions.<br><br>METHODS: Unstimulated saliva samples from BMS patients and healthy controls were analyzed using data-independent acquisition (DIA)-based proteomics and 16S rRNA gene sequencing. A multi-step strategy was applied to identify BMS-associated core salivary proteins. Biofilm formation, epithelial adhesion and injury, as well as molecular permeability using a transwell model were conducted to assess the mucosal barrier-microbe interactions.<br><br>RESULTS: Proteomic profiling defined 29 BMS-associated core proteins with MUC5B showing prominent differential expression. Microbiome analysis showed altered community structure in BMS saliva, including increased relative abundance of Rothia. Further in&#xa0;vitro explorations revealed that mucin triggered dispersal of the formed biofilms, reduced bacterial adhesion to oral epithelial cells, attenuated epithelial cell injury and decreased FITC-dextran permeability in a concentration-dependent manner.<br><br>CONCLUSION: BMS might be associated with mucin-related alterations in the salivary microenvironment, including reduced MUC5B and increased relative abundance of Rothia. Together with the in&#xa0;vitro findings, this might suggest that mucin-related barrier changes may be linked to altered host-microbe interactions in BMS.}, }
@article {pmid40555926, year = {2025}, author = {Wiele, N and de Melo Pereira, GV and da Silva Vale, A and de Mello Sampaio, V and Ribeiro-Barros, AI and Diniz de Souza, AF and Dos Santos, DVN and Góes-Neto, A and Soccol, CR}, title = {Comparative microbiomes reveal microbial signatures in coffee fermentation and flavor development across distinct Brazilian biomes.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {7}, pages = {207}, pmid = {40555926}, issn = {1573-0972}, support = {440343/2022-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; UIDB/00239/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, abstract = {Recent studies underscore the pivotal role of microbial terroir in shaping coffee fermentation and quality. However, the specific influence of regional microbiomes on flavor development remains underexplored. This study explored the link between the coffee farm microbiome and the resulting spontaneous fermentation process in Brazil’s Atlantic Forest and Semi-arid Cerrado biomes. Using Illumina-based amplicon sequencing, 972 prokaryotes and 435 eukaryotes were identified from coffee fruits, leaves, depulped coffee beans, over-ripe beans, soil, and temporal fermentation samples. During the fermentation process, microorganisms present in the pulped fruit (viz., Leuconostoc and Kazachstania) were the main microbial groups driving fermentation process across the two biomes, leading to the accumulation of primary (ethanol and lactic acid) and secondary (esters, aldehydes, higher alcohols, and ketones) metabolites. However, Leuconostoc and Kazachstania communities were significantly higher in the pulped fruit samples from the Atlantic Forest compared to the Cerrado biome. Therefore, the Atlantic Forest farm showed more stable microbial dynamics during the fermentation process and the formation of key flavor metabolites, such as methyl salicylate, linalool, ethyl linoleate, benzeneacetic acid ethyl ester, and phenylethyl alcohol. In contrast, the Cerrado samples exhibited higher microbial richness, leading to the emergence of co-dominant species such as Pantoea, Cutaneotrichosporon, Hyphopichia, Wickerhamomyces, and Cladosporium. Sensory evaluation revealed higher overall scores for the Atlantic Forest coffee, characterized by fruity, floral, and caramel notes, compared to earthy and herbal characteristics of Cerrado coffee. The findings demonstrate the influence of terroir-driven microbial communities on coffee fermentation and coffee quality, providing insights into optimizing fermentation for enhanced coffee flavor development and contributing to the growing field of microbial-assisted coffee production.}, }
@article {pmid41182402, year = {2025}, author = {Tekgül, ZB and Adıgüzel, A}, title = {Microbial viability assessment with PMA-qPCR: challenges, opportunities, and future directions.}, journal = {Archives of microbiology}, volume = {207}, number = {12}, pages = {343}, pmid = {41182402}, issn = {1432-072X}, abstract = {Since molecular analyzes are insufficient to distinguish living and non-living cells, lead to misleading results, and dead cells also multiply their DNA/RNA, a method that can give more sensitive results was needed. PMA (propidium monoazide), which is used to prevent the DNA of dead cells from negatively affecting the experimental results, is a viability indicator that binds only to the DNA of damaged cells and prevents them from being multiplied by PCR, and was first introduced in 2006. Recently the interest in the use of PMA in many fields such as microbiome and metagenomic studies, environmental microbiology, food microbiology, antibiotic and disinfectant effectiveness tests, clinical microbiology and diagnosis, and cell culture and biotechnology has increased considerably. Therefore, the purposes of use, principles, applications in various fields and limitations of PMA have been investigated. The current review of this vitality marker, which has a history of less than 20 years, will lead to its use of many new scientific studies and will provide convenience to scientists by bringing together studies on the use of this dye.}, }
@article {pmid41329407, year = {2025}, author = {Wang, W and Liang, Y and Cheng, T and Du, J and Zhang, Y and Jiang, L and Luo, X and Wang, Y}, title = {Gut Microbiota-Driven Modulation of Intestinal Barrier Function, Antioxidant Capacity, and Immune Response in Green-Footed Chicken by Dietary Fermented Chinese Herbal Compounds.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41329407}, issn = {1867-1314}, support = {16ZG6103//National Defense Basic Research Program/ ; }, abstract = {After the ban on antibiotics, fermented herbs have become an alternative. In the experiment, 960 one - day - old green - footed chickens were divided into four groups: T1 (basal ration), T2 (1% fermented herbs), T3 (3% fermented herbs), and T4 (5% fermented herbs). The experiment was conducted over a 69-day period. The health and growth of the chickens were assessed by evaluating growth performance, serum biochemistry, and gut microbiota. The results showed that during days 22–42 and 43–69, the average daily weight gain of T4 group chickens was significantly higher than that of T1 group (P < 0. 05). Serum biochemistry analysis showed that the IgA and IgG levels of T2, T3 and T4 group chickens were significantly higher than those of T1 group (P < 0. 05), while ALT activity was significantly lower than that of T1 group (P < 0. 05). In addition, the CD4+/CD8 + cell content in the blood of T2, T3 and T4 groups also increased (P < 0. 05). Notably, the Bursa of Fabricius Index in the T4 group was significantly enlarged (P < 0. 05). Gut immune and sequencing analyses showed that the villus height of the jejunum and duodenum increased significantly (P < 0. 05). 16s microbiome sequencing results showed that the gut markers of the test groups were Coriobacteriia, Subdoligranulum, and unidentified Actinobacteria. This study shows that fermentation of astragalus, cypress, dandelion, Scutellaria baicalensis, and honeysuckle herbs can modulate the intestinal microbial community structure through multiple pathways, promote gut health in broiler chickens, and thereby enhance growth performance.}, }
@article {pmid41372737, year = {2025}, author = {Shah, A and Doshi, G}, title = {Stress and neurodegeneration: mechanistic insights and therapeutic opportunities for preserving brain resilience.}, journal = {Acta neurologica Belgica}, volume = {}, number = {}, pages = {}, pmid = {41372737}, issn = {2240-2993}, abstract = {Neurodegenerative diseases such as Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, and Amyotrophic Lateral Sclerosis are strongly influenced by persistent stress, which accelerates both their onset and progression. This review explores the intricate interplay between chronic stressors, oxidative and metabolic imbalances, protein misfolding, inflammatory responses, and psychosocial adversity, and their cumulative impact on the aging brain’s capacity for homeostasis. The loss of cellular resilience due to prolonged stress leads to maladaptive outcomes, including mitochondrial dysfunction, sustained neuroinflammation, breakdown in proteostasis, and disruption of hypothalamic-pituitary-adrenal axis signaling, all of which amplify neuronal vulnerability. The detailed molecular pathways that underlie these phenomena, the article identifies key mediators such as Reactive Oxygen species, mitochondrial regulators, heat shock proteins, and proinflammatory cytokines that drive neurodegeneration. A comprehensive literature search was conducted using PubMed, Scopus, Web of Science, and Google Scholar up to 2025. Eligible publications included original research articles, clinical studies, and systematic reviews focusing on stress-related molecular pathways, oxidative metabolism, proteostasis, neuroinflammation, and therapeutic interventions in aging and neurodegenerative diseases. A qualitative synthesis of these studies was performed to identify key mechanisms, biomarkers, and emerging treatment strategies relevant to stress-induced neurodegeneration. Further, the review evaluates both established and emerging interventions aimed at mitigating these stress-driven processes. Lifestyle modifications such as aerobic exercise, calorie restriction, and cognitive behavioural therapies complement pharmacological agents like antioxidants, chaperone modulators, and anti-inflammatory drugs to enhance brain resilience and delay disease onset. Recent advances in the field, including integrated multi-omics profiling, biomarker discovery, and medicine approaches, promise to refine our ability to satisfy patients and deliver targeted therapies based on individual stress profiles. Additionally, the article discusses the neuroimmune-gut axis and the potential for interventions targeting microbiome-related inflammation. Early detection of stress-related biomarkers and personalized strategies holds considerable promise for improving clinical outcomes, enabling earlier diagnosis, and fostering tailored therapies that preserve cognitive function and independence in aging populations.}, }
@article {pmid41417288, year = {2025}, author = {Deng, J and Ji, J and Khan, A and Wang, Z and Xiang, W and Qiao, H and Salama, ES and Gu, J and Mao, C and Liu, P and Li, X}, title = {Antimicrobial Proteins from Limosilactobacillus fermentum GR-9 Inhibit Pathogens and Alleviate Salmonella Paratyphi B Infection in Mice.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41417288}, issn = {1867-1314}, support = {24ZDWA005//Natural Science Foundation of Gansu Province/ ; }, abstract = {Probiotics employ defense molecules that include antimicrobial peptides (AMPs) and lytic enzymes to inhibit pathogens; however, translating these mechanisms into applications remains challenging. In this study, Limosilactobacillus fermentum GR-9, isolated from “Jiangshui”, secretes AMPs and NlpC/p60 hydrolase, exhibiting 64%-77% of inhibition against both Gram-positive and Gram-negative pathogens. In mice model, GR-9 treatment reduced 93% of Salmonella Paratyphi B intestinal pathogen colonization effectively, similar to the antimicrobial norfloxacin. Moreover, GR-9 promoted beneficial microbiota, including Ligilactobacillus spp. and Bifidobacterium, highlighting its dual role in pathogen clearance and microbiome restoration. GR-9 further alleviated inflammation by modulating the immune response, significantly reducing the levels of pro-inflammatory cytokine (both TNF-α and IL-6) by 16% in both serum and intestinal tissues. Ultimately, this treatment highlights that probiotic-producing therapeutic compounds in situ offer a viable alternative to synthetic AMP production, addressing its critical challenges while providing a sustainable tool against antimicrobial-resistant pathogens.}, }
@article {pmid41432892, year = {2026}, author = {Seenivasan, SN and Vasudevan, SA and Raghupathy, AK and Rajan, F and Selvan, E and Sharma, SM and Muthusamy, RK and Paramasivam, L and Seethalakshmi, SP and Yogeswaran, S and Velmurugan, G}, title = {Intratumoural microbial metabolites in breast cancer: a longitudinal study on association with metastatic progression.}, journal = {Molecular and cellular biochemistry}, volume = {481}, number = {2}, pages = {1045-1057}, pmid = {41432892}, issn = {1573-4919}, support = {SRG/2020/001867//Science and Engineering Research Board/ ; }, abstract = {Delayed diagnosis and metastasis remain major challenges in breast cancer. While the gut microbiome’s influence on tumour progression is established, the presence and role of intratumoural microbial metabolites in breast cancer and their association with metastasis remain unexplored. Paired tumour and adjacent tissues were collected from 50 breast cancer patients at baseline. Patients were followed for five years; 10 who developed distant metastasis were classified as pre-metastatic, and 10 who remained disease-free formed the non-metastatic group. Untargeted LC–MS/MS-based metabolomics was performed to profile host and microbial metabolites. Multivariate analysis and pathway enrichment were used to identify discriminatory signatures. Elevated levels of carnitine, indole, tryptophan-derived metabolites, ceramides and polyamines were observed in tumour tissues on comparison with adjacent tissues. Interestingly, these metabolites were downregulated in tumour tissues of patients who progressed for metastasis (pre-metastatic) with increase in N-methylhistamine and taurolithocholic acid sulfate, suggesting metabolic reprogramming during metastatic priming. Baseline host–microbial metabolic disruptions in breast tumours are linked to future metastasis, with metabolites like indoles, bile acids, and polyamines showing promise as early biomarkers and therapeutic targets in precision oncology.}, }
@article {pmid41452511, year = {2025}, author = {Al-Adham, ISI and Ali Agha, ASA and Al-Remawi, M and Al-Akayleh, F and Al-Sheikh, A and Aburub, F and Collier, PJ}, title = {Probiotics, Psychobiotics, Paraprobiotics, and Postbiotics in Gut-Brain Axis Modulation: Multi-Omics and AI-Driven Precision Nutrition for Cognitive Health.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41452511}, issn = {1867-1314}, abstract = {The gut-brain axis has emerged as a key regulatory interface in cognitive function and neurological health, influenced by diet-driven microbial metabolism and host-microbiome interactions. Integrating multi-omics approaches with AI-driven precision nutrition offers novel insights into how diet modulates neuroimmune, neuroendocrine, and metabolic pathways. This article explores recent advances in microbiome research, highlighting the role of microbiota-derived extracellular vesicles (MEVs) as bioactive carriers that facilitate gut-brain communication by transporting neuroactive metabolites and immune modulators. These findings reveal an underexplored mechanism by which dietary interventions can reshape brain function at the molecular level. Additionally, synthetic biology and CRISPR-mediated microbiome engineering are advancing targeted interventions, allowing precise modulation of microbial gene expression to enhance neuroprotective pathways and mitigate neuroinflammation. Emerging strategies such as psychobiotics, paraprobiotics, and postbiotics further expand this therapeutic landscape, offering novel microbiome-based tools to influence neurotransmission, neuroimmune regulation, and cognitive resilience. Artificial intelligence (AI)-driven multi-omics integration further enables predictive modeling of microbiome-neurotransmitter interactions, hence refining personalized nutritional strategies for cognitive resilience and neuroprotection. However, challenges such as inter-individual variability, algorithmic biases, and ethical considerations in AI-driven dietary recommendations must be addressed to ensure the suitability of potential therapies. Future research should focus on in vivo validation of AI-guided dietary interventions through multi-modal neuroimaging, metabolomics, and transcriptomics. These advances position precision nutrition as a transformative tool in neuroscience, bridging microbiome science, AI, and personalized medicine to optimize brain health and mitigate neurodegenerative risks.}, }
@article {pmid41455009, year = {2025}, author = {Safari, F and Golafshan, F and Malekpour, E and Mirzaei, SA and Rouzbahani, H and Hajarzadeh, MO and Nasir Harandi, S and Nasirharandi, S and Noursina, A}, title = {Functional Proteins of Akkermansia Muciniphila: Impacts on Host Health and Metabolism.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41455009}, issn = {1867-1314}, abstract = {Akkermansia muciniphila, a mucin-degrading bacterium endemic to the human gut microbiome, plays a crucial role in modulating host physiology through the action of its functional proteins. This review compiles the latest insights into these proteins, elucidating their molecular mechanisms and their influence on host health. Notable proteins include Amuc_1100, Amuc_1631 (P9), Amuc_2109, and Amuc_1434, each of which is involved in key physiological processes. Amuc_1100 functions as an immune rheostat, engaging TLR2 and TLR4 pathways to modulate immune responses. Amuc_1631 enhances glucose homeostasis by promoting GLP-1 secretion, thereby linking gut microbiota to metabolic regulation. Amuc_2109 is implicated in the reinforcement of tight junctions, contributing to intestinal barrier integrity. In contrast, Amuc_1434 has demonstrated anti-tumor effects through the induction of apoptosis in colorectal cancer cells. Beyond these functions, these proteins also facilitate mucin degradation, support microbial cross-feeding, and promote resilience to gastrointestinal stressors. The review emphasizes their therapeutic potential for a range of conditions, including metabolic disorders, inflammatory bowel disease, cancer, and neuropsychiatric disorders. However, it also identifies translational hurdles such as the need for robust human clinical trials and the development of optimized delivery systems to harness their benefits fully. These findings position the proteins of A. muciniphila as promising targets for microbiota-centric therapeutic interventions.}, }
@article {pmid41483122, year = {2026}, author = {Aghdam, MM and Rezagholizadeh, L and Fazaeli, A and Moradi, A and Ojarudi, M}, title = {Nutritional modulation of metabolic signaling within the tumor microenvironment for cancer therapy.}, journal = {Molecular and cellular biochemistry}, volume = {481}, number = {3}, pages = {1155-1182}, pmid = {41483122}, issn = {1573-4919}, abstract = {The tumor microenvironment (TME) constitutes a complex ecosystem of cellular and non-cellular components. Together, these constituents exert a critical influence on cancer progression. A principal mechanism underlying this influence is metabolic reprogramming, in which tumor cells alter glucose, amino acid, and lipid metabolism to promote growth, survival, and immune evasion. Metabolic adaptation is further regulated by nutrient-sensing pathways, including mammalian target of rapamycin (mTOR), AMP-activated protein kinase (AMPK), and hypoxia-inducible factor (HIF), which often exhibit context-dependent and sometimes opposing functions in tumor and immune cells within the TME. Given this complexity, targeting metabolic vulnerabilities has become a promising therapeutic approach. In this context, nutritional interventions, such as caloric restriction, ketogenic diets, fasting-mimicking diets, protein or amino acid modulation, and lipid metabolism adjustments, aim to deprive tumors of essential nutrients, remodel the immunosuppressive TME, and increase cancer cell sensitivity to chemotherapy, radiotherapy, and immunotherapy. However, the efficacy of these interventions varies according to cancer type, oncogenic drivers, and immune contexture, and there is a risk of impairing anti-tumor immune function. Addressing these challenges will require personalized nutrition strategies that integrate tumor genetics, metabolic profiling, and the gut microbiome, together with technological advances for real-time monitoring. Progress in this area depends on a deeper mechanistic understanding of nutrient-immune interactions and the optimization of combination approaches for improved metabolic targeting in precision oncology. Accordingly, this review addresses a critical gap by synthesizing mechanistic and translational literature and outlining actionable priorities to advance nutritional modulation from preclinical research to clinical application.}, }
@article {pmid41493541, year = {2026}, author = {Dhiman, I and Nandni,  and Poria, V and Kumar, S and Yadav, R and Shaik, T and Bedwal, S and Wati, L}, title = {Plant growth promoting rhizobacteria (PGPR) mediated amelioration of plant tolerance to abiotic stresses: Drought, salinity, and heavy metals.}, journal = {Archives of microbiology}, volume = {208}, number = {2}, pages = {100}, pmid = {41493541}, issn = {1432-072X}, abstract = {Plants, being sessile organisms, are perpetually subjected to a spectrum of escalating abiotic stresses, which have detrimental repercussions on agriculture worldwide. In the forthcoming era of climate change and ecosystem degradation, fostering the use of beneficial microbiota in agroecosystems represents a major challenge towards sustainability. Some plant-associated bacteria, called Plant Growth Promoting Rhizobacteria (PGPR), may confer growth-promoting advantages to the host plant through enhancing nutrient uptake, altering hormone homeostasis, and/or improving tolerance to abiotic stress factors (drought, heavy metal, and salinity stress) in plants. These include promoting plant growth through the activation of antioxidant enzymes to detoxify reactive oxygen species, accumulation of compatible solutes to maintain osmotic homeostasis, suppression of lipid peroxidation to conserve membrane integrity, and emission of volatile organic compounds to induce systemic resistance. Additionally, PGPR synthesize phytohormones and exopolysaccharides that reinforce their persistence in soil, improve plant-water relations, and optimize nutrient uptake efficiency. In this regard, exploring the key ecological and evolutionary interactions between plants and their microbiomes is a prerequisite to developing innovative approaches and novel natural products that will complement conventional farming techniques. Collectively, these interactions fortify plant defense mechanisms, enhance physiological homeostasis, and promote adaptive plasticity in adverse environments. Herein, we describe the role of plant-microbe interactions in mitigating abiotic stress and fostering sustainable crop production. Leveraging multifactorial PGPR in agroecosystems strengthens the adaptive resilience of plants, reduces dependency on synthetic fertilizers, maintains soil microbiome integrity, cellular homeostasis, nutrient cycling, improves water retention, and ensures sustainable productivity in stress-prone and resource-limited regions.}, }
@article {pmid41524778, year = {2026}, author = {Sundaray, JK and Roy, D and Mohapatra, M and Mohanty, D and Das, II and Parida, CK}, title = {Metagenomic profiling of fish-associated microbiota: ecological perspectives from freshwater to marine environment-a review.}, journal = {Archives of microbiology}, volume = {208}, number = {2}, pages = {105}, pmid = {41524778}, issn = {1432-072X}, support = {Project Code: 1006449//Centre for Agricultural Bioinformatics (CABin) Project/ ; }, abstract = {Microorganisms play pivotal roles in maintaining host physiology and ecosystem balance, with fish-associated microbiomes offering unique insights due to the diverse habitats and feeding behaviours of their hosts. This review comprehensively explores the diversity, composition, and functional roles of gut and skin-associated microbial communities in fish across freshwater, brackish, and marine environments, with emphasis on recent advancements in metagenomic methodologies. Culture-independent techniques, particularly high-throughput and third-generation sequencing technologies, have revolutionized our ability to uncover microbial diversity, gene functions, and interspecies interactions. The fish gut microbiome, heavily influenced by factors such as diet, habitat, and host species, contributes significantly to nutrient metabolism, immune modulation, and physiological adaptation. Similarly, the skin microbiota provides a critical first line of defence, offering protection through competitive exclusion and antimicrobial activity. Functional metagenomics reveals microbial contributions to host metabolism, energy homeostasis, xenobiotic degradation, and environmental adaptation via the gut-brain axis and metabolic pathways. Emerging evidence highlights the bidirectional relationships between microbiota and host phenotypic plasticity. This review underscores the importance of integrative metagenomic approaches to decode complex microbial functions and their ecological relevance in aquaculture, with implications for sustainable fish health management, disease prevention, and improved productivity.}, }
@article {pmid41642480, year = {2026}, author = {Chriaa, O and Gdoura-Ben Amor, M and Mathlouthi, NEH and Slima, AB and Mhalhel, K and Turki, M and Kacem, FH and Germanà, A and Ben Ali, M and Gdoura, R}, title = {Probiotic intervention attenuates hypercholesterolemia and modulates gut microbiota in high-fat diet-fed rats.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {2}, pages = {74}, pmid = {41642480}, issn = {1573-0972}, abstract = {Hypercholesterolemia is a major risk factor for cardiovascular diseases and is often associated with lipid metabolism disturbances, liver dysfunction, and gut microbiota imbalances. Probiotics have emerged as promising agents to improve cholesterol management through gut microbiome modulation and anti-inflammatory effects. This study investigated the impact of probiotics on weight, lipid profiles, liver function, and gut microbiota composition in high-fat diet (HFD)-induced hypercholesterolemic rats. Rats were divided into five groups: normal diet (NG), HFD, HFD + Rosuvastatin (SG), HFD + probiotics (Lactobacillus spp.) (PG), and HFD + Rosuvastatin + probiotics (PSG). Probiotic supplementation significantly attenuated weight gain, reduced triglycerides (TG), total cholesterol (TCH), and LDL-C levels, and improved liver enzyme profiles (ALT, AST) compared to the HFD group. Histological analysis revealed that probiotics mitigated HFD-induced hepatocellular degeneration and decreased pro-inflammatory cytokine expression (IL-1β, TNF-α) in liver tissues. Gut microbiota analysis showed that probiotics modulated the relative abundance of key bacterial phyla and families, increasing beneficial taxa such as Lachnospiraceae and Lactobacillaceae. These findings suggest that probiotics can serve as a potential therapeutic strategy for managing hypercholesterolemia by improving lipid metabolism, protecting hepatic health, and reshaping the gut microbiome.Trial registration: CEREASFS4625/4022 (https//www.medecinesfax.org/fra/pages/518/projetscereas).}, }
@article {pmid41697296, year = {2026}, author = {Chengcheng, L and Yanduo, Z and Zhebin, W and Jianzhang, L and Yangtao, Z and Jun, L and Yu, L and Felemban, HR and Alyahyawy, OY and Alhomodi, AF and Hadadi, F and Shaibah, A and Bingzhi, L and Xianwei, W}, title = {Metagenomic analysis of fecal microbial communities in dairy goats from different farms.}, journal = {Protoplasma}, volume = {263}, number = {3}, pages = {1031-1045}, pmid = {41697296}, issn = {1615-6102}, abstract = {This study aims to investigate the differences in the microbial community structure of goat manure under various breeding environments, providing scientific evidence and theoretical support for healthy breeding practices. Gut microbiota is a key determinant of feed conversion, disease resistance and overall productivity in ruminants. The gut microbiome is an integral part of the digestive system. Its composition and functional traits markedly influence digestive efficiency, immune development, gut homeostasis and reproductive performance. Using four goat dairy farms in the Yangling, Shaanxi Province as study subjects, fecal samples were collected and analyzed using 16S rRNA sequencing technology, combined with α-diversity indices and β-diversity analysis. The results revealed significant differences in the microbial community structure of goat feces across different farms, with each farm exhibiting unique microbial communities. Each farm harboured distinct microbial signatures and functional profiles, providing microbiota-based targets for precision management of Guanzhong dairy goats.}, }
@article {pmid41731166, year = {2026}, author = {Zhang, X and Su, Q and Chen, X and Wang, S and Du, J and Chen, L and Xu, Q and Liu, C and Zhao, J}, title = {Inference of drowning sites of cases in the Pearl river based on microbial community profiling and random forest algorithm.}, journal = {International journal of legal medicine}, volume = {}, number = {}, pages = {}, pmid = {41731166}, issn = {1437-1596}, support = {82371901//National Natural Science Foundation of China/ ; 2024B04J0022//Funding by Science and Technology Projects in Guangzhou/ ; 2022JC35//Grant-in Aids for Scientific Research from Ministry of Public Security of the People's Republic of China/ ; 2022JC26//Grant-in Aids for Scientific Research from Ministry of Public Security of the People's Republic of China/ ; }, abstract = {Accurate inference of drowning sites remains a critical challenge in forensic investigations, particularly for corpses recovered from dynamic aquatic environments. Conventional methods, such as diatom testing, are limited by the absence or scarcity of diatoms in certain water bodies, labor-intensive morphological identification, and challenges in distinguishing morphologically similar species. In this study, we explored the feasibility of inferring drowning sites in human cases by integrating pulmonary microbial community profiling with machine learning. A total of 56 lung tissue samples from confirmed drowning victims were collected from four regions of the Pearl River’s Guangzhou section, including the central urban waterfront (site1), mid-reach brackish transition zone (site2), southern estuarine outflow zone (site3), and eastern tributary confluence (site4). High-throughput sequencing of the 16 S rRNA gene (V3 – V4 region) was performed to characterize microbial community composition. Significant spatial heterogeneity in pulmonary microbiota was observed across drowning sites, as demonstrated by alpha diversity analysis, unweighted UniFrac-based principal coordinates analysis, and differential abundance testing. Linear discriminant analysis effect size (LEfSe) further identified 111 differentially abundant microbial taxa, providing biological interpretation of spatial microbial variation among groups. To enable drowning site inference, microbial features at the genus level were subjected to feature engineering using a hybrid strategy combining variance thresholding and the Boruta algorithm. Through this process, 32 genera—including Ralstonia, Sphingomonas, Akkermansia, and Faecalibacterium—were selected as key microbial markers for geolocation. Multiple classification models, including Random Forest (RF), Decision Tree (DT), Support Vector Machine (SVM), and Logistic Regression (LR), were constructed and compared. The RF model exhibited the superior predictive performance, achieving a test set accuracy of 92.3% and a macro-average area under the receiver operating characteristic curve (AUC) of 0.949. External validation using five independent cases further confirmed the model’s practical utility, correctly predicting the drowning sites for four of the victims. Overall, This study preliminarily demonstrates the feasibility of inferring drowning locations through pulmonary microbiome analysis combined with machine learning in human samples, demonstrating the novel application of this approach to human cases. Future efforts should expand geographic sampling and integrate environmental metadata to enhance methodological robustness.}, }
@article {pmid41733709, year = {2026}, author = {Sahariah, P and Saikia, L and Bharali, A and Law, D and Sen, S and Dutta, PP}, title = {Modulation of mitochondrial biogenesis by flavonoids via SIRT1 signalling in metabolic syndrome: a systematic review.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {41733709}, issn = {1573-4978}, abstract = {Metabolic syndrome (MetS) is a complex cluster of metabolic abnormalities, including insulin resistance, central obesity, dyslipidemia, and hypertension. Dysregulated mitochondrial biogenesis has emerged as a key pathogenic feature of MetS, while flavonoids are increasingly recognised for their ability to modulate mitochondrial function through SIRT1-dependent pathways. This review aims to critically evaluate the role of flavonoids in modulating mitochondrial biogenesis via SIRT1 signalling in MetS, with emphasis on mechanistic evidence. A systematic review was conducted with a mechanistic focus, integrating preclinical and translational evidence to assess the role of flavonoids in MetS through SIRT1. A comprehensive literature search was performed in PubMed, Scopus, and Web of Science up to 2025 using the keywords “flavonoids,” “flavonols,” “SIRT1,” “AMPK,” “GLUT4,” and “metabolic syndrome.” Flavonols have emerged as the most extensively studied subclass of flavonoids in MetS models, with compounds such as quercetin, myricetin, and luteolin demonstrating consistent protective effects. These effects were mediated by AMPK activation, GLUT4 translocation, and mitochondrial biogenesis via SIRT1 signalling, thereby improving insulin resistance, dyslipidemia, and mitochondrial dysfunction. Despite robust mechanistic evidence, no clinical trials to date have evaluated flavonols in the context of MetS. Limitations, such as poor bioavailability, pharmacokinetic variability, and the absence of standardised formulations, continue to hinder their clinical translation. To overcome translational barriers, future research should prioritise randomised controlled trials, alongside innovative strategies such as nanoformulations, microbiome-targeted interventions, and flavonoid-inspired therapeutics. Addressing these gaps could establish the flavonoid–SIRT1 axis as a novel therapeutic avenue for MetS.}, }
@article {pmid41746458, year = {2026}, author = {Almeida, LF and Li, L and de Vries, RP and Sun, P and Maitan-Alfenas, GP}, title = {Enzymatic production of prebiotic xylooligosaccharides.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {3}, pages = {}, pmid = {41746458}, issn = {1573-0972}, abstract = {Xylooligosaccharides (XOS) have been shown to have prebiotic activities and therefore have beneficial effects on human and animal health. Production of these oligosaccharides from xylan often results in diverse mixtures, largely due to the variation in the xylan structure and the substrate specificities of the enzymes used to generate them. In this review, we will shortly describe the xylan structure and its variations, and the enzymes that are involved in its degradation. The use of these enzymes for the production of XOS and how this affects the variation in XOS structures will be addressed, which will then be linked to their prebiotic effects, especially related to modulation of the gut microbiome. The resulting health benefits will be summarized and finally the remaining challenges will be highlighted and suggestions for further improvement of their production will be provided.}, }
@article {pmid41779114, year = {2026}, author = {Medeiros, EB and Lidio, AV and Zabot, GC and Fenilli, GP and de Bem Silveira, G and Keller, GS and Carrion, FRA and De Felice, FG and Kluwe-Schiavon, B and Walls-Bass, C and Barichello, T and Budni, J}, title = {Exploring the Gut-Brain Connection: Are Probiotics the Next Frontier in Alzheimer's Disease Treatment?.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12602-026-10927-w}, pmid = {41779114}, issn = {1867-1314}, abstract = {Alzheimer’s disease (AD) is the most common form of dementia, historically considered exclusively as a neurological condition treated primarily with cholinergic and glutamatergic inhibitors. Recent evidence highlights the significant influence of peripheral systems, particularly the gut-brain axis, on AD pathology. The gut microbiota plays a critical role in both physiological and psychological functions, and its interactions may impact the integrity of the blood-brain barrier, potentially contributing to neurodegenerative processes. Emerging therapeutic strategies targeting the gut microbiome, including both pharmacological and non-pharmacological approaches such as probiotics and prebiotics, offer promising avenues for intervention. This review synthesizes current literature and illustrative data to elucidate the connections among the gut-brain axis, neuroinflammation, and neuroprotection, and their implications for the pathogenesis and potential treatment of AD.}, }
@article {pmid41793457, year = {2026}, author = {Hussain, B and Haouala, F and Fariduddin, Q}, title = {From night hormone to green signal: The journey of melatonin.}, journal = {Protoplasma}, volume = {}, number = {}, pages = {}, pmid = {41793457}, issn = {1615-6102}, support = {grant number IMSIU-DDRSP-RP25).//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)/ ; }, abstract = {Melatonin (MT), once considered exclusive to animals, is now recognized as a universal and multifunctional molecule in plants, playing pivotal roles in growth regulation, stress tolerance, and antioxidant defense. Since its discovery in plants in the mid-1990s, the presence of MT has been reported to be prevalent across diverse plant taxa. MT modulates plant responses to abiotic stresses such as heat, cold, salinity, drought, heavy metals, and UV radiation, as well as biotic stresses including pathogen attack and herbivory, primarily by regulating antioxidant enzymes, stress-responsive genes, hormone signaling pathways, and production of secondary metabolites. Advanced analytical techniques such as HPLC, LC-MS, and NMR have facilitated sensitive detection and structural characterization of MT in various plant species. Molecular studies have identified receptors of MT and its roles in regulating different processes, highlighting its integration with other phytohormones and signaling molecules. Genetic engineering tools have been proven effective in raising the level of endogenous MT levels, which has immense potential for enhancing crop resilience. Emerging evidence points to the role of MT in modulating the plant microbiome and systemic signaling, offering new avenues for research. Despite significant advances, key challenges remain in understanding the structure of receptors, signaling crosstalk, and the regulation of its biosynthesis under stress. This review discusses the methods for detecting MT in plants and evaluates its physiological, molecular, and functional aspects. Tracing the evolution of MT research in plants, from its initial discovery to the present day, key milestones, cross-talk, and signaling pathways of MT in plants have been discussed.}, }
@article {pmid41807782, year = {2026}, author = {Stevanoska, M and Cremona, M and Beekmann, K and Sturla, SJ and Aichinger, G}, title = {Interindividual variability in gut microbial formation of the hop phytoestrogen 8-prenylnaringenin results in elevated but sub-toxic internal exposures.}, journal = {Archives of toxicology}, volume = {100}, number = {6}, pages = {2397-2409}, pmid = {41807782}, issn = {1432-0738}, support = {SCAHT-AP_22_02//Swiss Centre for Applied Human Toxicology/ ; }, abstract = {The gut microbiome converts the prenylated polyphenol isoxanthohumol (iXN), a natural constituent of hops found in beer, into 8-prenylnaringenin (8-PN), a potent phytoestrogen associated with endocrine-disrupting effects. Following oral exposure, interindividual differences in microbiome composition may lead to variable systemic 8-PN concentrations and consequently to differences in susceptibility to toxicity. To characterize the contribution of gut microbiota to health effects of hop polyphenols, a human physiologically based kinetic (PBK) model that includes microbial 8-PN formation was developed. Ex vivo fecal fermentation coupled to LC–MS/MS revealed substantial interindividual variation in biotransformation capacity. Derived kinetic parameters were incorporated into the PBK model, which was subsequently used to predict systemic 8-PN exposure while accounting for interindividual variability. Model simulations indicated that high iXN metabolizers experience approximately two-fold more internal 8-PN exposure than low metabolizers. Estrogenicity of the predicted uterine 8-PN concentrations was assessed via alkaline phosphatase induction in Ishikawa cells. Even in high metabolizers, systemic 8-PN concentrations appeared to remain below levels of concern regarding endocrine disruption. These findings highlight the importance of accounting for interindividual variability in gut microbial biotransformation when predicting xenobiotic toxicokinetics and illustrate the applicability of microbiome-competent PBK modeling for predicting the systemic fate of gut microbial metabolites.}, }
@article {pmid41831055, year = {2026}, author = {Longoria, CR and DeSio, DD and Oydanich, M and Su, X and Chiles, EN and Kerkhof, LJ and Ibironke, O and Häggblom, MM and Wages, NP and Guers, JJ and Vatner, DE and Vatner, SF and Campbell, SC}, title = {Disruption of the gut microbiota in regulator of G protein signaling 14 knockout (RGS14 KO) mice alters the metabolome and reduces enhanced exercise capacity.}, journal = {European journal of applied physiology}, volume = {}, number = {}, pages = {}, pmid = {41831055}, issn = {1439-6327}, support = {826640//Office of Naval Research/ ; R01HL37368//NHLBI Division of Intramural Research/ ; R01HL106511//NHLBI Division of Intramural Research/ ; P30CA072720-6852//Division of Cancer Prevention, National Cancer Institute/ ; }, abstract = {Regulator of G-protein Signaling 14 Knockout (RGS14 KO) mice exhibit enhanced exercise capacity and health span, however the contribution of the gut microbiota to this phenotype remains unclear. This study integrated long-read rRNA operon amplicon sequencing and metabolomics to first determine how microbial composition and tissue metabolite profiles differ between RGS14 KO and their wild-type littermates. Next, we investigated how administration of antibiotics to perturb the gut microbiota may affect the RGS14 KO phenotype. Prior to antibiotic treatment (ABX), RGS14 KO mice outperformed WT littermates in maximal running distance and work performed, accompanied by elevated skeletal muscle citrate synthase, complex IV activity, and nitric oxide production. One week of ABX significantly reduced exercise capacity in both genotypes and markedly suppressed mitochondrial activity in RGS14 KO skeletal muscle. Gut microbiota profiling revealed similar phylum-level structure between genotypes but distinct species- and strain-level signatures. Metabolomics of brown adipose tissue (BAT) and quadriceps identified genotype-specific metabolic programs that were disrupted by ABX, including pathways related to amino acid metabolism, nucleotide turnover, and mitochondrial energetics. Collectively, these findings demonstrate that RGS14 KO mice harbor unique microbial and metabolic networks that support enhanced thermogenesis and exercise performance, and that microbiota depletion eliminates these advantages. This work establishes a mechanistic foundation connecting the gut microbiota to BAT and skeletal muscle metabolism, highlighting potential microbiome-targeted strategies to improve metabolic health and physical performance.}, }
@article {pmid41872932, year = {2026}, author = {Imtiaz, H and Liu, R and Li, QH and Zhou, CZ and Ying, YT and Tan, X}, title = {Reduction in microbiota-derived short-chain fatty acids contributes to the pathogenesis of pulmonary arterial hypertension.}, journal = {Respiratory research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12931-026-03591-9}, pmid = {41872932}, issn = {1465-993X}, support = {31872444//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Pulmonary arterial hypertension (PAH) is a progressive and fatal cardiopulmonary disorder, with growing evidence implicating proinflammatory gut dysbiosis in its pathogenesis. Fast growing broiler chickens (Gallus gallus) spontaneously develop PAH with histopathological features that closely resemble those of the human disease, providing a robust translational model. METHODS: Gut microbiota composition in PAH-afflicted broilers was compared to that of healthy controls to identify disease-associated microbial alterations. Microbiota depletion was achieved using a broad-spectrum antibiotic cocktail, and oral supplementation with calcium acetate, a short-chain fatty acid (SCFA) salt, was administered to assess therapeutic potential. Pulmonary cytokine expression was measured to evaluate inflammation. RESULTS: PAH-afflicted broilers exhibited gut microbial alterations similar to those observed in human patients, characterized by a reduction in bacterial genera involved in the production of anti-inflammatory metabolites, particularly SCFAs, and an increase in arginine- and tryptophan-producing taxa. Microbiota depletion selectively enriched SCFA-producing bacteria and prevented the onset of PAH. Calcium acetate supplementation significantly mitigated disease progression and reduced pulmonary expression of proinflammatory cytokines. CONCLUSIONS: These findings establish a causal relationship between microbiome-derived metabolites and pulmonary vascular remodeling, supporting SCFA-based interventions as a promising therapeutic strategy for PAH.}, }
@article {pmid41885972, year = {2026}, author = {Peng, B and Feng, Q and Wang, S and Zhao, X and Sheng, T and Wang, S and Liu, W and Liu, W and Huang, W and Meng, S and Zeng, S and Lin, R}, title = {Salivary microbiota composition and caries status in children with hearing impairment: a cross-sectional comparative study.}, journal = {Clinical oral investigations}, volume = {30}, number = {4}, pages = {}, pmid = {41885972}, issn = {1436-3771}, support = {201904010085//the Science and Technology Planning Project of Guangzhou/ ; 2025-2027-12//the Key Project of Medicine Discipline of Guangzhou/ ; }, abstract = {OBJECTIVES: To characterize the salivary microbiota structure in children with hearing impairment using 16 S rRNA gene sequencing and explore its potential association with caries burden. METHODS: A total of 114 hearing-impaired children aged 6–16 years underwent oral clinical examination and completed a questionnaire. From this cohort, 20 children (HI group) and 20 age- and sex-matched healthy children (HS group) were randomly selected for salivary microbiome sequencing. Analyses included alpha and beta diversity, LEfSe, and caries-stratified subgroup comparisons. RESULTS: Hearing-impaired children carried a heavy caries burden (overall prevalence: 93.9%; mean DMFT/dmft: 6.4 ± 3.9). Oral hygiene practices were generally suboptimal, with only 54.5% brushing twice daily and 41.6% using fluoride toothpaste. Beta diversity analysis significantly differed between groups (ANOSIM, R[2] = 0.057, P < 0.05). The HI group exhibited trends of increased Proteobacteria, Neisseria, and Gemella and decreased Veillonella and Capnocytophaga (all P > 0.05). LEFSe analysis revealed richer signature taxa in controls (e.g., Selenomonas, Tannerella), whereas hearing-impaired children showed limited enriched taxa, especially in the low-caries subgroup, indicating microbiota simplification. CONCLUSIONS: The oral microbiome of hearing-impaired children displays alterations in overall community structure, characterized by reduced diversity of signature microbial taxa and a trend toward ecological simplification. CLINICAL RELEVANCE: These findings identify oral microbial trends associated with hearing impairment, providing potential insights for early caries risk assessment and tailored preventive interventions in this vulnerable population.}, }
@article {pmid41915144, year = {2026}, author = {Liu, S and Zhang, H and Jin, C and Geng, X and Li, R and Wu, N and Wang, Y}, title = {Pediococcus pentosaceus JNL0053 Mitigates DSS-induced Colitis in Mice Via the IL-22-Gut Barrier Pathway.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41915144}, issn = {1867-1314}, support = {2023YFC2506000//National Key R&amp;D Program of China/ ; ZR2024QH412//Natural Science Foundation of Shandong Province/ ; JNL-2023010Q//Research Project of Jinan Microecological Biomedicine Shandong Laboratory/ ; }, abstract = {Ulcerative colitis (UC) is a chronic, relapsing inflammatory bowel disease that imposes a growing socioeconomic burden worldwide. Among emerging live biotherapeutics, the probiotic Pediococcus pentosaceus has shown therapeutic promise against UC, yet its molecular mode of action remains poorly understood. In this study, we isolated a novel strain P. pentosaceus JNL0053 from traditional Inner Mongolian cheese. By integrating transcriptomics, untargeted metabolomics, and 16 S rRNA gene profiling, we elucidated its protective efficacy in the dextran sulfate sodium (DSS)-induced murine colitis model. Mice receiving P. pentosaceus JNL0053 exhibited reduced body-weight loss, lower disease activity index scores and attenuated histopathological damage. This treatment reshaped the gut microbiota and was accompanied by a more balanced immune microenvironment, as evidenced by markedly decreased serum levels of pro-inflammatory cytokines interleukin (IL)-6 and IL-1β, alongside significantly elevated anti-inflammatory IL-10. N-acetylmuramate, identified as a key differential metabolite, potently promoted Th17 cell differentiation, leading to the secretion of IL-22 and IL-17 F. This, in turn, increased the expression of mucin 2 and occludin, thereby protecting the intestinal barrier against pathogens. Collectively, P. pentosaceus JNL0053 orchestrated multi-level crosstalk between host immunity and the gut microbiome to alleviate DSS-induced colitis. By activating the IL-22–MUC axis and restoring epithelial integrity, this food-derived P. pentosaceus JNL0053 represents a compelling therapeutic strategy for UC.}, }
@article {pmid41917507, year = {2026}, author = {Suparmin, A and Cahyani, LE and Ngadiman,  and Sudibyo, H and Handayani, DP and Kirana, RP}, title = {First genomic report of Enterobacter mori strain Pna8 from Pandanus conoideus with antagonistic activity against plant wilt pathogen Fusarium odoratissimum and Ralstonia solanacearum.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41917507}, issn = {1573-0972}, support = {Academic Excellence Program C of Universitas Gadjah Mada 431/UN1.P1/KPT/HUKOR/2024//Universitas Gadjah Mada/ ; }, abstract = {Plant wilt diseases are among the most destructive threats to global agriculture, largely due to the rapid adaptive capacity and treatment resistance of their causal pathogens. Endophytic bacteria represent a promising, sustainable alternative for disease management. Here, we report the first isolation and characterization of an endophytic bacterium, Enterobacter mori strain Pna8, from Pandanus conoideus, a tropical plant whose microbiome has remained unexplored. Strain Pna8 displayed strong antagonistic activity, inhibiting the fungal pathogen Fusarium odoratissimum by 55.9% and suppressing the growth of the bacterial wilt pathogen Ralstonia solanacearum, demonstrating dual biocontrol potential against both fungal and bacterial wilt diseases. Whole-genome sequencing revealed a 4.81 Mb genome comprising 4,433 coding sequences enriched in functions related to carbohydrate metabolism, phytohormone biosynthesis, phosphate solubilization, and stress tolerance. Importantly, Pna8 lacks pectinolytic CAZymes commonly associated with pathogenic E. mori, supporting its non-destructive, endophytic lifestyle. The genome also encodes unique biosynthetic gene clusters, including a lassopeptide absent from pathogenic relatives and siderophore variants related to frederiksenibactin. Comparative genomic analysis identified 119 singleton genes involved in transcriptional regulation, ion transport, and biofilm formation, indicating niche-driven evolution and ecological specialization. Collectively, these results highlight E. mori Pna8 as a novel and promising biocontrol resource for sustainable agriculture and tropical crop protection.}, }
@article {pmid41998320, year = {2026}, author = {Chaitra, HS and Pandiyan, K and Singh, J and Kalia, VK}, title = {Influence of sex and geographical location on culturable midgut bacterial diversity of pink bollworm, Pectinophora gossypiella larvae and their enzyme production potential.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {5}, pages = {}, pmid = {41998320}, issn = {1573-0972}, abstract = {Gut microbes play a dynamic role in many metabolic and physiological activities in insects. Recent studies have shown the difference in the gut microbiota associated with both sex and geographical locations. Deciphering the gut microbiota hosted with respect to their function in an economic pest like pink bollworm, Pectinophora gossypiella, is essential to understand the relationship between insect and its gut microbiome. In the present study, culturable midgut bacteria were isolated from Bt cotton resistant P. gossypiella larvae (male and female) collected from different cotton growing regions across India. A total of 37 bacterial isolates, 21 from male and 16 from female were obtained and identified based on 16S rRNA gene sequence. All the isolates belonged to two major phyla, Proteobacteria and Firmicutes. Only three isolates, Enterococcus casseliflavus, Enterobacter hormaechei subsp. xiangfangensis and Bacillus cereus were common to both the sexes, while the rest were specific to each sex. The study also indicated a higher bacterial diversity in populations collected from two locations, Adilabad and Khandwa. All the isolates were screened for extracellular hydrolytic enzyme production, protease, amylase, cellulase, xylanase and chitinase. The results revealed that, among 37 bacterial isolates, 33, 7, 6 and 4 isolates exhibited protease, cellulase, chitinase and amylase activity, respectively. Maximum production of protease was noticed in Pantoea dispersa GM2 (0.39 ± 0.02 U/ml), amylase from B. cereus RF2 (0.17 ± 0.04 U/ml), cellulase from Burkholderia contaminans KhF1 (endoglucanase – 8.29 ± 1.60 U/ml; exoglucanase – 12.77 ± 1.5 U/ml; β-glucosidase – 10.01 ± 0.7 U/ml) and chitinase from E. hormaechei subsp. xiangfangensis AuF (87 ± 0.02 U/ml). The findings suggest that the gut bacterial community is influenced by both sex and geographical locations and the enzyme production are confined to specific locations. Further molecular studies would reveal the factors responsible for microbial community diversity and enzyme production.}, }
@article {pmid42020671, year = {2026}, author = {Cruz, D and Saati-Santamaria, Z and Achury-Arrubla, L and Garcia-Fraile, P}, title = {From Wild to Farm: Gut Bacteriome Differences and Probiotic Potential of Pantoea Agglomerans in Two-Spotted Cricket (Gryllus Bimaculatus) Rearing.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {42020671}, issn = {1867-1314}, abstract = {The gut microbiome plays a crucial role in insect nutrition and performance, yet its targeted exploitation in cricket farming remains underexplored. Here, we combined gut microbiota profiling of wild and farmed Gryllus bimaculatus with probiotic testing of host-derived bacterial isolates to explore microbiome-informed strategies for sustainable cricket farming. Wild crickets exhibited higher Shannon diversity but lower phylogenetic diversity than farmed counterparts. Wild populations were enriched in Oscillospiraceae and Christensenellaceae families, while farmed crickets showed higher abundance of Parabacteroides. From 199 bacterial isolates, wild populations showed higher frequencies of uricolytic capabilities (44% vs. 31%), related to nitrogen recycling, while farmed crickets had more pectinolytic isolates (70% vs. 50%), linked to plant fiber degradation. Pantoea agglomerans I53BLB, which demonstrated broad enzymatic capabilities, was selected for probiotic evaluation; we further provide its genome sequence and analysis to contextualize its metabolic and probiotic potential. A feeding experiment with a 2 × 3 factorial design (two diets × three probiotic treatments, n = 10 replicates per group) compared control chicken feed versus a high-fiber diet formulated with agricultural by-products, each supplemented with water, live or heat-inactivated P. agglomerans. A significant diet × probiotic interaction was observed for weight gain (χ[2] = 18.8, p = 0.0021) and adult emergence (χ[2] = 17.7, p = 0.0033). Live P. agglomerans enhanced performance only when combined with the high-fiber diet, with individuals reaching a mean wet weight of 0.602 g compared to 0.451 g (heat-inactivated, p = 0.035) and 0.427 g (water control, p = 0.003), and a significantly higher adult emergence rate (37%) compared to all other treatment combinations (13%, p < 0.05), suggesting a symbiotic effect likely related with carbohydrate digestion. No effects were observed on survival or reproductive output. Notably, the high-fiber diet alone performed comparably to commercial feed, suggesting potential for sustainable cricket production using agricultural by-products. These findings demonstrate the feasibility of microbiome informed probiotic strategies to enhance cricket farming efficiency while reducing feed costs.}, }
@article {pmid42020676, year = {2026}, author = {Purohit, HV and Chakraborty, J and Kothari, RK and Bhatt, AR}, title = {Gene Exchange Mechanisms in Natural and Engineered Probiotics Within the Human Gut Implications for Antibiotic Resistance and Metabolic Modulation.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {42020676}, issn = {1867-1314}, abstract = {The human gut microbiome is a dynamic and densely populated ecosystem where microbial gene exchange plays a central role in shaping both ecological interactions and host physiology. This review critically examines the mechanisms and implications of horizontal gene transfer (HGT) among natural and engineered probiotics within the human gut, with a specific focus on antibiotic resistance dissemination and metabolic modulation. We provide an in-depth analysis of the molecular pathways of conjugation, transformation, and transduction under anaerobic gut conditions, highlighting their roles in the spread of mobile genetic elements, including antibiotic resistance genes (ARGs) and functional metabolic traits. Special emphasis is placed on the dual nature of gene exchange: while beneficial traits such as vitamin biosynthesis and polysaccharide degradation can be horizontally acquired to enhance probiotic efficacy and host-microbe symbiosis, the uncontrolled dissemination of ARGs or synthetic constructs poses significant clinical and ecological risks. Through a synthesis of recent findings from metagenomics, microbial ecology, and synthetic biology, we explore how natural probiotics may act as reservoirs of ARGs, and how engineered strains—if not properly contained—may contribute to genetic instability in the gut. We also evaluate current containment strategies such as chromosomal integration, kill switches, auxotrophy, and orthogonal circuit design to limit horizontal spread, alongside emerging tools for in situ gene transfer monitoring. Finally, we discuss regulatory challenges and propose a context-dependent risk assessment framework in which the consequences of probiotic gene exchange are determined by cargo properties, host ecological niche, gut inflammatory status, and biocontainment design.}, }
@article {pmid42020691, year = {2026}, author = {Vávrová, P and Janďourek, O and Coraça-Huber, DC and Spiegel, C and Nachtigal, P and Krátký, M and Konečná, K}, title = {Host soluble plasma factors increase dual-species Staphylococcus epidermidis and Candida albicans biofilm biomass without enhancing stress tolerance.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-49557-1}, pmid = {42020691}, issn = {2045-2322}, support = {SVV 260 664//Univerzita Karlova v Praze, Czechia/ ; NW24-05-00539//Ministerstvo Zdravotnictv&#xed; Cesk&#xe9; Republiky/ ; }, abstract = {Staphylococcus epidermidis (S. epidermidis) and Candida albicans (C. albicans) are common members of the human microbiome and opportunistic pathogens, forming mixed biofilms, leading to catheter-associated bloodstream infections or wound infections. They are increasingly difficult to treat, highlighting the urgent need for new antibiofilm strategies. Understanding how host environmental factors affect microbial communities is crucial for their development. Based on our previous findings, we investigated whether higher levels of host soluble factors in human plasma (HP) and freeze-thaw lysed sheep red blood cells (FT-RBC) support the formation of S. epidermidis-C. albicans dual-species biofilm and increase resilience. Tryptic soy broth, RPMI 1640, and Lubbock media with HP or FT-RBC supplementation were used for in vitro biofilm formation. Total biomass, individual microorganisms, key matrix components (carbohydrates, proteins, eDNA), and antimicrobial tolerance were evaluated. Our results showed that although higher concentrations of HP in Lubbock medium support the formation of complex dual-species biofilm biomass, this does not correlate with enhanced antimicrobial tolerance. In contrast, higher adaptive resistance was detected in less heterogeneous biofilms formed under nitrogen-limited conditions in RPMI 1640-supplemented medium. These findings indicate that biofilm resilience is not solely dependent on biomass amount and complexity, underscoring the need to better understand host-biofilm interactions.}, }
@article {pmid42020874, year = {2026}, author = {Xia, Y and Chen, S and Deng, Z and Ye, C and Wu, H and Wang, Y and Guo, S and Guo, N and Yang, J and Tao, Z and Xiong, X and Guo, Y and Shang, Y}, title = {Soil microbial succession for forensic estimation of postmortem interval and decomposition site identification.}, journal = {International journal of legal medicine}, volume = {}, number = {}, pages = {}, pmid = {42020874}, issn = {1437-1596}, support = {82402196//Natural Science Foundation of China/ ; 82572150//Natural Science Foundation of China/ ; 2024JJ6546//Natural Science Foundation of Hunan Province/ ; }, abstract = {Estimating the postmortem interval (PMI) and identifying decomposition sites are important challenges in forensic science. The soil microbiome has shown potential in both applications. This study used pig models to simulate human decomposition and analyzed soil microbial succession over both short (0–11 days) and mid-to-long-term (up to 10 months) intervals to develop a PMI estimation model, while simultaneously comparing control and decomposition soils to assist in identifying potential corpse deposition sites. We built KNN (K-nearest neighbors) models at the genus level, which achieved high performance in short-term PMI estimation. Furthermore, a Linear Discriminant Analysis (LDA) model demonstrated robust performance in long-term PMI estimation, relying primarily on animal-associated microbial genera. Additionally, the KNN machine learning model effectively distinguished soils impacted by cadavers. This study provides a promising tool for estimating PMI and identifying potential body deposition sites.}, }
@article {pmid42031861, year = {2026}, author = {Kamyab, M and Motamedi, H}, title = {Introducing silica-solubilizing and plant growth-promoting bacteria from sugarcane as inducers of drought stress tolerance.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-48745-3}, pmid = {42031861}, issn = {2045-2322}, abstract = {Today’s sugarcane cultivation is faced with abiotic stresses including drought, salinity, heat and water limitation leading to, its reduced growth, yield, and economic productivity. Given the significant role of silica in alleviating these negative effects as well as pathogens, silica solubilizing bacteria opens an eco-friendly and sustainable approach to overcome these challenges. The aim was to find native silicate solubilizing bacteria from sugarcane and assessment their plant growth-promoting potential. Extensive screening was done from five sugarcane fields and symbiont bacterial species were qualitatively and quantitatively selected with regard to silicate solubilization. The isolates were explored for plant growth-promoting traits. As a result, Pantoea ananatis ASEna, Pantoea dispersa E345Se, and Pseudomonas migulae DSb were identified as high silica solubilizers. These also exhibited antifungal activity; phosphorus and potassium solubilization; sulfur oxidation; protease and cellulose production; auxin, hydrogen cyanide, and ammonia synthesis; nitrogen fixation; tolerance to heat, salinity (10%), drought, and pH stresses. The identified genera are part of the core sugarcane microbiome, and this is for the first time that these species have been documented as possessing growth-promoting traits for sugarcane and silicate-solubilizing capabilities. Currently, sugarcane producers are seeking for solutions to mitigate biotic and abiotic stresses and enhance crop yield in sugarcane fields. The strategic selection of bacteria that not only solubilize silica but also possess growth-promoting traits and can supply other essential nutrients to stimulating plant growth through various mechanisms, can enhance the effectiveness of silicate-solubilizing bacteria and make them suitable candidates for development of biofertilizers.}, }
@article {pmid42032090, year = {2026}, author = {Wang, R and Li, W and Yin, Y and Jiang, S and Yang, B and Yu, R}, title = {Human milk-derived Bifidobacterium longum subsp. infantis CCFM1269 alleviates food allergy by modulating gut microbiota and restoring intestinal barrier.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-50287-7}, pmid = {42032090}, issn = {2045-2322}, abstract = {Food allergy (FA) is an immune-mediated disorder increasingly linked to intestinal dysbiosis and epithelial barrier dysfunction. This study evaluated the protective effects of Bifidobacterium longum subsp. infantis CCFM1269, a human milk-derived probiotic, using a β-lactoglobulin-induced FA mouse model. Oral administration of CCFM1269 significantly reduced allergic symptoms, including poor weight gain, diarrhea, and elevated allergy scores. The probiotic restored immune balance by downregulating IL-4 and IL-17 A and upregulating IL-10 and IFN-γ in both serum and jejunal tissues. It also alleviated oxidative stress by increasing superoxide dismutase activity and decreasing malondialdehyde levels. CCFM1269 enhanced intestinal barrier integrity through the upregulation of tight junction proteins Occludin, Claudin-1, and ZO-1. Microbiome analysis showed that CCFM1269 reshaped the gut microbial structure by increasing Helicobacter and reducing Alloprevotella and Bacteroides, taxa strongly associated with FA severity. Correlation analysis confirmed that these microbial changes were linked to improvements in immune and barrier function. Collectively, these findings indicate that human milk-derived CCFM1269 alleviates FA through microbiota modulation and epithelial restoration, supporting its potential as a probiotic strategy for preventing and treating FA.}, }
@article {pmid42032553, year = {2026}, author = {Somarathna, MT and Leuke Bandara, D and Gunasekare, SKV and Nawarathna, LS and Wijetunge, S and Paranagama, MP and Gunawardhana, ND}, title = {Molecular detection of Helicobacter pylori in saliva of Sri Lankan adults with periodontitis, gastritis or both conditions.}, journal = {BMC oral health}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12903-026-08421-4}, pmid = {42032553}, issn = {1472-6831}, support = {Multidisciplinary Research Grant -2024 (MRG) 500//University Research Council, University of Peradeniya, Peradeniya, Sri Lanka/ ; }, abstract = {BACKGROUND: Periodontitis is an immuno-inflammatory disease affecting the tooth-supporting structures, primarily caused by dysbiosis of the oral microbiome. The involvement of one of the gastric pathogens, Helicobacter pylori, has been reported among individuals with periodontitis. However, the evidence regarding the association between oral H. pylori, periodontitis, and gastritis remains inconsistent and has not been investigated in Sri Lanka. Therefore, this study aimed to detect the oral H. pylori in a cohort of Sri Lankan adults and to evaluate its association with periodontitis and gastritis. METHODS: This cross-sectional study recruited 214 adults from two tertiary care institutes in Sri Lanka. Participants were categorized into four groups: (A) periodontitis only (n = 60), (B) gastritis only (n = 51), (C) both periodontitis and gastritis (n = 48), and (D) healthy controls without periodontitis or gastritis (n = 55). Unstimulated saliva samples were collected, DNA was extracted, and H. pylori was detected using PCR targeting the 16S rRNA gene. Positive samples were confirmed by ureA gene amplification. Detection rates were compared using Fisher’s exact test with Holm correction for multiple comparisons (p < 0.05). RESULTS: H. pylori was detected in 44 of 214 participants (20.6%; 95% CI 15.4–26.5%): periodontitis only 20.0%, gastritis only 21.6%, both conditions 31.3%, and controls 10.9%. The highest detection rate was observed in individuals with both periodontitis and gastritis (31.3%; OR 3.71, 95% CI 1.31–10.55). Although this difference did not reach statistical significance after Holm correction (adjusted p = 0.084), it represents a biologically meaningful trend warranting further investigation with larger sample sizes. No significant associations were found with age or sex (p > 0.05). CONCLUSION: H. pylori DNA is detectable in the saliva of Sri Lankan adults, with the highest detection rate observed in individuals with both periodontitis and gastritis (31.3%). This clinically relevant trend suggests that the inflamed periodontium may provide a favorable niche for the pathogen, although larger studies are needed to confirm statistical significance. This study represents the first investigation in Sri Lanka to identify the oral cavity as a potential extragastric niche for H. pylori using salivary detection. However, PCR-based detection cannot distinguish viable colonization from transient contamination. Longitudinal studies with culture-based methods and viability testing are required to clarify whether the oral cavity serves as an active reservoir for H. pylori transmission and reinfection.}, }
@article {pmid42043454, year = {2026}, author = {Oyedokun, PA and Alade, TA and Olawale, IJ and Laoke, TS and Adeyemi, MO and Oyedokun, MD and Olaolu, OA and A S, LS and Olayemi, SB and Ndako, JA}, title = {Translating microbial dysbiosis into brain health interventions: a focus on the oral-gut-reproductive inflammatory pathways.}, journal = {Archives of microbiology}, volume = {208}, number = {7}, pages = {}, pmid = {42043454}, issn = {1432-072X}, abstract = {Alterations in the microbial communities along the oral, gut, and reproductive (OGR) axis are increasingly recognized as major contributors to systemic inflammation, endocrine dysregulation, and neuroimmune pathophysiology. Scientific evidence has demonstrated that OGR dysbiosis is associated with neuroimmune signaling potentially by the leakage of lipopolysaccharides and cytokine cascades, with associated disruption of blood-brain barrier integrity, degeneration of the neurovascular unit, dysregulation of the hypothalamic-pituitary-adrenal axis, and disruption of neurotransmitter balance via abnormal tryptophan metabolism. The mechanisms have been implicated in the development of several neuropsychiatric and neurodegenerative disorders across preclinical and human observational models. Novel microbiome-targeted approaches, including antimicrobial therapy, prebiotics, probiotics, dietary modifications, and hormone-microbiota-targeting treatment, demonstrate potential to restore microbial balance and reduce neuroinflammation, with mechanistic effects on neurotransmitter production, barrier protection, and immune tolerance. However, these effects have been demonstrated predominantly in preclinical and animal models; robust evidence from well-powered human clinical trials is currently limited. Accordingly, these approaches should be considered exploratory and hypothesis-generating rather than established clinical strategies, and their translation to patient care requires rigorous evaluation in controlled human trials. This review addresses the gap in understanding how dysbiosis in these interdependent microbial ecosystems transmits inflammatory and metabolic signals that impair neurophysiology. This review presents a translational perspective on OGR-axis modulation as a frontier for the prevention and management of brain disorders, integrating microbial, immune, endocrine, and neural perspectives. Exploring these insights would birth a paradigm shift from symptom-management-based brain health interventions to microbiota-specific interventions.}, }
@article {pmid42043591, year = {2026}, author = {Hu, Y and Lin, H and Jiang, M and Lin, C and Li, H and Sun, J and Chen, K and Yu, Y and Liu, C}, title = {Host-derived Bacillus velezensis enhances intestinal structure, antioxidant capacity, and pathogen resistance in the American bullfrog (Aquarana catesbeiana).}, journal = {Archives of microbiology}, volume = {208}, number = {7}, pages = {}, pmid = {42043591}, issn = {1432-072X}, support = {KB23Y1101//Application Research and Extension of Fermented Chinese Herbal Medicine in Bullfrog Farming under the 2023 Rural Revitalization Strategy/ ; }, abstract = {The development of host-derived probiotics presents a forward-looking nutritional component strategy for sustainable aquaculture. However, research on host-associated probiotics for the globally farmed American bullfrog (Aquarana catesbeiana) is limited. The research put Bacillus velezensis (BLS) isolated from bullfrog guts determine its probiotic potential. Bullfrogs were divided into two groups: one fed a control diet and the other fed a diet enriched with 1 × 10[8] CFU/g BLS for 7 weeks. BLS supplementation significantly enhanced growth performance and markedly decreased mortality after challenge with Streptococcus agalactiae. Relative to controls, the BLS cohort demonstrated heightened activity of essential antioxidant enzymes (CAT, GSH-Px, and SOD) and lower malondialdehyde levels in liver and intestinal tissues. Moreover, BLS supplementation enhanced intestinal structure, demonstrated by markedly increased villus height and goblet cell count, alongside enhanced hepatocyte arrangement and tissue integrity. Gut microbiome analysis revealed that BLS elevated the proportion of Firmicutes while decreasing the proportion of harmful genera such as Elizabethkingia. These findings suggest that the probiotic effects are mediated through the modulation of gut barrier function and microbial community. In conclusion, dietary supplementation with B. velezensis BLS enhanced growth, pathogen resistance, antioxidant capacity, and bowel health in bullfrogs through enhanced intestinal morphology and microbiome regulation. Consequently, supplementation holds significant promise as a probiotic in bullfrog farming.}, }
@article {pmid42050727, year = {2026}, author = {Ivanova, M and Svensmark, B and Bruun Jensen, EE and Aarestrup, FM and Vigre, H and Otani, S}, title = {Metagenomics provides broad detection of pathogens, antimicrobial resistance, and virulence genes in pig diarrhoea and complement conventional methods.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00577-2}, pmid = {42050727}, issn = {2524-4671}, abstract = {BACKGROUND: Post-weaning diarrhoea (PWD) remains a major cause of morbidity in pig production and is commonly associated with enterotoxigenic Escherichia coli (ETEC). Conventional diagnostics rely on culturing and targeted qPCR, which provide limited resolution of pathogen diversity, virulence and antimicrobial resistance. Here, we evaluated Oxford Nanopore Technologies (ONT) metagenomic sequencing as a diagnostic tool for direct detection of pathogens, virulence factors and antimicrobial resistance genes (ARGs) from diarrhoeal pig faeces. RESULTS: Twenty-six diarrhoeal and six healthy pig faecal samples were analysed using culture, qPCR and ONT metagenomics with both high-output and rapid workflows. Culturing recovered 26 haemolytic E. coli and nine Clostridium perfringens isolates. PromethION metagenomics detected a significantly higher diversity of bacterial species, virulence factors and ARGs compared with GridION. Direct read mapping achieved 71–96% genome coverage for six E. coli isolates. Fourteen high- and medium-quality E. coli metagenome-assembled genomes (MAGs) were reconstructed, of which seven clustered closely with corresponding cultured isolates. All virulence factors detected in isolates were captured by metagenomics, while metagenomics identified additional fimbrial and enterotoxin genes not recovered by culture. Metagenomic ARG profiling identified resistance to 16 antibiotic classes, compared to eight classes in cultured isolates. No ESBL, carbapenemase or mcr genes were detected. CONCLUSIONS: Long-read ONT metagenomics enables culture-independent, strain-resolved characterisation of the pig gut microbiome during PWD, capturing pathogen diversity together with virulence and antimicrobial resistance profiles. This approach reveals within-sample strain heterogeneity and functional potential that are not resolved by conventional culturing, supporting its value for studying microbial ecology and dysbiosis in diseased animal microbiomes.}, }
@article {pmid42280338, year = {2026}, author = {Zhang, S and Liu, K and Shi, L and Yan, C and Wang, A and Liu, A and Guo, H and Xie, A and Kong, XJ}, title = {Development of a Metagenomics-Guided Personalized Synbiotic Protocol for Children with Autism Spectrum Disorder: An Exploratory Case Series.}, journal = {Nutrients}, volume = {18}, number = {11}, pages = {}, pmid = {42280338}, issn = {2072-6643}, support = {92436//Boston Children's Hospital/ ; 233263//Massachusetts General Hospital/ ; }, mesh = {Humans ; *Synbiotics/administration &amp; dosage ; *Metagenomics/methods ; Child, Preschool ; *Autism Spectrum Disorder/microbiology/therapy ; Male ; Child ; Female ; Pilot Projects ; Feces/microbiology ; *Gastrointestinal Microbiome ; Treatment Outcome ; *Precision Medicine/methods ; }, abstract = {BACKGROUND/OBJECTIVES: Gut microbiota dysregulation has been increasingly implicated in the pathophysiology of autism spectrum disorder (ASD), yet clinical responses to standardized probiotic interventions remain inconsistent, likely reflecting substantial inter-individual variability in baseline microbiome composition, host-microbe interactions, immune tone, and metabolic function. Here, we present a pilot implementation of a metagenomics-guided, personalized synbiotic intervention in children with ASD using the Systematic Microbiome Assessment and Reconstruction Therapy (SMART) framework.<br><br>METHODS: Seven children (aged 5-12 years) underwent longitudinal fecal shotgun metagenomic profiling, and dietary habits, food sensitivities, and regional dietary background were recorded as contextual factors potentially influencing microbiome composition and response to intervention. Individualized synbiotic formulations were constructed based on microbial taxonomic composition and inferred functional capacity and iteratively refined over time. Gastrointestinal outcomes were assessed through caregiver-reported clinical observations, whereas behavioral changes were evaluated using standardized instruments.<br><br>RESULTS: Several participants demonstrated improvements in gastrointestinal symptoms and selected behavioral domains. Notably, in a subset of participants, improvements in gastrointestinal function preceded measurable behavioral changes.<br><br>CONCLUSIONS: Although limited by a small sample size and lack of a control group, these findings provide preliminary evidence supporting the feasibility of implementing a metagenomics-guided personalized synbiotic framework in ASD and generate hypotheses for future investigation. This work presents a preliminary conceptual framework for integrating microbial composition and inferred functional profiling into individualized intervention design and highlights the potential value of microbiome-informed stratification in future studies of treatment response. Larger controlled studies with objective outcome measures are warranted to further evaluate feasibility, reproducibility, and potential clinical utility.}, }
@article {pmid42280343, year = {2026}, author = {Biagioli, V}, title = {Probiotics, Maternal Microbiome, and Early-Life Programming: A One Health Perspective on Perinatal and Infant Health.}, journal = {Nutrients}, volume = {18}, number = {11}, pages = {}, pmid = {42280343}, issn = {2072-6643}, mesh = {Humans ; *Probiotics/administration &amp; dosage ; *Gastrointestinal Microbiome/physiology ; *Infant Health ; Female ; Pregnancy ; Infant ; Infant, Newborn ; Developmental Origins of Health and Disease ; Maternal Nutritional Physiological Phenomena ; }, abstract = {In recent years, the role of the gut microbiota in regulating human health has gained increasing scientific attention, particularly during early life [...].}, }
@article {pmid42280356, year = {2026}, author = {Kim, EJ and Hong, DK and Choi, ID and Shim, JJ and Lee, JH and Jung, WK}, title = {Effect of Latilactobacillus curvatus HY7601 and Lactiplantibacillus plantarum KY1032 on Serum Triglyceride Levels and the Gut-Metabolic Axis: A Randomized, Double-Blind, Placebo-Controlled Clinical Trial.}, journal = {Nutrients}, volume = {18}, number = {11}, pages = {}, pmid = {42280356}, issn = {2072-6643}, mesh = {Humans ; Double-Blind Method ; *Triglycerides/blood ; *Probiotics/administration &amp; dosage/therapeutic use ; Female ; Male ; *Gastrointestinal Microbiome ; Middle Aged ; *Hypertriglyceridemia/blood/therapy/microbiology ; Adult ; Cholesterol, LDL/blood ; Biomarkers/blood ; *Lactobacillaceae ; *Lactiplantibacillus plantarum ; Overweight/blood ; }, abstract = {Background/Objectives: Hypertriglyceridemia is a critical cardiovascular risk factor, and the probiotic combination of Latilactobacillus curvatus HY7601 and Lactiplantibacillus plantarum KY1032 (HY+KY) has emerged as a potential therapeutic strategy, though clinical validation in adults with mild hypertriglyceridemia (HTG) is needed. Methods: In this randomized, double-blind, placebo-controlled, 12-week trial, a total of 100 overweight participants with mild HTG were randomized (n = 50 per group). Ultimately, 80 participants completed the study without major protocol violations and were evaluated in the Per-Protocol Set (probiotics group: n = 41; placebo group: n = 39). Primary outcomes included changes in serum lipid profiles such as triglycerides (TG) and LDL cholesterol (LDL), metabolic biomarkers, and gut microbiota composition analyzed via 16S rRNA gene sequencing. Results: HY+KY supplementation led to significant reductions in serum TG (158.61 ± 23.17 to 139.54 ± 54.31 mg/dL, p = 0.009) and LDL (129.22 ± 28.45 to 111.34 ± 21.03 mg/dL, p = 0.005) compared to baseline, while the placebo group showed no significant changes. Furthermore, the HY+KY group exhibited a significant increase in Apolipoprotein CII (ApoC2, p = 0.034) and a reduction in fasting glucose levels (p = 0.021). Microbiome analysis revealed that HY+KY significantly increased alpha diversity (Shannon index, p = 0.012) and significantly altered the microbial community structure (beta diversity, p = 0.015). Co-occurrence network analysis identified Lactiplantibacillus as a highly connected central node that is strongly associated with the favorable shifts in clinical biomarkers. Conclusions: HY+KY supplementation was associated with improved fasting TG and LDL profiles in adults with mild HTG, alongside coordinated changes in ApoC2, fasting glucose, and gut microbiota structure. These findings support the potential of probiotic supplementation as a preventive nutritional approach in borderline HTG.}, }
@article {pmid42280361, year = {2026}, author = {Chiesa, A and Generali, L and Butera, A and Filippini, T and Lanteri, V and Veneri, F}, title = {Oral Microbiota Characteristics in Relation to Different Dietary Patterns: A Systematic Review.}, journal = {Nutrients}, volume = {18}, number = {11}, pages = {}, pmid = {42280361}, issn = {2072-6643}, mesh = {Humans ; *Microbiota/physiology ; *Mouth/microbiology ; *Diet/methods ; Diet, Mediterranean ; Oral Health ; Female ; Diet, Vegetarian ; *Feeding Behavior/physiology ; Male ; Adult ; Diet, Vegan ; }, abstract = {Background: Diet is a key modifiable factor influencing oral health and may shape the oral microbiota. While individual nutrients, especially free sugars, have been widely studied, the role of overall dietary patterns remains unclear. This systematic review aimed to evaluate the association between dietary patterns and oral microbiota in humans. Methods: PubMed/MEDLINE, Embase, and Web of Science were searched up to 18 March 2026. Studies assessing defined dietary patterns (Mediterranean, vegan, vegetarian, omnivorous) and oral microbiota using sequencing-based methods in healthy individuals were included. Due to heterogeneity in study design, dietary assessment, and microbiome analysis, a narrative synthesis was conducted. Results: Six studies (n = 448 participants) were included. Dietary patterns showed limited impact on overall microbiota structure, with no consistent changes in alpha and beta diversity. However, differences were observed at the taxonomic level. The Mediterranean diet was generally associated with a lower abundance of periodontopathogenic taxa. Plant-based and omnivorous diets showed distinct microbial profiles, particularly involving Neisseria, Haemophilus, Prevotella, and Streptococcus. Functional activity and metabolomic profiles appeared more sensitive to dietary variation than taxonomic composition alone. Conclusions: The oral microbiota appears relatively stable across dietary patterns, although diet may influence specific taxa and functional pathways relevant to oral health. The Mediterranean diet shows the most consistent association with beneficial microbial shifts. However, evidence is limited by heterogeneity and cross-sectional designs, highlighting the need for longitudinal and interventional studies.}, }
@article {pmid42280378, year = {2026}, author = {Cabri, G and Bhatti, SFM and Hemeryck, LY and Boon, P and Volk, HA and Hesta, M and Verdoodt, F}, title = {Canine Idiopathic Epilepsy as a Natural Animal Model for Human Epilepsy: A Scoping Review Highlighting Metabolic Perspectives Beyond the Brain.}, journal = {Nutrients}, volume = {18}, number = {11}, pages = {}, pmid = {42280378}, issn = {2072-6643}, support = {1297623N//Research Foundation - Flanders/ ; }, mesh = {Animals ; Dogs ; Humans ; *Disease Models, Animal ; *Epilepsy/metabolism/veterinary ; *Dog Diseases/metabolism ; Brain/metabolism ; }, abstract = {Background: Emerging evidence indicates that epilepsy extends beyond the brain, involving systemic metabolic, immune, and microbiome perturbations that shape neuronal excitability and treatment response. Canine idiopathic epilepsy (CE) offers a naturally occurring model with strong electrophysiological, pharmacological, and clinical homology to human epilepsies. Methods: This scoping review was conducted according to the PRISMA-ScR guidelines. A systematic literature search was performed in Web of Science and MEDLINE (PubMed) to identify original studies reporting metabolic, immunometabolic, or neurochemical alterations in CE compared with healthy controls. Eligible studies included peer-reviewed original research involving client-owned dogs diagnosed with CE according to international consensus criteria (IVETF guidelines). Studies focusing exclusively on genetics or neuroimaging without metabolic outcomes were excluded. Titles, abstracts, and full texts were screened for eligibility, and data were extracted from included studies using a standardized approach. Identified metabolic domains were synthesized narratively and grouped into functional systems, including amino acid and lipid metabolism, micronutrients, neurotransmission, oxidative stress, inflammation and immunology, endocannabinoid signalling, microRNAs, and gut-brain axis-related pathways. In a second step, the identified metabolic domains were evaluated for translational relevance through a targeted, non-systematic narrative synthesis of the human epilepsy literature. This approach aimed to assess cross-species parallels and to provide a conceptual framework to guide future research, rather than to perform a comprehensive systematic review of metabolic alterations in human epilepsy. Results: Across CE studies, consistent alterations were observed in multiple interconnected functional systems, including metabolic, immune, and gut-brain axis pathways, in agreement with findings reported for human epilepsy. These data support a model of epileptogenesis involving systemic dysfunction beyond the central nervous system. Translationally, these findings suggest opportunities for biomarker development, patient stratification, and mechanism-based interventions, including dietary and metabolic approaches (e.g., medium-chain triglyceride supplementation), microbiome modulation, and immunometabolic targeting. The current evidence is limited by small and heterogeneous cohorts, potential confounding effects of antiseizure medications, variability in dietary and fasting conditions, breed-related effects, and a predominance of associative over causal relationships. Conclusions: This review positions CE as a reference framework for future research into epilepsy metabolism, integrating current evidence and its translational relevance to human disease. The findings support a shift toward a systems-level view of epileptogenesis, involving interconnected metabolic, immune, and gut-brain axis pathways beyond the brain. CE represents a valuable translational model to identify shared mechanisms, inform biomarker discovery, and guide the development of mechanism-based therapeutic strategies across veterinary and human epilepsy.}, }
@article {pmid42280379, year = {2026}, author = {Xie, A and Yuan, L and Yang, B}, title = {Immune Responses Against Allergic Asthma Following Intervention with Lacticaseibacillus paracasei DMLA16017 and Vitamin D in Rats.}, journal = {Nutrients}, volume = {18}, number = {11}, pages = {}, pmid = {42280379}, issn = {2072-6643}, mesh = {Animals ; *Asthma/immunology/therapy ; *Vitamin D/pharmacology/administration &amp; dosage ; Rats ; Cytokines/blood ; Disease Models, Animal ; Male ; Gastrointestinal Microbiome/drug effects ; Lung/pathology/immunology ; Ovalbumin ; Immunoglobulin E/blood ; Rats, Sprague-Dawley ; }, abstract = {OBJECTIVES: Allergic asthma (AA) is an increasing public health concern. The aim of this study was to investigate the potential effects of immune responses against AA in rats following intervention with Lacticaseibacillus paracasei DMLA16017 and vitamin D (VD).<br><br>METHODS: L. paracasei DMLA16017 was identified using 16S rDNA sequencing, while a rat model of AA was established via ovalbumin (OVA) induction. Subsequently, samples were collected for biomarker analysis in peripheral blood and lung tissue (including serum OVA-immunoglobulin E (IgE) and cytokines) using enzyme-linked immunosorbent assays and assessment of the composition of the intestinal microbiota and species diversity using 16S rRNA sequencing.<br><br>RESULTS: In the rat model, OVA-induced sensitization induced significant physiological alterations, including pulmonary tissue damage, elevated white cell counts, increased serum levels of OVA-IgE and cytokines interleukin (IL)-4 and IL-17, and reduced levels of IFN-&#x3b3; and TGF-&#x3b2;. These changes were accompanied by dysbiosis of the gut microbiota and decreased species diversity. Co-administration of VD and DMLA16017 effectively ameliorated the physiological disturbances and histopathological abnormalities in rats with AA, restored the balance between cellular and immune responses, and improved the composition of the gut microbiota and species diversity.<br><br>CONCLUSIONS: Combined intervention with VD and DMLA16017 can be used to treat AA disorders, with potential long-term modulation of the immune system.}, }
@article {pmid42280407, year = {2026}, author = {Acierno, C and Caturano, A and Barletta, F and Rinaldi, L and Sasso, FC and Adinolfi, LE and Nevola, R}, title = {Nutritional Interventions Targeting the Gut Microbiome in MASLD: From Prebiotics and Probiotics to Postbiotics and Fecal Microbiota Transplantation.}, journal = {Nutrients}, volume = {18}, number = {11}, pages = {}, pmid = {42280407}, issn = {2072-6643}, mesh = {Humans ; *Prebiotics/administration &amp; dosage ; *Fecal Microbiota Transplantation ; *Probiotics/administration &amp; dosage ; *Gastrointestinal Microbiome ; *Fatty Liver/therapy/microbiology ; Synbiotics/administration &amp; dosage ; Dysbiosis ; }, abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is a highly prevalent liver-centred manifestation of systemic metabolic dysfunction. The gut-liver axis provides a biologically credible therapeutic rationale because intestinal dysbiosis, impaired barrier integrity, microbial metabolites, bile acid signalling, short-chain fatty acids, and trimethylamine N-oxide may influence hepatic steatosis, inflammation, and fibrogenesis. This narrative review critically evaluates dietary patterns, prebiotics, probiotics, synbiotics, postbiotics, and fecal microbiota transplantation (FMT) as microbiome-directed strategies in MASLD. The comparative framework prioritises disease-specific human evidence, clinically meaningful endpoints, trial duration and sample size, reproducibility, safety, and feasibility. Dietary optimisation remains the most clinically grounded intervention, whereas probiotics and synbiotics show modest and heterogeneous signals on biochemical or metabolic surrogate endpoints. Prebiotics are mechanistically coherent but supported by limited liver-centred trials. Postbiotics and microbiome-mediated bioactives remain early-stage and require stricter definitional boundaries. FMT is investigational and should not be extrapolated from its established role in recurrent Clostridioides difficile infection. Most available evidence across all intervention categories relies principally on surrogate endpoints-including aminotransferases, insulin resistance indices, lipid parameters, and microbiome compositional shifts-rather than on validated liver-centred outcomes such as histological improvement or quantitative liver fat assessment; this constrains the strength of conclusions that can currently be drawn. Across all categories, microbiome modulation does not by itself establish liver disease modification, and no microbiome-targeted nutritional intervention has yet demonstrated histological benefit in MASLD. Future trials in this field should prioritise validated hepatic endpoints, phenotype-stratified patient enrolment, adequate follow-up duration, and direct comparisons between intervention categories to determine which microbiome-directed strategies, if any, deliver measurable and reproducible hepatic benefit beyond surrogate markers.}, }
@article {pmid42280409, year = {2026}, author = {Ostrowska, M and Komoń-Janczara, E and Mikołuć, B and Iłowiecka, K and Jarczak, J and Zagórska, J and Zambrzycka, P and Turroni, S and Szczerba, H}, title = {Oral Mycobiome Alterations in Children with Phenylketonuria: Associations with Dietary Intake and Metabolic Context-A Pilot Study.}, journal = {Nutrients}, volume = {18}, number = {11}, pages = {}, pmid = {42280409}, issn = {2072-6643}, support = {2022/06/X/NZ9/00519//National Science Centre/ ; }, mesh = {Humans ; *Phenylketonurias/microbiology/metabolism ; Pilot Projects ; Male ; Female ; Child ; *Diet ; *Saliva/microbiology ; *Mycobiome ; Child, Preschool ; Case-Control Studies ; *Mouth/microbiology ; *Fungi/classification ; }, abstract = {BACKGROUND: Phenylketonuria (PKU) is a metabolic disorder requiring a strict low-phenylalanine diet. Oral health impairment, including bacteriome dysbiosis, is common in PKU, yet the mycobiome remains poorly defined. This pilot study aimed to characterise the salivary oral mycobiome of children with PKU compared with controls and to explore associations with dietary intake.<br><br>METHODS: Saliva samples from 18 children, including 8 patients with PKU and 10 age-matched controls, were profiled using internal transcribed spacer (ITS) amplicon sequencing. Alpha/beta diversity, taxonomic composition, diet-fungi correlations, discriminative taxa and LEfSe were analysed.<br><br>RESULTS: Alpha diversity did not differ significantly between groups after correction for multiple comparisons, although exploratory subgroup analyses suggested lower evenness in PKU children aged <10 years compared with older controls. Beta diversity differed by diagnosis (PERMANOVA: F = 1.7251, p = 0.0062) and in the age-diagnosis model (F = 1.8502, p = 0.0004). Taxonomic analyses identified nominal differences in several fungal taxa, including Candida (p = 0.011), Saccharomycetales_fam_Incertae_sedis (p = 0.011), Naganishia (p = 0.020), and Aspergillaceae (p = 0.036) in PKU samples; however, these findings should be interpreted as exploratory because many did not remain significant after FDR correction. Diet-mycobiome analyses identified selected FDR-supported associations, including an inverse relationship between phenylalanine intake and Naganishia in PKU.<br><br>CONCLUSIONS: This pilot study suggests preliminary compositional differences in the oral mycobiome of children with PKU that may be related to dietary therapy and metabolic context. These exploratory findings require validation in larger cohorts with detailed oral health assessment and control of confounders.}, }
@article {pmid42280416, year = {2026}, author = {Kim, J and Lee, J}, title = {Nutritional Regulation of Ovarian Bioenergetics: Implications for Reproductive Aging and Female Infertility.}, journal = {Nutrients}, volume = {18}, number = {11}, pages = {}, pmid = {42280416}, issn = {2072-6643}, support = {RS-2025-00513071//National Research Foundation of Korea/ ; }, mesh = {Female ; Humans ; *Energy Metabolism/physiology ; *Infertility, Female/metabolism/physiopathology ; *Aging/metabolism/physiology ; *Ovary/metabolism ; Animals ; *Reproduction/physiology ; Mitochondria/metabolism ; }, abstract = {Ovarian function is critically dependent on tightly coordinated cellular energy metabolism, which governs follicular development, oocyte competence, and reproductive longevity. Increasing evidence indicates that metabolic dysregulation, including mitochondrial dysfunction, oxidative imbalance, and impaired NAD[+] metabolism, contributes to the pathophysiology of major ovarian disorders such as PCOS, ovarian aging, and DOR. In parallel, emerging studies suggest that nutritional factors influence ovarian function by modulating mitochondrial bioenergetics, redox homeostasis, and nutrient-sensing signaling pathways. This review summarizes current knowledge on the molecular basis of ovarian energy metabolism and its disruption in female reproductive disorders. We further discuss nutritional strategies targeting ovarian bioenergetics, including antioxidants, NAD[+] precursors, mitochondrial cofactors, and dietary metabolic interventions. In addition, we highlight recent advances in metabolomics, microbiome research, epigenomics, and multi-omics integration that are shaping emerging nutrition-based approaches in reproductive medicine. Collectively, positioning ovarian metabolism at the center of nutritional reproductive research may provide a conceptual framework for understanding metabolic regulation in ovarian function and for guiding future research on reproductive health.}, }
@article {pmid42280426, year = {2026}, author = {Arshad, F and Akbar, A and Chinnappan, R and Khan, MI and Yaqinuddin, A and Arora, I}, title = {Dietary Polyphenols and Selected Nutraceuticals in Hepatocellular Carcinoma: Mechanistic Insights, Translational Evidence, and Clinical Prospects.}, journal = {Nutrients}, volume = {18}, number = {11}, pages = {}, pmid = {42280426}, issn = {2072-6643}, mesh = {Humans ; *Dietary Supplements ; *Liver Neoplasms/prevention &amp; control ; *Carcinoma, Hepatocellular/prevention &amp; control ; *Polyphenols/pharmacology/administration &amp; dosage ; Animals ; Signal Transduction/drug effects ; Diet ; }, abstract = {BACKGROUND: Hepatocellular carcinoma (HCC) develops predominantly from chronic liver injury, with diet representing a clinically actionable yet mechanistically complex modulator of hepatic carcinogenesis. Despite advances in immunotherapy, long-term survival remains poor, underscoring the need for complementary preventive and adjunctive strategies.<br><br>METHODS: We conducted a narrative review of epidemiological, experimental, and clinical literature on dietary patterns, polyphenols, and non-polyphenol nutraceuticals for HCC prevention and management, with a focus on underlying molecular and cellular mechanisms.<br><br>RESULTS: Dietary polyphenols and selected nutraceuticals exert pleiotropic effects on signaling pathways implicated in HCC, including NF-&#x3ba;B, STAT3, TGF-&#x3b2;/SMAD, PI3K/AKT, and Wnt/&#x3b2;-catenin, while modulating hepatic stellate cell activation, immune cell polarization, and microbiome-derived metabolites. Preclinical studies suggest that some compounds may enhance antitumor immunity and sensitize tumors to systemic therapies; however, clinical translation is constrained by limited bioavailability, pharmacokinetic variability, formulation heterogeneity, and a lack of high-quality trials.<br><br>CONCLUSIONS: This review highlights the potential of dietary patterns and nutraceuticals in HCC prevention and as adjunctive therapies. It outlines key translational priorities, including etiologic stratification, biomarker-driven trial design, and rigorous safety evaluation.}, }
@article {pmid42280436, year = {2026}, author = {Hwang, JH and Choi, YK}, title = {Effects of Herbal and Natural Product Interventions on Gut Microbiota and Clinical Outcomes in Patients Receiving PPI-Containing Therapy: A Systematic Review and Meta-Analysis.}, journal = {Nutrients}, volume = {18}, number = {11}, pages = {}, pmid = {42280436}, issn = {2072-6643}, support = {NRF-2022R1A2C1013518//National Research Foundation of Korea/ ; }, mesh = {Humans ; *Proton Pump Inhibitors/adverse effects/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; *Biological Products/pharmacology/therapeutic use ; Helicobacter Infections/drug therapy/microbiology ; Treatment Outcome ; *Plant Preparations/pharmacology ; Helicobacter pylori/drug effects ; Female ; *Phytotherapy ; Male ; Middle Aged ; }, abstract = {Proton pump inhibitor (PPI)-containing regimens, including bismuth quadruple therapy, may perturb gut microbiota through combined exposure to acid suppression, antibiotics, bismuth, and underlying disease context. Herbal medicines and natural products have been proposed as adjunctive interventions to mitigate treatment-related microbiota perturbations; however, systematic synthesis of the clinical evidence remains limited. This systematic review and meta-analysis evaluated the effects of herbal and natural product interventions on gut microbiota and clinical outcomes in patients receiving PPI-containing therapy. Six databases (PubMed, EMBASE, Web of Science, Scopus, CENTRAL, and CNKI) were searched from their inception to March 2026. Risk of bias was assessed using RoB 2.0 and ROBINS-I. This review was prospectively registered in PROSPERO (CRD420261346672). Eighteen studies (17 randomized controlled trials, 1 observational study; n = 1984 participants) were included in the final analysis. Meta-analysis demonstrated significantly higher Helicobacter pylori eradication rates (pooled relative risk (RR) = 1.20, 95% confidence interval (CI) 1.14-1.27; I[2] = 33%). Chinese-style total effective rate was also higher in the herbal groups (RR = 1.19, 95% CI 1.14-1.25; I[2] = 0%), but this non-standardized outcome should be interpreted cautiously. Exploratory microbiome meta-analyses suggested higher post-treatment Bifidobacterium and Lactobacillus levels; however, substantial heterogeneity limited interpretability. Narrative synthesis revealed potential preservation of α-diversity and attenuation of pathobiont proliferation in herbal groups. Overall, herbal and natural product interventions may be associated with favorable clinical outcomes and potential microbiota-modulating effects in patients receiving PPI-containing therapy, but certainty remains limited due to methodological concerns, outcome indirectness, and heterogeneity. High-quality trials stratified by antibiotic exposure are warranted.}, }
@article {pmid42280437, year = {2026}, author = {Samiksha, F and Singh, D and Harbool, SS and Di Martino, L and Kruithoff, C and S McCormick, T and Ghannoum, M}, title = {Fungal β-1,3-glucans: Cell Wall Constituents That Promote Gut Health Through Innate Immune Modulation.}, journal = {Nutrients}, volume = {18}, number = {11}, pages = {}, pmid = {42280437}, issn = {2072-6643}, mesh = {Humans ; *beta-Glucans/pharmacology/immunology ; *Immunity, Innate/drug effects ; *Cell Wall/chemistry/immunology ; Animals ; *Gastrointestinal Microbiome/drug effects/immunology ; *Fungi/chemistry ; Innate Immunity Recognition ; Prebiotics ; Intestinal Barrier Function ; }, abstract = {Fungal β-1,3-glucans are structurally conserved polysaccharide components of the fungal cell wall that exhibit potent immunomodulatory activity. These molecules are recognized by pattern recognition receptors, Toll-like receptors, complement receptor 3, lactosylceramide, scavenger receptors, and EphA2. Binding of β-1,3-glucans through these receptors triggers coordinated innate and adaptive immune responses such as cytokine production, phagocytosis, and trained immunity. In addition to receptor-mediated immune activation, dietary β-1,3-glucans function as fermentable prebiotic fibers that modulate gut microbiota composition, increase short-chain fatty acid production, and strengthen epithelial barrier integrity. These combined immunological and microbiome-mediated effects position β-1,3-glucans as key regulators of gut homeostasis. Preclinical and emerging clinical evidence supports broad therapeutic potential across multiple disease domains, including inflammatory bowel disease, metabolic disorders, respiratory infections, and cancer. In oncology, β-1,3-glucans enhance anti-tumor immunity, improve responses to monoclonal antibodies and chemotherapy, and serve as promising adjuvants in vaccine-based strategies. Additionally, β-1,3-glucan is widely used as a biomarker for invasive fungal infections and represents a validated target of antifungal therapies such as echinocandins. Despite these advances, clinical translation remains limited by heterogeneity in glucan source, structure, and formulation, as well as a lack of appropriately powered, standardized human clinical trials. Future efforts should focus on clarifying mechanisms of action, as well as rigorous clinical evaluation, to fully define the therapeutic utility of fungal β-1,3-glucans.}, }
@article {pmid42280469, year = {2026}, author = {Ang, MY and Choo, SW}, title = {The Nutri-Exposome Intelligence Framework: Integrating Multi-Omics, Machine Learning, and Digital Nutrition for Precision Chronic Disease Prevention.}, journal = {Nutrients}, volume = {18}, number = {11}, pages = {}, pmid = {42280469}, issn = {2072-6643}, support = {Reference Number: 5000105//High-Level Talent Recruitment Program for Academic and Research Platform Construction/ ; Grant Number: KY20250604000448//IFIRI Talents Program/ ; }, mesh = {Humans ; Multiomics ; *Machine Learning ; Chronic Disease/prevention &amp; control ; *Precision Medicine/methods ; Digital Health ; *Exposome ; Nutrigenomics/methods ; Data Analytics ; Diet ; }, abstract = {Background/Objectives: Precision nutrition is moving beyond population-based guidance and isolated gene-diet interactions toward integrative models of dietary response. However, current approaches remain fragmented across nutrigenomics, microbiome research, multi-omics profiling, digital health, and machine learning. This review proposes the Nutri-Exposome Intelligence Framework as a conceptual, data science-driven model for integrating cumulative dietary, environmental, microbial, molecular, clinical, and digital exposures for precision chronic disease prevention. Methods: This conceptual review synthesizes the literature on precision nutrition, nutrigenetics, nutrigenomics, exposomics, gut microbiome research, multi-omics integration, wearable and biomarker-based monitoring, and machine learning in nutrition studies. Evidence was organized into a framework linking exposure assessment, host susceptibility, microbiome-mediated biotransformation, molecular response profiling, computational modelling, personalized intervention, and longitudinal feedback. Results: The proposed framework consists of seven interconnected layers: diet, environment, and lifestyle exposures; host genome and microbiome; multi-omics molecular responses; machine learning-based integration; risk prediction and responder stratification; personalized dietary intervention; and wearable and biomarker-based feedback. It positions the nutri-exposome as a cumulative exposure-response system and highlights how machine learning can support data harmonization, feature engineering, predictive modelling, responder classification, explainable interpretation, and adaptive refinement of dietary recommendations. Key applications include obesity, type 2 diabetes, cardiovascular disease, metabolic dysfunction-associated steatotic liver disease, cardiovascular-kidney-metabolic syndrome, and broader cardiometabolic prevention. Conclusions: Nutri-exposome intelligence offers a structured pathway for transforming complex nutrition data into predictive, explainable, and adaptive precision nutrition strategies. Implementation will require longitudinal and multi-ethnic cohorts, standardized metadata, causal validation, interpretable machine learning, ethical governance, and equitable access to support responsible clinical and public health translation globally.}, }
@article {pmid42280542, year = {2026}, author = {Zhou, T and He, Y and Liew, A and Wang, M and Cheong, KL}, title = {Polysaccharides from the Peel of Hylocereus undatus Promote Wound Healing by Reshaping the Skin Microbiome and Regulating Immune Balance.}, journal = {Polymers}, volume = {18}, number = {11}, pages = {}, pmid = {42280542}, issn = {2073-4360}, support = {2025A1515010078//Natural Science Foundation of Guangdong Province/ ; 2024ZDZX2084//Key Research Project of High Education of Guangdong Province/ ; }, abstract = {Polysaccharides isolated from the peel of Hylocereus undatus exhibit promising anti-inflammatory activity; however, the underlying mechanisms-particularly their modulatory effects on cutaneous microbiota composition and host immune responses-remain incompletely characterized. This study investigates the therapeutic potential of polysaccharides isolated from the peel of Hylocereus undatus in the management of inflammatory cutaneous wounds. The polysaccharide extracted from the peel of Hylocereus undatus via ultrasound-assisted extraction is an acidic heteropolysaccharide, with galacturonic acid and rhamnose as its dominant monosaccharide components. It exhibits low crystallinity, a porous structure, and good thermal stability. In a mouse wound model, treatment with the polysaccharide extracted from the peel of Hylocereus undatus significantly accelerated wound closure as early as day 3 (** p < 0.01). By day 9, the wound closure rate approached that of the positive control group and remained significantly higher than that of the untreated group (** p < 0.01), exceeding 90%. Treatment with the polysaccharide advanced the inflammatory peak, as evidenced by elevated anti-inflammatory cytokines (IL-10 and TGF-β) and suppression of the pro-inflammatory cytokine IL-6. Immunofluorescence staining confirmed that polysaccharide promoted cell proliferation and neovascularization at the wound site. In conclusion, polysaccharides isolated from the peel of Hylocereus undatus accelerate skin wound healing by modulating the skin microbiota, enhancing the anti-inflammatory response, and promoting tissue regeneration, highlighting its potential as a natural wound dressing.}, }
@article {pmid42280664, year = {2026}, author = {Hashemi, SM and Graeff, M and Nai, EA and Savidov, N}, title = {Cultivation System Dominates Cucumber Performance and Root-Zone Microbiomes Across Biochar Particle Sizes.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {11}, pages = {}, pmid = {42280664}, issn = {2223-7747}, abstract = {Hydroponic (HP) and aquaponic (AQ) systems are widely known in greenhouse production; however, the combined effects of nutrient delivery system and substrate physical structure on crop performance and root-zone microbiomes remain insufficiently understood. Substrate physical properties influence water retention and aeration, which can affect root-associated microorganisms, plant growth, and yield. This study evaluated cucumber (Cucumis sativus L.) growth, yield, nutrient dynamics, physiological stress responses, and bacterial community composition under HP and AQ systems using bamboo-derived biochar substrates and coconut coir as a control. Vegetative growth was enhanced under AQ, with the greatest plant elongation (1102 ± 40.1 cm) and stem diameter (15.1 ± 1.0 mm) observed in biochar-grown plants. Total yield was consistently higher under AQ than HP, with the highest yield recorded in the coarse biochar treatment (28.6 kg m[-2]). Aquaponic systems were associated with greater nutrient availability under the conditions evaluated during mid to late season production, including nitrate concentrations of up to 226 mg L[-1]. Physiological stress monitoring indicated lower stress exposure under aquaponic conditions in plants grown in medium and coarse biochar substrates across both systems, with 78 to 81% of the growing season classified within low to balanced stress conditions. Bacterial community composition was primarily shaped by cultivation system, which explained 19.3% of the observed variation, whereas substrate treatment did not significantly alter overall bacterial community structure. Overall, cultivation system was the dominant factor associated with variation in cucumber performance and root-zone bacterial communities, while biochar substrates supported improved plant growth, yield, and reduced physiological stress.}, }
@article {pmid42280669, year = {2026}, author = {Zhang, L and Dong, J and Zhao, J and Jiang, H and Zhang, W}, title = {Rhizosphere Functional Plasticity and the Keystone Taxon Sphingomonas Facilitate Sweet Cherry Adaptation to Semi-Arid Stress.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {11}, pages = {}, pmid = {42280669}, issn = {2223-7747}, support = {2023LHMS03007//Department of Science and Technology of Inner Mongolia Autonomous Region/ ; }, abstract = {Translocation of elite cultivars across distinct climatic regions often induces transplantation shock. Although the rhizosphere microbiome can facilitate host acclimation, the underlying functional mechanisms remain unclear. Here, we investigated microbiome-mediated adaptation in "Hongdeng" sweet cherry (Prunus avium L.) moved from a humid coastal region (Dalian, DL) to a semi-arid inland habitat (Hohhot, HS). We integrated plant physiological assays, metagenomic sequencing, and structural equation modeling (SEM) to compare the source population (DL), the introduced population (HS), and a locally acclimated reference cultivar ("Summit", HSY). The introduced trees adjusted physiologically to the semi-arid environment by elevating proline levels and antioxidant enzyme activities. Although environmental stress reduced microbial alpha diversity, the core taxonomic framework persisted. Community assembly analysis indicated that the semi-arid climate intensified environmental filtering. Network analysis identified Sphingomonas as a keystone taxon; notably, it maintained a highly connected topological role despite a stable relative abundance. Furthermore, structural equation modeling showed that the environmental stress index positively correlated with the upregulation of microbial DNA repair pathways (R = 0.81, p < 0.001). Ultimately, the SEM demonstrated that environmental stress primarily shapes microbial functional profiles rather than driving species turnover, thereby contributing to host adaptation. The successful establishment of introduced sweet cherry in semi-arid regions is tied more closely to rhizosphere functional plasticity than to taxonomic restructuring. These findings highlight the role of the keystone taxon Sphingomonas in maintaining rhizosphere homeostasis, offering a theoretical framework for targeted microbiome engineering to mitigate transplant shock and enhance crop resilience.}, }
@article {pmid42280740, year = {2026}, author = {Ding, Y and Zhao, Y and Xie, Y and Sun, C and Yang, L and Sun, Z and Yang, L and Wang, Y and Zhang, J and Han, Z}, title = {Aspergillus neoalliaceus MR-86 Promotes the Growth of Saposhnikovia divaricata by Regulating the Rhizosphere Microbiome.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {11}, pages = {}, pmid = {42280740}, issn = {2223-7747}, support = {20260204099YY, 20260204045YY//Jilin Province Science and Technology Department/ ; JLAUHLRG20102006//Jilin Agricultural University high-level researcher grant/ ; D23007//The 111 Project, Northeast Advantageous Characteristic Resources and Health Food Discipline Innovation Introduction Base/ ; }, abstract = {Plant growth-promoting fungi (PGPF) have shown broad potential to improve soil conditions and enhance root growth and development. However, few studies have examined the effects of exogenous PGPF inoculation on the growth of the medicinal plant Saposhnikovia divaricata and the associated changes in the rhizosphere microbiome. In this study, Aspergillus neoalliaceus MR-86 exhibited phosphate solubilization, growth in nitrogen-free medium, potassium solubilization, IAA production, and siderophore production. PCR assays did not detect the aflatoxin biosynthesis-related genes aflR, aflS, and omtA in strain MR-86. Pot trials demonstrated that inoculation with MR-86 significantly increased the plant height and root dry weight of S. divaricata by 10.32% and 21.05%, respectively (p < 0.05). In the rhizosphere, soil pH decreased, whereas soil alkaline-hydrolyzable nitrogen and available phosphorus levels, as well as the activities of protease, urease, and cellulase, increased significantly. Illumina NovaSeq sequencing revealed that MR-86 inoculation altered the soil microbial community structure and specifically enriched several microbial taxa, including Talaromyces, Subulicystidium, and Aspergillus. Moreover, MR-86 inoculation did not alter the composition of dominant bacterial and fungal phyla, but significantly modified microbial interactions and the topology of microbial networks. Correlation analysis indicated that the specific microbial taxa Subulicystidium, Aspergillus, and Talaromyces were positively associated with soil nutrient indices, enzyme activities, and plant growth parameters. Functional prediction analysis indicated that MR-86 treatment was predicted to be enriched bacterial metabolic pathways, including flavone and flavonol biosynthesis and ether lipid metabolism, and was predicted to increase the relative abundance of functional fungal groups such as ectomycorrhizal and wood-decomposing fungi. In summary, A. neoalliaceus MR-86 may contribute to improved growth of S. divaricata by enhancing nutrient availability and transformation and by modulating the structure and function of the rhizosphere microbiome.}, }
@article {pmid42280750, year = {2026}, author = {Liu, J and Haider, FU and Liu, Y and Zhang, P and Liu, T and Li, X and Li, S}, title = {Reframing Partial Root-Zone Irrigation: A Spatial Stress-Priming Mechanism for Crop Adaptation to Abiotic Stresses.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {11}, pages = {}, pmid = {42280750}, issn = {2223-7747}, support = {2024YFD1501500//The National Key R&amp;D Program of China/ ; 20240101010JJ//Jilin Province Science and Technology Department/ ; }, abstract = {Abiotic stresses limit crop productivity by disrupting water relations, carbon assimilation, nutrient acquisition, membrane stability, and redox homeostasis. Partial root-zone irrigation (PRI), commonly implemented as partial root-zone drying (PRD), is often viewed as a deficit-irrigation strategy to improve water-use efficiency; however, this view underestimates the biological consequences of spatial root-zone heterogeneity. This review evaluates PRI as a spatially structured, priming-like framework for crop adaptation to abiotic stress. Available evidence indicates that localized drying and wet-side water uptake can coordinate root sensing, hydraulic-chemical signaling, abscisic acid delivery, hormone crosstalk, xylem-mediated regulation, and stomatal control. Beyond gas exchange, PRI is associated with photosynthetic maintenance, osmotic adjustment, antioxidant and redox regulation, root architectural plasticity, nutrient acquisition, and metabolic reprogramming. Evidence is strongest for drought, whereas responses to low temperature, salinity, heat-associated evaporative demand, and combined stresses remain more context-dependent. Emerging work also links PRI to rhizosphere restructuring and microbiome shifts, but the causal mechanisms and field reproducibility remain unresolved. We argue that future progress requires matched PRI-deficit-irrigation comparisons, standardized switching thresholds, shared physiological and molecular readouts across crops, high-resolution root biology, and commercially realistic field validation. This framing distinguishes conserved physiological outcomes from mechanisms that may differ among crops, genotypes, and irrigation designs.}, }
@article {pmid42280785, year = {2026}, author = {Nunes, A and Minello, LVP and Oliveira, ER and Schneider, AR and Dutra, FS and Guizolfi, T and Santos, LRB and Gelli, VC and Granada, CE and Sperotto, RA and Moura, S and Maraschin, M and Lima, GPP}, title = {Impact of Kappaphycus alvarezii Biostimulant on Growth, Biochemistry, Essential Oil, and Rhizosphere of Basil (Ocimum basilicum) Plants.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {11}, pages = {}, pmid = {42280785}, issn = {2223-7747}, support = {2023/03886-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 25/2551-0002537-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Rio Grande do Sul/ ; 22/2551-0001641-3//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Rio Grande do Sul/ ; 88887.696139/2022-00//Coordena&#xe7;&#xe3;o de Aperfeicoamento de Pessoal de N&#xed;vel Superior/ ; 405949/2022-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 306495/2023-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 303956/2023-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 405779/2022-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 305135/2021-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 314977/2025-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 311719/2023-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 24/2551-0001302-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Rio Grande do Sul/ ; 2024TR002499//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa e Inova&#xe7;&#xe3;o do Estado de Santa Catarina/ ; 408526/2024-6//Institutos Nacionais de Ci&#xea;ncia e Tecnologia/ ; }, abstract = {Seaweed-derived biostimulants are a promising strategy for improving crop performance in sustainable agriculture. In this context, this study evaluated the effects of foliar application of Kappaphycus alvarezii extracts, obtained from two Brazilian regions (São Paulo: Kal-SP and Santa Catarina: Kal-SC), at different concentrations (1%, 3%, 5%, and 7%) on the growth, biochemical profile, essential oil yield, and rhizosphere microbiome of Ocimum basilicum under field conditions. Morphological analysis indicated that the 5% and 7% concentrations increased plant height, biomass, root development, and inflorescence production, with biomass gains of up to 51% and essential oil production increases of up to 142% compared to the control. Biochemical responses varied by extract origin, with Kal-SC promoting greater increases in photosynthetic pigments, antioxidant activity, and carbon-related metabolites, whereas Kal-SP induced only minor metabolic changes. The algal biostimulant modulated essential oil yield and composition, promoting treatment-dependent shifts in major terpenoid compounds. Microbiome analysis showed no significant changes in alpha diversity, but significant shifts in beta diversity and functional groups, such as Bacillaceae, indicating rhizosphere reorganization. Overall, the effectiveness of K. alvarezii-based biostimulants depends on concentration and biomass source, highlighting their potential as sustainable agricultural bioproducts and the importance of standardized extraction for consistent outcomes.}, }
@article {pmid42280795, year = {2026}, author = {Geng, H and Xin, Y and Jin, H and Zheng, Z and Pan, T and Zeng, Z}, title = {Physiological Responses, Molecular Basis, and Integrated Regulation of Heat Tolerance in Soybean.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {11}, pages = {}, pmid = {42280795}, issn = {2223-7747}, support = {LQ24C130001//Zhejiang Provincial Natural Science Foundation/ ; CARS-04-CES33//China Agriculture Research System-Soybean/ ; 2022LFR109//Program for Research and Development of Zhejiang A&amp;F University/ ; }, abstract = {Global warming has led to frequent occurrences of extreme heat, posing a huge threat to soybean (Glycine max L.) yield. As a major source of plant protein and oil, soybean is particularly sensitive to heat stress during its growth and development, especially in critical stages such as flowering and seed filling. Heat tolerance in crops is a complex trait governed by polygenic networks and environmental interactions; although existing studies have identified several heat-tolerance-related genes, the molecular regulatory networks regulating crop responses to heat stress remain elusive. This review synthesizes recent advances in soybean heat tolerance research, with a particular emphasis on physiological responses and molecular regulatory mechanisms under heat stress. We further evaluate the potential of modern technologies, including gene editing, marker-assisted selection, and pan-genomics, for the precise improvement of heat tolerance in soybean. Additionally, we outline sustainable agronomic practices and field management strategies to mitigate heat stress. The development of heat-tolerant soybean varieties depends not only on the identification of superior alleles but also requires a shift from gene-centric genetic improvement toward a system-wide solution that integrates "Genotype × Environment × Management".}, }
@article {pmid42281243, year = {2026}, author = {Stanford, J and Hoedt, EC and Gómez-Martín, M and Clarke, ED and Duncanson, K and Burrows, T and Collins, CE}, title = {Contrasting dietary patterns remodel gut microbial function and generate multi-omic signatures associated with cardiometabolic markers.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2685381}, doi = {10.1080/19490976.2026.2685381}, pmid = {42281243}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Multiomics ; Feces/microbiology ; Biomarkers/urine/blood ; Female ; Adult ; Male ; *Diet ; Australia ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Cross-Over Studies ; Middle Aged ; Metabolome ; Metabolomics ; Blood Pressure ; }, abstract = {Diet is a modifiable determinant of gut microbiome composition, yet the impact of contrasting whole-dietary patterns on microbial metabolic capacity and coordinated host metabolic signatures remains incompletely characterized. In a randomized crossover feeding trial, 34 Australian adults were provided with a Healthy Australian Diet (HAD), aligned with national dietary guidelines, and a Typical Australian Diet (TAD), reflecting average population intake for two weeks each, separated by a two-week washout. Fecal microbiome composition and function were assessed using shotgun metagenomics, plasma and urine metabolites by untargeted metabolomics, with cardiometabolic markers including blood pressure, plasma lipids, and glucose quantified. HAD was associated with reduced taxonomic and functional alpha diversity relative to baseline, with no change following TAD. Species-level responses were modest, 105 functional pathways differed between diets, with 99 increasing following HAD, predominantly related to amino acid and nucleotide biosynthesis and vitamin/cofactor metabolism. Multi-omic integration using DIABLO achieved strong discrimination of dietary responses (held-out accuracy 91.7%; permutation p = 0.005). In total, 77 individual omic feature-cardiometabolic outcome associations survived FDR correction (q < 0.05), spanning microbial gene functions, plasma metabolites, and urinary metabolites linked to cholesterol, blood pressure, and triglyceride responses. These exploratory findings suggest that integrated microbiome-metabolome profiling may capture inter-individual variation in dietary cardiometabolic responses, though replication in larger, independent, robustly designed studies is needed before translational personalized nutrition strategies can be assessed.}, }
@article {pmid42281266, year = {2026}, author = {Hu, M and Li, Y and Zhao, L and Cha, S and Xue, Y and Han, Y and Xue, C and Dong, N}, title = {Engineered Lactococcus lactis for Oral Delivery of an Antimicrobial Peptide against Enterotoxigenic Escherichia coli in Weaned Piglets.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c17784}, pmid = {42281266}, issn = {1520-5118}, abstract = {Food-grade strategies against foodborne pathogens while preserving intestinal health are gaining attention. Here, we developed a regulated delivery platform using Lactococcus lactis engineered to secrete a tandem dimeric antimicrobial peptide (SD). The engineered strain (SDLactis) exhibited stable growth, genetic stability, and tolerance to simulated gastrointestinal conditions. Chloride-responsive SD secretion enabled effective antibacterial activity against enterotoxigenic Escherichia coli (ETEC) K88 in vitro. In ETEC-challenged piglets, oral SDLactis alleviated diarrhea, improved growth, and reduced intestinal injury and inflammation. It strengthened intestinal barrier integrity by upregulating tight junction proteins (ZO-1, Claudin-1,Occludin) and downregulating CFTR. Microbiome analysis revealed that SDLactis partially restored gut microbial diversity, reducing Escherichia-Shigella while enriching Lactobacillus and short-chain fatty acid-producing genera. Overall, food-grade engineered lactic acid bacteria serve as controllable delivery vehicles for antimicrobial peptides, offering a nonantibiotic strategy for pathogen control and gut health management in food and feed applications.}, }
@article {pmid42281376, year = {2026}, author = {Zhang, R and Li, X and Chen, X and Shen, A and Zhang, X and Peng, C and Qiu, J}, title = {Charge-Competition AIEgens Induce Mitochondrial Dysfunction for Selective Eradication of Candida albicans while Restoring Vaginal Microbiota.}, journal = {Journal of microbiology and biotechnology}, volume = {36}, number = {}, pages = {e2601074}, doi = {10.4014/jmb.2601.01074}, pmid = {42281376}, issn = {1738-8872}, mesh = {Female ; *Candida albicans/drug effects ; Animals ; *Antifungal Agents/pharmacology/chemistry ; *Candidiasis, Vulvovaginal/drug therapy/microbiology ; *Vagina/microbiology ; *Mitochondria/drug effects ; Biofilms/drug effects ; Lactobacillus/drug effects/growth &amp; development ; Mice ; *Microbiota/drug effects ; Humans ; Disease Models, Animal ; }, abstract = {The principal therapeutic challenge in vulvovaginal candidiasis (VVC) is that the non-selective nature of conventional antifungal drugs, which frequently perturb vaginal microecological homeostasis and disrupt Lactobacillus barrier, lead to the emergence of recurrent infection and drug resistance. This study aims to develop novel antifungal agents capable of efficiently and selectively eradicating pathogenic fungi while protecting and promoting the growth of Lactobacilli, with real-time monitoring capabilities and significant potential for clinical application. Harnessing the principle of charge-competition, we engineered a cationic amphiphilic aggregation-induced emission luminogens (AIEgens, named as TPE-ET), where hydrophobic chain length served as a key determinant governing membrane affinity, aggregation propensity, and antimicrobial selectivity. This design empowered potent eradication of Candida albicans (C. albicans) while concomitantly favoring the proliferation of beneficial Lactobacilli. Moreover, TPE-ET disrupted C. albicans biofilms and suppressed virulence genes related to adhesion, invasion, and drug resistance. In a murine VVC model, TPE-ET reduced fungal burden by over 90%, facilitating the repair of damaged vaginal epithelium and the reconstitution of a Lactobacillus-dominat vaginal microbiome. Remarkably, TPE-ET outperformed clotrimazole in restoring healthy microecological balance, as manifested by diminished Proteobacteria abundance alongside increased Firmicutes (notably Lactobacillus) and Bacteroidetes. Mechanistic studies revealed that TPE-ET exerted its remarkable antifungal activity by targeting the mitochondrial inner membrane, disrupting the metabolism-inflammation axis and eliciting mitochondrial dysfunction. Collectively, this dual merits of membrane charge-selective targeting and AIEgens-mediated visualization established an innovative therapeutic strategy for VVC, featuring superior efficacy, exquisite selectivity, and real-time monitoring capability with significant clinical potential.}, }
@article {pmid42281379, year = {2026}, author = {Bae, Y and Kim, DJ and Seo, Y and Noh, Y and Lee, S and Kwon, SK}, title = {Large-Scale Microbiome Profiling of Brown Algae Identifies a Specific Vibrio aphrogenes Clade Strain That Promotes Gametophyte Settlement.}, journal = {Journal of microbiology and biotechnology}, volume = {36}, number = {}, pages = {e2604061}, doi = {10.4014/jmb.2604.04061}, pmid = {42281379}, issn = {1738-8872}, mesh = {Biofilms/growth &amp; development ; *Microbiota ; *Vibrio/classification/physiology/isolation &amp; purification/genetics ; *Phaeophyceae/microbiology/physiology ; Symbiosis ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; }, abstract = {Marine macroalgae are foundation species of coastal ecosystems, maintaining close interactions with their microbiome for development and environmental adaptation. Although secure attachment to substrates is essential for both morphological development and survival, the potential causal link between microbial symbionts and this fundamental attachment process remains poorly understood. To address this gap, we integrated large-scale field sampling with functional validation to identify bacteria that influence the attachment of brown algae, specifically comparing attached and drifted individuals of Undaria pinnatifida and Ecklonia cava. Notably, Vibrio was consistently enriched in attached algae, whereas Marinomonas dominated drifted individuals. Translating these field observations into lab-scale validation, we isolated and evaluated their biofilm-formation capacity and impact on gametophyte settlement. A specific isolate belonging to the Vibrio aphrogenes clade exhibited superior biofilm formation and significantly enhanced algal abundance 2.57-fold in co-culture with U. pinnatifida gametophytes. These findings provide a scientific basis for developing bacterial inocula for seaweed seedling production and support broader macroalgae restoration strategies under changing environmental conditions.}, }
@article {pmid42281420, year = {2026}, author = {Góngora, E and Altshuler, I and Ellis, M and Okshevsky, M and Greer, CW and Whyte, LG}, title = {In Situ Mesocosm Experiment Shows the Capability of the Microbial Community of a Canadian High Arctic Shoreline to Degrade the New Generation of Ship Fuels.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c10583}, pmid = {42281420}, issn = {1520-5851}, abstract = {The warming effects of climate change are leading to a reduction in sea ice, which could open new shipping routes across the Arctic, leading to the possibility of hydrocarbon spills washing onto a shoreline. The behavior and biodegradability of new low-sulfur fuels (LSFs), currently being used by vessels worldwide, has not been assessed on Arctic beaches. We deployed mesocosm experiments on a remote Canadian high Arctic beach for 33 days using two LSFs (marine diesel and ultra-low-sulfur fuel oil, ULSFO) and Bunker C fuel oil (currently being phased out). Bunker C was mostly removed from beach sediments by natural attenuation (14.6% biodegradation, 62.8% nonbiological removal), while the LSFs were more easily biodegraded (37.6-72.8% biodegradation, 2.9-10.0% nonbiological removal). Native beach sediment microorganisms, including putatively novel taxa, adapted to the presence of fuel by expressing multiple aliphatic hydrocarbon biodegradation genes, but only few aromatic hydrocarbon degradation genes. Our results suggest that, while not as biodegradable as marine diesel, ULSFO appears to be a more environmentally friendly alternative to Bunker C due to its higher biodegradability under in situ Arctic environmental conditions. However, limited aromatic hydrocarbon biodegradation under cold and nutrient-poor environmental conditions could negatively affect the efficacy of natural attenuation.}, }
@article {pmid42281424, year = {2026}, author = {Garland, S and Orr, VT and Hall, JPJ and Harrison, E}, title = {Invasive plasmids as ecosystem engineers-from mechanism to application.}, journal = {Essays in biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1042/EBC20250040}, pmid = {42281424}, issn = {1744-1358}, support = {APP37189//UKRI | Biotechnology and Biological Sciences Research Council (AFRC)/ ; NE/X009971/1//UKRI | Natural Environment Research Council (NERC)/ ; MR/W02666X/1//UKRI | Medical Research Council (MRC)/ ; }, abstract = {Horizontal gene transfer, mediated by mobile genetic elements such as conjugative plasmids, is recognised as a major driver of bacterial innovation. While predominantly explored in the context of change within individual strains and species, the broad host ranges of many plasmids mean that they can invade not just lineages but communities. This has far-reaching implications for both the fate of the plasmid and our understanding of bacterial adaptation, as well as applications for the functional engineering of microbial communities. In comparison to single-strain systems, in which plasmid invasion is largely determined by a now well-defined set of parameters-conjugation rate, fitness cost of carriage, and segregation loss-the spread of plasmids into communities is vastly more complex: governed by the wide range of dynamics within strains, but also by community dynamics, spatial heterogeneity, and the interactions between strain- and community-level selection. Here, we review the processes by which plasmids can invade communities and discuss how community complexity both constrains and facilitates plasmid spread. We further explore how this mechanistic understanding can be harnessed to enhance microbial community function.}, }
@article {pmid42281763, year = {2024}, author = {Winston, JA and Suchodolski, JS and Gaschen, F and Busch, K and Marsilio, S and Costa, MC and Chaitman, J and Coffey, EL and Dandrieux, JRS and Gal, A and Hill, T and Pilla, R and Procoli, F and Schmitz, SS and Tolbert, MK and Toresson, L and Unterer, S and Valverde-Altamirano, &#xc9; and Verocai, GG and Werner, M and Ziese, AL}, title = {Clinical Guidelines for Fecal Microbiota Transplantation in Companion Animals.}, journal = {Advances in small animal care}, volume = {5}, number = {1}, pages = {79-107}, pmid = {42281763}, issn = {2666-450X}, }
@article {pmid42282017, year = {2026}, author = {Chaulagain, D and Paul, B and Leslie, S and Artigues-Lleixà, M and Cros, MP and Toloza, L and Tang, Z and Hoover, A and Güell, M and Karig, D}, title = {Rational assembly of synthetic marine biofilm community with chitinase production.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-9419003/v1}, pmid = {42282017}, issn = {2693-5015}, abstract = {Highly diverse multispecies biofilms are ubiquitous in microbial ecosystems; however, our current understanding of biofilm dynamics is limited to single species or low richness studies. We aimed to design a multispecies biofilm with a targeted function, chitinase production, using natural marine bacteria. We present a top-down assembly approach to design functional biofilm communities. Using our method, we found that final community membership was established within 24 hours, regardless of nutrient availability. However, cultivation in nutrient-rich media enabled rapid identification of the competitive dominant taxon, Pseudoalteromonas , among the 17 initial isolates used in the assembly. By repeating community assembly in a low-nutrient medium without these highly competitive taxa, we achieved the highest species diversity in the biofilm. The resulting multispecies biofilm exhibited chitinase production and maintained ~ 50% persistence during peak invasion. By comparison, a single species chitinase-producing biofilm formed lower biomass and suffered higher displacement during invasion. Importantly, one member that withstood invasion challenge in the multispecies community was completely undetectable at seven days post-invasion as a single species biofilm, indicating collective invasion resilience in the multispecies community. Further evidence of cooperation for coexistence is supported by increased β-N-acetylglucosaminidase, enzyme that hydrolyzes chitin oligomers, in the 14-member community at later timepoints, while the detected exochitinase activity remained stable. Our findings present a streamlined strategy to assemble diverse and functional biofilm communities for targeted biofilm engineering in marine and applied microbiome contexts, and our achievement of engineered function using natural bacteria offers a powerful complement to synthetic biology.}, }
@article {pmid42282041, year = {2026}, author = {Schutz, C and Queiroz, A and Mota, T and Ward, A and Barr, D and Janssen, S and Shey, M and Wilkinson, R and Wilkinson, K and Burton, R and Lelouvier, B and Andrade, B and Meintjes, G}, title = {Microbial product translocation and mortality in adults hospitalised with HIV-associated tuberculosis: a prospective observational cohort study.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-9856875/v1}, pmid = {42282041}, issn = {2693-5015}, abstract = {Background: HIV-associated tuberculosis (HIV-TB) results in unacceptably high mortality rates despite appropriate treatment. Patients hospitalized with HIV-TB often have disseminated tuberculosis and sepsis syndrome which may result in gastro-intestinal barrier dysfunction and facilitate microbial product translocation. Microbial product translocation may contribute to HIV-TB deaths by driving systemic inflammation. Objectives: To assess microbial product translocation and gastrointestinal epithelial damage in patients hospitalized with HIV-TB and the association with 12-week mortality and biomarkers of tuberculosis dissemination. To describe the bacterial blood microbiome (abundance and diversity) in patients with HIV-TB, its association with mortality and tuberculosis dissemination and compare to outpatient controls. Methods: Patients hospitalized with a new diagnosis of HIV-TB were enrolled and prospectively followed for 12 weeks. Markers of microbial product translocation and gastrointestinal damage were measured in a subset (n=373) and bacterial 16s rDNA was quantitated and metagenomic sequencing performed in 235 patients. Microbial product translocation and gastrointestinal epithelial damage marker concentrations were compared between hospitalized patients who died and survivors and inpatients compared to HIVpositive outpatient controls. Logistic regression analysis was performed to determine associations with mortality. Bacterial abundance, diversity and immune perturbation was measured and analysed across patient outcome groups and in patients with tuberculosis dissemination. Results: Patients hospitalized with HIV-TB had significantly higher concentrations of bacterial 16s rDNA, soluble CD14 (sCD14), lipopolysaccharide binding protein (LBP), trefoil factor 3 (TFF3) and lower endotoxin core antibody IgM (EndoCAB), compared to outpatient controls. Soluble CD14 and TFF3 were significantly higher and EndoCAB lower in inpatients who died versus survivors. TFF3 was independently associated with mortality. LPS, sCD14, LBP, EndoCAB and TFF3 showed significant trends in patients with positive biomarkers of tuberculosis dissemination. Metagenomic sequencing showed higher diversity in hospitalised HIV-TB patients compared to controls, but diversity was not different between outcome groups. Mycobacterium genus proportions were increased in hospitalised patients who died compared to survivors. Conclusion: We found evidence of increased gastrointestinal epithelial damage and microbial product translocation in patients hospitalized with HIV-TB and in patients with positive biomarkers for tuberculosis dissemination, however, only TTF3 (a marker of gastrointestinal epithelial damage), was independently associated with mortality.}, }
@article {pmid42282125, year = {2026}, author = {Zhang, S and Chen, J and Lai, Y and Wang, C}, title = {Migrasomes program tissue microenvironment: from physiology to oncology, future perspectives in clinical advances.}, journal = {Journal of the National Cancer Center}, volume = {6}, number = {3}, pages = {219-233}, pmid = {42282125}, issn = {2667-0054}, abstract = {Cancer remains a critical global health challenge, necessitating an in-depth investigation into spatiotemporal dimensions. Migrasomes, a class of migration-dependent organelles that sequester spatiotemporal and biochemical cues, offer a previously overlooked pathway for microenvironmental programming during tumor evolution. At the cellular level, migrasomes mediate extensive intercellular communication and material transfer, while facilitating cellular quality control via the extrusion of damaged organelles. Within tissue microenvironments, these organelles exert context-dependent, bidirectional effects, modulating homeostasis in processes such as wound healing, senescence, inflammation, and microbial infection, while being exploited in cancer to drive proliferation, angiogenesis, immunomodulation, and metastasis. This review elucidates the intricate role of migrasomes within tumor microenvironments and other tissue settings, discusses their potential involvement in the transition from tissue homeostasis to malignancy, and evaluates their potential implications for clinical therapeutic strategies, as well as diagnostic and prognostic biomarkers.}, }
@article {pmid42282175, year = {2026}, author = {Dedon, LR and Lee, DJ and Lin, Q and Yuan, H and Chi, J and Li, L and Gu, H and Tennen, H and Covault, JM and Zhou, Y}, title = {Baseline Gut Microbiome-Metabolome Signatures Are Associated with Drinking Severity and Reduction Following Dutasteride Treatment in Alcohol Use Disorder.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.26.26354041}, pmid = {42282175}, abstract = {The gut microbiome has been implicated in alcohol use disorder (AUD), but its relationship to drinking intensity and treatment response remains poorly understood. We conducted a longitudinal multi-omics analysis of stool samples collected at baseline and endpoint (after 12 weeks) from 122 participants enrolled in a double-blind, placebo-controlled trial of dutasteride for AUD. Gut microbiome composition was characterized using 16S rRNA gene sequencing, and fecal metabolites were measured by LC-MS-based metabolomics. At baseline, drinking intensity was associated with increasingly lower microbial richness. Genera in the class Clostridia emerged as key microbial hubs associated with drinking intensity in an age- and sex-dependent manner. Drinking intensity promoted co-enrichment of [ Ruminococcus ] gnavus group and [ Clostridium ] inocuum group with amino acid catabolites, as well as the co-depletion of diverse Clostridia taxa and lipid metabolites. Dutasteride treatment and drinking reduction had minimal impact on gut microbiome composition. Random forest models integrating baseline clinical, microbiome, and metabolome data improved the classification of clinically meaningful drinking reduction compared to models using clinical data alone. These findings show that a coupled baseline gut microbiome-metabolome signature is associated with drinking intensity and future treatment response in AUD, highlighting the potential for multi-omics integration to inform precision treatment approaches.}, }
@article {pmid42282268, year = {2026}, author = {Frame, LA and Warren, A and Al Qalam, A and Corr, PG and Farah, M and Karam, M and Rangoussis, K and Fahim Devin, M and Celikkol, Z and Gordon, L and Villarreal, D and Catto, E and Udam, Y and Thompson, K and Lubinski, O and Samman, A and Badawi, A and Hack, H and Hunter, M and Hines, I and Servetas, S and Jackson, SA and Hasan, NA and Kogan, M}, title = {Brain health and the gut microbiome (bMicrobiome Study): a proof-of-concept, feasibility study integrating shotgun metagenomics, metrology, and multidimensional phenotyping across the cognitive aging spectrum.}, journal = {Gut microbes reports}, volume = {3}, number = {1}, pages = {2679810}, pmid = {42282268}, issn = {2993-3935}, abstract = {BACKGROUND: Associations between the gut microbiome and cognitive decline remain inconsistent, reflecting methodological variability, small cohorts, and limited integration of behavioral and lifestyle factors. The microbiota-gut-brain axis may influence cognition through metabolic, immune, and neuroendocrine pathways affecting mood, decision-making, and health behaviors.<br><br>METHODS: This prospective, proof-of-concept study integrated multidimensional phenotyping with metagenomic sequencing (shotgun) in adults (50-90&#x2009;y) around Washington, DC. Participants were classified as healthy controls (HC) or mild cognitive impairment (MCI) by clinical history; early Alzheimer's disease (eAD) participants were unable to complete study requirements. Longitudinal assessment used Boston Cognitive Assessment (BoCA), patient-reported outcomes (PROMIS-29), dietary intake and quality (DietID&#x2122;), readiness-for-change (adapted URICA), at-home stool sample collection.<br><br>RESULTS: Seventeen participants completed sufficient assessments (HC n&#x2009;=&#x2009;11; MCI n&#x2009;=&#x2009;6). Substantial overlap in gut microbiome composition was observed between HC and MCI. Poorly characterized or uncommon taxa drove trends; unassigned taxa were common. Assessment revealed high diet quality and variability in dietary patterns and key components (vegetables, whole grains, fat, fish). Participants demonstrated high readiness to engage in nutritional behavior change, with individuals with MCI reporting greater concern about maintaining changes and a stronger desire for external support.<br><br>CONCLUSIONS: Integrating multidimensional phenotyping with metagenomics is feasible in cognitive decline. Findings highlight biological and behavioral heterogeneity, limitations of species-level inference, and diet and behavioral readiness as modifiable contextual factors.}, }
@article {pmid42282286, year = {2026}, author = {Jain, M and Jain, T and Nayak, R and Saad, T and Karale, AW and Ilyas, M and Arjariya, R}, title = {Estimation of gut microbiome motif associated with active tuberculosis - A case control study.}, journal = {Bioinformation}, volume = {22}, number = {4}, pages = {2083-2086}, pmid = {42282286}, issn = {0973-2063}, abstract = {Tuberculosis (TB) is the most tenacious health issue affecting individuals globally. Therefore, it is of interest to estimate gut microbiota motifs associated with the outbreak of active TB by incorporating the insights from human case-control data. 106 respondents were categorised into 2 groups: group A with TB and group B controls with 53 respondents in each category. The Shannon diversity index was substantially diminished in affected individuals. The active TB cases exhibited substantially decreased micro-biomes (P < 0.001). Thus, we show the need to develop microbiome-targeted strategies to reduce the incidence of active TB cases and improve their effective management.}, }
@article {pmid42282445, year = {2026}, author = {Zhu, L and Wen, X and Zhu, W and Hu, X and Xu, Y and Peng, X}, title = {Enteromorpha prolifera Polysaccharide Alleviates Type 2 Diabetes via the Gut Microbiota-Liver Axis to Modulate Cholesterol Metabolism.}, journal = {Food science &amp; nutrition}, volume = {14}, number = {6}, pages = {e71998}, pmid = {42282445}, issn = {2048-7177}, abstract = {Enteromorpha prolifera polysaccharide (EPP), a major bioactive sulfated polysaccharide derived from green algae, possesses potent hypoglycemic and hypolipidemic properties. This study aimed to evaluate the therapeutic efficacy of EPP in a murine model of type 2 diabetes mellitus (T2DM) and elucidate its underlying molecular mechanisms through an integrated multi-omics approach-comprising 16S rRNA microbiomics, untargeted metabolomics, and transcriptomics. Our findings demonstrate that EPP intervention significantly suppressed fasting blood glucose (FBG) levels, attenuated dyslipidemia, and enhanced systemic insulin sensitivity. At the microbiome level, EPP restored intestinal homeostasis by enriching beneficial taxa, specifically Lactobacillus, Ligilactobacillus, and Dubosiella, while depleting the T2DM-associated genus Blautia. These microbial shifts correlated with significantly elevated fecal concentrations of short-chain fatty acids (SCFAs), including acetate, propionate, and branched-chain fatty acids (isobutyrate and isovalerate). Integrated pathway analysis revealed that EPP significantly modulates steroid hormone biosynthesis; integrated pathway analysis suggested that EPP potentially modulates pathways related to steroid hormone biosynthesis, cholesterol metabolism, and primary bile acid synthesis. Quantitative RT-PCR validation confirmed that EPP treatment was accompanied by the upregulation of critical genes involved in bile acid and steroidogenesis (Cyp17a1, Cyp11a1, Hsd3b7, and Stard1) and the downregulation of Srebf2 and Hnf4α, the master transcriptional regulators of cholesterol biosynthesis and hepatic gluconeogenesis, respectively. Correlation analyses further indicated potential links between gut microbiota alterations, SCFA production, and glycemic control. Collectively, these results suggest that EPP may alleviate T2DM symptoms, which is associated with the modulation of the gut microbiota-hepatic cholesterol metabolism axis, positioning it as a promising functional food ingredient or therapeutic candidate for metabolic disorders.}, }
@article {pmid42282557, year = {2026}, author = {Adelfio, M and Bonzanni, M and Callen, GE and Diaz, AR and Paster, BJ and He, X and Hasturk, H and Ghezzi, CE}, title = {Profiling Gingival Inflammation in a 3D Oral Tissue Model Reveals Early Features of Disease Progression.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.06.05.730462}, pmid = {42282557}, issn = {2692-8205}, abstract = {Gingival health depends on a balanced interplay among the gingival epithelium, immune system, and oral microbiome. Disruption of this equilibrium through sustained biofilm accumulation and host inflammatory responses leads to gingivitis, a highly prevalent yet reversible condition which if left untreated could progress into more severe and irreversible condition called periodontitis. The early onset of gingivitis remains poorly defined due to subtle clinical presentation and pronounced interindividual variability. Current diagnostic approaches rely largely on clinical assessment and endpoint biomarkers, limiting insight into the early host-microbiome interactions that drive disease initiation. Here, we employ a previously validated, physiologically relevant oral tissue model (OTM) to longitudinally investigate epithelial-microbiome interactions following inoculation with patient-derived dysbiotic microbiomes from early-stage gingivitis. The OTM maintained host tissue integrity and microbial viability over a seven-day period, preserving epithelial barrier function, dynamic inflammatory responses, and disease-associated microbial signatures. Notably, we establish, for the first time in an in vitro platform, clinical calibration against gingival crevicular fluid (GCF), demonstrating that OTM responses recapitulate inoculum-dependent inflammatory signatures, increased microbial dissimilarity under dysbiotic conditions, and coordinated host-microbiome metabolic interactions. While pro-inflammatory responses were most pronounced at early time points, subsequent modulation toward anti-inflammatory states highlights the temporal complexity of host responses and suggests that longer culture durations may further resolve disease trajectories. Collectively, these findings validate the OTM as a robust, physiologically relevant platform that captures key features of periodontal health and inflammation. By integrating host viability, microbial ecology, and clinical benchmarking, this system enables mechanistic interrogation of early disease-driving processes and provides a translational framework for advancing predictive diagnostics and preventive therapeutic strategies in periodontal disease.}, }
@article {pmid42282600, year = {2026}, author = {Corbett, CM and O'Shall, AE and Niedringhaus, M and West, EA}, title = {Behavioral flexibility and gut microbiome as potential predictors of oral oxycodone self-administration.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.06.02.729613}, pmid = {42282600}, issn = {2692-8205}, abstract = {Prescription opioids such as oxycodone have been widely used in the United States and have contributed to the ongoing opioid epidemic. While many individuals limit use to prescribed contexts, a subset transitions to misuse and, in some cases, to illicit opioid use. Identifying behavioral and biological factors that predict this vulnerability is critical for improving prevention and intervention strategies. Here, we investigated whether individual differences in behavioral flexibility and gut microbiome composition are associated with future oxycodone intake using a translationally relevant model of oral oxycodone self-administration in male and female Long-Evans rats. We established a model in which distinct intake phenotypes emerged, characterized by animals with high versus low oxycodone consumption. Behavioral flexibility, assessed using a contingency degradation task, was associated with oxycodone intake, identifying it as a potential behavioral biomarker of vulnerability. In parallel, oral oxycodone exposure altered gut microbiome composition, and microbiome features were associated with both behavioral flexibility and drug-taking behavior. These findings support a framework in which individual differences in opioid intake arise from the interaction of pre-existing behavioral traits and biological states, including gut microbiome composition which provides a foundation for identifying predictive biomarkers and developing individualized strategies to mitigate risk for opioid misuse.}, }
@article {pmid42282663, year = {2026}, author = {Torres-Morales, J and Dewhirst, F and Kauffman, KM and Mark Welch, J and Borisy, G}, title = {Site-specialization of human oral Porphyromonas species.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.06.02.729646}, pmid = {42282663}, issn = {2692-8205}, abstract = {Site-specificity within the human oral cavity reflects adaptation mechanisms such as genome divergence and metabolic specialization. Members of the genus Porphyromonas are distributed across oral sites in health and disease, yet the specific distribution of taxa and the functional basis of their site-specificity remain poorly understood. We analyzed 1,242 metagenomes from nine oral sites in healthy individuals and 24 subgingival plaque samples from individuals with periodontitis. Competitive mapping to a dereplicated genus-level pangenome of 84 reference genomes, combined with phylogenomic, gene-level detection, and functional profiling, revealed distinct site-specific distribution patterns, ecotype differentiation, and metabolic specialization across Porphyromonas taxa. Porphyromonas pasteri was the most abundant and widespread taxon in healthy subjects, comprising two ecotypes--one mucosal, one plaque-associated. Porphyromonas gingivalis was rare in healthy subjects but present in periodontal disease, although detected in only half of periodontitis samples. P. gingivalis exhibited the broadest metabolic repertoire, suggestive of a survival strategy adaptive to disparate conditions. In contrast, Porphyromonas catoniae, restricted to healthy dental plaque, lacked biosynthetic pathways for cobalamin, biotin, and serine, implying nutritional dependency on other taxa or the host. Porphyromonas endodontalis, detected in subgingival plaque across both health and disease, also lacked several metabolic pathways. A 44 kb conjugative element identified in P. gingivalis was detected across healthy and periodontitis subgingival plaque microbiomes independently of the P. gingivalis chromosome, indicating horizontal transfer. These findings reveal genomic divergence and complex metabolic specialization among Porphyromonas taxa, refining our understanding of their role in the ecological structure of the human oral microbiome.}, }
@article {pmid42282679, year = {2026}, author = {Laurin, PJ and Garud, NR}, title = {Complex adaptive architectures constrain the pace of adaptations sweeping across human gut microbiomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.06.01.729358}, pmid = {42282679}, issn = {2692-8205}, abstract = {Recent work has shown that commensal gut bacteria can evolve rapidly within hosts on short timescales of days to months, fueled by the enormous mutational input generated daily in the microbiome. Yet how rapidly adaptations spread across gut microbiomes of different hosts remains unclear. We address this question by estimating the number of independent origins of gene-specific sweeps spreading via recombination across bacterial populations. Multiple origins (soft sweeps) indicate that adaptive mutations arise rapidly whereas one origin (hard sweeps) indicate slower mutational input. Contrary to expectations of rapid adaptation, we find that many gene-specific sweeps have only one or a few origins. We show that this requires that sweeps arise from adaptive mutation rates orders of magnitude lower than single base pair mutation rates. This implies that gene-specific sweeps bear difficult-to-mutate complex adaptations such as structural or epistatic variants. Consistent with this interpretation, we find that identified sweep regions exhibit patterns of nucleotide diversity and linkage disequilibrium inconsistent with a single adaptive mutation rising to high frequency. We conclude that recombination across human gut microbiomes enables the spread of adaptations with complex genetic architectures that otherwise would require a long waiting time to generate de novo within an individual host.}, }
@article {pmid42282687, year = {2026}, author = {Woods, E and Jones, D and Gorden, O and Nusbacher, N and Kofonow, J and Dumont, G and Frank, DN and Friedman, NR and Herrmann, BW and Lozupone, C and Verneris, MR}, title = {Altered Tonsillar Microbiome in Children with Down Syndrome and Obstructive Sleep Apnea.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.29.728812}, pmid = {42282687}, issn = {2692-8205}, abstract = {BACKGROUND AND OBJECTIVES: Children with Down syndrome (DS) have a high prevalence of obstructive sleep apnea (OSA) due to anatomic, neuromuscular, immunological and metabolic factors, yet the contribution of the tonsillar microbiome to airway obstruction in this population remains unexplored. We hypothesized that DS-associated OSA would be associated with a distinct tonsillar microbiome compared to non-DS OSA.<br><br>METHODS: Tonsillar tissue from 22 DS and 18 NDS participants were analyzed by 16S rRNA sequencing. Alpha and beta diversity were assessed using Faith's phylogenetic diversity and UniFrac distances, respectively, and significantly different taxa were identified with ANCOM-BC and Mann-Whitney testing.<br><br>RESULTS: Although overall microbial richness and community structure were similar between groups, overweight DS participants demonstrated increased phylogenetic diversity compared to normal-weight DS peers. Taxonomic profiling of the entire patient cohort revealed that in DS tonsils there were selective alterations in key genera with selective depletion of Haemophilus and enrichment of Staphylococcus , Rothia , and Lactobacillales . Haemophilus abundance correlated positively with tonsil weight in both cohorts.<br><br>CONCLUSIONS: These findings suggest that while global diversity is preserved, specific microbial shifts distinguish the DS tonsillar niche, potentially reflecting altered immune and metabolic environments associated with trisomy 21. Understanding these microbial differences may reveal mechanisms underlying the higher incidence and persistence of OSA in DS and inform targeted therapeutic strategies.}, }
@article {pmid42282707, year = {2026}, author = {Blumstein, DM and Patel, A and Schiro, G and Suzuki, TA}, title = {Beyond distance-decay: The Mississippi River shapes gut microbiome communities in the Peromyscus maniculatus species complex.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.06.03.729934}, pmid = {42282707}, issn = {2692-8205}, abstract = {Biogeographic barriers are fundamental in shaping the distribution of animals and plants, yet the role of discrete landscape features in constraining microbial dispersal remains poorly understood. Identifying the barriers that partition gut microbial communities is essential for modeling the distribution of hosts and their symbionts across physical space and evolutionary time. The deer mouse (Peromyscus maniculatus species complex), which inhabits nearly all terrestrial environments in North America, provides an ideal model for testing these biogeographic drivers of the mammalian gut microbiome. Using NSF NEON biorepository samples, we characterized the gut microbiomes of 13 populations across the contiguous United States using full-length 16S rRNA long-read sequencing. While we observed a consistent distance-decay relationship across the continent, our results reveal that the Mississippi River acts as a major biogeographic break, significantly increasing microbial dissimilarity beyond the levels predicted by geographic distance alone. This "river effect" suggests that large fluvial systems impose a discrete barrier to microbial transmission, likely due to restricted host dispersal. Furthermore, we identified specific microbial lineages that exhibit differential sensitivity to this barrier, suggesting a gradient in microbial acquisition patterns ranging from the environment to host-host transmission. Together, these findings demonstrate that the gut microbiome may act as a sensitive bio-indicator of landscape-level ecological connectivity, revealing that large-scale landscape barriers disrupt microbial transmission even among closely related host populations that lack reproductive barriers.}, }
@article {pmid42282751, year = {2026}, author = {Duchamp-Smith, C and Burchat, N and Pantula, LG and Mitchell, SB and Aydemir, TB and Sampath, H}, title = {Hepatic stearoyl-CoA desaturase-1 is specifically suppressed by dextran sodium sulfate but does not influence colitis sensitivity.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.29.728832}, pmid = {42282751}, issn = {2692-8205}, abstract = {UNLABELLED: The delta-9 desaturase stearoyl-CoA desaturase-1 (SCD1) catalyzes the conversion of saturated fatty acids to monounsaturated fatty acids (MUFA) and is highly expressed in liver and adipocytes. Previous studies have demonstrated that treating mice with dextran sulfate sodium (DSS), a chemical inducer of ulcerative colitis, results in severe downregulation of SCD1 in the liver. However, the specific role of hepatic SCD1 in modulating colitis severity, as well as the impact of DSS on SCD1 and other lipogenic factors in other tissues has not been investigated. Here we show that downregulation of hepatic SCD1 following DSS treatment is not accompanied by changes to other lipogenic genes in the liver. In contrast, adipose tissue demonstrates coordinated reductions in lipogenic genes, including SCD1 and SCD2, while the colon does not display any perturbation of these targets. Furthermore, we demonstrate that the downregulation of hepatic SCD1 occurs independently of sterol regulatory element binding protein-1c (SREBP-1c) and does not require an intact gut microbiome. Interestingly, a distinct model of colitis induced by IL-10 deficiency does not result in downregulation of hepatic SCD1. Concomitant with transcriptional changes, DSS treatment is associated with significant remodeling of the hepatic lipidome, including reductions in total phospholipids (PLs) and reduced MUFA-containing PLs and triacyglycerols (TAGs), consistent with the observed reduction in SCD1. Interestingly, hepatic cholesterol esters and plasma lipids including free cholesterol and glycerophospholipids were significantly elevated following DSS treatment. Given the significant reduction in hepatic SCD1 following DSS treatment, we tested a role for liver SCD1 in modulating colitis sensitivity. Mice with a targeted deletion of hepatic SCD1 were not more prone to colitis, indicating that the loss of hepatic SCD1, while a consequence of DSS-induced colitis, does not mediate colitis sensitivity in vivo.<br><br>SYNOPSIS: Hepatic SCD1 does not modulate colitis severity upon DSS exposure. However, DSS-induced colitis elicits significant lipid metabolism dysfunction, demonstrated by elevated plasma and liver lipids, particularly plasma cholesterol and hepatic cholesterol esters, highlighting a role for gutliver crosstalk following colonic inflammation.}, }
@article {pmid42282818, year = {2026}, author = {Richmond, GR and Cunha, E and Kelly, L and Dias, &#xd3; and Chang, RL}, title = {Nutrient control enables metabolic reconstruction of L. rhamnosus GG and analysis of secretions.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.06.02.729517}, pmid = {42282818}, issn = {2692-8205}, abstract = {Lacticaseibacillus rhamnosus GG (LGG) is an important gut commensal bacterial strain that has been extensively studied in both industrial and health settings. Despite its long history of study, a high-quality genome-scale metabolic network model (GEM) for LGG has yet to be reconstructed. Only automatically-generated draft models have been published, which have notoriously limited functional accuracy. Furthermore, comprehensive nutrient requirements have not been established for well-controlled in vitro study. Here we present the first curated GEM for LGG using a new approach for reconstruction and validation that leverages multiple automatically-generated draft models, applied study literature, and high-throughput defined media experiments. In addition, our results include a series of chemically defined media, extensive single-component nutrient dropout growth data, insights from in silico and in vitro experiments into major secretion products lactate and indole-3-carboxaldehyde, a minimal medium and in silico characterization of LGG's nutrient requirements. Our approach for developing interdisciplinary research tools for LGG metabolism comprises a new framework that could be applied to many understudied microorganisms, particularly useful in studying bacteria within the human microbiome.}, }
@article {pmid42282998, year = {2026}, author = {Zeng, B and Maitikuerban, M and Chen, L and Wang, DK and Li, J and Yang, L and Lao, XM and Zhang, SE and Liao, GQ and Liang, YJ}, title = {Microbiome dynamics and early microbial signatures predict bone regeneration in marsupialized jaw lesions: a longitudinal 16S sequencing cohort study.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2684137}, pmid = {42282998}, issn = {2000-2297}, abstract = {BACKGROUND: Marsupialization is a conservative treatment for odontogenic jaw lesions but is hampered by protracted, unpredictable bone regeneration, lacking early biomarkers. Furthermore, whether these intraosseous lesions harbour a unique microbiome remains unknown. We aimed to characterize microbial dynamics during treatment and develop a prognostic model to address clinical unpredictability.<br><br>METHODS: A prospective longitudinal study was conducted with multi-site sampling (saliva, tissue, luminal fluid and swabs) across three phases: primary surgery, 3-month follow-up and secondary surgery. Bacterial 16S rRNA gene sequencing was subsequently performed. Microbial dynamics were analyzed using diversity analysis and source tracking. A prognostic model was constructed using a hybrid feature selection strategy to predict 12-month bone regeneration using 3-month post-operative swabs.<br><br>RESULTS: Baseline analysis revealed that odontogenic jaw lesions harbour a unique, biologically selected microbiome enriched in Fusobacterium and Clostridia, which are distinct from saliva. Marsupialization induced a profound microbial remodelling, transforming this closed niche into an open, stochastic ecosystem dominated by salivary commensals. Long-term analysis indicated a secondary succession, where primary pathogens were replaced by a Bacteroidia-enriched community. Crucially, after a rigorous feature selection process, a streamlined microbial signature accurately predicted 12-month bone regeneration (AUC&#x2009;=&#x2009;0.937). Poor bone regeneration was associated with the persistence of the primary Clostridia core, whereas favourable regeneration was linked to a shift towards Bacteroidia and Proteobacteria.<br><br>CONCLUSION: Marsupialization drives the lesion microbiome from a pathogenic niche toward a stochastic, commensal-like state. This succession trajectory is associated with clinical outcome. Our prognostic model offers a novel precision tool to optimize lesion management.}, }
@article {pmid42283379, year = {2026}, author = {Eleftherianos, I and Zhang, W and Mohamed, A and Al-Akeel, RK and Alkhaibari, AM and Keyhani, N and Smagghe, G}, title = {Microbiome-mediated chemical communication in insects: Implications for pest management.}, journal = {Pest management science}, volume = {}, number = {}, pages = {}, doi = {10.1002/ps.71015}, pmid = {42283379}, issn = {1526-4998}, support = {32472644//National Natural Science Foundation of China/ ; QiankehePingtaiCXPTXM[2025]-026//Guizhou Provincial S&amp;T Innovation Platform Research Project/ ; }, abstract = {Insects rely on semiochemicals to regulate aggregation, mating, foraging, and host selection. This review synthesizes evidence that insect-associated microbiota shape these chemical signals and evaluates their potential for pest management. The literature supports four principal routes by which microbes influence insect chemical communication: (i) direct production of volatile organic compounds; (ii) microbial provision or modification of pheromone precursors; (iii) microbiome-mediated effects on sensory and neural function; and (iv) context dependence driven by diet, development, quorum sensing, and environmental microbiomes. The strongest evidence comes from loss-gain-rescue studies, including German cockroach fecal volatiles and Wolbachia-linked effects on Drosophila paulistorum mating chemistry. Translationally, fermentation-based lures for fruit flies and microbial deterrents such as Xenorhabdus-derived metabolites show clear promise, whereas most other systems remain correlative because gene-to-metabolite-to-behavior chains are incomplete and field validation is limited. Microbiome-semiochemical interactions offer a credible platform for next-generation attractants, repellents, and symbiont-based pest control. Progress will depend on rigorous mechanistic validation, standardized behavioral assays, and biosafety-aware field testing to convert promising discoveries into scalable integrated pest management tools. © 2026 The Author(s). Pest Management Science published by John Wiley &amp; Sons Ltd on behalf of Society of Chemical Industry.}, }
@article {pmid42283450, year = {2026}, author = {Pishchany, G and Fryling, KE and Vasukuttan, V and Shin, YH and Mortimer, TD and Grad, YH and Clardy, J}, title = {Aerocavin Is an Antibiotic with Potent and Specific Anti-Neisserial Activity.}, journal = {ACS infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1021/acsinfecdis.6c00197}, pmid = {42283450}, issn = {2373-8227}, abstract = {Gonorrhea, caused by Neisseria gonorrhoeae, is a widespread sexually transmitted disease that is becoming resistant to all currently used antibiotics. Therefore, new therapeutics for gonorrhea are desperately needed. Here, we show that a natural product, aerocavin, is highly potent and specific against Neisseria. Aerocavin accumulates in N. gonorrhoeae at high levels and inhibits bacterial RNA polymerase (RNAP) by binding the switch region. Aerocavin resistance mutations evolve in N. gonorrhoeae at a low rate and are absent in clinical isolates. Previously overlooked narrow-spectrum antimicrobials like aerocavin may enable microbiome-sparing treatments of gonorrhea.}, }
@article {pmid42283564, year = {2026}, author = {Ardizzone, CM and Lammons, JW and Lan, RS and Elnaggar, JH and Lillis, RA and Toh, E and Pack, LM and Mott, PD and Jacobs, CD and Yeruva, L and Taylor, CM and Quayle, AJ}, title = {Integrated multi-omics analysis uncovers cervicovaginal ecological networks and their association with Chlamydia trachomatis load.}, journal = {Infection and immunity}, volume = {}, number = {}, pages = {e0068125}, doi = {10.1128/iai.00681-25}, pmid = {42283564}, issn = {1098-5522}, abstract = {Chlamydia trachomatis (Ct) is a causal agent of upper reproductive tract pathology. There is a broad spectrum of cervical Ct load in infected women, and upper tract infection is associated with higher cervical Ct load. Recent studies indicate that bacterial vaginosis (BV) can modulate host-Ct outcomes. To identify features associated with BV status and Ct load, we performed an integrated multi-omics analysis of the cervicovaginal microbiome, tryptophan metabolome, and cytokines. Samples were analyzed using 16S rRNA gene sequencing, targeted UPLC-MS/MS quantification of tryptophan metabolites, and multiplex cytokine profiling. Ordination analyses showed that BV status was separated by the microbiome, metabolome, and cytokines, whereas Ct load was separated only by cytokines. K-means clustering of tryptophan metabolites defined three metabolome state types (MSTs). MST I, associated primarily with Lactobacillus crispatus-dominated community state type (CST) I, exhibited high tryptophan availability, indole-3-lactic acid, and complete kynurenine-pathway activity. Both MST II and MST III were associated with BV-associated CST IV and showed marked tryptophan depletion. MST II was broadly depleted of most tryptophan metabolites, while MST III was enriched in downstream microbially derived indole pathway metabolites and kynurenic acid. Hierarchical all-against-all association testing revealed coordinated relationships linking clusters of bacterial taxa, metabolites, and cytokines. Importantly, multi-omics network analyses identified integrated microbial-metabolic-immune modules that predicted high versus low Ct load, highlighting CXCL9, CXCL10, IL-17, BV-associated taxa, and indole pathway metabolites as key discriminative features. Results demonstrate that cervical Ct load reflects coordinated microbial-metabolic-immune ecological states rather than microbiome composition alone and refine current models of Ct-BV interactions.}, }
@article {pmid42283770, year = {2026}, author = {Liu, H and Tian, J and Sun, X and Li, R and Gao, W and Zhang, D and Dong, G}, title = {Divergent Colorectal Cancer Risks Following Metabolic Bariatric Surgery: Anatomical Remodeling and the Genotoxic Microenvironment.}, journal = {Obesity surgery}, volume = {}, number = {}, pages = {}, pmid = {42283770}, issn = {1708-0428}, abstract = {Metabolic bariatric surgery (MBS) reduces overall cancer incidence, yet colorectal cancer (CRC) risk diverges by procedure. Roux-en-Y gastric bypass (RYGB) has been associated with increased long-term CRC risk (HR 1.55 at 10-14 years), whereas sleeve gastrectomy (SG) shows no equivalent elevation, though shorter follow-up (mean 4.5 vs. 8.5 years) precludes definitive conclusions. This review develops a biologically plausible mechanistic framework for these divergent outcomes. RYGB-induced anatomical bypass and accelerated transit are proposed to drive distal substrate overload, with an associated shift of the colonic microbiome toward proteolytic fermentation. The proposed genotoxic luminal environment is characterized by convergent actions of secondary bile acids, tyramine, and hydrogen sulfide, compounded by butyrate depletion. By preserving gastrointestinal continuity, SG is hypothesized to avoid these alterations. These considerations support integrating baseline CRC risk into surgical selection and procedure-specific surveillance after RYGB.}, }
@article {pmid42283822, year = {2026}, author = {Santos, ACC and Corrêa, JL and de Lima, DS and Andrade, ACAS and Junqueira, CN and Dos Santos, AR and Augusto, SC and Bonetti, AM and Ueira-Vieira, C}, title = {Gut microbiome composition and cellulolytic bacteria associated with the carpenter bee Xylocopa frontalis.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-026-13911-0}, pmid = {42283822}, issn = {1432-0614}, abstract = {Carpenter bees of the genus Xylocopa interact extensively with woody substrates during nest construction, suggesting that associated microorganisms may contribute to the degradation of plant-derived polymers. Despite their ecological relevance, the gut microbiome and functional potential of Xylocopa species remain poorly characterized. In this study, we investigated the bacterial and fungal gut microbiome of Xylocopa frontalis using 16S rRNA and ITS amplicon sequencing, complemented by culture-dependent approaches. The gut microbiome was dominated by bacterial taxa commonly associated with bees, including Bombiscardovia, Bifidobacterium, and Frischella, whereas fungal communities were more variable and included genera such as Aspergillus and Cladosporium. Several taxa were consistently detected across samples, indicating recurrent community members; however, a consistent core microbiome was not clearly observed. We established a collection of cultivable microorganisms, including a bacterial isolate capable of utilizing cellulose as a carbon source, as demonstrated by plate assays. Phylogenetic and genomic analyses identified this isolate as Bacillus velezensis strain Xf, which harbors genes associated with cellulose and hemicellulose degradation. These findings suggest the potential for lignocellulose-related metabolism in the gut microbiome. Together, our results provide a combined culture-independent and culture-dependent characterization of the X. frontalis gut microbiome and identify microorganisms with relevant functional traits. Although based on a limited sample size, this study expands current knowledge of microbial associations in carpenter bees and establishes a foundation for future investigations into their functional roles. KEY POINTS: • Gut microbiome of Xylocopa frontalis was characterized by amplicon sequencing • Bacillus velezensis strain Xf showed cellulolytic activity in vitro • Gut-associated microbes showed genes linked to lignocellulose degradation.}, }
@article {pmid42283827, year = {2026}, author = {Wiśniewski, P and Maździarz, M and Kwietniewska, K and Krawczyk, K}, title = {Shifts in Rhizosphere Bacterial Community Composition and Predicted Functional Potential Associated with Impatiens parviflora Invasion in Temperate Forest.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02807-1}, pmid = {42283827}, issn = {1432-184X}, support = {No. 12.610.002-110//Uniwersytet Warmi&#x144;sko-Mazurski w Olsztynie/ ; No. 12.610.002-110//Uniwersytet Warmi&#x144;sko-Mazurski w Olsztynie/ ; No. 12.610.002-110//Uniwersytet Warmi&#x144;sko-Mazurski w Olsztynie/ ; }, abstract = {Impatiens parviflora is a widespread invasive plant in temperate European forests, yet its influence on rhizosphere microbial communities remains poorly understood. This study provides initial metagenomic insights into taxonomic shifts and predicted functional potential of bacterial communities associated with this invader. Rhizosphere soils were collected from eight I. parviflora-invaded and eight non-invaded control plots in a mixed coniferous forest in northern Poland and analysed using Oxford Nanopore shotgun sequencing, with functional inference performed using the taxonomy-dependent FAPROTAX database. Bacterial richness was significantly higher in invaded soils, whereas Shannon and Simpson diversity indices did not differ between treatments, indicating an expansion of rare taxa without changes in overall diversity structure. The invaded rhizosphere was characterised by a uniform depletion of dominant bacterial orders, with no significantly enriched taxa detected, contrasting with the selective enrichment of microbial groups often reported for other invasive plant species. FAPROTAX-based predictions indicated consistently lower inferred abundances of 37 metabolic processes in invaded plots, including those related to nitrogen cycling and degradation of complex plant polymers. Because these functional predictions are derived from taxonomic composition, they represent inferred ecological potential rather than measured activity. Overall, these results generate testable hypotheses regarding plant-soil feedbacks and highlight the utility of long-read metagenomics for exploring microbial dynamics potentially contributing to the ecological success of I. parviflora in temperate forests.}, }
@article {pmid42283898, year = {2026}, author = {Hu, T and Li, Y and Li, A and Liu, M and Li, S and Zheng, L and Zhang, J and Liu, R and Zhong, W}, title = {Application of a native Weissella starter to modulate the microbiome, metabolome, and quality characteristics of fermented Ma bamboo shoots.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {7}, pages = {}, pmid = {42283898}, issn = {1573-0972}, support = {32402036//National Natural Science Foundation of China/ ; LQ23C010004//Natural Science Foundation of Zhejiang Province/ ; }, mesh = {*Weissella/metabolism/isolation &amp; purification/classification/genetics ; Fermentation ; *Microbiota ; *Metabolome ; *Fermented Foods/microbiology/analysis ; Food Microbiology ; *Plant Shoots/microbiology/chemistry ; Bacteria/classification/genetics/isolation &amp; purification ; Metabolomics ; Food, Processed ; *Bambusa/microbiology ; }, abstract = {Spontaneous fermentation of bamboo shoots often leads to unstable quality and safety risks, such as nitrite accumulation. To solve this problem, two native Weissella strains (N2-1 and N2-2) with fast acid-producing and nitrite-degrading abilities were isolated from traditionally fermented Ma bamboo shoots. This study evaluated their use as a starter culture. High-throughput sequencing showed that inoculation quickly changed the microbial community. Weissella became the dominant genus, while the diversity of other bacteria and fungi decreased. In addition, metabolomics analysis revealed major changes in the metabolites. The Weissella fermentation increased umami-related nucleotides (adenine and adenosine) and flavor volatiles, while speeding up the breakdown of bitter phenolics and dipeptides. These chemical changes improved the texture: both raw and cooked bamboo shoots showed higher chewiness and cohesiveness, and lower hardness. Correlation analysis confirmed that the dominance of Weissella was closely linked to these positive changes. In conclusion, using this native Weissella starter is a practical way to standardize the safety, microbial stability, and sensory quality of fermented bamboo shoots.}, }
@article {pmid42283913, year = {2026}, author = {Zhang, Y and Yu, X and Shi, L and Qi, C and Wang, H}, title = {The role of the microbiome in uterine cancer: insights into tumorigenesis, therapeutic implications, and clinical prospects.}, journal = {Journal of the Egyptian National Cancer Institute}, volume = {38}, number = {1}, pages = {}, pmid = {42283913}, issn = {2589-0409}, mesh = {Humans ; Female ; *Microbiota/immunology ; Tumor Microenvironment/immunology ; *Uterine Neoplasms/therapy/microbiology/etiology/pathology/diagnosis ; Prognosis ; *Carcinogenesis ; }, abstract = {Malignant tumors of the uterine cavity are a leading cause of cancer-related mortality in women worldwide. In recent years, the tumor microenvironment, as a novel biological concept, has garnered increasing attention. The microenvironment plays a crucial role in the initiation, progression, and response to treatment of tumors. Although research on the microenvironment of malignant uterine tumors is in its early stages, preliminary findings suggest that alterations in the microbial communities of cervical and endometrial cancers are closely associated with tumorigenesis, immune evasion, metastasis, and treatment resistance. Notably, specific microbial community changes have potential diagnostic and prognostic implications, offering novel insights into the management of these cancers.This review aims to summarize and analyze the current state of research on the microenvironment of malignant uterine tumors, particularly its role in cervical and endometrial cancers. We first overview the epidemiological landscape and microenvironmental features of these tumors, emphasizing how microbial communities influence tumor initiation and progression. This influence occurs through immune modulation, metabolic changes, and alterations within the tumor microenvironment. Second, the potential role of the microenvironment in tumor therapy is explored, particularly its application prospects in chemotherapy, radiotherapy, and immunotherapy. In addition, the application potential of microbial communities in early tumor diagnosis, efficacy monitoring, and prognosis assessment is discussed.}, }
@article {pmid42284092, year = {2026}, author = {Astolfi, A and Potenza, M and Ciavarella, C and Moramarco, A and Bonci, P and Zaghi, A and Foschi, C and D'Eliseo, LA and D'Eliseo, D and Lazzarotto, T and Fontana, L and Versura, P}, title = {Distinct Ocular Surface Microbial Profiles in Corneal Transplant Candidates.}, journal = {Cornea}, volume = {}, number = {}, pages = {}, doi = {10.1097/ICO.0000000000004088}, pmid = {42284092}, issn = {1536-4798}, support = {RC-2022/51//Ministero della Salute/ ; }, abstract = {PURPOSE: To characterize the ocular surface microbiome in patients undergoing corneal transplantation and to evaluate microbial shifts associated with corneal endothelial decompensation and surgical history.<br><br>METHODS: In this single-center case-control study, conjunctival swabs were collected from 54 adults scheduled for lamellar or penetrating keratoplasty and from 16 healthy controls. Sampling was performed under sterile conditions immediately before surgery. Bacterial DNA was analyzed by 16S rRNA gene sequencing targeting the V3-V4 regions. Alpha and beta diversity indices were calculated using the Shannon index and Bray-Curtis dissimilarity. Taxonomic composition was compared across groups stratified by clinical status and prior ocular surgery.<br><br>RESULTS: Pretransplant patients showed significantly higher alpha diversity than healthy controls (P = 0.04), and beta diversity analysis confirmed distinct microbial community structures between groups (P = 0.002). The patient group exhibited enrichment of Enterobacteriaceae, Pseudomonas, and Escherichia-Shigella, whereas Bacteroidota and Bacteroidia predominated in healthy subjects. No significant differences in diversity or composition were observed between decompensated and nondecompensated cases. Patients with prior penetrating keratoplasty displayed higher microbial diversity than those with previous phacoemulsification (P = 0.03).<br><br>CONCLUSIONS: Corneal transplant candidates exhibit distinct ocular surface microbial profiles characterized by increased diversity and enrichment of opportunistic taxa. Although endothelial decompensation did not significantly alter microbial composition, prior surgical history appeared to influence diversity patterns. These exploratory findings provide preliminary evidence that the ocular surface microbiome may play a role in the preoperative assessment and postoperative outcomes of corneal transplantation.}, }
@article {pmid42284364, year = {2026}, author = {Li, M and Sun, P and Zhou, X and Yang, X and Li, W}, title = {Microbial modulation of CNS remyelination in multiple sclerosis: the missing link in gut-brain axis research.}, journal = {Nutritional neuroscience}, volume = {}, number = {}, pages = {1-16}, doi = {10.1080/1028415X.2026.2686736}, pmid = {42284364}, issn = {1476-8305}, abstract = {Multiple sclerosis (MS) is a chronic, immune-mediated disorder of the central nervous system (CNS) marked by demyelination and neurodegeneration. While much attention has focused on immune dysregulation and neuroinflammation, the failure of effective remyelination is a key driver of disease progression, especially in progressive MS. Recently, the gut microbiome has emerged as a potent modulator of systemic immunity and CNS function, influencing processes such as neuroinflammation and neurogenesis. This review examines current evidence on microbiota-derived metabolites, including short-chain fatty acids (SCFAs), indole derivatives, and bile acids, and their potential roles in pathways associated with oligodendrocyte precursor cell (OPC) biology and remyelination. Evidence from preclinical models, including germ-free systems, fecal microbiota transplantation (FMT), and probiotic interventions, suggests that microbial signals can modulate immune responses and CNS environments that may indirectly affect demyelination and repair processes. However, direct causal effects on OPC differentiation and functional remyelination remain incompletely established. We critically evaluate the strengths and limitations of existing studies, highlighting inconsistencies across experimental models and the context-dependent nature of microbiota-host interactions. Clinical evidence remains limited, with current studies primarily assessing inflammatory or metabolic outcomes rather than direct measures of remyelination. Key translational challenges include uncertainties regarding metabolite bioavailability in the CNS, cell-specific mechanisms of action, and reproducibility of microbiome-targeted interventions.}, }
@article {pmid42284458, year = {2026}, author = {Palayyan, SR and Siddiqui, AH and Jiang, P and Margolskee, RF and Sukumaran, SK}, title = {Expression of Calca gene-derived peptides in the murine taste system.}, journal = {Chemical senses}, volume = {}, number = {}, pages = {}, doi = {10.1093/chemse/bjag014}, pmid = {42284458}, issn = {1464-3553}, abstract = {Taste cell regeneration and taste signaling are regulated by myriad growth factors and signaling molecules secreted by neurons and taste papillae-resident cells. 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 and trigeminal 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 CGRP1R subunits are expressed in taste stem/progenitor cells and by subsets of fibroblasts and immune cells in the lingual mesenchyme. We confirmed this expression pattern using quantitative polymerase chain reaction (qPCR) and histological techniques. qPCR of geniculate and nodose-petrosal-jugular ganglia revealed that both express Cgrp and CGRP1R subunit mRNAs, but not preprocalcitonin and Calcr. This interesting expression patterns suggests that procalcitonin and CGRP might reciprocally regulate the CGRP1R in the taste papillae and potentially influence taste signaling, taste cell regeneration and the taste microbiome.}, }
@article {pmid42284780, year = {2026}, author = {Gu, D and Cao, X and Wang, D and Chen, D and Yao, J and Song, M}, title = {Respiration-coupled redox metabolism supports Cr(VI) reduction by an indigenous Bacillus in soil-groundwater systems.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142691}, doi = {10.1016/j.jhazmat.2026.142691}, pmid = {42284780}, issn = {1873-3336}, abstract = {Reliable in situ remediation of Cr(VI)-contaminated soil-groundwater systems remains challenging because introduced microorganisms often show poor persistence, competitiveness, and functional stability under site-specific subsurface conditions. Indigenous microorganisms may provide a more adaptable alternative, yet how their respiratory metabolism, ecological fitness, and community interactions support sustained Cr(VI) reduction and immobilization under field-relevant conditions remains insufficiently understood. Here, an indigenous Cr(VI)-reducing strain GS was isolated and evaluated in aqueous batch cultures, soil microcosms, and a pilot-scale in situ trial, supported by multi-omics and microbiome analyses. Strain GS maintained high Cr(VI) reduction across wide temperature and pH ranges in aqueous cultures. In soil microcosms (100-1000 mg kg[-1] Cr(VI)), strain GS bioaugmentation achieved 66-77% Cr(VI) reduction and shifted chromium from labile pools to more stable solid-phase fractions, indicating effective immobilization. Transcriptomic and metabolomic profiling indicated that Cr(VI) stress activated a respiration-coupled redox response, characterized by enhanced heme/porphyrin metabolism, increased respiration-associated redox activity, and strengthened carbon/redox metabolism. Community analyses identified Bacillus as a key taxon associated with Cr(VI) reduction. A 180-day field trial achieved rapid Cr(VI) depletion in soil and groundwater within 30-120 days and showed no rebound over 180 days. These findings support indigenous Bacillus-based in situ bioremediation as a sustainable strategy for Cr(VI)-contaminated soil-groundwater systems.}, }
@article {pmid42284849, year = {2026}, author = {Salia, S and Swift-Gallant, A}, title = {Hormones, sex differences, and autism: From single-cause theories to integrated developmental systems.}, journal = {Hormones and behavior}, volume = {183}, number = {}, pages = {105964}, doi = {10.1016/j.yhbeh.2026.105964}, pmid = {42284849}, issn = {1095-6867}, }
@article {pmid42284942, year = {2026}, author = {Yang, X and Peng, AD and Huang, YH and Cheng, JH and Zhong, HT and Zhou, HT and Liu, PQ and Ji, XH and Li, C and Zhang, SR and Lai, JL and Luo, XG}, title = {Ecological risk assessment of 1,4-thioxane and its remediation by a synthetic microbiome based on a sulfur transformation system: From multi-omics to water application.}, journal = {Water research}, volume = {303}, number = {}, pages = {126258}, doi = {10.1016/j.watres.2026.126258}, pmid = {42284942}, issn = {1879-2448}, abstract = {Among the chemicals in weapons abandoned by Japan in China during World War II, 1,4-thioxane, a typical degradation product of mustard gas, has environmental persistence and potential ecological risks. However, its toxicity mechanism and efficient remediation strategy remain unclear. This study first employed multi-omics technologies (16S sequencing, metagenomics, and metabolomics) to analyze the toxic effects of 1,4-thioxane (0-100 mg·L[-1], 120 days) on water microecology. Subsequently, an efficient degrader, Pseudomonas sp. M1, was screened, and transcriptome analysis revealed significant upregulation of Fe-S cluster assembly-related genes (sufB, sufU, sufS), which are key components of the SUF sulfur conversion system. These three genes were heterologously expressed in Escherichia coli to construct three engineered strains, each capable of degrading 1,4-thioxane via the SUF system. When mixed in equal proportions to form a synthetic microbiome, they completely degraded 100 mg·L[-1] 1,4-thioxane in culture medium within 16 h and achieved 100% removal in simulated polluted water within 15 days. Integrated multi-omics analysis demonstrated that 1,4-thioxane is highly persistent (residual rate > 98%) but significantly inhibits nitrogen cycling, manifested by NH4[+] accumulation (1.5-3.1-fold increase) and NO3[-] depletion (24.9-87.6% decrease), along with reduced ammonia monooxygenase, nitrite oxidoreductase, and nitrate reductase activities (67.8-91.0%, 53.2-90.1%, and 42.8-80.9% reductions, respectively). Ionome analysis showed K and P accumulation and Mo depletion; 16S sequencing revealed reduced microbial diversity, suppression of nitrogen-cycling genera, and enrichment of Pseudomonas; metagenomics uncovered widespread suppression of nitrogen metabolism pathways, dysregulation of antibiotic resistance genes, and decreased viral abundance; and metabolomics confirmed global inhibition of the alanine-aspartate-glutamate pathway. This is the first study to combine multi-omics toxicity analysis with synthetic microbiome remediation based on the SUF sulfur conversion system. The findings provide a theoretical basis and technical support for ecological risk assessment and bioremediation of sites contaminated by relic Japanese chemical weapons.}, }
@article {pmid42285364, year = {2026}, author = {Bieber, T and Bochner, BS and Boyce, JA and Kabashima, K and Barrett, N and Holloway, JW and Izuhara, K and Jenmalm, M and Kraft, M and Sagi-Eisenberg, R and Sehmi, R and Wenzel, SE and Vercelli, D and , }, title = {Highlights from the 2025 Symposium of the Collegium Internationale Allergologicum.}, journal = {The Journal of allergy and clinical immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jaci.2026.05.028}, pmid = {42285364}, issn = {1097-6825}, }
@article {pmid42285653, year = {2026}, author = {Manikandan, C and Devi V K, A and Manivasagam, G and Pereira, A and Mano, JF and Borges, J and Jaiswal, AK and Udduttula, A}, title = {Nature's blueprint: Exopolysaccharides linking microbiome dynamics to advanced bone tissue engineering.}, journal = {Carbohydrate polymers}, volume = {387}, number = {}, pages = {125447}, doi = {10.1016/j.carbpol.2026.125447}, pmid = {42285653}, issn = {1879-1344}, mesh = {*Tissue Engineering/methods ; Humans ; *Bone and Bones/metabolism ; Animals ; *Polysaccharides, Bacterial/chemistry ; Tissue Scaffolds/chemistry ; Bone Regeneration ; *Microbiota ; *Gastrointestinal Microbiome ; Osteoarthritis/therapy ; Osteogenesis ; }, abstract = {Emerging evidence increasingly suggests a strong correlation linking the human gut microbiome and bone health, particularly in its ability to modulate bone metabolism and the genesis of bone disorders. It is essential to properly understand the mechanisms of the human microbiome to prevent and treat such bone complications. While several therapeutic and analytical techniques have been explored in the past, tissue engineering has recently gained prominence as a strategy that can take advantage of the microbiome's potential. Within this context, microbial exopolysaccharides represent a promising yet largely overlooked source of functional and structural polysaccharides. These natural polymers have significant potential offering meaningful advancements in creating effective materials for bone repair and regeneration. Their potential roles span from enhancing scaffold architecture and mechanical integrity to modulating immune response and promoting osteogenic activity. This review investigates the dynamic interplay between microbiome and bone health through exopolysaccharide-driven tissue engineering. The use of both gut-derived and non-gut microbial EPS in bone tissue engineering has been emphasized. Further EPS driven strategies and their potential for treating bone dysbiosis and contributing to the development of cell-free scaffolds for bone disorders like osteoporosis and osteoarthritis have been discussed.}, }
@article {pmid42285833, year = {2026}, author = {Zyzynska, K and Rodziewicz, M and Grycner, K and Tretiakow, D and Lipska-Zietkiewicz, BS and Skorek, A}, title = {Early childhood asthma and adenotonsillectomy: From upper airway microbiota to type 2 biomarkers and clinical outcomes.}, journal = {Paediatric respiratory reviews}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.prrv.2026.05.008}, pmid = {42285833}, issn = {1526-0550}, abstract = {Early childhood asthma is one of the most common chronic diseases in children, and its course may be modified by coexisting upper airway obstruction. It remains uncertain whether adenoidectomy or adenotonsillectomy can improve asthma control or reduce exacerbations in children with asthma and obstructive symptoms. Emerging evidence links asthma phenotype, type 2 inflammatory biomarkers (fractional exhaled nitric oxide, blood eosinophilia, periostin, chitinase) and changes in upper airway microbiota with variable clinical responses to surgery. This narrative review summarises studies evaluating the impact of adenoidectomy and adenotonsillectomy on asthma outcomes in paediatric populations, including secondary analyses of major randomised controlled trials (CHAT, PATS). Across heterogeneous cohort and database studies, surgery is associated with improved symptom control and reductions in hospitalisations and emergency visits in selected children, particularly younger patients with severe obstruction and poorly controlled disease despite pharmacotherapy. A post-hoc analysis of the CHAT trial demonstrated a significant reduction in wheezing after adenotonsillectomy, and a secondary analysis of the PATS trial showed a trend toward improved asthma symptom burden, although neither trial was designed with asthma as a primary endpoint. Conversely, some large population-based analyses suggest a neutral effect or even an increased long-term risk of asthma in specific subgroups, underscoring substantial uncertainty. Critically, no randomised controlled trial has evaluated asthma control or exacerbation rate as a primary outcome after adenotonsillectomy, and overall evidence quality is low to very low. Adenotonsillectomy should therefore be considered a targeted option for a carefully selected subgroup of young children with documented upper airway obstruction and poorly controlled asthma, rather than a routine intervention. Well-designed multicentre prospective studies with standardised asthma endpoints, detailed phenotyping and microbiome and biomarker assessment are needed to clarify which patients derive durable benefit and to define the role of surgery within personalised asthma management.}, }
@article {pmid42285959, year = {2026}, author = {Lyu, C and Wang, Z and Zhao, R and Zhao, H and Liu, S and Lian, H and Wang, X}, title = {Preoperative gut microbial network alterations and BCAA-Related metabolic disturbance in postoperative delirium after cardiac surgery: a prospective matched multi-omic study.}, journal = {Translational psychiatry}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41398-026-04161-9}, pmid = {42285959}, issn = {2158-3188}, abstract = {Postoperative delirium (POD) is a frequent neuropsychiatric complication after cardiac surgery, yet the biological basis of individual susceptibility remains unclear. In this prospective cohort study, 317 adults undergoing elective on-pump cardiac surgery were enrolled and followed for POD during the first 7 postoperative days. Thirty patients who developed POD were then matched 1:1 with 30 non-POD controls by age, sex, and primary diagnosis for multi-omic analyses. Preoperative fecal samples were collected from the first bowel movement after admission and before prophylactic antibiotic administration, and postoperative fecal samples were collected from the first postoperative bowel movement. Paired fecal samples underwent shotgun metagenomic sequencing, and perioperative serum samples underwent untargeted metabolomic profiling. Preoperatively, α- and β-diversity were comparable between groups, but patients who subsequently developed POD exhibited a less connected and less integrated microbial network structure. Postoperatively, gut microbial composition differed significantly between groups (PERMANOVA R[2] = 0.053, P < 0.001). Metagenomic profiling identified 35 differentially abundant species and 16 differentially enriched KEGG level 3 pathways, with POD-associated features showing inferred functional shifts toward amino-acid catabolism, including branched-chain amino acid (BCAA)-related pathways. Untargeted metabolomics demonstrated marked perioperative remodeling in both groups, but POD was associated with a 27-metabolite panel characterized predominantly by lower postoperative levels or impaired recovery, with pathway enrichment converging on valine, leucine, and isoleucine metabolism. Integrative analyses further linked POD-associated microbial taxa with amino-acid catabolic pathways and lower levels of BCAA-related serum metabolites. These findings suggest that POD is associated with preoperative alterations in microbial network organization and a postoperative microbiome-metabolome disturbance pattern centered on amino-acid metabolism, particularly the BCAA axis.}, }
@article {pmid42286232, year = {2026}, author = {Byrd, DA and Zouiouich, S and Wahl, D and Pardini, B and Gomez Morales, MF and Tarallo, S and Bulfamante, S and Francavilla, A and Francescato, G and Hogue, SR and Armaroli, P and Bellisario, C and Ferrante, G and Vogtmann, E and Wan, Y and Hua, X and Shi, J and Gunter, M and Naccarati, A and Senore, C and Sinha, R}, title = {Fecal immunochemical tests from population-based colorectal cancer screening programs support prospective microbiome cohorts.}, journal = {British journal of cancer}, volume = {}, number = {}, pages = {}, pmid = {42286232}, issn = {1532-1827}, abstract = {BACKGROUND: Large, prospective cohorts are needed to research the gut microbiome's role in colorectal cancer (CRC) risk. We evaluated the gut microbiome leveraging residual fecal immunochemical tests (FIT) from a CRC screening program in Turin, Italy, and conducted one of the largest population-based case-control studies across the adenoma-carcinoma sequence to date.<br><br>METHODS: We extracted DNA from residual FIT stool, used whole-genome shotgun sequencing, and included those with CRC (N&#x2009;=&#x2009;44), advanced adenomas (N&#x2009;=&#x2009;269), early adenomas (N&#x2009;=&#x2009;134), and FIT-negative controls (N&#x2009;=&#x2009;478). Alpha diversity, beta diversity, and species, gene, and pathway relative abundances were estimated. Multivariable logistic regression models were used to estimate associations of these metrics with colorectal neoplasms.<br><br>RESULTS: Alpha diversity was mostly inversely associated with colorectal neoplasms, particularly early adenomas (OR: 0.45, 95% CI: 0.25-0.80; P&#x2009;=&#x2009;0.01). Presence of oral pathogens, including Parvimonas micra, was associated with higher odds of CRC. Furthermore, Escherichia coli and Bacteroides fragilis were strongly associated with higher odds of all colorectal neoplasms. Several genes and pathways were associated with colorectal neoplasms.<br><br>CONCLUSIONS: Our findings align with smaller studies of the gut microbiome and colorectal neoplasms, supporting that CRC screening programs provide opportunities to prospectively study the gut microbiome's association with cancer risk in large populations.}, }
@article {pmid42286247, year = {2026}, author = {Glass, EM and Kolling, GL and Papin, JA}, title = {Genome-scale metabolic modelling identifies vaginal microbiome members as potential probiotics.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {42286247}, issn = {2058-5276}, support = {R01-AI154242//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; R01-AT010253//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; 1 T 32 GM 145443-1//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; GRFP award number 1842490//National Science Foundation (NSF)/ ; }, abstract = {Probiotic supplements are marketed for diverse health benefits, yet species inclusion often lacks functional rationale. Our survey of 352 over-the-counter probiotic products available in the USA revealed 36 unique microbial species. However, there is no clear link between species inclusion and the intended health benefit. Here, to address this gap, we developed HaPaPro, a collection of 1,012 genome-scale metabolic models spanning pathogenic, probiotic and host-associated bacteria, constructed from publicly available genome sequences. Flux balance analysis revealed that probiotic species fail to capture the metabolic diversity of host-associated microbes. Focusing on vaginal health, we computationally identified vaginal microbes with metabolic profiles overlapping Gardnerella vaginalis. In vitro spent media assays using 11 vaginal isolates showed variable inhibition of G. vaginalis, primarily driven by D-lactic acid production, which was also produced by non-Lactobacillus species. These findings highlight the need for function-based probiotic design and demonstrate a scalable framework integrating metabolic modelling with experimental validation.}, }
@article {pmid42286383, year = {2026}, author = {Feng, Y and Zhou, Y and Wang, Y and Wang, Y and Liu, X and Sun, T and Xu, J}, title = {The gut-liver axis: exploring microbial dysbiosis and specific biomarkers in hepatocellular carcinoma.}, journal = {AMB Express}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13568-026-02082-w}, pmid = {42286383}, issn = {2191-0855}, support = {2020-48-3-1//Shenyang Breast Cancer Clinical Medical Research Center/ ; 22-321-31-04//Shenyang Public Health R&amp;D Special Project/ ; 82373113//National Natural Science Foundation of China/ ; 2025-MSLH-421//Natural Science Foundation of Liaoning Province/ ; XLYC1907160//LiaoNing Revitalization Talents Program/ ; }, abstract = {Hepatocellular carcinoma represents a major global health challenge, with its link to the commensal microbiota being clearly established. However, developing reproducible microbial biomarkers for early-stage hepatocellular carcinoma diagnosis across diverse populations remains challenging. We conducted an integrative analysis of 13 studies, examining 16S rRNA sequencing data from 607 fecal samples and 263 liver tissue samples. Data processing utilized VSEARCH, QIIME, and R packages (vegan, phyloseq, cooccur, random forest), with PICRUSt for functional prediction. Alpha diversity analysis revealed significant differences in liver microbiota but not in gut microbiota between hepatocellular carcinoma patients and non-cancer individuals. Linear Discriminant Analysis Effect Size identified Blautia and Streptococcus as biomarker shared across the gut and liver micro-niches. Based on the internal data, the models constructed using gut and liver microbiome characteristics demonstrated high discriminative ability (gut model AUC = 0.8064; liver model AUC = 0.9645). Mendelian randomization analysis revealed a potential association between Streptococcus and the development of hepatocellular carcinoma. KEGG enrichment analysis further indicated marked functional differences in microbiota, primarily linked to metabolic irregularities, between cancer patients and controls. Therefore, this study reveals unique gut-liver microbial community features in patients with hepatocellular carcinoma, identifies potential cross-site diagnostic biomarkers, and constructs gut and liver predictive model with good performance, providing preliminary evidence for the application of microbial biomarkers in the early diagnosis and screening of hepatocellular carcinoma.}, }
@article {pmid42286462, year = {2026}, author = {Dai, W and Jahangir, M and Li, T and Guo, WJ}, title = {Early-life stress and adolescent circadian dysrhythmia drives unique behavioral and microbial profiles in rats.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05287-y}, pmid = {42286462}, issn = {1471-2180}, support = {82171487//National Natural Science Foundation of China/ ; 2024C03006//"Pioneer" and "Leading Goose" R&amp;D Program of Zhejiang/ ; TD2024003//Leading innovation and entrepreneurship team of Hangzhou/ ; }, abstract = {OBJECTIVES: Early life adversity and circadian disruptions are known to impact neurodevelopment and physiology. This study investigated the effects of maternal separation (MS), adolescent circadian dysrhythmia, and their combination (double hit) on anxiety-like behavior and gut microbiota composition in rats.<br><br>METHODS: Rats were divided into four groups: CL (control group: normal early-life conditions with a standard light/dark cycle during adolescence), MS&#x2009;+&#x2009;N (maternal separation (MS) with a standard light/dark cycle (N=normal)) during adolescence), N&#x2009;+&#x2009;ALD (normal early-life conditions (N) with an altered light/dark cycle (ALD) during adolescence), and MS&#x2009;+&#x2009;ALD (combined exposure: MS with an altered light/dark cycle (ALD) during adolescence). Anxiety-like behavior and locomotor activity were assessed using the Open Field Test. Gut microbial diversity and taxonomic composition were analysed to identify microbial shifts across groups.<br><br>RESULTS: Behavioral analysis indicated that the combined stress group (MSLD) spent significantly (p&#x2009;<&#x2009;0.05) more time in the center of the arena compared to the CL, MS&#x2009;+&#x2009;N, and N&#x2009;+ ALD groups, suggesting a compromise in risk assessment ability due to dual stress exposure. Microbiome profiling revealed that while a core microbiome was conserved, each stressor generated a unique taxonomic signature. The N&#x2009;+&#x2009;ALD group appeared as the most distinct outlier, characterized by the lowest number of unique features and a specific enrichment of the viral species of phylum Uroviricota. Conversely, the MS&#x2009;+&#x2009;ALD group was distinguished by an enrichment of Bacteroidota species, including Muribaculum intestinale and Phocaeicola vulgatus, while the MS&#x2009;+&#x2009;N group showed enrichment in Bacteroides acidifaciens. Mycobiome analysis showed that early-life stress was the primary driver of fungal restructuring, distinguishing maternal separation groups by the loss of Neocallimastix species and the competitive expansion of Piromyces finnis. While adolescent circadian disruption alone largely preserved the baseline mycobiome, the cumulative dual-hit stress (MS&#x2009;+&#x2009;ALD) generated a distinct dysbiotic profile evident by the unique proliferation of Anaeromyces robustus.<br><br>CONCLUSIONS: In conclusion, the developmental timing of stress exposure drives distinct dysbiotic shifts. Specifically, adolescent circadian disruption selectively targets the virome, whereas early-life stress causes shift in the microbiome which endures a long-term foundation for adolescent psychiatric vulnerability. Notably, the cumulative effect of early life and adolescence stressors results in a unique microbial and behavioral profile, highlighting that the specific developmental window of exposure is a decisive factor in gut-brain axis dysfunction.}, }
@article {pmid42286497, year = {2026}, author = {Gao, X and Sanui, A and Rasmika Dewi, DAP and Lucaci, AG and Mason, CE and Suzuki, H}, title = {Shotgun metagenomic dataset of surface microbiomes at a train station in Shinagawa, Tokyo.}, journal = {BMC genomic data}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12863-026-01451-5}, pmid = {42286497}, issn = {2730-6844}, support = {U54AG089334//National Institute for Health and Care Research/ ; JPMJCR20H1//JST CREST/ ; 20K10436//JSPS KAKENHI/ ; JAHMEC.G-02, 2022//Japan Architectural Health, Management and Education Center Research grant/ ; }, abstract = {OBJECTIVES: The urban microbiome is a significantly underexplored ecosystem which contributes to the health and resilience of the human population and less is known about the microbiome of urban transportation systems that commuters interact with daily. Shotgun metagenomic sequencing data from swab samples were collected at a representative medium-scale urban commuter railway station in Tokyo, Japan, with daily passenger volumes on the order of tens of thousands, in October 2021. The dataset was generated as part of the nationwide "Urban Microbiomes in Japan" project and provides a resource for comparative analyses of urban microbial diversity and future public health surveillance studies in urban environments.<br><br>DATA DESCRIPTION: Three surface swab samples were collected in October 2021 from concrete floor areas near ticket gates at a major railway station in Shinagawa, Tokyo. Samples were collected using Isohelix swabs with DNA/RNA Shield stabilization solution. Metagenomic DNA was extracted and subjected to shotgun sequencing, generating 2 &#xd7; 150 bp paired-end reads.}, }
@article {pmid42286567, year = {2026}, author = {Wu, J and Wu, S and He, T and Fang, S and Zhu, H}, title = {Postoperative exercise modulating gut microbiota and associated metabolites to facilitate bone-tendon healing in rotator cuff tears.}, journal = {BMC musculoskeletal disorders}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12891-026-10083-w}, pmid = {42286567}, issn = {1471-2474}, support = {BPB-2024FSH//Fujian Provincial Finance Project/ ; 2025Y9098//Joint Funds for the Innovation of Science and Technology, Fujian Province/ ; }, abstract = {BACKGROUND: Rotator cuff tear is a prevalent shoulder injury, and postoperative exercise is considered to facilitate healing. However, the effect of postoperative exercise on rotator cuff tear healing through gut microbiota and metabolites remains unclear.<br><br>METHODS: The control (con) group (n&#x2009;=&#x2009;10) underwent sham surgeries, while the model (mod) and postoperative exercise (sport) groups (each n&#x2009;=&#x2009;10) underwent supraspinatus tendon repair surgeries. Starting on postoperative day 7, the sport group underwent treadmill exercise at 10&#xa0;m/min for 20&#xa0;min/day, 5 days/week, for 4 consecutive weeks. Subsequently, the supraspinatus tendon-humerus complex, fecal, and serum samples were collected.<br><br>RESULTS: Synchrotron radiation micro-CT and histological studies indicated that postoperative exercise was associated with reduced bone loss and enhanced new bone formation at tendon-bone sites. Gut microbiome profiling revealed that exercise was associated with reshaped microbial composition, with increased Proteobacteria and Dubosiella, and decreased Lachnoclostridium and Allobaculum in the sport group compared with the model group. Functional analyses showed that the HIF-1 signaling pathway and &#x3b2;-Alanine metabolism were notably enriched following exercise. Network correlation analysis suggested that Dubosiella functioned as a central taxon within the microbial community. Metabolomics suggested that exercise was associated with altered metabolite abundances like Val-Pro-Asp-Pro-Arg, which correlated with pathways like gap junction. Moreover, metabolomics further identified &#x3b2;-Alanine metabolism as the key overlapping pathway connecting microbial alterations with serum metabolic changes, with &#x3b2;-alanyl-L-arginine as a representative metabolite. Seven microbe-metabolite pairs showed significant correlations. Among them, Parabacteroides exhibited strong associations with multiple metabolites, including cycloheptyl derivatives, and demonstrated predictive value for tendon-bone healing (AUC&#x2009;=&#x2009;0.88).<br><br>CONCLUSION: In a murine model, postoperative exercise following rotator cuff tear repair surgery was associated with modulating gut microbiota and metabolites, which may contribute to rotator cuff tear healing. This finding provides preclinical insights into integrating postoperative exercise into rotator cuff tear recovery strategies.}, }
@article {pmid42286580, year = {2026}, author = {Li, L and Li, L and Yang, Y and Wang, C and Lan, Z and Liu, J and Zhu, X and Zhao, C and Yang, M and Ma, Y and Liu, Y and Ren, Z}, title = {The oral microbiome is associated with the diagnosis, prognosis and radiotherapy sensitivity of esophageal cancer.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {42286580}, issn = {1479-5876}, support = {YXKC2022004//Henan Youth and Middle-aged Health Science and Technology Innovation Leaders Training Project/ ; SBGJ202401004//Henan Medical Science and Technology Tackling Program of Provincial-Ministry Joint Major Project/ ; HNSWJW-2022011//Henan Health Young and Middle-aged discipline Leader Project/ ; }, mesh = {Humans ; *Esophageal Neoplasms/radiotherapy/diagnosis/microbiology ; *Microbiota/genetics/radiation effects ; Prognosis ; *Mouth/microbiology ; Female ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Aged ; }, abstract = {BACKGROUND: Esophageal cancer (EC) is a leading cause of cancer-related mortality worldwide and early detection strategies and precise postoperative interventions must be developed. However, the identification of noninvasive biomarkers for the diagnosis and prognosis remains limited.<br><br>METHODS: We performed 16S rRNA gene sequencing on tongue-coating samples from 440 participants, including 157 EC patients, 167 healthy controls (HCs) and 120 EC patients who received radiotherapy. We characterized the oral microbiome and constructed microbial diagnostic and prognostic classifiers. Furthermore, the oral microbiome of EC who received radiotherapy (n&#x2009;=&#x2009;120) was characterized.<br><br>RESULTS: The oral microbial diversity of EC patients was increased, with differences in the microbial community between EC patients and HCs. In EC, the genera Veillonella, Streptococcus and Actinomyces were enriched, whereas Porphyromonas and Rothia were depleted. The classifier based on six optimal microbial markers was constructed using random forest algorithm and achieved area under the curves (AUCs) of 93.69% and 95.18% in discovery and validation groups, respectively. After radiotherapy, the oral microbial diversity and richness were significantly reduced. The prevalence of opportunistic pathogens, including Fusobacterium and Porphyromonas, decreased, whereas the prevalence of Streptococcus and Actinomyces increased in EC patients after radiotherapy. Through six months of follow-up, patients were categorized into a progression group (PG) (n&#x2009;=&#x2009;26) and a nonprogression group (NPG) (n&#x2009;=&#x2009;106) based on the presence of tumor recurrence, metastasis, and death. A prognostic model based on 13 selected amplicon sequence variants (ASVs) of the oral microbiome was constructed, with an AUC of 99.29%. The random forest analysis identified six key differential ASVs between the PG and the NPG, including Fusobacterium and Gemella. Additionally, twenty-five ASVs associated with nine clinical indicators were identified.<br><br>CONCLUSIONS: Our study provides a comprehensive characterization of the oral microbiome in both EC patients and EC patients after radiotherapy, highlighting the potential of the oral microbiome as noninvasive biomarkers for determining the diagnosis and prognosis of EC.}, }
@article {pmid42286668, year = {2026}, author = {Lawther, K and Dimonaco, NJ and Donnelly, P and Guinguina, A and Krizsan, SJ and Huws, SA}, title = {Dietary inclusion of Asparagopsis taxiformis significantly reduces methane emissions in dairy cows by mechanistically altering vitamin B12-dependent and other methanogenesis precursor pathways.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02447-0}, pmid = {42286668}, issn = {2049-2618}, abstract = {BACKGROUND: Ruminant products are widely consumed due to their high protein and micronutrient content, but ruminant production contributes significantly to greenhouse gas emissions, with methane (CH4) accounting for 33% of anthropogenic emissions. CH4 is generated via fermentative processes by the rumen microbiome, primarily through hydrogen utilisation by methanogenic archaea. Feeding beef cattle the red seaweed Asparagopsis taxiformis (ASP) has been shown to reduce CH4 emissions by up to 80%. However, the microbial mechanisms underlying this reduction remain poorly understood. In this study, Nordic Red dairy cows (122 ± 13.7 days in milk) were fed grass silage and concentrate (60:40 dry matter basis) either with or without 0.5% ASP (organic matter basis) in a Latin square design, and rumen fluid was collected 19 days into each of the 3 experimental periods.<br><br>RESULTS: ASP supplementation reduced CH&#x2084; yield by 54% (g CH&#x2084;/kg DM). Metagenomic analysis revealed genes encoding pyruvate and propionate production pathways were more abundant in ASP treated animals, while those associated with acetate and CH&#x2084; were reduced. Additionally, genes encoding vitamin B12 biosynthesis enzymes showed reduced abundances (e.g., adenosylcobinamide-GDP ribazoletransferase, EC 2.7.8.26, -29.92%). Vitamin B12 and its related cofactors are&#xa0;critical for methanogenic methyltransferases and C1 metabolism. Dominant taxa including Prevotella and Methanobrevibacter declined, while less abundant taxa increased their contribution to methane-related pathways, indicating niche displacement and community restructuring. CONCLUSION&#xa0;: ASP supplementation modulates the rumen microbiome through mechanisms extending beyond direct methanogen inhibition. The reduced abundance of genes involved in C1 metabolism and vitamin B12-dependent methanogenic processes suggest methane suppression is linked to broader restructuring of microbial metabolic networks. The redistribution of methane-related functions from dominant taxa to a wider taxonomic community indicates ecological reorganisation and functional resilience of the rumen microbiome. Collectively, these results reveal the multiple modes of action of ASP, establishing its promise as an effective methane mitigation strategy. Video Abstract.}, }
@article {pmid42286710, year = {2026}, author = {Kang, D and Shin, Y and Cho, YK and Park, JM and Jung, SH and Choi, MG}, title = {Integrated analysis of gastric microbiome and clinical features for the diagnosis of gastric neoplasms.}, journal = {Gut pathogens}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13099-026-00843-3}, pmid = {42286710}, issn = {1757-4749}, support = {HI22C0226//Ministry of Health and Welfare/ ; RS-2024-00450891//National Research Foundation of Korea/ ; KCHUGR -201902503//Korean College of Helicobacter and Upper Gastrointestinal Research/ ; }, abstract = {BACKGROUND: Gastric cancer (GC) progression is closely associated with microbial dysbiosis. However, microbial alterations in the intermediate stage of gastric adenoma (GA) remain under-characterized. This study investigated stage-specific microbiome changes and evaluated predictive models integrating microbial and clinical features.<br><br>METHODS: We analyzed 231 subjects (129 GA, 73 GC, 29 healthy controls [HC]) using 16&#xa0;S ribosomal DNA sequencing of paired oral, non-lesional gastric mucosa (GM), and gastric lesion (GL) samples. Random Forest models were constructed using microbial genera and clinical features, validated via leave-one-out cross-validation.<br><br>RESULTS: Stepwise microbial dysbiosis was observed during GC progression. Alpha diversity was significantly lower in GC-GL than in HC-GM and GA-GL. Helicobacter pylori infection was associated with reduced alpha diversity in GL samples. Genera such as Streptococcus, Neisseria, and Haemophilus were enriched in GC-GL, while Phocaeicola, Faecalibacterium, and Bifidobacterium were depleted. A gastric neoplasm prediction model incorporating 33 microbial genera and six clinical variables (age, sex, BMI, hypertension, smoking, and atrophy) demonstrated superior predictive performance (AUC&#x2009;=&#x2009;0.830) in distinguishing gastric neoplasms from HCs, compared to models using either microbial genera (AUC&#x2009;=&#x2009;0.790) or clinical variables (AUC&#x2009;=&#x2009;0.715) alone. The combined model also accurately distinguished between GA and GC (AUC&#x2009;=&#x2009;0.807).<br><br>CONCLUSIONS: The gastric microbiome profile changes dynamically during GC progression, highlighting its potential role in tumor development. Integrating microbial signatures with clinical features enables robust classification of gastric neoplasms and may serve as a valuable adjunctive tool for diagnosis and risk stratification in endoscopic practice.}, }
@article {pmid42286833, year = {2026}, author = {Mäki, JM and Kirjavainen, PV and Täubel, M and Tuoresmäki, P and Piippo-Savolainen, E and Backman, K and Pekkanen, J and Karvonen, AM}, title = {The role of dog keeping in the home microbiota and its impact on children's health.}, journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology}, volume = {37}, number = {6}, pages = {e70408}, pmid = {42286833}, issn = {1399-3038}, support = {296814//Academy of Finland/ ; 296817//Academy of Finland/ ; 139021//Academy of Finland/ ; 287675//Academy of Finland/ ; 308253//Academy of Finland/ ; 308254//Academy of Finland/ ; 201710468//Juha Vainio S&#xe4;&#xe4;ti&#xf6;/ ; //The Foundation for Pediatric Research/ ; //Yrj&#xf6; Jahnssonin S&#xe4;&#xe4;ti&#xf6;/ ; //Suomen Kulttuurirahasto/ ; //Kuopion Seudun Hengityss&#xe4;&#xe4;ti&#xf6;/ ; //Terveyden ja hyvinvoinnin laitos/ ; //Tampereen Tuberkuloosis&#xe4;&#xe4;ti&#xf6;/ ; //P&#xe4;ivikki ja Sakari Sohlbergin S&#xe4;&#xe4;ti&#xf6;/ ; //Maatalousyritt&#xe4;jien el&#xe4;kelaitos - Mela/ ; }, mesh = {Animals ; Dogs ; Humans ; Female ; *Microbiota ; *Dust/immunology ; Male ; Infant ; Finland/epidemiology ; Bacteria/isolation &amp; purification ; *Child Health ; Anti-Bacterial Agents/therapeutic use ; Fungi/isolation &amp; purification ; *Pets ; Fever/epidemiology ; Otitis/epidemiology ; }, abstract = {BACKGROUND: Children with dog contacts in early childhood are healthier and use less antibiotics during the first year of life. We have earlier identified dog-associated bacterial and fungal signals in house-dust microbiota. The aim of this study was to determine whether these signals in house dust mediate the dog keeping associated positive health effects in the first year of life.<br><br>METHODS: We studied 368 Finnish children from pregnancy and collected weekly diary data on otitis, fever, usage of antibiotics, and dog keeping from 9th to 52nd postnatal weeks. The dog-associated signals in house dust microbiota included the abundance of 12 bacterial and two fungal genera, which were determined alongside richness with Illumina MiSeq sequencing from floor dust samples collected at the child age of 2&#x2009;months. Bacterial cell concentrations in floor dust were measured with quantitative PCR (qPCR). Generalized estimating equations (GEE) were used for statistical analyses of the microbe-health associations.<br><br>RESULTS: Eight of the dog-associated genera individually explained 10%-23% of the protective associations between dog keeping and at least one health outcome. The strongest effect was observed for the Pasteurella in relation to fever weeks. In addition, three correlated bacterial genera together explained 25% of the dog-associated reduction in antibiotic use. Bacterial or fungal richness, total cell concentrations, or proportion of human-sourced bacteria in house dust did not significantly mediate the dog-associated health effects.<br><br>CONCLUSIONS: Specific dog-associated bacterial and fungal genera in house dust, but not richness, explained partly the associations between dog keeping and lower prevalence of respiratory infections.}, }
@article {pmid42286837, year = {2026}, author = {Gavanji, S and Suhail, M and Bencurova, E and Dandekar, T and Othman, EM}, title = {Recent advances and clinical relevance of microbiome dynamics in health and disease.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2679197}, doi = {10.1080/19490976.2026.2679197}, pmid = {42286837}, issn = {1949-0984}, mesh = {Humans ; Probiotics/administration &amp; dosage ; Dysbiosis/microbiology/therapy ; Prebiotics ; *Microbiota ; *Gastrointestinal Microbiome ; Animals ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Gastrointestinal Tract/microbiology ; Fecal Microbiota Transplantation ; }, abstract = {The human microbiome, comprising trillions of bacteria, viruses, fungi, and archaea, represents an essential partner in human biology rather than a passive collection of microbes. These microbial communities inhabit diverse niches, including the gut, skin, oral cavity, respiratory tract, and urogenital system, where they contribute to digestion, vitamin biosynthesis, immune development, and regulation of host metabolism. Their dynamic interactions form a complex ecosystem that profoundly shapes health across the lifespan. However, with ever increasing reports on the microbiome including perceived health benefits, diagnostic use, detrimental species and immune modulation, we synthesize findings from multiple biomedical fields for this review. It first describes beneficial functions of commensal microbes in maintaining immune tolerance and metabolic balance, then analyzes the effect of diet, geography and medication exposure, the consequences of dysbiosis in gastrointestinal, metabolic, neurological, cardiovascular, autoimmune, and oncological disorders. The article examines the functional potency of the gut microbiome, keystone taxa as well as disease-stage-specific and general dynamics, how microbiomes modulate drug absorption, metabolism, and efficacy, thereby influencing individualized responses to therapy. Furthermore, it evaluates therapeutic approaches, including probiotics, prebiotics, fecal microbiota transplantation, and engineered microbial strategies that seek to restore microbial equilibrium. The significance of this review lies in its integrative perspective, as it links microbiome research to precision medicine, emphasizing that safeguarding microbial diversity is crucial for prevention, early diagnosis, and the personalization of future medical interventions.}, }
@article {pmid42286862, year = {2026}, author = {Othman, EM and Bencurova, E and Ferretti, P and Bork, P and Rodriguez Del Rio, A and Huerta-Cepas, J and Caruana, I and Abdel-Latif, R and Akash, A and Albacete, A and Lafi, F and Dandekar, T and Naseem, M}, title = {Diet and microbiome shape small-molecule cytokinin pools in mammals.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2679497}, doi = {10.1080/19490976.2026.2679497}, pmid = {42286862}, issn = {1949-0984}, mesh = {Animals ; *Cytokinins/blood/metabolism ; Humans ; Mice ; *Diet ; *Gastrointestinal Microbiome ; *Mammals/metabolism ; Metabolomics ; Metagenomics ; Feces/chemistry ; Swine ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Microbiota ; }, abstract = {Cytokinins (CKs) are adenine-derived metabolites traditionally characterized as plant hormones, yet their origin, distribution, and functions in mammalian systems remain largely undefined. Using integrated metabolomics, microbiome, and metagenomics approaches, we provide a systematic characterization of CK occurrence and potential sources in mammals. Serum profiling across five animal species revealed consistent detection of multiple CK derivatives, with concentrations markedly lower than in plant tissue. The CK storage form, zeatin-O-glucoside, predominated in mammalian sera, followed by trans-zeatin and kinetin, indicating a CK composition distinct from that in plants. Species-specific differences, such as reduced trans-zeatin in mice and lower kinetin in humans, further suggest divergent regulatory patterns. In mice, CKs were present in vascular tissues of the kidney, heart, and liver, demonstrating systemic distribution. Dietary manipulation showed that starvation significantly reduced CK abundance in serum, colon, feces, and urine, confirming that diet is a major contributor to the mammalian CK pool. Meta-omics analysis of gut microbiomes identified CK-related genes across multiple microbial taxa, with the highest representation in human microbiomes, followed by those of mouse and pig. Germ-free mouse experiments showed substantially lower CK levels than conventionally raised counterparts, establishing a microbiome-dependent contribution. Collectively, our findings identify CKs as diet and microbiome modulated metabolites in mammals, warranting future investigation to elucidate their physiological significance in mammalian biology.}, }
@article {pmid42286863, year = {2026}, author = {Bartold, M and Cheah, CW and Vaithilingam, RD}, title = {Periodontitis and Rheumatoid Arthritis-Mechanistic Evidence.}, journal = {Journal of periodontal research}, volume = {}, number = {}, pages = {}, doi = {10.1111/jre.70132}, pmid = {42286863}, issn = {1600-0765}, abstract = {Current evidence strongly supports an association between periodontitis and rheumatoid arthritis (RA) in a subset of susceptible individuals. The relationship between these conditions is underpinned by a complex interplay between chronic inflammation and subgingival bacterial infection. Several hypotheses have been proposed to explain the mechanistic basis of this association. Among these, the "two-hit" model is particularly compelling, as it suggests that inflammation, infection, or a combination of both may contribute to the initiation and progression of RA in predisposed individuals. According to this model, the progression of gingivitis and periodontitis, together with associated microbial dysbiosis, may promote protein citrullination, carbamylation, and the formation of malondialdehyde-acetaldehyde (MAA) adducts. These post-translational modifications may subsequently induce the production of autoantibodies before the clinical onset of joint inflammation and RA. Once synovial inflammation develops, additional citrullination, carbamylation, and MAA adduct formation may occur within the joint microenvironment, further amplifying autoantibody production. In previously sensitized individuals, such as those with chronic gingivitis or periodontitis, this secondary immune response may be substantially enhanced, resulting in increased joint inflammation and tissue destruction. Subgingival bacteria may also contribute directly, or indirectly, to the periodontitis/RA axis through translocation to distant tissues, induction of protein citrullination and other protein post-translational modifications, stimulation of autoantibody production, and exacerbation of inflammatory responses. Central to the role bacteria play in the periodontitis/RA axis is the emergence of functional alterations in the microbiome. Dysbiosis in the subgingival microenvironment, and the emergence and proliferation of recognized periodontal pathobionts, underpins these key elements. This, along with bacterial-induced inflammation and direct influence on immune player trafficking, results in a complex synergy within the mechanistic processes involved in the relationship between periodontitis and RA. In this narrative review, we critically examine the inflammatory and microbial mechanisms implicated in the interaction between periodontitis and RA and propose an updated framework integrating inflammation, dysbiosis, and autoimmunity.}, }
@article {pmid42286866, year = {2026}, author = {Correale, C and Morandi, M and Gil-Gomez, A and Silvestri, A and Gatti, A and Braga, D and Maroli, A and Foppa, C and De Zanet, S and Algieri, F and Lizier, M and Rossetti, R and Carloni, S and Penna, G and Spinelli, A and Brescia, P and Rescigno, M}, title = {Muribaculum as a microbial contributor of rifaximin-induced mucosal protection during chemotherapy.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2685994}, doi = {10.1080/19490976.2026.2685994}, pmid = {42286866}, issn = {1949-0984}, mesh = {Animals ; *Rifaximin/pharmacology/administration &amp; dosage ; Fluorouracil/adverse effects ; Humans ; *Intestinal Mucosa/drug effects/microbiology/pathology ; Mice ; *Gastrointestinal Microbiome/drug effects ; Intestinal Barrier Function ; *Mucositis/chemically induced/prevention &amp; control/microbiology/drug therapy ; Mice, Inbred C57BL ; *Antineoplastic Agents/adverse effects ; Disease Models, Animal ; Male ; *Anti-Bacterial Agents/pharmacology ; }, abstract = {Chemotherapy-induced intestinal mucositis is a frequent and dose-limiting toxicity that compromises cancer treatment outcomes and lacks effective targeted interventions. Here, we investigate the mechanisms by which the nonabsorbable antibiotic rifaximin mitigates chemotherapy-induced intestinal injury, focusing on microbiota-mediated preservation of epithelial barrier integrity. In a murine model of 5-fluorouracil (5-FU)-induced intestinal injury, rifaximin pretreatment reduced mucosal inflammation and tissue damage, preserved epithelial and mucus barrier integrity, and limited systemic endotoxemia. Importantly, rifaximin did not impair the antitumor efficacy of 5-FU in Apc[Min/+]C3arKO mice. To assess translational relevance, we employed a human intestinal ex vivo organ culture system (EVOC) and found that rifaximin preserved mucosal architecture, mucus balance, and tight junction integrity following inflammatory challenge. Microbiome profiling revealed that rifaximin reshaped the intestinal microbial community, preventing the depletion of health-associated taxa, including Muribaculum and Parasutterella. Functional experiments demonstrated that Muribaculum intestinale supplementation alone attenuated 5-FU-induced injury, reproducing key protective features of rifaximin treatment. Together, these findings identify Muribaculum as a microbial contributor to rifaximin's protective effects, supporting its potential role as a safe adjunctive strategy to improve gastrointestinal tolerability of cancer treatment.}, }
@article {pmid42286894, year = {2026}, author = {Evers, MJAP and Krom, BP and de Jongh, CA}, title = {A mechanistic framework linking the oral microbiome to Alzheimer's disease through neuroinflammation.}, journal = {Journal of Alzheimer's disease : JAD}, volume = {}, number = {}, pages = {13872877261456324}, doi = {10.1177/13872877261456324}, pmid = {42286894}, issn = {1875-8908}, abstract = {Alzheimer's disease (AD) is a growing problem in our society and the most common form of dementia. This neurodegenerative disease is characterized by neuroinflammation and the accumulation of amyloid-β (Aβ) and tau. Previous studies have found associations between the oral microbiome and AD. This review aims to elucidate the role of the oral microbiome in AD, through neuroinflammation, and reviews the relationship between AD and bacteria and fungi. Studies have found bacteria (e.g., Porphyromonas gingivalis) and fungi (e.g., Candida albicans) in postmortem AD brains. Moreover, mice models have shown that oral microbes are able to cross the blood-brain barrier (BBB), and were correlated with activated microglia, neuroinflammation, and Aβ load. This review introduces a mechanistic framework that describes how oral microbes cause an inflammatory response resulting in AD pathology. Specifically, oral dysbiosis causes oral pathogens to disseminate into the bloodstream, this triggers an inflammatory response, subsequently activating microglia, ultimately resulting in AD pathology. This process can follow two pathways: First, there is a direct response of the immune system in the brain to oral pathogens that migrate through the bloodstream and cross the BBB, which causes neuroinflammation and activates microglia, leading to AD pathology. Second, an early-life systemic inflammation causes microglia to get into a "hyperactive" state, in which they respond in an exaggerated way to normal stimuli triggering immune responses throughout a person's life that result in AD pathology. This mechanistic framework provides new line of thought for future research on the question of causality of AD.}, }
@article {pmid42286957, year = {2026}, author = {Raho, GS}, title = {Probiotics in allergic disease: from adjunct supplement to immune-modifying strategy (2026 update).}, journal = {Current opinion in allergy and clinical immunology}, volume = {}, number = {}, pages = {}, doi = {10.1097/ACI.0000000000001171}, pmid = {42286957}, issn = {1473-6322}, abstract = {PURPOSE OF REVIEW: Allergic diseases continue to increase globally, and accumulating evidence implicates early-life microbial exposures as central determinants of immune tolerance. This review synthesizes advances from 2024 to 2026 regarding probiotic-mediated immune modulation and their translational implications in allergy prevention and therapy.<br><br>RECENT FINDINGS: Recent studies confirm strain-specific expansion of Foxp3+ regulatory T cells, suppression of Th2 polarization, reinforcement of epithelial barrier integrity, and durable epigenetic stabilization mediated by short-chain fatty acids such as butyrate. Clinical trials demonstrate benefit in perinatal prevention of atopic dermatitis, modulation of allergic rhinitis symptoms, early-life asthma risk reduction, and probiotic-adjuvanted oral immunotherapy.<br><br>SUMMARY: Probiotics are evolving from adjunctive supplements to biologically active immune modulators with disease-modifying potential. Integration with allergen immunotherapy and precision microbiome profiling may redefine preventive and therapeutic strategies in allergic disease.}, }
@article {pmid42286999, year = {2026}, author = {Felten, V and West, EA and Martini, F and Favrot, C and Unterer, S and Suchodolski, J and Scharl, M and Renz, H and Fischer, NM and Rostaher, A}, title = {Faecal Microbiota Transplantation Reduces Lesion Severity and Medication Use in Canine Atopic Dermatitis: A Randomised, Placebo-Controlled, Double-Blinded Clinical Trial.}, journal = {Veterinary dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/vde.70092}, pmid = {42286999}, issn = {1365-3164}, support = {215128/WT_/Wellcome Trust/United Kingdom ; 03162//American Kennel Club Canine Health Foundation/ ; //Westie Foundation of America/ ; }, abstract = {BACKGROUND: Faecal microbiota transplantation (FMT) is an established therapy for gastrointestinal disease, yet its role in canine atopic dermatitis (cAD) remains unclear.<br><br>HYPOTHESIS/OBJECTIVES: We hypothesised that adjunctive FMT improves clinical severity and reduces symptomatic medication use in dogs with cAD. The objective was to evaluate efficacy and safety versus placebo.<br><br>ANIMALS: Forty-six client-owned dogs with naturally occurring cAD were enrolled from a referral hospital population; 40 completed the study (FMT n&#x2009;=&#x2009;20, placebo n&#x2009;=&#x2009;20).<br><br>MATERIALS AND METHODS: Prospective, randomised, placebo-controlled, double-blinded clinical trial. Dogs received daily oral lyophilised FMT capsules for 90&#x2009;days plus three monthly rectal FMT administrations (Day [D]0, D30, D60) or placebo capsules with sham handling. Concomitant symptomatic therapies were permitted. Outcomes included Canine Atopic Dermatitis Extent and Severity Index, fourth iteration (CADESI-04), pruritus Visual Analog Scale (PVAS), Medication Score (D0-90) and Owner Global Assessment of Treatment Efficacy (OGATE, D90).<br><br>RESULTS: CADESI-04 scores were lower with FMT at month (M) 2 (7&#x2009;&#xb1;&#x2009;6 vs. 16&#x2009;&#xb1;&#x2009;12; p&#x2009;=&#x2009;0.006) and month 3 (8&#x2009;&#xb1;&#x2009;6 vs. 15&#x2009;&#xb1;&#x2009;12; p&#x2009;=&#x2009;0.020). Sustained responders (&#x2265;&#x2009;50% CADESI-04 improvement at M2 and M3) were more frequent with FMT (35% vs. 5%; p&#x2009;=&#x2009;0.044). In the FMT group, the medication scores were lower at M2 (16&#x2009;&#xb1;&#x2009;10 vs. 23&#x2009;&#xb1;&#x2009;11; p&#x2009;=&#x2009;0.033) and M3 (13&#x2009;&#xb1;&#x2009;10 vs. 24&#x2009;&#xb1;&#x2009;15; p&#x2009;=&#x2009;0.007) compared to placebo. PVAS decreased in both groups without between-group differences. OGATE favoured FMT (p&#x2009;=&#x2009;0.028). FMT was well tolerated.<br><br>Adjunctive FMT reduced lesion severity and medication requirements, supporting its use as a safe microbiome-based add-on therapy in cAD.}, }
@article {pmid42287050, year = {2026}, author = {Gao, J and Li, W and Li, X and Tan, Y and Li, Y and Duan, L and Wu, T and Chen, D and Hu, Y and Wang, M}, title = {[Association between wearable-derived physical activity patterns and gut microbiota in older adults].}, journal = {Beijing da xue xue bao. Yi xue ban = Journal of Peking University. Health sciences}, volume = {58}, number = {3}, pages = {551-559}, pmid = {42287050}, issn = {1671-167X}, mesh = {Humans ; Aged ; *Wearable Electronic Devices ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Exercise/physiology ; Male ; Female ; Feces/microbiology ; China ; }, abstract = {OBJECTIVE: To identify real-world physical activity patterns in older adults using objective measurements from wearable devices, and to analyze the associations between these patterns and gut microbiota composition.<br><br>METHODS: Based on data collected from a real-world health management project, a total of 743 participants from Eastern, Central, and Northern China were enrolled between January 2018 and June 2025. A 180-day objective physical activity dataset prior to fecal sampling was collected via smart wearable devices to extract features including mean daily steps, coefficient of variation of steps, and the proportion of active days. Fecal samples underwent 16S ribosomal RNA (rRNA) gene (V3-V4 region) amplicon sequencing to obtain genus-level relative abundance matrices. Covariates, including demographics, lifestyle, and chronic disease history, were collected via questionnaires and physical examinations. The discriminative dimensionality reduction via learning a tree (DDRTree) algorithm combined with K-means clustering was applied to identify physical activity phenotypes. Alpha diversity was evaluated using the Shannon index (Kruskal-Wallis test), and beta diversity was assessed using covariate-adjusted permutational multivariate analysis of variance (PERMANOVA) based on Bray-Curtis distance. Multivariable linear regression with false discovery rate (FDR) correction was used to screen differential taxa. A microbial risk score (MRS) was constructed based on taxa with a raw P < 0.05, defined as the difference between the standardized abundance of beneficial and harmful taxa. Co-occurrence networks were constructed to evaluate micro-ecological topological structures.<br><br>RESULTS: The cohort comprised 381 (51.3%) individuals aged 60-74 years and 362 (48. 7%) aged &#x2265;75 years. Compared with the 60-74 group, the &#x2265;75 group had higher prevalences of hypertension (45.9% vs. 36.7%, P=0.045) and heart disease (34.0% vs. 25.2%, P=0.032), higher systolic blood pressure (median 130 mmHg vs. 120 mmHg, P < 0.001), and fewer mean daily steps (median 6 200 steps vs. 7 000 steps, P < 0.001). Clustering identified three activity patterns: active group (n=143, 19.2%; high steps, low variation, high adherence), moderate group (n=429, 57.7%), and irregular group (n=171, 23.0%; low steps, high variation, low adherence). The active group exhibited the lowest prevalences of hypertension (35.0%) and heart disease (21.7%), and the lowest systolic blood pressure (mean 124.4 mmHg), whereas the irregular group showed the highest values (51.5%, 40.4%, and 127.6 mmHg, respectively). Alpha diversity showed no significant differences among the groups. After adjusting for covariates, physical activity patterns showed no statistically significant effect on beta diversity (R[2]=0.003 7, P=0.115). Compared with the irregular group, two genera in the active group showed significant differences (P < 0.05). Specifically, the relative abundance of Roseburia in the active group was significantly lower than that in the irregular group (P < 0.05), and the relative abundance of Butyricimonas was also significantly lower than that in the moderate group (P < 0.01). However, these differences did not remain statistically significant after FDR correction. The MRS exhibited a significant gradient distribution across the groups, with the active group scoring the highest (P < 0.001). Co-occurrence network analysis revealed that the active group had the highest network density and proportion of positive correlations (84.5%), whereas the irregular group had the lowest (60.3%).<br><br>CONCLUSION: Physical activity patterns identified from wearable device data are associated with gut microbiota composition and ecological network characteristics in older adults. Active and regular physical activity patterns indicate a higher MRS and more stable microbial co-occurrence networks, suggesting potential associations between activity regularity and gut microbial ecology, though causal inference requires longitudinal confirmation.}, }
@article {pmid42287428, year = {2026}, author = {Yang, L and Liu, B and Gu, X}, title = {Genetic evidence for potential causal associations between gut microbiota and site-specific urolithiasis risk: a two-sample mendelian randomization study.}, journal = {Urolithiasis}, volume = {54}, number = {1}, pages = {}, pmid = {42287428}, issn = {2194-7236}, mesh = {Humans ; Mendelian Randomization Analysis ; *Urolithiasis/genetics/microbiology/epidemiology ; *Gastrointestinal Microbiome/genetics ; Genome-Wide Association Study ; Polymorphism, Single Nucleotide ; }, abstract = {Urolithiasis is a common and recurrent condition with substantial clinical burden. Although observational studies have linked the gut microbiome to stone formation, causal inference is limited by confounding and reverse causation. We applied two-sample Mendelian randomization (MR), a genetic epidemiological approach that uses germline genetic variants as instrumental variables to minimize confounding and reverse causation bias, to evaluate the potential causal associations between gut microbial taxa and site-specific urolithiasis subtypes. Genetic association estimates for gut microbiota were obtained from the MiBioGen consortium. Summary statistics for urolithiasis subtypes were sourced from two independent European-ancestry GWAS datasets. Instrumental variables were selected per taxon at P < 5 × 10[-6], LD-clumped (r[2]<0.01, 1000 kb), harmonized across datasets, and screened via PhenoScanner to remove variants associated with potential confounders at genome-wide significance. Weak instruments were excluded (F < 10). Primary causal estimates were obtained using inverse-variance weighted (IVW), with complementary analyses using weighted median, MR-Egger, simple mode, and weighted mode. Sensitivity analyses included Cochran's Q, MR-Egger intercept, MR presso analysis, leave-one-out analyses, and reverse MR. After applying multiple testing correction and sensitivity filtering, three taxa showed evidence of potential causal associations with specific urolithiasis subtypes. Genetically predicted higher abundance of family Prevotellaceae (id.960) was associated with decreased risk of bladder calculus (OR = 0.88, 95% CI 0.79-0.97, p = 8.85 × 10[-3]). Higher abundance of class Bacilli (id.1673) was associated with decreased risk of ureter calculus (OR = 0.59, 95% CI 0.42-0.84, p = 2.72 × 10[-3]). Higher abundance of genus Coprobacter (id.949) was associated with increased risk of renal calculus (OR = 1.37, 95% CI 1.14-1.66, p = 9.79 × 10 [-4]). Sensitivity analyses indicated no evidence of heterogeneity, directional pleiotropy, or horizontal pleiotropy. Leave-one-out and reverse MR analyses supported robustness and directionality. Our study provides genetic evidence supporting potential causal associations within the gut-stone axis, suggesting that specific gut microbial taxa may influence the risk of site‑specific urolithiasis.}, }
@article {pmid42287442, year = {2026}, author = {Shin, JH and Song, EJ and Lim, MY and Choi, HJ and Kim, J and Nam, YD}, title = {Plant-based diet quality and gut microbiota in relation to cardiometabolic risk in Korean adults.}, journal = {European journal of nutrition}, volume = {65}, number = {4}, pages = {}, pmid = {42287442}, issn = {1436-6215}, support = {E0252500-01//Ministry of Science and ICT/ ; RS-2025-00513735//Ministry of Science and ICT/ ; E0170600-09//Ministry of Science and ICT/ ; }, mesh = {Humans ; Republic of Korea/epidemiology ; *Gastrointestinal Microbiome/physiology ; Female ; *Diet, Plant-Based ; Cross-Sectional Studies ; Male ; Adult ; Middle Aged ; *Cardiometabolic Risk Factors ; Obesity/epidemiology ; *Cardiovascular Diseases/epidemiology ; *Diet, Vegetarian ; Cholesterol, HDL/blood ; Blood Glucose ; }, abstract = {PURPOSE: This study investigated the association between plant-based diet quality and gut microbiota and explored whether integrating microbiota profiles with dietary indices improved strength of association with selected cardiometabolic outcomes.<br><br>METHODS: In this cross-sectional study, we analyzed cohort data collected from 2,388 Korean adults between 2017 and 2019. Dietary quality indices, including the overall plant-based diet index (PDI), healthful PDI (hPDI), and unhealthful PDI (uPDI), were derived from a food frequency questionnaire. Gut microbiota were profiled using 16S rRNA gene sequencing. Cardiometabolic risk factors included obesity, abdominal obesity, elevated fasting glucose, elevated triglycerides, low high-density lipoprotein cholesterol (HDL-C), and elevated blood pressure.<br><br>RESULTS: A higher hPDI score was associated with reduced obesity risk (OR&#x2009;=&#x2009;0.72; 95% CI, 0.57-0.91) and improved gut microbiota &#x3b1;-diversity. A higher uPDI score was associated with increased risk of elevated fasting glucose (OR&#x2009;=&#x2009;1.23; 95% CI, 1.00-1.52) and low HDL-C levels (OR&#x2009;=&#x2009;1.35; 95% CI, 1.07-1.70), and lower &#x3b1;-diversity. hPDI and uPDI scores were also associated with differences in gut microbial community structure. For obesity and elevated fasting glucose, models integrating plant-based diet indices with gut microbiome features showed higher area under the curve than dietary-only models. Genus-level analyses identified key bacterial genera associated with dietary scores and metabolic traits. The predictive performance for low HDL-C remained modest across models.<br><br>CONCLUSIONS: Plant-based diet quality was associated with gut microbiota composition and cardiometabolic health. Integrating gut microbiome features with dietary assessments provided greater explanatory value for obesity and elevated fasting glucose, although longitudinal studies are needed to clarify temporal relationships and causal pathways.}, }
@article {pmid42287443, year = {2026}, author = {Pires, D and Castañeda, F and Galvez, L and Balendres, MA}, title = {Soil as a Battlefield and a Reservoir: Linking Soil Components to the Epidemiology of Soilborne Plant Diseases.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02810-6}, pmid = {42287443}, issn = {1432-184X}, abstract = {This paper focuses on how microbial diversity, soil organic matter, and soil structure influence the activities of soilborne pathogens and plant disease epidemiology. Microbial diversity, soil organic matter, and soil structure are soil components that can reshape plant-pathogen-soil interactions by altering nutrient dynamics and the composition of the soil microbiome. When beneficial microorganisms are enriched in soil ecosystems, suppression of soilborne pathogens may be enhanced, thereby decreasing disease incidence and severity. However, microbial diversity, soil organic matter, and soil structure may also promote pathogen growth or facilitate cooperative microbial interactions that improve pathogen persistence, thereby elevating disease risk. Future progress requires a shift from descriptive surveys toward functional and predictive approaches, as these soil components influence epidemiological processes that can either suppress or intensify the development of plant diseases caused by soilborne plant pathogens. Rather than acting as deterministic drivers of disease outcomes, microbial diversity, soil organic matter, and soil structure modify the ecological context in which host-pathogen interactions occur, altering the likelihood of pathogen establishment, persistence, and transmission. This paper highlights the importance of soil management in regulating microbial community dynamics and supporting plant disease control within this probabilistic ecological framework.}, }
@article {pmid42287449, year = {2026}, author = {Mertin, AA and Blackall, LL and Brumley, DR and Liew, ECY and van der Merwe, M}, title = {Host Species Mediate Distinct Seed Microbiome Responses to Restoration.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02802-6}, pmid = {42287449}, issn = {1432-184X}, abstract = {Microbial diversity is a key driver of ecosystem function, yet it remains poorly integrated into ecological restoration frameworks. While seeds are the primary dispersal unit of plants and the foundation of most restoration programs, the microbial communities they carry are rarely considered. Here, we assess whether sites that have undergone restoration have altered seed-associated microbial communities. We do this by comparing bacterial and fungal seed microbiomes across natural and restored landscapes. Using a landscape-scale sampling design, seeds were collected from multiple plant host species and populations across 41 sites spanning a broad latitudinal gradient. High-throughput sequencing of the 16S rRNA gene and ITS2 region was used to characterise bacterial and fungal communities, respectively, and differences in diversity, composition, and network structure were assessed using multivariate and network-based approaches. Seed microbiomes differed between natural and restored sites, but the magnitude and nature of these changes varied among host species. Restored sites were associated with shifts in microbial diversity, community composition, and network structure, including changes in the retention of putative keystone taxa. In some species, restoration was linked to pronounced restructuring of seed-associated microbial communities, whereas in others, microbiomes remained comparatively stable. Together, these results demonstrate that restoration can alter seed microbial communities in ways that are not consistently predicted by soil-focused restoration outcomes and that host identity mediates these responses. Incorporating seed microbiome data into restoration monitoring may therefore provide a complementary and previously overlooked indicator of restoration success, with implications for improving plant germination and health.}, }
@article {pmid42287489, year = {2026}, author = {da Silveira Bastos, IMA and Cardoso, MS and Laux, M and Ribeiro, RR and García, GJY and Bahia, PA and de Sousa, PMV and Alves, BGT and de Rezende, DHC and Rosado, AS and Bezerra, JDP and Landell, MF and Melo, VMM and Tavares, TCL and Góes-Neto, A}, title = {Worldwide diversity and ecology of mangrove fungi: a systematic review of ITS metabarcoding studies and a quantitative, integrative analysis of raw sequence data.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {7}, pages = {}, pmid = {42287489}, issn = {1573-0972}, mesh = {*Fungi/classification/genetics/isolation &amp; purification ; *DNA Barcoding, Taxonomic ; *Biodiversity ; *Wetlands ; *Mycobiome ; Basidiomycota/genetics/classification ; Geologic Sediments/microbiology ; *Rhizophoraceae/microbiology ; Ecosystem ; Ascomycota/genetics/classification/isolation &amp; purification ; Phylogeny ; }, abstract = {Fungi are integral components of the mangrove microbiome, playing critical roles in decomposition, nutrient cycling, and symbiosis. Our study synthesizes the findings from a global systematic review of fungal ITS metabarcoding studies conducted in mangrove ecosystems. This review consolidates data from 23 original research articles (1,154 samples) and provides a comprehensive overview of the diversity, community structure, and ecological functions of fungi in these critical coastal habitats. The analyses revealed a consistent core fungal mycobiome in mangroves worldwide. This community is dominated by Ascomycota, with Basidiomycota as the second most abundant phylum. A consistent set of ten highly abundant genera underpins this core community, and fungal diversity and composition are strongly influenced by the specific substrate. Non-rhizospheric sediment harbors the highest diversity, while live plant organs host a more specialized and less diverse community, slightly dominated by potential plant pathogens. Rhizospheric sediment supports a unique assemblage rich in wood-decomposing fungi. The primary ecological role of fungi in mangroves is decomposition, which is essential for breaking down lignocellulosic litter, cycling nutrients, and storing carbon in sediments. A surprisingly high relative abundance of fungi classified as plant pathogens was identified on mangrove plant tissues, suggesting an underappreciated role of fungal diseases in these ecosystems. Metabarcoding provides a far broader view of fungal diversity than traditional collection and culturing methods. It has uncovered a vast number of uncultured taxa and has been particularly effective in revealing the significant, and likely underestimated, presence of macrofungi in mangrove soils. Our study also highlights that current short-read metabarcoding can severely underestimate certain fungal groups, particularly the endomycorrhizal Glomeromycota, due to technical limitations. Altogether, our synthesis provides a global baseline against which future mangrove mycobiome studies can be benchmarked.}, }
@article {pmid42287544, year = {2026}, author = {Han, J and Su, D and Guo, Y and Luo, H and Zhao, S and Li, C and Zhan, Y}, title = {The Modern Environment and Childhood Asthma: The Role of Air Pollution and Heavy Metal Exposure.}, journal = {Current allergy and asthma reports}, volume = {26}, number = {1}, pages = {}, pmid = {42287544}, issn = {1534-6315}, mesh = {Humans ; *Asthma/epidemiology/etiology ; *Environmental Exposure/adverse effects ; Child ; *Air Pollution/adverse effects ; *Metals, Heavy/adverse effects ; *Air Pollutants/adverse effects ; Particulate Matter/adverse effects ; Pregnancy ; }, abstract = {PURPOSE OF REVIEW: Childhood asthma is the most common chronic non-communicable disease in children and a major global public health challenge. Although genetic predisposition contributes to asthma susceptibility, the high burden of disease-particularly in high-sociodemographic-index regions-points to a central role of environmental exposures characteristic of the modern environment. This review synthesizes current evidence linking ambient air pollution and heavy metal exposure to childhood asthma, with a focus on early-life vulnerability, underlying biological mechanisms, and implications for prevention.<br><br>RECENT FINDINGS: We reviewed epidemiological, toxicological, and mechanistic studies published through November 2025, prioritizing systematic reviews and meta-analyses while integrating recent cohort studies, intervention trials, and experimental research. Epidemiological findings consistently demonstrate that prenatal and early-childhood exposure to particulate matter (PM&#x2082;.&#x2085;, PM&#x2081;&#x2080;), traffic-related air pollutants (e.g., NO&#x2082;, black carbon), and ozone is associated with increased asthma incidence, wheezing, reduced lung function, and higher rates of exacerbations and healthcare utilization. In contrast, evidence for metal-related exposures is more heterogeneous. Toxic metals and metalloids, transition metals in particulate matter, and essential trace-element status may contribute to asthma risk through biologically plausible pathways, but associations appear to depend on exposure timing, exposure source, biomarker type, co-exposures, and population context. Mechanistic studies reveal shared and interacting pathways involving oxidative stress, airway epithelial barrier disruption, immune dysregulation, epigenetic modifications, and microbiome alterations. The effects of these exposures are magnified during critical developmental windows and modified by genetic susceptibility and social determinants of health, contributing to marked environmental health inequities. Overall, childhood asthma is strongly shaped by early-life exposure to air pollution and heavy metals through interconnected biological and social pathways. Addressing these preventable environmental risks is essential for effective asthma prevention and for reducing global disparities.}, }
@article {pmid42287552, year = {2026}, author = {Khongkool, K and Taweechotipatr, M and Payungporn, S and Sawaswong, V and Lertworapreecha, M}, title = {Prophylactic effects of native swine probiotics on Salmonella Typhimurium infection: evidence from immune responses and gut microbiome stability.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {7}, pages = {}, pmid = {42287552}, issn = {1573-0972}, support = {NRCT5-RGJ63005-085//the National Research Council of Thailand (NRCT)/ ; }, mesh = {Animals ; *Probiotics/administration &amp; dosage/therapeutic use ; *Salmonella typhimurium/drug effects/immunology ; *Gastrointestinal Microbiome/drug effects ; Mice ; Swine ; Immunoglobulin A, Secretory ; *Salmonella Infections/prevention &amp; control/immunology/microbiology ; Disease Models, Animal ; Intestines/microbiology ; Female ; Bacterial Translocation ; Saccharomyces cerevisiae ; Spleen/microbiology ; Body Weight ; }, abstract = {Probiotics provide strain-specific health benefits and may help protect against enteric pathogens. This study examined the protective effects of single- and multi-strain probiotics against Salmonella Typhimurium infection in a mouse model. Mice received Lactiplantibacillus plantarum TBRC-15420, Bacillus amyloliquefaciens TBRC-15434, Saccharomyces cerevisiae TBRC-19857, or a mixture of the three strains for 30 days before oral challenge with S. Typhimurium. Clinical outcomes, body weight change, pathogen clearance, histopathology, intestinal secretory IgA, and gut microbiota composition were then evaluated. No mortality was observed during the experiment, although infected mice showed transient clinical signs after challenge. Probiotic-treated mice lost less body weight than control mice, with the multi-strain treatment showing the most pronounced effect among the treatments tested and L. plantarum TBRC-15420 showing the strongest effect among the single-strain treatments. Intestinal sIgA values were descriptively higher in several probiotic-treated mice, particularly in the TBRC-15434 and TBRC-15420 groups. Probiotic treatment was also associated with lower S. Typhimurium recovery from the small intestine and reduced bacterial translocation to the liver and spleen, with no detectable bacteria in probiotic-treated groups by day five. Histological observations from representative sections suggested better-preserved intestinal, liver, and spleen architecture in probiotic-treated mice. Microbiome profiling showed descriptive compositional patterns, including relatively higher Bacteroidetes abundance and lower Proteobacteria abundance in several probiotic-treated groups. Overall, these findings suggest that native swine probiotics may help reduce S. Typhimurium burden and support host resilience during infection, although larger studies are needed to confirm the immune and microbiome-related effects.}, }
@article {pmid42287567, year = {2026}, author = {Hao, YY and Zhao, ZA and Zhang, LM and Zhao, ZG}, title = {Targeting the gut-brain axis: microbial interventions for neurological disorders.}, journal = {Metabolic brain disease}, volume = {41}, number = {1}, pages = {}, pmid = {42287567}, issn = {1573-7365}, support = {82570586//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Nervous System Diseases/microbiology/therapy/metabolism ; Animals ; *Gastrointestinal Microbiome/physiology ; *Brain/metabolism ; Probiotics/therapeutic use ; *Fecal Microbiota Transplantation/methods ; *Brain-Gut Axis/physiology ; Diet, Ketogenic/methods ; Blood-Brain Barrier/metabolism ; }, abstract = {The pathogenesis of neurological disorders involves complex interactions among genetic, environmental, immunological, and metabolic factors. Characterized by high disability rates and prolonged disease courses, these conditions impose a significant burden on patients and society. As a dynamic and modifiable component of the internal environment, gut microbiota plays a central role in the onset and progression of neurological disorders through the "gut-brain axis." Bidirectional communication occurs between gut microbiota and the central nervous system via neural, immune, and endocrine pathways. This interplay regulates blood-brain barrier integrity, modulates neuroinflammatory responses, and maintains neurotransmitter balance, thereby influencing disease progression. This review systematically summarizes current evidence on the role of gut microbiota in representative neurological disorders, such as traumatic brain injury, stroke, and epilepsy, and critically evaluates the therapeutic potential of microbiota-targeted interventions, including fecal microbiota transplantation, ketogenic diets, and probiotics. Collectively, this review provides novel insights into disease pathogenesis and highlights innovative microbiome-based therapeutic strategies for the prevention and management of neurological diseases.}, }
@article {pmid42287603, year = {2026}, author = {Ravichandran, N and Uvarajan, D and Karuppusamy, PA and Gnanarajan, R and Govindharaj, J and Mohanraj, SVP and Ravikumar, M and Mahendran, K and Vellingiri, B and Narayanasamy, A}, title = {Molecular and Immunological Mechanisms Underlying the Anticancer Effects of Bifidobacterium.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {42287603}, issn = {1867-1314}, abstract = {The genus Bifidobacterium, a prominent member of the human gut microbiota, has attracted increasing attention for its potential role in cancer prevention and treatment. Growing evidence suggests that Bifidobacterium species can modulate host immune responses, regulate inflammation, induce apoptosis, and inhibit tumour progression by modulating key oncogenic signalling pathways. This review highlights the molecular and immunological mechanisms underlying the anticancer effects of Bifidobacterium, with particular emphasis on its role in enhancing cancer immunotherapy. Recent studies have indicated that the abundance of Bifidobacterium is associated with improved responses to immune checkpoint inhibitors (ICIs) and other immunotherapeutic strategies, suggesting its potential as a microbiome-based adjuvant in cancer treatment. Moreover, advances in drug delivery approaches, including encapsulation technologies and genetically engineered Bifidobacterium strains, have improved their stability and tumour-targeting capabilities in preclinical models. Although promising results have been reported in experimental and animal studies, well-designed clinical trials are required to validate their therapeutic efficacy and safety in humans. Overall, this review summarizes the current evidence on the molecular pathways, immune modulation, and emerging therapeutic applications of Bifidobacterium, highlighting its potential as a novel microbiome-based strategy to improve cancer immunotherapy outcomes.}, }
@article {pmid42287798, year = {2026}, author = {Winssy, TD and Anandham, R and Maragatham, S and Uma, D and Karthikeyan, S and Balachandar, D}, title = {Long-term nutrient management shapes soil microbial and metabolic signatures in a century-old semi-arid agroecosystem.}, journal = {Journal of environmental management}, volume = {411}, number = {}, pages = {130209}, doi = {10.1016/j.jenvman.2026.130209}, pmid = {42287798}, issn = {1095-8630}, abstract = {Semi-arid tropical soils inherently contain low soil organic carbon (SOC) and limited nutrient reserves, resulting in poor productivity. Intensive cropping with synthetic fertilizers, further deteriorate soil quality and impair ecosystem functioning. In contrast, organic amendments alone or combined with synthetic fertilizers sustain soil biodiversity through microbially mediated processes. However, how long-term nutrient management shapes soil microbiomes and their functional diversity in semi-arid tropical systems remains largely unknown. To address this gap, we investigated a 116-year-old long-term nutrient management experiment using a multi-omic framework. Shotgun metagenomics characterized the total microbiome (bacteria, archaea, and eukaryota) and associated carbon- and nitrogen-cycling genes under four contrasting nutrient management practices: unfertilized control, inorganic fertilizer alone (IC), organic amendment alone (OM), and integrated nutrient management combining organic and inorganic inputs (INM). OM and INM significantly improved soil nutrient stocks, SOC, microbial biomass, and enzyme activities compared with IC and Control. These treatments also enhanced microbial diversity and shifted communities toward copiotrophic and functionally beneficial taxa, whereas IC and Control were dominated by stress-tolerant oligotrophs. Pathway analysis showed that carbon fixation dominated the C-cycling gene pool, with alternative autotrophic pathways prevailing over the Calvin cycle, particularly under OM and INM. These treatments also supported higher abundances of methanogenic and decomposition-associated genes, indicating enhanced carbon turnover. Nitrogen-cycling functions exhibited pathway-specific responses: OM enriched N-fixation and assimilatory nitrate reduction genes, whereas INM enhanced denitrification and dissimilatory nitrate reduction pathways. IC showed increased nitrification potential but the weakest biologically regulated N pathways. Volatomics profiling showed that OM and INM produced more diverse and metabolically active volatile organic compounds that were strongly associated with SOC and key biological attributes. Collectively, our study underscores the importance of carbon-rich organic inputs in rebuilding soil carbon stocks, reinforcing biological processes, and enhancing nutrient cycling for long-term sustainability of agriculture in semi-arid tropical regions.}, }
@article {pmid42287872, year = {2026}, author = {Wu, J and Wang, B and Li, Y and Zhang, X and Peng, Y and Liu, Q and Zhang, C and Lian, B and Cao, H and Li, K and Wang, H}, title = {Divergent responses of prokaryotic and eukaryotic microbiomes drive assembly, stability, and functional dynamics in the Bohai sea.}, journal = {Marine environmental research}, volume = {220}, number = {}, pages = {108193}, doi = {10.1016/j.marenvres.2026.108193}, pmid = {42287872}, issn = {1879-0291}, abstract = {Coastal oceans, critical for biodiversity and biogeochemistry, are increasingly altered by anthropogenic pressures that interact with natural spatiotemporal variability. However, the relative influence of spatial versus temporal drivers on microbiomes assembly, association, and function remains unclear. To resolve this, we integrated multi-kingdom amplicon and metagenomic sequencing to analyze microbial communities across spatial (Laizhou Bay vs. open Bohai Sea) and temporal (seasonal to interannual) gradients in the Bohai Sea, a semi-enclosed coastal system heavily influenced by recurrent human activities. Our results demonstrate that temporal variation exerts relatively stronger influences than spatial heterogeneity on the structure and dynamics of microbial communities in the Bohai Sea. Microeukaryotes exhibited the greatest responsiveness to spatiotemporal change, followed by archaea, with bacteria showing the highest stability. Archaeal and microeukaryotic communities were primarily governed by stochastic processes, whereas bacterial assembly transitioned from deterministic to stochastic control along spatiotemporal gradients. Microbiome co-occurrence networks were increasingly complex but less stable under spatiotemporal variability, dominated by competitive interactions and demonstrating a clear complexity-stability trade-off. Metagenomic analysis revealed a scale-dependent hierarchy of environmental drivers regulating metabolic pathways, with temperature predominant at the regional scale, DO in summer, and DON within homogeneous sub-regions. Two parallel microbial strategies for coping with anthropogenic pressure were identified, including enhanced catabolic pathways for xenobiotic degradation and a seasonally dynamic, mobile antibiotic resistome. This study provides a multidimensional and systematic perspective by demonstrating that temporal dynamics are the principal regulator of coastal microbiomes structure, stability, and function, with critical implications for predicting the responses of anthropogenically stressed coastal ecosystems under continuous environmental change.}, }
@article {pmid42287874, year = {2026}, author = {Vilaplana, MI and Jiménez-Ramos, R and Rodríguez-Romero, A and Fortunato, A and Vergara, JJ and Egea, LG}, title = {Sunscreen pollution alters the role of detached seagrass leaves in the coastal carbon cycle.}, journal = {Marine environmental research}, volume = {220}, number = {}, pages = {108199}, doi = {10.1016/j.marenvres.2026.108199}, pmid = {42287874}, issn = {1879-0291}, abstract = {Seagrass macrophytodetritus plays a crucial role in coastal carbon dynamics, but little is known about primary production and dissolved organic carbon (DOC) release from freshly detached leaves and their associated microbiome. Although this detritus is often exposed to sunscreen pollution in shallow coastal areas, the effects of sunscreen-derived compounds on macrophytodetritus decomposition also remain largely unknown. In this study, we exposed freshly detached leaves of the seagrass Cymodocea nodosa to a mixture of five commercial sunscreens in a 63-day mesocosm experiment. In the control treatment, leaves exhibited measurable primary production net biomass change, and net DOC release, throughout the experiment. Much of this production was attributed to residual photosynthetic activity in the leaves and a high relative abundance of phototrophic bacterial families in the phyllosphere microbiome. In contrast, sunscreen exposure caused severe metabolic disruption, accelerating necrosis, promoting DOC consumption until day 40, and shifting the leaf carbon metabolism towards net heterotrophy. These results demonstrate that freshly detached seagrass leaves are an active and dynamic component of coastal carbon cycling. Our results also reveal how sunscreen pollution associated with coastal tourism can alter the role of seagrass detritus as a source of DOC, trophic subsidies, and potential precursor to long-term oceanic carbon sequestration.}, }
@article {pmid42287910, year = {2026}, author = {Li, H and Li, Y and Zhang, Z and Li, X and Zhao, K and Fan, Z and Liu, K}, title = {The ablation cycle drives glacier microbiome dynamics and downstream dissemination risk of the resistome.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142686}, doi = {10.1016/j.jhazmat.2026.142686}, pmid = {42287910}, issn = {1873-3336}, abstract = {Glacial ecosystems on the Tibetan Plateau undergo pronounced hydrological shifts across the glacial ablation cycle, driven by the onset and retreat of the Indian summer monsoon. To elucidate how transitions between four distinct hydrological ablation stages (pre-ablation, early ablation, late ablation, and frozen) shape microbial community structures and antibiotic resistance gene (ARG) profiles, we analyzed 112 samples collected across four stages from multiple glacier catchments on the southeastern Tibetan Plateau using metagenomic sequencing. Our results indicated that warmer stages favored thermotolerant Proteobacteria and reduced overall community diversity and evenness. ARG abundances exhibited ablation-dependent fluctuations, with Betaproteobacteria identified as predominant potential hosts. Furthermore, ARGs and virulence factors associated with mobile genetic elements were enriched during early and late ablation stages relative to the frozen stage, suggesting elevated potential for horizontal gene transfer coinciding with peak meltwater discharge. Notably, while upstream meltwaters generally exhibited higher ARG abundances, the upstream-downstream disparity tended to diminish from the pre-ablation to the late ablation stage, likely reflecting enhanced microbial mixing driven by glacier melt. Together, these findings reveal that glacier meltwater microbiomes are primarily shaped by ablation dynamics rather than spatial heterogeneity. More importantly, dynamics across the glacial ablation cycle drive shifts in meltwater hydrology that facilitate the downstream environmental mobility of glacial resistomes, posing growing antimicrobial resistance risks within the One Health framework.}, }
@article {pmid42287915, year = {2026}, author = {Bai, J and Wen, J and Cao, Q and Pang, M and Ma, L and Man, S}, title = {Integrated microbiome and metabolomics analyses reveal gut-lung axis alteration following waterborne Pseudomonas aeruginosa exposure.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142645}, doi = {10.1016/j.jhazmat.2026.142645}, pmid = {42287915}, issn = {1873-3336}, abstract = {Pseudomonas aeruginosa (P. aeruginosa) is frequently detected in drinking water systems and premise plumbing, representing a persistent environmental microbial hazard. However, the systemic effects of waterborne P. aeruginosa exposure beyond localized pulmonary infection remain poorly characterized from an environmental risk perspective. In this study, we employed an integrated microbiome-metabolomics approach to characterize coordinated pulmonary, intestinal, and systemic host-microbiome-metabolite responses in a P. aeruginosa exposure-induced acute pneumonia murine model. Respiratory challenge with P. aeruginosa resulted in severe lung inflammation and epithelial barrier disruption, and accompanied with coordinated microbial and metabolic remodeling across distal compartments. Lachnospiraceae_NK4A136_group was enriched in both pulmonary and intestinal microbiota, suggesting its potential as a candidate environmental indicator of host responses to waterborne P. aeruginosa exposure in this acute pneumonia murine model. Metabolomic analyses revealed pronounced reprogramming of tryptophan metabolism, which was characterized by compartment-specific redistribution of the microbiota-derived metabolite like indole-3-propionic acid (IPA), with increased abundance in lung tissue and decreased abundance in serum and intestinal contents. These findings support IPA acts as a candidate metabolic indicator of systemic host-microbiome-metabolite alteration. Mechanistically, P. aeruginosa exposure was associated with altered aryl hydrocarbon receptor (AhR) signaling and compromised epithelial barrier integrity across pulmonary and intestinal tissues. Prophylactic IPA supplementation restored AhR activation, reinforced barrier function, and attenuated inflammatory injury. Collectively, these findings propose a candidate framework in which waterborne P. aeruginosa exposure is associated with coordinated pulmonary, intestinal, and systemic host-microbiome-metabolite alterations that may contribute to distal toxicological responses. Our work provides preliminary mechanistic support for microbiome- and metabolite-based effect indicators in environmental health assessment of waterborne pathogens, and pends validation in additional exposure models and human-relevant cohorts.}, }
@article {pmid42287941, year = {2026}, author = {Ye, X and Jing, X and Li, Z and Jia, L and Zhong, F and Luo, XG}, title = {Dynamic dual roles of gut microbial metabolites in Alzheimer's disease: Translational insights for gut-brain axis interventions.}, journal = {Microbiological research}, volume = {311}, number = {}, pages = {128587}, doi = {10.1016/j.micres.2026.128587}, pmid = {42287941}, issn = {1618-0623}, abstract = {Alzheimer's disease (AD) is a complex neurodegenerative disorder in which the microbiome-gut-brain axis (MGBA) plays a crucial regulatory role through microbial metabolites. This review analyzes the concentration trajectories of representative metabolites across different disease stages and compartments, and synthesizes current preclinical evidence on how these metabolites influence AD pathogenesis, with particular attention to the mechanisms underlying their dual roles. We integrate evidence for bidirectional pathological crosstalk: gut dysbiosis accelerates central neurodegeneration through altered metabolite signaling, while AD-related neuropathology concurrently disrupts gut homeostasis. The review also evaluates MGBA-targeted intervention strategies and critically identifies key limitations that hinder clinical translation, including unclear dose-response relationships and insufficient patient stratification. We note that brain-to-gut mechanistic evidence remains considerably less developed than that for the gut-to-brain direction, and that signaling crosstalk among multiple metabolites is poorly characterized. Future studies should prioritize the neuroendocrine and immune pathways linking central pathology to gut dysbiosis, the dose-response relationships of individual metabolites, and standardized multi-metabolite profiling within prospective longitudinal cohorts. Addressing these gaps will advance mechanism-guided, precision-targeted interventions that mitigate the prevalent gut dysfunction in AD and confer global therapeutic benefits.}, }
@article {pmid42288047, year = {2026}, author = {Maire, A and Laurenceau, R and Rolhion, N and Bikard, D}, title = {In situ genetic modification of gut bacteria.}, journal = {Current opinion in microbiology}, volume = {92}, number = {}, pages = {102766}, doi = {10.1016/j.mib.2026.102766}, pmid = {42288047}, issn = {1879-0364}, abstract = {The crucial role of the gut microbiome in human health has driven a need to understand bacterial function within their complex native ecosystem. However, traditional functional genomic methods require isolating, cultivating, and modifying bacteria in vitro before their reintroduction in vivo. This process often necessitates the use of axenic animals or antibiotic treatments, creating artificial conditions that disrupt key microbial interactions and can obscure relevant phenotypes. This review highlights emerging tools for precise, in situ genetic manipulation of bacteria directly within the gut. We cover diverse technologies, including DNA delivery systems (e.g. engineered temperate phages, phagemids, and conjugative plasmids), and genetic perturbation strategies (e.g. CRISPR-Cas tools and transposons). These methods offer the opportunity to engineer unculturable microbes in their natural habitat and conduct genetic screens to investigate the role of specific genes and pathways. Finally, we explore the potential therapeutic applications of in situ microbiome editing.}, }
@article {pmid42288147, year = {2026}, author = {Künstner, A and Abdelhamid, A and Casetti, F and Rodriguez, E and Busch, H and Has, C}, title = {Cutaneous dysbiosis in inherited ichthyoses/epidermal differentiation disorders: a prospective case-control study.}, journal = {The Journal of investigative dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jid.2026.05.029}, pmid = {42288147}, issn = {1523-1747}, }
@article {pmid42288363, year = {2026}, author = {Hotca, AE and Lin, OM and Piawah, S and Mendiola, DM and Yom, SS and Kuon, C and Atreya, CE}, title = {The Role of the Microbiome and Gut Health in Patients With Digestive Tract Cancers.}, journal = {Seminars in radiation oncology}, volume = {38}, number = {}, pages = {151032}, doi = {10.1016/j.semradonc.2026.151032}, pmid = {42288363}, issn = {1532-9461}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Gastrointestinal Neoplasms/microbiology/therapy ; Dysbiosis ; }, abstract = {The purpose of this review is to provide a practical and clinically relevant overview of the role of the microbiome in the development and treatment of digestive tract cancers. We describe the established associations between microbes and malignancy, such as Helicobacter pylori and Fusobacterium nucleatum, in gastric and colorectal cancer, respectively. We also review emerging evidence identifying additional microorganisms that may play a role in digestive tract cancer initiation and progression. We discuss the impact of microbial composition on the efficacy and toxicity of cancer-directed therapies, including radiation therapy and systemic chemotherapy. Beyond outlining gut microbial risk factors, we also highlight interventions on the oral and gut microbiome to prevent or alleviate symptoms associated with dysbiosis, along with proposed strategies to improve therapeutic outcomes in the future. Finally, we examine opportunities to support gut microbial health, including suggestions to reduce exposure to environmental toxins that may increase cancer risk.}, }
@article {pmid42288372, year = {2026}, author = {Mishra, KK and Mao, J}, title = {Integrative Oncology and Radiation Therapy: An Essential Evolution.}, journal = {Seminars in radiation oncology}, volume = {38}, number = {}, pages = {151028}, doi = {10.1016/j.semradonc.2026.151028}, pmid = {42288372}, issn = {1532-9461}, mesh = {Humans ; *Integrative Oncology/methods ; *Radiation Oncology/methods ; *Neoplasms/radiotherapy/therapy ; Complementary Therapies ; Quality of Life ; Patient-Centered Care ; *Radiotherapy ; }, abstract = {Radiation oncology has long paired precision with compassion, technical excellence with daily human connection. Integrative oncology extends that legacy, advancing a shift from reactive symptom management to proactive, coordinated care; from fragmented referrals to integrated pathways; and from isolated pilot efforts to implementation-ready science. In this volume of Seminars in Radiation Oncology international experts reflect on the collective toolbelt of integrative oncology, the maturation of the science, and the exciting opportunity before us in radiation oncology. By integrating complementary approaches alongside conventional treatment, integrative oncology seeks to improve symptom control, functional outcomes, treatment adherence, and quality of life, with emerging evidence supporting benefits in disease-free and overall survival in select settings. Integrative approaches include nutrition and the microbiome, physical activity, mind-body and nature-based interventions, acupuncture and East Asian medicine, Ayurveda, massage and manual therapy, yoga, tai chi, qi gong, music therapy, stress management, sleep medicine, herbs and supplements, psycho-oncology, and supportive care. Across this collection, three central themes emerge: (a) patient-centered care targeting symptoms that matter most to patients and caregivers; (b) data-driven practice grounded in clinical trials, guidelines, and mechanistic science; and (c) operational compatibility with radiation oncology workflows. We hope readers leave with two clear outcomes: practical integrative strategies applicable to patients beginning radiation therapy tomorrow, and a sharper understanding of the research and systems infrastructure required to make integrative oncology a standard and equitable component of care. The work presented here signals a structural evolution -aligning tumor control and survival with symptom science, biologic insight, and whole-person care. In doing so, radiation oncology is uniquely positioned not merely to participate in, but to lead the redefinition of integrative cancer care for the decades ahead.}, }
@article {pmid42288488, year = {2026}, author = {Yan, Q and Chen, W and Kang, J and Zhou, X and He, Z and Tan, Z}, title = {Goat gut microbiome as a reservoir for microorganism-encoded short peptides: regulation by host development age and nematode challenge.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01051-2}, pmid = {42288488}, issn = {2055-5008}, abstract = {Short peptides are a promising class of antimicrobial agents with efficacy against multidrug-resistant pathogens. While host-derived defense peptides from animals and plants have been widely characterized, the landscape of microbial-encoded short peptides, particularly those with antimicrobial activity that can mitigate antibiotic resistance, remains underexplored. In this study, we identified 1147 novel microorganism-encoded short peptides (MSPs) from the goat gut microbiome, most of which lack homology to existing database entries. The microbial communities producing these MSPs were altered by the developmental stage of the goat, whereas the overall composition and diversity of these populations remained unchanged during nematode infection, despite significant correlations between certain MSPs and type 2 immunity. Notably, two MSPs demonstrated potent antimicrobial activity with lower cytotoxicity, exhibiting remarkable efficacy against methicillin-resistant Staphylococcus aureus and Streptococcus agalactiae. Collectively, our findings establish the goat gastrointestinal tract microbiome as a distinctive and promising reservoir for the discovery of antimicrobial and immunoregulatory peptides.}, }
@article {pmid42288512, year = {2026}, author = {Jappe, U and Behrends, J and Schromm, AB}, title = {Lipid ligand binding and membrane interactions of a novel food-derived lipid transfer protein enhance basophil allergic responses.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42288512}, issn = {2045-2322}, mesh = {*Carrier Proteins/immunology/metabolism ; *Basophils/immunology/metabolism ; Humans ; *Antigens, Plant/immunology/metabolism ; Liposomes/metabolism ; Ligands ; *Plant Proteins/immunology/metabolism ; Lupinus/immunology/chemistry ; *Allergens/immunology/metabolism ; Prunus persica/immunology ; *Food Hypersensitivity/immunology ; Protein Binding ; }, abstract = {Non-specific (ns) lipid transfer proteins (LTPs) are lipid-binding allergens whose natural ligands are not fully known. To elucidate the function and allergenic relevance of nsLTP-lipid complexes, purified natural Lupinus luteus (L. luteus) nLTP and recombinant peach LTP, rPru p 3, were tested for membrane interaction and lipid transport activity using liposome assays and Förster-resonance-energy-transfer (FRET) in a case-level proof-of-principle investigation. Allergenic relevance of the LTP-lipid interaction was evaluated in the presence of oleic acid (OA), phosphatidylcholine (PC), phosphatidylglycerol (PG), and phosphatidylserine (PS) in a basophil activation test (BAT) with effector cells from an LTP-allergic patient. Both LTPs interacted with neutral PC and negatively charged PS liposomal membranes. A novel transport activity for anionic PG species was identified for both proteins, indicating a shared functional preference for the glycerol headgroup. LTP-dependent lipid exchange/mixing were consistent with transfer. However, fusion/mixing mechanisms cannot be excluded with the current readout. In BAT, both LTPs showed enhanced activation in combination with OA, PC, PG, and PS. As PG is a key component of bacterial membranes, the PG specificity of the lipid interaction of L. luteus nLTP and rPru p 3 is likely of relevance in allergen interaction with the gut microbiome and for enhancement of allergic symptoms. These findings highlight lipid-specific functional properties and lipid-dependent modulation of allergenic activity in plant nsLTPs.}, }
@article {pmid42288685, year = {2026}, author = {Lin, ML and Gao, HN}, title = {Transplantation of encapsulated fecal microbiota: research progress and future trends.}, journal = {World journal of pediatrics : WJP}, volume = {}, number = {}, pages = {}, pmid = {42288685}, issn = {1867-0687}, support = {2022YFC2304500//National Key Research and Development Program/ ; 2021YFA1301104//National Key Research and Development Program/ ; }, abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) demonstrates significant efficacy in treating intestinal disorders, such as recurrent Clostridioides difficile infection (rCDI). However, traditional FMT relies on invasive delivery methods (e.g., colonoscopy or use of a nasoenteric tube) and lacks standardized donor screening, limiting its widespread clinical adoption and scalability. As a key formulation of live biotherapeutic products (LBPs), encapsulated FMT represents a transition from empirical microbial transfer to engineered biotherapeutics, offering a safer and more convenient approach for clinical application.<br><br>DATA SOURCES: This review synthesizes, compares, and integrates data in a narrative fashion from PubMed and the China National Knowledge Infrastructure.<br><br>RESULTS: Research on encapsulated FMT in adults has progressed toward standardization and the exploration of new indications. In contrast, pediatric studies remain primarily focused on rCDI treatment and lack large-scale randomized controlled trials. Evolution toward encapsulated, standardized products is driving a shift from whole-community microbial formulations toward more defined consortia and, ultimately, synthetic biology-based innovations. Concurrent significant regulatory challenges persist, as definitions of LBPs remain inconsistent and clear, harmonized international guidelines are yet to be established.<br><br>CONCLUSIONS: This review summarizes progress and emerging research priorities in encapsulated FMT while also examining current regulatory challenges and innovative directions within the LBP framework. Future developments are poised to advance encapsulated FMT from whole-community transplantation toward the precise modulation of functional microbial consortia. This progression will help drive microbial therapeutics toward greater standardization and personalization, offering improved treatment strategies for intestinal and other microbiome-associated diseases.}, }
@article {pmid42289130, year = {2026}, author = {Algazina, T and Azanbayeva, D and Tsoy, N and Touir, G and Kotlyarova, T}, title = {CYTOKINE - ASSOCIATED PARAMETERS OF THE IMMUNE RESPONSE IN PSORIASIS AND THEIR CORRELATIONS WITH ALPHA - AND BETA - DIVERSITY OF THE GUT MICROBIOME.}, journal = {Georgian medical news}, volume = {}, number = {373}, pages = {204-210}, pmid = {42289130}, issn = {1512-0112}, mesh = {Humans ; *Psoriasis/immunology/microbiology/genetics/pathology ; Female ; Male ; *Cytokines/immunology ; *Gastrointestinal Microbiome/immunology/genetics ; Adult ; Feces/microbiology ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Severity of Illness Index ; }, abstract = {OBJECTIVE: The aim of this study was to evaluate the relationship between cytokine-associated immune response parameters in patients with psoriasis and indices of gut microbiome alpha- and beta-diversity.<br><br>METHODS: The study included 91 patients with mild-to-moderate psoriasis and 92 nominally healthy volunteers in the control group. Disease severity was assessed using the Psoriasis Area and Severity Index (PASI). Cytokine profiling was performed in fecal samples using multiplex analysis to evaluate a panel of inflammatory mediators, including IL-1&#x3b1;, IL-4, IL-6, IL-8, IL-12p70, IL-17, IFN-&#x3b3;, and TNF-&#x3b1;. Gut microbiome composition was analyzed using 16S rRNA gene sequencing. Microbial diversity was assessed using alpha-diversity indices (Shannon and Simpson) and beta-diversity measures (Bray-Curtis dissimilarity and principal coordinates analysis).<br><br>RESULTS: Elevated levels of pro-inflammatory cytokines were observed in patients with psoriasis, with the most pronounced increases in IL-12p70 and IL-1&#x3b1;. Significant positive correlations were identified between PASI scores and the levels of IL-4, IL-8, and EGF, indicating an association between immune markers and disease severity. Beta-diversity analysis suggested a trend toward differences in microbial community structure between groups; however, these findings were not confirmed by PERMANOVA. Additionally, differences in the relative abundance of specific bacterial taxa were observed.<br><br>CONCLUSIONS: Psoriasis is associated with both immune dysregulation and alterations in gut microbiota composition. The observed relationships between fecal cytokine levels, microbiome characteristics, and disease severity support the concept of the gut-skin axis and highlight the potential of the gut microbiome as a biomarker and therapeutic target in psoriasis.}, }
@article {pmid42289429, year = {2026}, author = {Liu, G and Zhang, X and Lai, X and Zhu, X and Su, L and Wang, J}, title = {A comparative study of machine learning models for microbiome-based diagnosis and multi-class staging of colorectal cancer.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-53441-3}, pmid = {42289429}, issn = {2045-2322}, support = {62572389//National Natural Science Foundation of China/ ; }, abstract = {Colorectal cancer (CRC) is closely associated with gut microbiota dysbiosis; however, comprehensive benchmarking of machine learning models that integrate case-control differentiation with TNM staging remains limited. To address this gap, we systematically evaluated eight machine learning algorithms using 16S rRNA sequencing data derived from fecal samples. Our analysis included traditional methods (Logistic Regression), classic machine learning algorithms (Random Forest, XGBoost, SVM, KNN), and advanced deep learning architectures (CNN, MLP, GCN). These models were applied to both binary classification (CRC vs. healthy controls) and multi-class classification (TNM staging) tasks. Two complementary feature selection strategies (LEfSe and RFCV) were employed, followed by hyperparameter optimization, five-fold cross-validation on the training set (n = 510). Model performance was assessed on internal test sets (n = 210) and multiple independent cohorts (total n = 1039), with bootstrap analysis conducted to provide robust performance estimates. For binary classification, Random Forest achieved the highest and most consistent AUCs across all validation cohorts (0.8633-0.8672), significantly outperforming most other models (p < 0.05). For multi-class classification (Control vs. TNM I/II vs. TNM III/IV), Random Forest again demonstrated superior macro-average AUCs (0.7736-0.7816) on the independent validation set, with particularly high sensitivity (0.8571) for early-stage detection. Based on this comprehensive evaluation, Random Forest emerges as a highly robust and versatile algorithm for CRC diagnosis based on microbiome data, demonstrating balanced performance, effective feature selection, and promising potential for clinical staging applications.}, }
@article {pmid42289444, year = {2026}, author = {Masuoka, H and Miyatake, T and Park, J and Negishi, H and Kurokawa, R and Tsuchihashi, H and Makino, S and Suda, W}, title = {Fatigue-associated gut bacteria in Japanese healthy adults characterized by metagenomic analysis.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-56821-x}, pmid = {42289444}, issn = {2045-2322}, support = {J24K18210//Japan Society for the Promotion of Science, Japan/ ; J24K01676//Japan Society for the Promotion of Science, Japan/ ; }, abstract = {Emerging evidence suggests that fatigue caused by accumulated stress may serve as a prodromal symptom of psychiatric disorders, and gut microbiome dysbiosis has been reported in many such conditions. However, little is known about microbial and metabolic signatures associated with fatigue in otherwise healthy individuals. This study aimed to investigate associations between fatigue, the gut microbiome, and fecal metabolites in healthy Japanese adults. We identified characteristic microbial and metabolic differences specific to fatigued healthy individuals. Taxonomic analysis revealed a reduction in potentially beneficial bacteria and an enrichment of Escherichia coli in their gut microbiome. Functional profiling demonstrated enrichment of KEGG orthologs related to oxidative stress and depletion of energy-producing pathways. Correspondingly, key energy metabolites such as citrate were decreased. Notably, some fatigue-associated bacterial alterations overlapped with findings from external datasets on psychiatric disorders and myalgic encephalomyelitis/chronic fatigue syndrome, suggesting associative overlap in gut microbial alterations. These findings suggest associations between host fatigue and gut microbiome alterations involving oxidative stress and impaired energy metabolism. The consistent overlap of fatigue-associated microbial changes with those observed in psychiatric disorders highlights the potential relevance of gut microbial signatures in fatigue-related biological states. This study provides a foundation for future studies on gut microbial and metabolic pathways.}, }
@article {pmid42289473, year = {2026}, author = {Kim, H and Choi, J and Hitayezu, E and Chang, L and Chung, YS and Baek, JK and Yun, BH and Cha, KH and Seo, SK and Kwon, HK}, title = {Symptom-linked disruption of the vaginal Lactobacillus-IL-2/IFN-γ axis in genitourinary syndrome of menopause related symptoms.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-55963-2}, pmid = {42289473}, issn = {2045-2322}, support = {6-2025-0065//Yonsei University College of Medicine/ ; RS-2024-00396964//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry/ ; RS-2025-00561456, RS-2022-NR067484, RS-2019-NR040072//National Research Foundation of Korea/ ; }, abstract = {Genitourinary syndrome of menopause (GSM) is a common disease; however, the underlying mechanisms are unclear. This study aimed to identify the vaginal cytokine and microbiome signatures associated with symptom severity and explore the immune-microbial interactions underlying GSM. Vaginal fluid samples were collected from 66 women (42 controls and 24 patients with GSM). Cytokine levels were measured using a 25-cytokine multiplex assay. Microbiome profiles were obtained by 16S ribosomal RNA sequencing of the same samples; 61 samples passed quality control (37 controls, 24 patients). Most cytokines were downregulated in patients compared with controls, with interleukin (IL)-2, interferon (IFN)-γ, tumor necrosis factor-α, IL-4, and IL-10 showing the greatest reductions. Cytokine levels were negatively correlated with symptom severity, independent of menopausal status. Among post-menopausal women, IL-2 and IFN-γ levels were significantly lower in those with severe symptoms. Microbiome analysis revealed reduced alpha diversity and depletion of the Lactobacillus species, especially L. crispatus and L. iners, with increased levels of intestinal bacteria such as Enterococcus and Bacteroides. Correlation analysis demonstrated a strong positive association between L. crispatus and IL-2 (r = 0.56, p < 0.05) and a weaker trend with IFN-γ. Vaginal cytokine and microbiome profiles were altered in proportion to symptom severity, rather than menopausal status. The IL-2-Lactobacillus crispatus axis appears to help maintain the mucosal immune balance, suggesting its potential diagnostic and therapeutic value for restoring immune-microbial homeostasis in patients with vaginal atrophy.}, }
@article {pmid42289535, year = {2026}, author = {van Eerten, FJC and Plate, JDJ and Groenwold, RHH and Schweitzer, VA and Kluytmans, JAJW and Hietbrink, F}, title = {The effect of selective decontamination on antimicrobial resistance in intensive care patients: a systematic review and meta-analysis.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-57127-8}, pmid = {42289535}, issn = {2045-2322}, abstract = {Selective Digestive Decontamination (SDD) and Selective Oropharyngeal Decontamination (SOD) are applied to prevent infections amongst Intensive Care Unit (ICU) patients and have proven to reduce mortality and infection rates. However, concerns about the development of antimicrobial resistance persists, specifically after ICU discharge. The aim of this study was to assess the occurrence of antimicrobial resistance during ICU stay and after ICU discharge in patients who had received SDD, or SOD compared to control, explicitly at individual-patient level. A previous systematic review, which included studies on antimicrobial resistance after SDD or SOD published before 01-02-2012, was updated. All studies analyzing antimicrobial resistance during and after ICU stay, were included. All outcomes related to resistant pathogens, whether detected through colonization or infection, were included. Pooled odds ratios and 95% confidence intervals were calculated using the Mantel-Haenszel method with random effects. Analyses were done separately for SDD and SOD. Twenty-seven studies were included in the meta-analysis on the occurrence of antimicrobial resistance during ICU stay, yielding a protective association in patients receiving SDD; OR 0.73 (95%-CI 0.54;0.98, I[2] 75%), which consisted of significant heterogeneity. Four studies investigated antimicrobial resistance after ICU discharge, of which two demonstrated protective results and two observed an increase in resistance in patients who had received SDD or SOD. A prospective long-term follow-up study is required to investigate the long-term effect of SDD and SOD on antimicrobial resistance. During ICU stay, SDD was not associated with increased antimicrobial resistance to specific antibiotics, consistent with previous findings, although study heterogeneity was considerable. This current review emphasizes the limited amount of data on the long-term effect of antimicrobial decontamination strategies on antimicrobial resistance, without addressing the population level effects on resistance rates and changes in gut-microbiome. Understanding this long-term effect is essential when deciding whether to implement preventative antibiotics.}, }
@article {pmid42289567, year = {2026}, author = {Hirsch, T and Moser, U and Wolf, A and Andrianakis, A}, title = {Sinonasal microbiome remains stable during dupilumab therapy in chronic rhinosinusitis: a pilot study.}, journal = {European archives of oto-rhino-laryngology : official journal of the European Federation of Oto-Rhino-Laryngological Societies (EUFOS) : affiliated with the German Society for Oto-Rhino-Laryngology - Head and Neck Surgery}, volume = {}, number = {}, pages = {}, pmid = {42289567}, issn = {1434-4726}, abstract = {PURPOSE: This prospective pilot study aimed to evaluate whether dupilumab therapy induces measurable changes in the sinonasal microbiome of patients with chronic rhinosinusitis with nasal polyps (CRSwNP).<br><br>METHODS: Eight CRSwNP patients fulfilling criteria for biologic therapy were treated with dupilumab 300&#xa0;mg biweekly for six months. Nasal swabs from the middle meatus were collected immediately before therapy initiation and after six months. Alpha diversity and beta diversity metrics were assessed, and differential abundance analysis was performed.<br><br>RESULTS: Dupilumab therapy did not result in significant changes in alpha diversity, beta diversity, or taxonomic composition. Minor, non-significant reductions in richness and Shannon diversity were observed. Principal coordinate analysis showed extensive overlap between pre- and post-treatment samples, supported by a non-significant PERMANOVA. No statistically significant differentially abundant taxa were detected. In contrast to the microbiome results, clinical outcomes improved markedly over the same period, with all patients showing a reduction in SNOT-22 of at least 12 points and a decrease in Nasal Polyp Score of at least 1 point.<br><br>CONCLUSION: In this pilot CRSwNP cohort, no significant changes in sinonasal microbial diversity or composition were detected over six months of dupilumab therapy, despite marked clinical improvement. Larger, controlled studies are required to detect subtle or delayed microbial changes.}, }
@article {pmid42289648, year = {2026}, author = {Huang, C and Ding, Z and Guo, Y and Ma, X and Li, J and Guo, L}, title = {Sex-specific adaptive strategies and rhizosphere microbiome responses to drought stress in Bouteloua dactyloides.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05275-2}, pmid = {42289648}, issn = {1471-2180}, support = {LJKMZ20221053//Foundation of Liaoning Province Education Administration/ ; X2021012//Shenyang Agricultural University/ ; }, abstract = {Drought is becoming more frequent and severe under global climate change. Bouteloua dactyloides (Nutt.) (hereafter, B. dactyloides) is a dioecious, drought-tolerant warm-season turfgrass, but whether males and females use different adaptive strategies under drought remains unclear. We conducted a pot experiment to compare male and female plants under well-watered (90% field capacity) and drought-stressed (30% field capacity) conditions. We hypothesized that male and female B. dactyloides plants would exhibit sex-specific adaptive strategies in physiological traits and rhizosphere microbial communities under drought stress. Drought increased malondialdehyde and proline contents and enhanced superoxide dismutase and ascorbate peroxidase activities in both sexes, while peroxidase activity decreased. Under well-watered conditions, females had a higher drought resistance index than males, whereas no significant sex difference was detected under drought. Sex-specific responses were still evident; females showed a higher root-shoot ratio, whereas males exhibited increased catalase (CAT) activity. Drought and plant sex also jointly altered rhizosphere microbial communities. Drought increased fungal alpha diversity only in males, whose rhizospheres were enriched in Basidiomycota and Glomeromycota. Drought suppressed bacterial aerobic metabolism and sulfur respiration functions, as well as saprotrophic and pathogenic fungi in both sexes. Notably, male rhizospheres were significantly enriched in symbiotic fungi, particularly arbuscular mycorrhizal fungi (AMF). Overall, female B. dactyloides mainly enhances drought adaptation through morphological plasticity, whereas males rely more on a microbiome-mediated strategy centered on AMF recruitment. These findings reveal sex-specific physiological and rhizosphere microbiome adaptation pathways and underscore the role of the microbiome in drought response, providing a basis for cultivar selection in arid-region turf management.}, }
@article {pmid42289756, year = {2026}, author = {Jia, P and Dong, L and Ma, T and Bi, Y and Tu, Y and Diao, Q}, title = {Variations in methane emissions from dairy cows: associations with rumen microbial synergy and metabolic pathway divergence.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42289756}, issn = {1674-9782}, support = {2024YFD1300200//the National key Research and Development Program/ ; CAAS-ASTIP//the Agricultural Science and Technology Innovation Program/ ; }, abstract = {BACKGROUND: Methane (CH4) is a metabolic by-product of rumen microbial fermentation, contributing significantly to global warming and dietary energy loss. Elucidating the mechanisms underlying natural variation in rumen methanogenesis is essential for the development of effective CH4 mitigation strategies. Here, we applied rumen metagenomics to identify the microbial mechanisms for differences in enteric CH4 emissions among dairy cows.<br><br>RESULTS: Enteric CH4 emissions from 111 lactating dairy cows under normal feeding conditions were utilized to characterize the natural variation in rumen methanogenesis. Metagenomic analysis revealed that the comprehensive effects of bacteria involved in starch degradation, lactate metabolism, and volatile fatty acid biosynthesis provide distinct amounts of hydrogen for rumen methanogenesis in high-methane-producing (HMP) and low-methane-producing (LMP) cows. Ciliate protozoa were universally abundant in HMP cows (P&#x2009;<&#x2009;0.05), whereas methanogens enrichment exhibited heterogeneity, with the dominant methanogen Methanobrevibacter exhibiting negative correlations with the other 11 methanogens (P&#x2009;<&#x2009;0.05). Six nutrient metabolic pathways modulating methanogenesis were identified, and HMP-associated methanogenesis was further driven by upregulated formate metabolism and acetoclastic pathways (P&#x2009;<&#x2009;0.05). Random forest model analysis screened 34 microbial genera as biomarkers for CH4 production.<br><br>CONCLUSIONS: This study excluded extrinsic confounders exist for rumen microbiome and CH4 emissions in dairy cows. These findings elucidated the causal microbial and metabolic mechanisms underlying rumen methanogenesis, providing actionable targets for microbiome-based strategies to mitigate CH4 emissions from livestock farming.}, }
@article {pmid42289812, year = {2026}, author = {Pellegrinetti, TA and Santos, AA and Molligan, J and Pérez-López, E}, title = {Can the leafhopper microbiome unlock new strategies for its control?.}, journal = {Journal of economic entomology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jee/toag166}, pmid = {42289812}, issn = {1938-291X}, abstract = {Leafhoppers (Hemiptera: Cicadellidae) are significant agricultural pests worldwide, causing direct feeding injury and transmitting plant pathogens. Conventional management still relies heavily on insecticides, but resistance development, non-target effects, and environmental concerns increasingly limit their effectiveness. Recent progress in leveraging insect microbiomes for sustainable pest control, mostly in well-studied groups such as mosquitoes, whiteflies, and aphids, suggests that symbiotic manipulation could offer new tools. Whether such strategies can be developed for leafhoppers remains an open question, given how little is currently known about their microbial partnerships. Here, we synthesize current knowledge of leafhopper-associated microbial communities and evaluate approaches that could complement existing integrated pest management programs. We discuss approaches ranging from the characterization and isolation of symbionts to biotechnology strategies. We present a case study examining microbiome dynamics in the corn leafhopper (Dalbulus maidis) as a conceptual demonstration of how microbiome data can generate testable management hypotheses. We highlight both the opportunities and challenges associated with manipulating microbial partners, including ecological predictability, host specificity, and evolutionary feedback. Framing leafhoppers as holobionts, our review outlines a roadmap for translating microbiome research into compatible control technologies for agricultural systems.}, }
@article {pmid42290122, year = {2026}, author = {Kumar, A and Hira, P and Sood, U and Lata, P and Anand, S and Saxena, A and Singh, AK and Verma, H and Negi, V and Singhvi, N and Dua, A and Nigam, A and Garg, N and Jali, B and Reecha,  and Solanki, R and Singh, P and Bala, K and Nagar, S and Gupta, V and Tripathi, C and Kaur, J and Kaur, J and Kumari, R and Mahato, NK and Kumar, R and Verma, M and Kaur, P and Shukla, P and Biswas, SM and Dua, M and Subudhi, S and Kumari, R and Garg, G and Makhija, S and Toteja, R and Rawat, CD and Singh, R and Lal, S and Ramos, JL and Timmis, K and Lal, R}, title = {Promoting Microbiology Literacy and Holistic Health: IMiLI and IMiLI-SAC Perspectives on Microbes, Diet, Lifestyle and Society-A 5-Year Journey.}, journal = {Microbial biotechnology}, volume = {19}, number = {6}, pages = {e70400}, doi = {10.1111/1751-7915.70400}, pmid = {42290122}, issn = {1751-7915}, mesh = {Humans ; Life Style ; India ; *Holistic Health ; Microbiota ; *Microbiology/education ; Diet ; }, abstract = {This manuscript summarises the 5-year journey of the International Microbiology Literacy Initiative (IMiLI) and its South Asian Regional Centre (IMiLI-SAC). The main focus of the centre has been to propagate microbiology literacy and at the same time translate microbiome science into society. IMiLI-SAC played an important role in engaging audiences from diverse backgrounds across India and beyond by conducting lectures, organising workshops and outreach programs. In addition, it has also translated many educational resources in regional and cultural languages for wider presentation. IMiLI-SAC played a pivotal role in connecting microbial science with real-world issues like sustainable development, human health, dietary choices, lifestyle, preventive healthcare and planetary health. This initiative practically translates the role of microbes in different contexts using examples like microbiome studies in India, extremophiles and their biotechnological applications, and bioremediation of contaminated sites. It emphasises the important role of microbes as essential players to sustain life on earth, and changing the perception of society that views microbes as harmful or pathogens. It also supports the concept of 'food as medicine' and 'antibiotic stewardship'. However, there are certain challenges like financial constraints, resources limitations and not as much awareness. Yet, IMiLI-SAC proposes that coordinated and multilingual community engagement will address this gap between science and society. The long-lasting vision of IMiLI-SAC is to incorporate microbiology literacy into school curricula, policies and public health to have a sustainable and healthy world.}, }
@article {pmid42290147, year = {2026}, author = {Adhikary, K and Ganguly, K and Ansari, MY and Chowdhury, SR and Choudhury, S and Sadhu, D and De, S and Roy, N and Banerjee, P and Mahanti, B and Majumder, S and Maiti, R}, title = {State-of-the-Art Review on Probiotics, Synbiotics, and Microbial Metabolites: Molecular Mechanisms Shaping Host Immunity, Metabolic Health, and Chronic Disease Prevention.}, journal = {Molecular nutrition &amp; food research}, volume = {70}, number = {11}, pages = {e70528}, doi = {10.1002/mnfr.70528}, pmid = {42290147}, issn = {1613-4133}, mesh = {Humans ; *Probiotics/pharmacology ; *Synbiotics ; *Gastrointestinal Microbiome/physiology ; Chronic Disease/prevention &amp; control ; Animals ; Reactive Oxygen Species/metabolism ; }, abstract = {The human digestive system is first colonized at birth with many microorganisms that impact on the overall health of the individual via various metabolic, immune, and neuroendocrine pathways. Such microorganisms are referred to as probiotics, according to the FAO and WHO, and they exert effects on host and microbiota interaction primarily through strain-specific bioactive metabolites that act both locally and systemically. The current review will detail the various types of bioactive metabolites and their roles in regulating redox homeostasis via the reduction of reactive oxygen species (ROS) and increases in antioxidant defenses. These include catalase, glutathione peroxidase, and superoxide dismutase, which are believed to be responsible for reducing inflammation and improving epithelial barrier function. In addition to the traditional single-strain approach to probiotics, synbiotics represent an alternative strategy to improve microbial survival, functional stability, and microbiome homeostasis. Synbiotics consist of a combination of probiotic organisms and selective prebiotics that enhance the survivability and functional capacity of the individual strains and thus the overall functional resilience of the gut microbiome. Emerging evidence from mechanistic, experimental, and clinical studies demonstrates the increasing relevance of synbiotics in both therapeutic and translational contexts in the modern healthcare system.}, }
@article {pmid42290242, year = {2026}, author = {Parikh, A and O'Rorke, R and Carroll, EL and Vermeulen, E and Harcourt, R and Plön, S and Rayment, WJ and Chariton, A}, title = {DNA Metabarcoding Reveals Unexpected Predator-Prey-Microbial Dynamics in the Southern Right Whale (Eubalaena australis).}, journal = {Molecular ecology}, volume = {35}, number = {12}, pages = {e70442}, doi = {10.1111/mec.70442}, pmid = {42290242}, issn = {1365-294X}, mesh = {Animals ; *Whales/microbiology/genetics ; *DNA Barcoding, Taxonomic ; Feces/microbiology ; *Diet ; *Food Chain ; *Predatory Behavior ; *Gastrointestinal Microbiome/genetics ; Decapoda ; Euphausiacea ; }, abstract = {Southern right whale (Eubalaena australis; SRW) populations are recovering from the impacts of commercial whaling, however, recovery has been spatially variable, with strong associations between reproduction and prey availability. The diet of SRWs has not been widely examined, and with SRW foraging shifting away from high-latitude foraging grounds dominated by krill, it is essential to understand their diet at different locations. The gut microbiome is closely linked to diet, and characterising gut bacterial composition can help evaluate long-term changes in prey and ecosystem dynamics. We used DNA metabarcoding to characterise the diet and faecal microbiome of SRWs from three calving/socialising grounds and a low-latitude foraging ground. SRW feeding was more opportunistic than previously documented. Decapoda emerged as a key component of the SRW diet, being consistently detected at higher frequency and relative read abundance than euphausiids and copepods in whales from both calving/socialising and foraging grounds. The expected prey of Calanoida were also prominent in whales from the foraging ground, as were Stomatopoda, Cumacea and Semaeostomeae. A significant correlation between diet composition and faecal bacterial composition was observed, with euphausiids being the strongest predictor of bacterial variation. Our findings provide a new understanding of the breadth and diversity of the diet of SRWs. We also provide a baseline for monitoring diet-gut microbiome interactions. Collectively, these results offer a glimpse into the trophic dynamics of a Southern Ocean predator being impacted by climate-driven changes in zooplankton distribution, with implications for long-term population recovery.}, }
@article {pmid42290394, year = {2026}, author = {Li, X and Lv, J and Zhao, L and Chang, Q and Zhao, K and Chen, X and Liu, Y and Yin, C and Mao, Z}, title = {The biocontrol potential of Streptomyces polychromogenes YKL-11 against apple replant disease: Inhibition of the growth of pathogenic Fusarium and remodelling of soil microbial flora.}, journal = {Plant biology (Stuttgart, Germany)}, volume = {}, number = {}, pages = {}, doi = {10.1111/plb.70243}, pmid = {42290394}, issn = {1438-8677}, support = {2024CXGC010903//Key Technology Research and Development Program of Shandong Province/ ; CARS-27//China Agriculture Research System of Ministry of Finance and Ministry of Agriculture and Rural Affairs/ ; NO.tsqn202408119//Taishan Scholar Funded Project/ ; NO.ts20190923//Taishan Scholar Funded Project/ ; 2022TZXD0037//Key R&amp;D program of Shandong Province/ ; 2023YFD2301003//National Key Research and Development Program of China/ ; 32502619//The National Natural Science Foundation of China/ ; ZR2023QC164//Natural Science Foundation of Shandong Province/ ; ZR2024QC036//Natural Science Foundation of Shandong Province/ ; }, abstract = {Apple replant disease (ARD) severely restricts the sustainable development of the apple industry. Streptomyces is important for the development of biocontrol bacteria for plant diseases and has broad prospects for use in agriculture. This study focused on Fusarium, one of the main pathogens involved in the development of ARD. The antagonistic strain Streptomyces polychromogenes YKL-11 was isolated from the rhizosphere soil of healthy apple trees in old orchards. High-throughput sequencing was used to investigate the effects of YKL-11 on the microbial community in replanted soil, and its biocontrol efficacy was evaluated through pot and field experiments. YKL-11 can significantly erode and disrupt the mycelial structure of Fusarium, causing its spores to atrophy and deform, thereby efficiently inhibiting the growth of this fungus. The results of the pot experiment showed that the application of YKL-11 could significantly promote the growth of apple seedlings, while effectively reducing the soil population of Fusarium oxysporum, F. moniliforme, F. solani and F. proliferatum. A microbiome analysis revealed that YKL-11 optimizes the microbial community. Composition in replanted soil by enriching beneficial genera such as Chaetomium and Trichoderma while inhibiting harmful genera, including Fusarium, Cephalotrichum and Neocosmospora. Overall, S. polychromogenes YKL-11 can effectively alleviate ARD. The results of this study provide a new theoretical basis and practical ideas for the green biological control of ARD.}, }
@article {pmid42290500, year = {2026}, author = {Oriquat, G and Abdelgawwad El-Sehrawy, AAM and K Abdulsahib, W and Waleed Mustafa, W and Jyothi, SR and Priyadarshini Nayak, P and Janney, JB and Singh, G and Sinha, A and Yazdi, F}, title = {Probiotic, synbiotic effects on the gut-liver axis: omics-enabled mechanisms and therapeutic windows.}, journal = {Future microbiology}, volume = {}, number = {}, pages = {1-18}, doi = {10.1080/17460913.2026.2684877}, pmid = {42290500}, issn = {1746-0921}, abstract = {The gut-liver axis is a two-way communication network where gut microbes and their metabolites affect liver function, while the liver regulates the intestinal environment through bile acids, immune factors, and antimicrobial substances. Disruption of this balance contributes to various liver diseases, including nonalcoholic fatty liver disease, alcohol-associated liver disease, cirrhosis, and liver cancer. Probiotics and synbiotics are potential therapies that aim to restore microbial balance, strengthen the intestinal barrier, and regulate inflammation and metabolism. Recent omics technologies, such as metagenomics, metabolomics, transcriptomics, and proteomics, have helped uncover how these interventions influence important pathways involving short-chain fatty acids, bile acids, and microbial metabolites. Studies suggest that probiotics and synbiotics may improve liver health through effects on metabolism, immune regulation, and fibrosis, although results vary depending on the specific microbial strains and patient characteristics. Emerging approaches include next-generation probiotics, targeted synbiotic combinations, and personalized microbiome-based treatments. Combining multi-omics data with digital health tools may help identify patients who are most likely to benefit. Overall, microbiota-targeted therapies show promise as personalized strategies for managing liver diseases, but further research is needed to overcome challenges in translating findings into consistent clinical applications.}, }
@article {pmid42290511, year = {2026}, author = {Brito, JS and Lima, LS and Coelho, EB and Berretta, A and Mafra, D}, title = {Jaboticaba (Plinia cauliflora), a typical Brazilian fruit, as a strategy to modulate inflammation, oxidative stress and gut dysbiosis in patients with chronic kidney disease: study protocol for a randomised, controlled dietary crossover trial.}, journal = {The British journal of nutrition}, volume = {}, number = {}, pages = {1-8}, doi = {10.1017/S0007114526107636}, pmid = {42290511}, issn = {1475-2662}, abstract = {Jaboticaba, Plinia cauliflora [Mart.] Kausel (Myrtaceae) is a native Brazilian fruit high in bioactive compounds with potent antioxidant and anti-inflammatory properties. We present the first protocol (randomised crossover with a washout period) for a clinical trial investigating the effects of consuming jaboticaba peel extract on inflammation, oxidative stress and gut dysbiosis in patients with chronic kidney disease (CKD) undergoing haemodialysis. Thirty eligible patients will be randomly assigned to the intervention group (3·3 g/d of jaboticaba peel extract, providing 650 mg/d of phenolic compounds) or to the placebo group (corn starch). The total daily dose will be administered as four capsules, divided into two doses per day, for 2 months. Following the washout period (2 months), patients will continue the supplementation in a crossover design for the same duration. Blood and fecal samples, food intake data and anthropometric measurements will be evaluated. Inflammatory markers and antioxidant enzymes will be assessed using real-time protein chain reaction, cytokine plasma levels will be measured by Luminex, and uremic toxin plasma levels will be analysed using high-performance LC. The fecal microbiome will be evaluated through high-throughput sequencing of the 16S rRNA gene amplicons. Conducting a rigorously designed trial using jaboticaba will provide essential information and generate new evidence to support nutritional strategies that utilise typical Brazilian fruits for patients with CKD.}, }
@article {pmid42290718, year = {2026}, author = {Zheng, K and Zhou, SH and Liao, S and Mu, J and Han, ZB and Wang, B}, title = {The respiratory microbiome influences the occurrence of respiratory diseases in children.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1734912}, pmid = {42290718}, issn = {2296-2360}, abstract = {Respiratory diseases are common and frequently occurring illnesses in children. In recent years, studies have confirmed that the respiratory microbiome is closely associated with the susceptibility and severity of respiratory diseases in children, and its microbial composition and metabolites are involved in the occurrence and development of respiratory infections, allergic airway inflammation, asthma and other disorders. Based on the cutting-edge research findings of the past 2-3 years, this review systematically summarizes the composition and sources of the respiratory microbiome in children, the characteristics of its colonization and dysbiosis, the interaction mechanisms with the host immune system, as well as the correlation rules with common respiratory diseases. It also focuses on elaborating novel therapeutic strategies such as probiotic therapy, phage therapy, and antimicrobial peptide (AMP) therapy, aiming to provide new ideas and directions for the research on the pathogenesis and clinical precision treatment of childhood respiratory diseases.}, }
@article {pmid42290790, year = {2026}, author = {Kiadii, O and Li, L}, title = {Managing the rumen hydrogen economy to improve feed efficiency and climate-smart livestock production.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1843670}, pmid = {42290790}, issn = {2297-1769}, abstract = {Enteric methane (CH4) emissions from ruminant livestock present dual challenges for agricultural sustainability: contributing to greenhouse gas emissions while reducing feed conversion efficiency and animal productivity. Methane is produced by methanogenic archaea utilizing metabolic hydrogen (H2) generated during ruminal fermentation. This hydrogen economy is central to fermentation efficiency, nutrient utilization, and methane formation. Conventional mitigation strategies have primarily focused on inhibiting methanogenesis; however, these approaches often yield inconsistent results across production systems and lack an integrative framework for systematic application. This narrative review proposes a shift in perspective from methane suppression to the management of H2 flow within the rumen hydrogen economy and introduces two complementary conceptual frameworks to guide this approach. The genetic-microbiome co-evolution framework conceptualizes the rumen microbiome as a partially heritable trait shaped by host genetic and environmental selection, providing a theoretical basis for selecting low-emission, feed-efficient animals. The conceptual fermentation kinetics framework provides a mechanistic basis for understanding how dietary inputs and microbial interactions influence the distribution of hydrogen among competing metabolic pathways, including methanogenesis and propionate formation. Together, these frameworks establish a systems-level perspective that may inform the development of integrated strategies combining host genetic selection, precision nutrition, and microbial management. While substantial validation remains necessary, this approach provides a conceptual foundation for advancing methane mitigation from descriptive observation toward mechanistic interpretation, with the ultimate goal of supporting climate-smart livestock production systems.}, }
@article {pmid42290922, year = {2026}, author = {Temple, AM and Golden, D and Temple, JD and D'Adamo, CR}, title = {An online program focusing on modifiable lifestyle and environmental interventions was associated with improved pediatric eczema symptoms: results from a retrospective observational study.}, journal = {Frontiers in allergy}, volume = {7}, number = {}, pages = {1759379}, pmid = {42290922}, issn = {2673-6101}, abstract = {BACKGROUND: Pediatric eczema is a highly prevalent condition that often causes substantial suffering among affected children and their families. The goal of this study was to evaluate the effects of an integrative program for parents of children with eczema that simultaneously addressed multiple modifiable lifestyle and environmental risk factors.<br><br>METHODS: Children with eczema diagnosis who began the online eczema program and provided outcomes data from May 2024 to May 2025 were eligible. The primary outcome was the Patient-Oriented Scoring Atopic Dermatitis (PO-SCORAD), a validated measure of eczema symptoms and burden. Outcomes were assessed at baseline and at one month, two months, and six months after beginning the program. Changes in mean PO-SCORAD scores from baseline throughout the duration of the study were assessed with analysis of variance (ANOVA). Multivariate linear regression modeling of PO-SCORAD scores using population-averaged generalized estimating equations (GEE) were also constructed accounting for baseline PO-SCORAD scores and adjusting for age, sex, presence of any allergy, use of topical corticosteroids, and use of antihistamines.<br><br>RESULTS: 197 participants were included in the study. The mean baseline PO-SCORAD score was 51.4, which is considered severe eczema. PO-SCORAD scores improved over the course of the study (p&#x2009;<&#x2009;0.0001) and there were statistically significant and clinically meaningful improvements noted after one month (11.3 points, 22.0% improvement), two months (17.8 points, 34.6% improvement), and six months (27.2 points, 52.9% improvement) in the program (p&#x2009;<&#x2009;0.0001). After accounting for baseline PO-SCORAD scores and covariates in regression modeling, there was a 22.5-point (p&#x2009;<&#x2009;0.0001) improvement in PO-SCORAD scores from baseline to final assessment. There was a 31.4-point decrease in PO-SCORAD scores from baseline to final assessment (p&#x2009;<&#x2009;0.0001, 47.2% improvement) among the subgroup of participants with severe eczema symptoms at baseline.<br><br>CONCLUSIONS: An online program focusing on modifiable lifestyle and environmental modifications was associated with clinically meaningful symptom improvements among children with eczema. Symptoms improved relatively quickly and the greatest improvements were noted among children with severe symptoms at baseline. Further prospective studies will help generate more conclusive evidence of the causal effects of multimodal intervention focused on modifiable lifestyle factors and environmental exposures on pediatric eczema symptoms.}, }
@article {pmid42290937, year = {2026}, author = {Sezer, E and Cevrioglu, AS and Ozozen, E and Koroglu, M and Yuvaci, HU and Aslan, MM and Bostanci, MS and Akdemir, N}, title = {Association Between Hysteroscopic Treatment of Cesarean Scar Disorder and Changes in the Endometrial Microbiome and Clinical Outcomes: A Prospective Observational Study.}, journal = {Reproductive medicine and biology}, volume = {25}, number = {1}, pages = {e70067}, pmid = {42290937}, issn = {1445-5781}, abstract = {PURPOSE: To evaluate the association between hysteroscopic treatment of cesarean scar disorder (CSDi), clinical improvement, and changes in the endometrial microbiome, as this remains unclear.<br><br>METHODS: This prospective observational study included 40 women diagnosed with symptomatic CSDi. Clinical outcomes, including symptom severity and ultrasonographic measurements, were assessed before and after hysteroscopic treatment. Endometrial microbiome analysis using 16S rRNA gene sequencing was performed in a predefined subgroup of 22 patients preoperatively and at 3&#x2009;months postoperatively. Microbial composition and diversity were analyzed and correlated with clinical findings.<br><br>RESULTS: Hysteroscopic treatment resulted in a significant reduction in isthmocele dimensions and improvement in clinical symptoms across the entire cohort (p&#x2009;<&#x2009;0.01). In the subgroup undergoing microbiome analysis, postoperative samples demonstrated a shift from a polymicrobial profile consisting mostly of Clostridia and Bacteroidia to a Lactobacillus-dominant microbial profile, accompanied by a decrease in microbial diversity (p&#x2009;<&#x2009;0.001). These microbiological changes occurred in parallel with clinical improvement.<br><br>CONCLUSIONS: Hysteroscopic treatment of CSDi is associated with favorable clinical outcomes and concurrent alterations in the endometrial microbiome. Although microbiome analyses were performed in a subset of patients, the findings suggest a potential relationship between anatomical correction and microbial environment. Larger, controlled studies are warranted to further elucidate this association.}, }
@article {pmid42290939, year = {2026}, author = {Kitaya, K and Kuroda, K and Jwa, SC and Kitajima, M and Ono, M and Kikuchi, I and Nakamura, T and Yamasaki, F and Koga, K and Yasuo, T and Tsuji, S and Kimura, F and Ito, A and Hirota, Y and Nomiyama, M and Iwami, N and Takimoto, K and Takehara, I and Sako, Y and Ota, K and Diao, L and Li, Y and Yan, L and Huang, W and Zhang, S and Wang, Q and Gu, F and Shu, J and Zargar, M and Kushnir, VA and Benadiva, C and Văduva, CC and Geysenbergh, B and Tsonis, O and Pérez-Medina, T and Moreno, I and Haimovich, S and Vitagliano, A and Cicinelli, E and Kusumi, M}, title = {International Expert Consensus Statement on Chronic Endometritis: A Comprehensive Literature Review and Modified e-Delphi Study.}, journal = {Reproductive medicine and biology}, volume = {25}, number = {1}, pages = {e70066}, pmid = {42290939}, issn = {1445-5781}, abstract = {PURPOSE: This study aimed to develop international expert consensus statements on chronic endometritis (CE) through a comprehensive literature review of existing evidence and a modified Delphi approach.<br><br>METHODS: Ten panelists of the Japan Society of Reproductive Medicine Female Reproductive Tract Special Interest Group on CE performed a comprehensive review of the literature and derived statements with related comments on six specific domains of interest on CE. A two-round modified e-Delphi questionnaire was conducted among 31 international experts to evaluate the statements.<br><br>RESULTS: Twenty-three out of 24 statements, including 43 detailed items, on epidemiology (associated diseases and risk factors), symptomatology (asymptomatic or oligosymptomatic nature with subtle and nondescript gynecologic manifestations), etiology and pathogenesis (inflammation, infection, and clinical course), microbiology (associated pathogens), diagnosis (histopathology, immunohistochemistry, hysteroscopy, and microbiome analysis), and treatment (antibiotics, surgery, and multidrug resistance) finally reached a consensus. Notably, for the histopathologic diagnosis of CE, a threshold of &#x2265;&#x2009;5 endometrial stromal plasma cells/10 high-power fields received an agreement rate of 81%.<br><br>CONCLUSIONS: This comprehensive literature review and Delphi study provide a real-world clinical perspective on CE from diverse international experts. These consensus statements have the potential to lay a foundation for diagnostic criteria and/or clinical guidelines on CE.}, }
@article {pmid42291110, year = {2026}, author = {Seok, MK and Lim, C and Seo, YJ and Lee, JY and Kyoung, H and Song, M and Kim, JM}, title = {Integrative multi-omics analysis reveals systemic and intestinal responses to heat stress in finishing pigs.}, journal = {Journal of animal science and technology}, volume = {68}, number = {3}, pages = {917-934}, pmid = {42291110}, issn = {2055-0391}, abstract = {Heat stress (HS) is a major environmental threat to swine production that impairs growth performance and health. Because of their limited thermoregulatory capacity, pigs are highly vulnerable to HS, which results in compromised intestinal integrity, systemic inflammation, and metabolic inefficiency. To elucidate the mechanisms underlying HS acclimation in pigs, we conducted a longitudinal multi-omics analysis integrating fecal microbiome, whole-blood transcriptome, and immune cell deconvolution in finishing pigs under thermoneutral (TN) or HS conditions. HS markedly reduced the average daily gain and feed intake. Microbiome profiling revealed condition-specific shifts: TN pigs showed enrichment of short-chain fatty acid (SCFA)-producing genera, such as Prevotella and Streptococcus, whereas HS pigs exhibited increased Clostridium sensu stricto 1. Functional predictions indicated preservation of the antioxidant and immunomodulatory pathways (glutathione, retinol, and aminoacyl-tRNA biosynthesis) in TN pigs, whereas HS pigs displayed branched-chain amino acid catabolism, reflecting metabolic acclimation under stress. Transcriptomic analysis revealed acute changes at week 1, with 516 differentially expressed genes enriched in hematopoiesis, focal adhesion, cytoskeletal remodeling, and thyroid hormone signaling. By Week 2, these gene responses had declined, suggesting partial acclimation. Network analysis identified cytoskeletal genes (ACTB, MYL9, ACTN4, and COL4A4) as the central regulators. Immune deconvolution further showed the HS-driven elevation of cytotoxic T and myeloid subsets, in contrast to B cell populations which were maintained under TN, highlighting divergent immune trajectories. Integration of the microbiome, transcriptome, and immune data revealed two axes: (1) cytotoxic T cells positively associated with Clostridium sensu stricto 1, but negatively associated with cytoskeletal genes, and (2) B cells positively linked to Prevotella, Lactobacillus, and structural genes. Only the B-cell structural axis formed a coherent cross-layer module, indicatin a recovery-oriented response. These findings demonstrate that resilience to HS requires the coordination of humoral immunity, cytoskeletal reinforcement, and SCFA-producing microbiota. The identified biomarker axis (Prevotella, B cells, and cytoskeletal genes) provides a mechanistic basis for developing precise strategies to enhance thermal tolerance in swine.}, }
@article {pmid42291117, year = {2026}, author = {Biswas, S and Kim, MH and Cho, S and Kim, IH}, title = {Impact of zinc oxide levels and probiotic supplementation in weaning-to-finishing pig diets: productivity, gut microbial composition, and environmental implications.}, journal = {Journal of animal science and technology}, volume = {68}, number = {3}, pages = {814-840}, pmid = {42291117}, issn = {2055-0391}, abstract = {The study aimed to assess the impact of dietary zinc oxide (ZnO) combined with probiotic supplementation on the performance, fecal characteristics, meat quality, noxious gas emissions, and microbiome composition in weaning-to-finishing pigs. The experiment was conducted using 200 weaned pigs (3 barrows and 2 gilts per pen) with an average body weight of 6.65 ± 0.66 kg, randomly distributed across four treatments, each repeated ten times. The dietary treatments were: 1) TRT1, basal diet + ZnO 75 ppm; 2) TRT2, basal diet + ZnO 75 ppm + probiotic 0.3% → basal diet + ZnO 75 ppm + probiotic 0.1% → basal diet + ZnO 75 ppm + probiotic 0.1%; 3) TRT3, basal diet + ZnO 2,500 ppm → basal diet + ZnO 2,500 ppm → basal diet + ZnO 75 ppm; 4) TRT4, basal diet + ZnO 2,500 ppm + probiotic 0.3% → basal diet + ZnO 2,500 ppm + probiotic 0.1% → basal diet + ZnO 75 ppm + probiotic 0.1%, TRT1 was consistent for all and variations in ZnO and probiotic doses in TRT2, TRT3, and TRT4 were applied phase-wise (weaning → growing → finishing). The treatment groups supplemented with probiotics (TRT2 and TRT4) exhibited significantly higher (p < 0.05) body weight and average daily gain at weeks 18 and 22, as well as increased (p < 0.05) average daily feed intake over the entire period compared to the TRT1 and TRT3 group. Additionally, these groups showed a marked reduction (p < 0.05) in NH3 and H2S emissions at weeks 18 and 22. Although no significant changes (p > 0.05) were observed in fecal scores or meat quality, ZnO with probiotic supplementation significantly increased (p < 0.05) gut microbiota diversity (alpha and beta), enhanced the abundance of beneficial bacteria such as Firmicutes, Prevotella, and Lactobacillus, and reduced pathogenic bacteria like Clostridium sensu stricto 1. Taxonomic analysis also revealed significant changes (p < 0.05) in bacterial composition. These findings demonstrate that combining probiotics with lower ZnO levels enhances growth performance, gut microbial composition, and environmental sustainability by reducing noxious gas emissions. This study highlights the potential of probiotic supplementation as a strategy to minimize reliance on high-dose ZnO while improving swine production efficiency and environmental impact.}, }
@article {pmid42291119, year = {2026}, author = {Park, J and Jang, KB and Kang, MG and Kyung, J and Yoon, J and Ryu, S and Kim, Y}, title = {Comparative pangenome analysis of methanogenic archaea from diverse ecosystems reveals potential targets for methane mitigation in rumen microbiome.}, journal = {Journal of animal science and technology}, volume = {68}, number = {3}, pages = {935-953}, pmid = {42291119}, issn = {2055-0391}, abstract = {Rumen methanogenesis is a major biological contributor to methane emissions in ruminants, yet the extent to which functional markers align with taxonomic relationships and how genome content varies across habitats, remains poorly resolved. In this study, we integrated broad phylogenetic frameworks with pangenome-resolved analysis to characterize methanogenic archaea from diverse ecosystems, including seawater, freshwater, sewage, rumen, human gut, soil, and cockroach sources. By combining these insights with pangenome reconstruction and KEGG-based pathway mapping of methanogenesis, we reveal key evolutionary and functional patterns. Notably, phylogenies based on 16S rRNA and mcrA genes showed limited concordance: only two clades exhibited overlap between trees, with most clustering patterns lacking environmental specificity. This discrepancy reflects the deep conservation of 16S rRNA compared with the evolutionary plasticity of mcr genes, shaped by lateral gene transfer, gene loss, and pathway modularity. The pangenome comprised of 8,695 orthogroups across 71 genomes, with core and soft-core genes enriched in translation, amino acid metabolism, and coenzyme biosynthesis, while the shell contained many poorly annotated orthogroups, highlighting annotation gaps in archaeal genomes. KEGG analysis revealed habitat-specific signatures: rumen methanogens were notably depleted in genes of the acetyl-CoA pathway, whereas human gut methanogens lacked key cofactor biosynthesis modules, including those for coenzymes M, B, F420, and methanofuran. From rumen-derived shotgun metagenomes, we identified 53 methane-producing, 4 canonical methanogenic, 10 potential competitor, and 1 methanotrophic metagenome-assembled genomes based on functional gene content. Competitor candidates included nitrate-reducing and Wood-Ljungdahl pathway-utilizing acetogens, suggesting hydrogen redirection under high-hydrogen or inhibitor conditions. These findings support a functional marker strategy that integrates 16S rRNA with pathway-specific genes and a pangenome framework to enhance ecological interpretations of methanogens and to prioritize potential targets for methane mitigation in ruminants.}, }
@article {pmid42291263, year = {2026}, author = {Guo, K and Zhang, Z and Zheng, X and Li, N and Qiu, D and Zhang, Z and Zhang, C and Li, L and Lin, H and Xu, C and Jiang, S and Ji, X and Yang, M and Feng, C and Deng, S and Li, X and Wu, Y and Zhang, L and Yao, Y and Davenport, M and Cai, C}, title = {Mental health in early pregnancy: Interplay of objectively measured lifestyles, gut microbiota, and metabolomics.}, journal = {iScience}, volume = {29}, number = {6}, pages = {116178}, pmid = {42291263}, issn = {2589-0042}, abstract = {Prenatal anxiety symptoms (AS) and depression symptoms (DS) in early pregnancy substantially impact maternal-infant health, but their pathophysiological mechanisms remain unclear. We conducted a multimodal assessment of 161 early-pregnant women. DS exhibited significantly longer standing/sitting durations and shorter nocturnal sleep and nap times (p < 0.05). AS was associated with lower fiber intake (p = 0.018). AS and DS had more complex microbial co-occurrence networks with more extensive metabolomic changes. DS was characterized by dysregulated cysteine/methionine metabolism and Bifidobacterium-mediated modulation of standing/sleep effects. Machine learning achieved best DS discrimination by combining physical activity, diet, and microbiome data (AUC = 0.877), while metabolomics alone best discriminated AS (AUC = 0.844). In conclusion, AS is associated with metabolomic dysregulation and fiber deficiency, while DS is associated with sedentary behavior and microbiota-metabolite disruption. This study establishes a precision framework prioritizing fiber interventions for AS and activity/sleep modulation targeting microbiota-metabolite pathways for DS.}, }
@article {pmid42291297, year = {2026}, author = {Ma, M and Wang, L and Chen, M and Shi, S and Gui, X and Huang, X}, title = {Metagenomic next-generation sequencing reveals microbial community characteristics during acute exacerbations of interstitial pneumonia and their associations with clinical phenotypes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1809022}, pmid = {42291297}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Lung Diseases, Interstitial/microbiology/diagnosis ; Female ; *Metagenomics/methods ; *Microbiota/genetics ; Retrospective Studies ; Male ; Bacteria/classification/genetics/isolation &amp; purification ; Aged ; Phenotype ; Middle Aged ; Sensitivity and Specificity ; Metagenome ; }, abstract = {OBJECTIVE: Accurate pathogen detection is crucial for clinical management of interstitial lung diseases (ILDs), but conventional culture methods (CMT) have limited sensitivity. This study evaluated the diagnostic performance of metagenomic next-generation sequencing (mNGS) versus CMT in ILD patients and characterized differences in lower respiratory microbiome between stable (Stable) and acute exacerbation (AE) stage, as well as their associations with clinical indicators.<br><br>METHODS: We retrospectively analyzed ILD patients admitted between September 2021 and November 2023. Multidisciplinary discussion (MDT)-based comprehensive diagnosis served as the reference standard. We compared the sensitivity, specificity, and accuracy of mNGS and CMT. Microbiome analyses were performed to assess community composition and diversity in the Stable and AE groups, and to explore correlations with clinical features (e.g., frequency of exacerbations, oxygenation index, inflammatory markers).<br><br>RESULTS: The sensitivity of mNGS (95.60%) was significantly higher than that of CMT (32.20%). In 61.80% of patients, only mNGS yielded positive results, highlighting its diagnostic advantage. A total of 77 microorganisms were detected; bacteria accounted for 66.67% (e.g., Streptococcus pneumoniae, Haemophilus parainfluenzae). Among fungi, Candida albicans and Pneumocystis jirovecii predominated. Microbial diversity was significantly lower in the AE group than in the Stable group (p&#xa0;<&#xa0;0.01). Candida albicans (p&#xa0;=&#xa0;0.032) and Abiotrophia defectiva (p=0.011) were enriched in AE, whereas Haemophilus parainfluenzae (p&#xa0;=&#xa0;0.038) and Prevotella pallens (p&#xa0;=&#xa0;0.022) were more abundant in Stable. Correlation analyses showed that Candida albicans was positively associated with exacerbation frequency (p&#xa0;<&#xa0;0.05), while Streptococcus salivarius correlated positively with the oxygenation index. Abiotrophia defectiva was positively associated with Erythrocyte Sedimentation Rate (ESR) and body temperature, but negatively associated with lymphocyte count.<br><br>CONCLUSION: Patients in the AE group exhibited altered microbial community structures, and increased fungal colonization may be associated with disease progression, suggesting new targets for clinical intervention.}, }
@article {pmid42291303, year = {2026}, author = {Jin, Y and Zhu, H and Fan, J and Xu, H}, title = {Gut microbial metabolites in colorectal cancer: dual roles in tumorigenesis, immune crosstalk, and therapeutic innovation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1693161}, pmid = {42291303}, issn = {2235-2988}, mesh = {Humans ; *Colorectal Neoplasms/microbiology/therapy/immunology/pathology/metabolism ; *Gastrointestinal Microbiome/physiology ; *Carcinogenesis ; Animals ; Dysbiosis ; Host Microbial Interactions ; }, abstract = {A substantial body of evidence has elucidated the critical role of gut microbiota in the development and progression of colorectal cancer (CRC). Gut dysbiosis, defined as the disruption of microbiome homeostasis, has been implicated in the pathogenesis of various diseases, including CRC, Parkinson's disease, and autoimmune liver disorders. In recent years, research has increasingly focused on microbial metabolites, with numerous studies confirming their association with CRC. This review systematically elucidates the dual roles of microbial metabolites in the initiation and progression of CRC: they can suppress tumors by strengthening the gut barrier, reducing inflammation, blocking abnormal cell growth, and triggering apoptosis; yet under dysbiotic conditions-like chronic inflammation or epithelial injury-they may promote cancer by releasing inflammatory cytokines, damaging DNA, and driving uncontrolled proliferation. We summarize key findings on these metabolites' functions in CRC, highlight emerging metabolite-targeted therapies, and identify major hurdles to clinical translation: metabolite instability, individual variation in host-microbe interactions, and absent biomarkers for patient selection. Because the gut microbiota-metabolite axis is central to CRC biology, targeting it rationally offers a promising path to more precise and effective treatments. Ultimately, gut metabolites are not just disease indicators-they are actionable therapeutic targets.}, }
@article {pmid42291307, year = {2026}, author = {Eysha, M and Fouani, M and Munir, M and Black, M and Long, A and Elchouemi, M and Singh, S and Abid, MB}, title = {The intricate interplay of microbial metabolomics and carcinogenesis: a spotlight on mechanistic pathways, clinical implications and methodological challenges.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1787954}, pmid = {42291307}, issn = {2235-2988}, mesh = {Humans ; *Metabolomics/methods ; *Carcinogenesis/metabolism ; *Neoplasms/metabolism/microbiology/pathology ; *Metabolome ; *Microbiota ; Metabolic Reprogramming ; Animals ; *Bacteria/metabolism ; }, abstract = {Cancer is increasingly recognized to involve profound metabolic reprogramming, where the resident human microbiome acts as a "second genome" that fundamentally influences health and disease. At the intersection of oncology and microbiology lies the microbial metabolome, a comprehensive set of small-molecule metabolites that serve as the primary functional effectors between the microbiome and the host. We synthesize mechanistic evidence across hematologic malignancies as well as solid tumors including colorectal, pancreatic, breast, liver, and head and neck cancers. Pro-carcinogenic metabolites, such as secondary bile acids and bacterial genotoxins like colibactin, drive malignancy through chronic inflammation, direct DNA damage, and oncogenic signaling. Conversely, protective metabolites, predominantly short-chain fatty acids like butyrate, counteract cancer progression through immune modulation, selective apoptosis, and epigenetic regulation. This review examines the microbial metabolome as a "double-edged sword" in carcinogenesis, detailing how these molecules can either promote or suppress tumorigenesis depending on their identity, concentration, and the host environment. The review further explores the translational potential of microbial metabolomics in clinical oncology. We highlight the emerging role of metabolites as diagnostic and prognostic biomarkers and their capacity to modulate the efficacy and toxicity of chemotherapy and immunotherapy. Finally, we address critical methodological hurdles, including the need for standardization and established causality while providing a roadmap for integrating metabolomic profiling into a new era of personalized precision oncology.}, }
@article {pmid42291308, year = {2026}, author = {Yang, S and Tian, C and Peng, D}, title = {Specific gut microbiota alterations and metabolic deficits in Parkinson's disease: a controlled comparison with functional constipation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1767241}, pmid = {42291308}, issn = {2235-2988}, mesh = {Humans ; *Constipation/microbiology/metabolism ; *Parkinson Disease/microbiology/metabolism/complications ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; *Dysbiosis/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Male ; Female ; Aged ; Sequence Analysis, DNA ; DNA, Bacterial/genetics/chemistry ; Glutathione/metabolism ; High-Throughput Nucleotide Sequencing ; DNA, Ribosomal/genetics/chemistry ; }, abstract = {OBJECTIVE: To isolate Parkinson's disease (PD)-specific gut dysbiosis from motility-related changes, this study compared the fecal microbiota of PD patients with constipation (PDC, n=20) against a functional constipation (FC, n=15) control group.<br><br>METHODS: High-throughput 16S rRNA gene sequencing and functional prediction were performed on fecal samples. Diversity metrics and taxonomic compositions were analyzed to identify PD-specific signatures.<br><br>RESULTS: The PDC group exhibited significantly higher microbial richness than the FC group (P&#xa0;=&#xa0;0.01). Despite structural similarities driven by the shared constipation phenotype (ANOSIM R&#xa0;=&#xa0;0.084), PDC was distinguished by specific compositional shifts, including the enrichment of Paraprevotella, Akkermansia, unclassified Ruminococcaceae, and Campylobacter. Functionally, the PDC microbiome showed significant deficits in tyrosine and glutathione metabolism pathways (P<0.05), indicating compromised dopamine precursor synthesis and antioxidant defense.<br><br>CONCLUSION: By controlling for colonic transit time, this study identified specific microbial alterations and metabolic deficits in PD independent of constipation. These findings support a "gut-first" etiology linked to specific pathobionts and barrier compromise.}, }
@article {pmid42291310, year = {2026}, author = {Shakhpazyan, NK and Mikhaleva, LM and Sadykhov, NK and Midiber, KY and Afanasev, RV and Gioeva, ZV and Mikhalev, AI and Bedzhanyan, AL}, title = {PCR profiling of tumor-associated microorganisms in tissue of primary epithelial malignant tumors of colorectal origin: associations with key clinicopathological characteristics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1793881}, pmid = {42291310}, issn = {2235-2988}, mesh = {Humans ; *Colorectal Neoplasms/microbiology/pathology ; Female ; Male ; Aged ; Middle Aged ; *Bacteria/genetics/classification/isolation &amp; purification ; *Adenocarcinoma/microbiology/pathology ; *Microbiota/genetics ; Bacterial Load ; Aged, 80 and over ; Real-Time Polymerase Chain Reaction ; }, abstract = {INTRODUCTION: Colorectal cancer is one of the most common malignancies worldwide, and microbiome research has strong potential to advance understanding of tumor biology and to support biomarker development and microbiome-targeted interventions. Most colorectal cancer microbiome studies rely on stool or mucosal sampling, but routine pathology archives contain abundant formalin-fixed, paraffin-embedded primary tumor tissue that could enable scalable assessment of tumor-associated microorganisms.<br><br>METHODS: We profiled tumor-associated microorganisms in primary colorectal adenocarcinoma specimens from 192 patients using a targeted quantitative PCR panel and evaluated associations with clinicopathological variables (tumor differentiation grade, primary tumor T category, and disease stage) using non-parametric tests, ordinal regression, regularized logistic regression, and within-panel profile ordination with permutation-based inference.<br><br>RESULTS: The most consistent signals were linked to tumor differentiation rather than stage. Tumors in the G2-G3 versus G1 comparison showed higher total bacterial load and a higher detection frequency of Ruminococcus spp., with both associations remaining significant after false discovery rate control; regression analyses corroborated these findings. A regularized logistic model achieved moderate discrimination for high-grade (G2-G3) disease (mean area under the receiver operating characteristic curve &#x2248;0.71) and yielded a compact signature dominated by total bacterial load and detection of Ruminococcus spp., with additional contributions from low-frequency taxa that warrant cautious interpretation. In contrast, models targeting primary tumor T category, invasiveness (T1-T2 vs T3-T4), or overall stage showed low discriminative performance (area under the curve &#x2264;0.59), and within-panel profile distances did not reveal robust global separation of groups.<br><br>CONCLUSIONS: Targeted quantitative PCR profiling of archived primary tumor tissue identifies reproducible microbiome signals that track tumor differentiation grade more strongly than stage, suggesting that tissue bacterial burden and selected taxa may reflect microenvironmental features associated with the G2-G3 versus G1 contrast. Broader tumor microbiome profiling should be required to capture diversity and refine clinically informative signatures.}, }
@article {pmid42291325, year = {2026}, author = {Wang, Y and Huang, Z and Zheng, J and Xu, O and Yu, H and Ye, X and He, Y}, title = {Profiling of human lung and gut microbiomes in different conditions of chronic obstructive pulmonary disease using ontology-based evidence synthesis and reasoning.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1771765}, pmid = {42291325}, issn = {2235-2988}, mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology ; *Lung/microbiology ; Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/isolation &amp; purification/genetics ; *Microbiota ; Host Microbial Interactions ; }, abstract = {Chronic Obstructive Pulmonary Disease (COPD) remains one of the leading global causes of morbidity and mortality, with increasing evidence highlighting microbial dysbiosis as a key factor in disease progression and exacerbation. To resolve the inherent heterogeneity in COPD microbiome research, we developed a standardized pipeline termed as Ontology-based Evidence Synthesis and Reasoning (O-ESR), utilizing the Ontology of Host-Microbiome Interactions (OHMI) framework. Our analysis included over 30 studies and identified more than 100 significantly altered bacterial taxa in the human airway and gut microbiomes of human COPD patients across three clinical conditions: COPD versus healthy controls, exacerbation versus stable states, and severe versus moderate diseases. Profiling across taxonomic levels revealed a marked airway expansion of pathogenic genera, including Haemophilus, Moraxella, Pseudomonas, and Burkholderia. Species-level analysis confirmed the specific enrichment of Haemophilus influenzae and Pseudomonas aeruginosa, supporting their roles in airway inflammation and exacerbation susceptibility. In contrast, the gut microbiome of COPD patients exhibited a decrease of beneficial anaerobes involved in short-chain fatty acid (SCFA) production, including Bifidobacterium bifidum, Faecalibacterium prausnitzii, and members of Lachnospiraceae and Ruminococcaceae. Notably, ontology-based reasoning identified a shared depletion of commensal genera such as Prevotella and Veillonella across both anatomical sites and all three clinical conditions, indicating a systemic and progressive loss of microbial diversity. This integrated analysis reveals a COPD-associated microbial landscape characterized by airway Proteobacteria expansion and gut SCFA-producer depletion, suggesting coordinated epithelial dysfunction, immune dysregulation, and gut-lung axis involvement. These findings demonstrate the power of ontological reasoning in decoding complex host-microbiome interactions, providing a robust foundation for microbiome-informed stratification and targeted interventions in COPD management.}, }
@article {pmid42035121, year = {2026}, author = {Zhang, X and Chi, Y and Zhang, Z and Wang, Y and Yi, F and Wang, P and Liu, Y and Hao, W}, title = {Gestational diabetes: from pathogenesis to therapeutic intervention.}, journal = {Diabetology &amp; metabolic syndrome}, volume = {18}, number = {1}, pages = {}, pmid = {42035121}, issn = {1758-5996}, abstract = {Gestational diabetes mellitus (GDM), affecting up to 15% of pregnancies worldwide, is a complex metabolic disorder arising from the interaction of pregnancy-induced insulin resistance and inadequate pancreatic β-cell compensation. This review synthesizes current advances in understanding the pathogenesis and therapeutic strategies of GDM. Mechanistically, GDM develops through a multifactorial network involving placental hormone–driven insulin resistance, impaired β-cell adaptive remodeling, genetic susceptibility, and epigenetic modifications that alter key metabolic regulators such as INSR and PDX1. Increasing evidence further implicates immunometabolic dysregulation—including neutrophil extracellular trap formation and placental inflammation—along with gut microbiota dysbiosis characterized by depletion of butyrate-producing bacteria and enrichment of lipopolysaccharide-producing taxa. Additional emerging contributors include circadian rhythm disruption and exposure to environmental endocrine-disrupting chemicals, both of which can interfere with glucose homeostasis and insulin signaling. These interacting mechanisms contribute not only to maternal hyperglycemia but also to adverse maternal and fetal outcomes, including macrosomia, preterm birth, and long-term cardiometabolic risk in both mothers and offspring. Current management strategies rely primarily on lifestyle interventions and pharmacotherapies such as insulin and metformin; however, novel therapeutic approaches—including GLP-1 receptor agonists, SGLT2 inhibitors, and microbiome-targeted interventions—are being explored, although their safety in pregnancy requires further validation. Looking forward, integrating multi-omics technologies, early biomarkers, and digital health monitoring may enable precision medicine approaches for earlier diagnosis, mechanistic subtyping, and individualized treatment of GDM, ultimately reducing its intergenerational metabolic burden.}, }
@article {pmid42278572, year = {2026}, author = {Khanduja, R and Frye, RE}, title = {A Systematic Review of Folate and the Human Enteric Microbiome: Biological Mechanisms and Clinical Implications.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27115048}, pmid = {42278572}, issn = {1422-0067}, mesh = {Humans ; *Folic Acid/metabolism ; *Gastrointestinal Microbiome/physiology ; Animals ; Probiotics ; Prebiotics ; }, abstract = {Folate (vitamin B9) is central to one-carbon metabolism, supporting nucleotide biosynthesis, methylation homeostasis, and epigenetic regulation. The gut microbiome both produces and consumes folate, creating a bidirectional axis influencing host health and disease. We systematically reviewed 159 original studies from MEDLINE, Google Scholar, Embase, and Scopus (inception through January 2026) examining enteric microbiota-folate interactions, with intervention evidence graded using the Oxford Centre for Evidence-Based Medicine 2011 framework. Only a minority of gut bacteria possess complete folate biosynthetic pathways; most depend on cross-feeding from prototrophic taxa including Bifidobacterium, Lactobacillus, and Streptococcus. Altered microbial folate metabolism was associated with metabolic, gastrointestinal, oncologic, neuropsychiatric, cardiovascular, immunologic, and reproductive disorders through convergent mechanisms of disrupted methylation, genomic instability, and immune dysregulation. Probiotic interventions achieved the strongest evidence, supported by multiple human controlled and observational trials and animal models. The evidence for prebiotic, dietary, and folate supplementation interventions was moderate due to the predominant animal models and in vitro data. Overall, the predominant associational and observational evidence base is insufficient to establish causal relationships, underscoring the need for adequately powered human randomized controlled trials with folate-specific endpoints, multi-omics integration, and precision approaches matching folate form and dose to individual microbiome and host genetic profiles.}, }
@article {pmid42278576, year = {2026}, author = {Kozhakhmetov, S and Kushugulova, A and Vinogradova, E and Rakhmankulova, A and Terzic, M and Bapayeva, G and Aimagambetova, G and Kamzayeva, N and Kim, Y and Primbetov, B and Imankulova, B and Kongrtay, K and Kadroldinova, N and Galym, M and Makhambetova, S and Nurgaliyeva, K and Abdiyeva, Z and Zhumakanova, Z and Baktybayeva, D and Smagulova, B and Ukybassova, T}, title = {Cervicovaginal Mycobiome Restructuring by HPV and Bacterial Community State Types in a Kazakhstani Shotgun Metagenomic Cohort: Lactobacillus iners as a Candida-Permissive Niche Associated with α-9 HPV in Cytologically Normal Women.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27115052}, pmid = {42278576}, issn = {1422-0067}, mesh = {Humans ; Female ; *Lactobacillus/genetics/physiology ; *Vagina/microbiology/virology ; *Candida/genetics/physiology ; *Cervix Uteri/microbiology/virology ; *Papillomavirus Infections/virology/microbiology ; *Mycobiome/genetics ; Metagenomics/methods ; Adult ; Microbiota ; Shotgun Sequencing ; Middle Aged ; *Human Papillomavirus Viruses/genetics ; }, abstract = {Cervicovaginal dysbiosis is an established co-factor of high-risk human papillomavirus (HPV) persistence and cervical neoplastic development, yet most studies address the bacterial compartment in isolation, leaving fungal communities and bacterial-fungal cross-kingdom interactions underexplored, particularly in Central Asian populations. We performed shotgun metagenomic sequencing (mNGS) of cervicovaginal samples from 311 Kazakhstani women undergoing routine cervical screening. HPV status was determined using combined PCR and mNGS methods, and cervical screening was completed using liquid-based cytology (NILM, ASC-US, LSIL, ASC-H). Bacterial, viral, and fungal taxa were profiled from a single shotgun dataset with Kraken2 pipeline. Bacterial community state types (CSTs) were determined based on dominant bacterial species, functional gene content was annotated against KEGG using eggNOG, and covariate-adjusted associations were estimated using MaAsLin3. Mycobiome β-diversity differed significantly by HPV status (p = 0.003). In particular, Candida positivity was significantly associated with HPV presence and with high-risk α-9 HPV in cytologically normal (NILM) samples (OR = 3.6, [1.6-9.6], p ≤ 0.001). Covariate-adjusted analysis was consistent with this positive association (q < 0.05). Concurrently, among CSTs, Lactobacillus iners-dominated CST III and dysbiotic Gardnerella vaginalis-dominated CST IV showed a 3-fold higher Candida albicans prevalence (p < 0.01). Further analysis demonstrated that, functionally, both of these CSTs had depleted capacity for lactate metabolism (ko00620, p < 0.0001) and, in particular, for the genetic capacity for pyruvate-dependent H2O2 generation (half that of the L. crispatus-dominated CST I). These findings support L. iners as a metabolically permissive rather than protective Lactobacillus and suggest cross-kingdom functional signatures as candidate biomarkers for HPV acquisition and persistence in Central Asia, a region previously absent from the cervicovaginal microbiome literature.}, }
@article {pmid42278930, year = {2026}, author = {McPherson, EJ and Chowdhry, M and Lin, A and Stavrakis, AI and Su, L}, title = {"Antimicrobial Brachytherapy" Protocol for Chronic Periprosthetic Joint Infection in Total Knee Arthroplasty: A Preliminary Case Series with 2-Year Results.}, journal = {Journal of clinical medicine}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/jcm15114070}, pmid = {42278930}, issn = {2077-0383}, abstract = {Background: The success rates of treating chronic periprosthetic joint infection (PJI) have plateaued in the last two decades utilizing exchange protocols combined with extended parenteral antimicrobials. At the same time, extended systemic antimicrobials carry well-recognized adverse effects, including organ toxicity, metabolic derangements, and disruption of host-microbiome balance, which may themselves impair host inflammatory responses and tissue healing. The defined challenge is to intensify local site eradication while minimizing systemic antimicrobial exposure and its associated host harms. This study introduces a tactical treatment shift focusing on local microbial biocidal treatment, that we aptly name "antimicrobial brachytherapy" protocol (ABP). Methods: A consecutive case series of 25 patients with chronic PJI in total knee arthroplasty (TKA) were treated with the ABP from 2019 to 2023. In brief, the protocol includes: (1) local multimodal antimicrobial therapy applied during debridement to reach and extinguish microbial reserves, (2) eliminating parenteral antimicrobials and limiting oral antimicrobials to 3 weeks, and (3) employing variable explantation times (longer when needed) via a 1.5 exchange technique allowing individualized host and limb rejuvenation. Patients were graded according to McPherson host scoring. Musculoskeletal Infection Society (MSIS) tier levels were used to rate success. All patients had a minimum two-year follow-up. Results: Eighty percent of the patients were significantly compromised, consisting of B and C hosts having 2 and 3 limb scores. Outcomes using the MSIS tier rating show 16/25 (64%) tier 1 success (infection-free without antimicrobial suppression). In these 16 patients, three were still using their 1.5 implant at a mean 4.2 years (2-5.5 years). There were two (8%) tier 3C outcomes (aseptic revision at <1 year), and six (25%) tier 3E failures (amputation, resection arthroplasty or arthrodesis) with four amputations for continued infection, and two who underwent a repeat 1.5 exchange for recurrent infection. Of the four patients amputated, three had fungal microbes identified in post-resection aspirations. Lastly, there was one (4.15%) tier 4a outcome (mortality at <1 year). Conclusions: The ABP concept is a tactical shift focusing antimicrobial therapy within the zone of infection, avoiding long course systemic antimicrobials, and allowing variable explantation time for host and limb rejuvenation. Success was comparable to published MSIS tier 1 outcomes using traditional two-stage exchange protocols with extended parenteral antimicrobials. Given the small sample size and absence of a comparator, the results should be regarded as hypothesis-generating, and require validation in larger, randomized, controlled studies.}, }
@article {pmid42279022, year = {2026}, author = {Babik, K and Bomze, Z and Szuba, M and Borek-Dzięcioł, B and Kociszewska-Najman, B}, title = {Impact of Early-Life Antibiotic Exposure on Gut Microbiome and Vaccine Immunogenicity in Infants: A Narrative Review.}, journal = {Journal of clinical medicine}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/jcm15114161}, pmid = {42279022}, issn = {2077-0383}, abstract = {Background: Neonatologists face a significant clinical challenge in balancing the life-saving effects of broad-spectrum antibiotics with an infant's ability to develop long-term vaccine-induced immunity. During the critical neonatal window, the gut microbiota acts as an essential endogenous adjuvant that promotes immune maturation through Toll-like receptor signaling and the production of microbial metabolites such as short-chain fatty acids. Methods: This narrative review was based on a comprehensive search of the PubMed and Google Scholar databases for studies published between 2014 and 2025. The search focused on the relationships between neonatal antibiotic exposure, gut microbiome development, and vaccine-induced immune responses in infants. Results: Early-life antibiotic exposure disrupts immune maturation by causing a marked reduction in commensal bacteria, particularly Bifidobacterium and Bacteroides. Clinical and epidemiological evidence indicates that this antibiotic-driven dysbiosis leads to significantly lower antibody titers following routine vaccinations, including PCV13, Hib, and DTaP, with measurable effects persisting up to 15 months of age. While antibiotics may paradoxically enhance oral rotavirus vaccine responses in resource-constrained settings by reducing environmental enteric dysfunction, an undisturbed native microbiota remains the optimal foundation for robust immunological memory. Conclusions: These findings highlight the necessity of improving antibiotic stewardship and exploring microbiota-restoring interventions, such as targeted probiotics, to optimize infant vaccination schedules and protect long-term immune health. Empirical antibiotic treatment should be promptly terminated once sepsis has been clinically excluded to preserve the gut-immune axis.}, }
@article {pmid42279061, year = {2026}, author = {Szwajkowski, M and Szwach, J and Shefa, S and Karwowska, A and Głębocka, A and Pazdro-Zastawny, K and Dorobisz, K}, title = {Molecular Characterization of the Middle Ear Microbiome in Pediatric Otitis Media with Effusion: Diagnostic and Clinical Implications.}, journal = {Journal of clinical medicine}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/jcm15114200}, pmid = {42279061}, issn = {2077-0383}, abstract = {Background: Otitis media with effusion (OME) is a highly prevalent pediatric condition and a leading cause of conductive hearing loss in children. Its pathogenesis remains uncertain, and diagnostic and therapeutic challenges make management difficult. Objectives: This review evaluates current evidence on the middle ear microbiome in pediatric OME, focusing on the diagnostic value of 16S ribosomal ribonucleic acid (16S rRNA) gene sequencing and its potential clinical implications. Methods: A literature review was conducted using the PubMed database, including studies published between 2006 and 2026. Eligible studies involved pediatric patients with OME and examined the sources and characteristics of microbiota potentially involved in disease pathogenesis. Microbiome analysis was performed using next-generation sequencing (NGS) techniques. Results: Growing evidence indicates that OME is associated with microbial dysbiosis and biofilm formation rather than a sterile inflammatory process. The most frequently detected genera include Haemophilus, Moraxella, Streptococcus, and Alloiococcus, although substantial variability exists between studies. Pathogens are believed to reach the middle ear through the Eustachian tube from two main reservoirs: the nasopharynx and the adenoids. The potential role of Helicobacter pylori infection and gastroesophageal reflux disease (GERD) in OME pathogenesis remains uncertain and requires further investigation. NGS methods, including 16S rRNA sequencing, demonstrate higher sensitivity than conventional culture techniques, enabling the detection of fastidious and previously unrecognized microorganisms. Evidence also highlights the limited effectiveness of antibiotic therapy in OME, the persistent issue of antibiotic overuse, and the relative advantages of conservative management and microbiome-modulating approaches compared with antibiotics and surgical interventions. Conclusions: Current evidence suggests that OME is closely associated with microbiota dysbiosis and bacterial biofilm formation. Given the limited efficacy of antibiotics, microbiome-focused strategies-particularly probiotics-should be further explored. Molecular diagnostic methods, especially NGS, show clear advantages over traditional culture-based techniques. Future research should further evaluate microbiome modulation as a potential adjunctive or preventive strategy.}, }
@article {pmid42279243, year = {2026}, author = {Radu, EA and Mocanu, E and Fulina, M and Rotar, V and Enache, F and Popescu, S and Șerbănescu, L}, title = {Maternal Oral Microbiome Dysbiosis and Adverse Pregnancy Outcomes: Microbial Signatures, Inflammatory Pathways, and Clinical Evidence.}, journal = {Journal of clinical medicine}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/jcm15114379}, pmid = {42279243}, issn = {2077-0383}, abstract = {Background/Objectives: Pregnancy is characterized by complex physiological, hormonal, and immunological changes that influence the oral environment and the microbial composition of the oral cavity. Emerging evidence suggests that maternal oral dysbiosis may be associated with systemic inflammatory responses and may potentially influence pregnancy outcomes. This systematic review aimed to evaluate the current clinical evidence regarding the association between maternal oral dysbiosis and adverse pregnancy outcomes, including preterm birth, low birth weight, and gestational complications. Methods: A systematic search of PubMed, Scopus, Web of Science, and Cochrane Library was conducted for studies published between January 2013 and September 2025. Observational studies and clinical trials examining the relationship between maternal oral dysbiosis or periodontal pathogens and pregnancy outcomes in pregnant women were included. Study selection was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA 2020) guidelines, and the review was prospectively registered in PROSPERO (CRD420261383855). Data were extracted on the study design, population characteristics, microbiological assessment methods, and reported pregnancy outcomes. Ten studies met the inclusion criteria of this review. Results: Seven of the ten included studies reported significant associations between the increased prevalence of periodontal pathogens, including Porphyromonas gingivalis, Fusobacterium nucleatum, and Prevotella intermedia, and adverse pregnancy outcomes, particularly preterm birth and low birth weight (LBW). Several studies have identified oral bacterial DNA in placental tissues, supporting the potential hematogenous microbial translocation pathways. However, heterogeneity in microbiological assessment techniques and study designs limits the comparability of the findings. Conclusions: Current evidence suggests that maternal oral dysbiosis may be associated with the inflammatory pathways linked to adverse pregnancy outcomes. Further prospective studies and standardized microbiome analyses are required to clarify the role of the oral microbiome in maternal and fetal health. Integrating oral health assessments into prenatal care may be an important strategy for improving maternal and neonatal outcomes.}, }
@article {pmid42279278, year = {2026}, author = {Liu, Z and Ang, MY and Kue, CS}, title = {Gut Microbiota in Colorectal Cancer: Mechanistic Insights, Clinical Strategies, and a Regional Perspective with a Focus on Sichuan, China.}, journal = {Cancers}, volume = {18}, number = {11}, pages = {}, doi = {10.3390/cancers18111693}, pmid = {42279278}, issn = {2072-6694}, abstract = {CRC remains a major cause of cancer-related morbidity and mortality worldwide. In recent years, the gut microbiota has gained increasing attention in CRC research. Intestinal microbes are not passive bystanders in tumor development. They may promote persistent inflammation, disrupt epithelial barrier integrity, alter microbial metabolites, and affect host immune and signaling pathways. Emerging evidence also suggests that microbiota-related metabolites and microbial functional alterations may influence host epigenetic regulation, including DNA methylation and chromatin-associated signaling, thereby further shaping colorectal carcinogenesis. Together, these changes can create a microenvironment that favors tumor initiation and progression. Several bacterial species, including Fusobacterium nucleatum, Parvimonas micra, and Peptostreptococcus anaerobius, have been repeatedly associated with CRC. In contrast, beneficial commensal microbes and their metabolites, especially short-chain fatty acids, may help maintain intestinal homeostasis and limit tumor-promoting processes. Because the gut microbiota is strongly shaped by diet, lifestyle, and environmental exposure, regional differences are also relevant. This is particularly important in Sichuan, China, where distinctive dietary habits and environmental features may influence microbial patterns associated with CRC risk and disease behavior. This review summarizes the main mechanisms linking the gut microbiota to CRC, examines the regional context of Sichuan, China, and discusses current and emerging clinical strategies. These include dietary intervention, probiotics, fecal microbiota transplantation, and microbiome-informed approaches to prevention, diagnosis, and treatment.}, }
@article {pmid42279294, year = {2026}, author = {Newell, LF and Twohey, E and Sweetnam, J and Skendzel, S and Stingle, J and Vartanian, KA and Davis, BA and Layman, CE and Carbone, L and Ray, K and Fei, SS and Karstens, L and He, FC and El Jurdi, N and Blaes, AH and Meyers, G and Cook, RJ and Baraki, A and Dengel, DR and Holtan, SG}, title = {Attenuation of Immune Senescence Markers After Intensive Cancer Therapy Through Resistance Training: A Pilot Study.}, journal = {Cancers}, volume = {18}, number = {11}, pages = {}, doi = {10.3390/cancers18111710}, pmid = {42279294}, issn = {2072-6694}, abstract = {Background: Chemotherapy and radiation accelerate aging of multiple systems, including the immune and musculoskeletal systems. Resistance training may mitigate some of the late physiologic effects of cancer therapy. Methods: We developed a community-based pilot study of resistance training for long-term cancer survivors meeting criteria for pre-frailty or frailty (N = 8; 6 allogeneic hematopoietic cell transplant, 1 autologous hematopoietic transplant, 1 breast cancer survivor) and their caregivers (N = 8 healthy controls) consisting of a baseline assessment, 10 weeks of personalized resistance training at least once weekly as a group and as many additional times on an individual basis as their schedule allowed, and an end-of-study assessment to measure change in strength and body composition. Blood samples were collected at the start of the study and after the 10-week training program to assess changes in peripheral blood mononuclear cell DNA methylation patterns, gene expression measured by RNA sequencing, and stool microbiome analysis using metagenomics. The median number of resistance training sessions was 25 sessions. Results: Cancer survivors and controls both more than doubled their squat and press volume after 10 weeks. At baseline, cancer survivors exhibited a pro-inflammatory transcriptomic and epigenetic profile with elevated interferon signaling and reduced naïve T cell signatures compared to healthy controls, consistent with immune senescence. After 10 weeks of resistance training, these differences normalized, suggesting that exercise exerted anti-inflammatory and immune-restorative effects in cancer survivors at both gene expression and methylation levels. Ten fecal microbial pathways that were lower in relative abundance in patients compared with controls at baseline were no longer significantly different post-exercise. Conclusions: Our data suggest that in addition to beneficial changes in body composition, resistance training may exert an immune restorative effect in cancer survivors.}, }
@article {pmid42279452, year = {2026}, author = {Yang, L and Meng, W and Yang, T and Zhu, Y and Wang, Z}, title = {Microbiomics: Novel Biomarkers of Colorectal Cancer Diagnosis and Prognosis.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {16}, number = {11}, pages = {}, doi = {10.3390/diagnostics16111582}, pmid = {42279452}, issn = {2075-4418}, abstract = {With colorectal cancer (CRC) accounting for over 1.9 million new cases and 930,000 deaths globally in 2020, there is a critical need for innovative indicators to forecast disease advancement and therapeutic outcomes. The gut microbiome has emerged as a fertile area for discovering such diagnostic and prognostic signals. This narrative review collected current evidence on intestinal microorganisms and their metabolic products as candidate markers for CRC control. Intestinal communities influence malignancy through diverse mechanisms, including metabolic shifts, immune modulation, inflammation, proliferation/apoptosis regulation, genotoxicity, and mucosal barrier disruption. Pathogenic species, such as Fusobacterium nucleatum and enterotoxigenic Bacteroides fragilis, facilitate tumorigenesis via FadA-mediated signaling and Th17/IL-17 responses. In contrast, beneficial taxa like Faecalibacterium prausnitzii and Akkermansia muciniphila provide protective effects through short chain fatty acid production. Macrophage phenotype physiological equilibrium is altered and inflammatory status fluctuates under the former. Metabolically, hydrogen sulfide damages mitochondrial DNA and secondary bile acids stimulate cellular proliferation. While 16S rRNA sequencing and shotgun metagenomics are established detection strategies, innovative platforms like organoids and gene arrays remain in the exploratory stage. Clinical data indicates that F. nucleatum aligns with advanced tumor stage, and its combined detection with colibactin-producing E. coli achieves high sensitivity for early-stage screening. Additionally, A. muciniphila levels can anticipate the efficacy of PD-1 blockade immunotherapy. Microbiota-derived tools represent a transformative direction in oncology. Future research must focus on standardizing protocols and validating multi-marker panels to enhance clinical translation.}, }
@article {pmid42279678, year = {2026}, author = {Ali, A and Cui, L}, title = {Metabolomic Characterization of Baby Spinach Phenolics Transformation During Gastrointestinal Digestion and Microbiome-Mediated Metabolism.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/foods15111893}, pmid = {42279678}, issn = {2304-8158}, abstract = {Gastrointestinal digestion and colonic fermentation determine phenolic transformation and reciprocal microbiome modulation, influencing the generation of gut-derived metabolites associated with epithelial integrity, inflammatory regulation, and metabolic homeostasis. Baby spinach phenolics possess antioxidant and microbiome-modulating potential; however, their functional efficacy is constrained by storage-induced degradation and limited gastrointestinal bioaccessibility. This study investigated phenolic transformation in fresh and stored baby spinach (4 °C and 25 °C) during simulated gastrointestinal digestion and subsequent colonic fermentation. Standardized in vitro digestion revealed limited phenolic bioaccessibility (10-15%), with storage at 25 °C accelerating oxidative degradation and reducing antioxidant capacity. Storage at 25 °C reduced TPC from approximately 465 to 265 µg GAE/g and decreased antioxidant activity by nearly 30%, whereas refrigerated storage (4 °C) better preserved phenolic stability and antioxidant capacity throughout the storage period. LC-MS/MS-based untargeted metabolomics characterized digestion-driven structural remodeling and identified diverse colonic metabolites generated during human fecal fermentation. Despite storage-induced alterations in precursor phenolics, 16S rRNA sequencing demonstrated microbiome relative microbial stability, with fermentation time exerting a stronger influence on community assembly than storage conditions. Microbial metabolism produced shared downstream metabolites, particularly phenylpropionic and flavonoid-derived intermediates. These results suggest that storage modifies phenolic availability during digestion, while gut microbial metabolism sustains the production of functionally relevant metabolites.}, }
@article {pmid42279781, year = {2026}, author = {Yi, X and Deng, W and Gao, K and Ou, X and Tang, K and Zeng, Q and Ni, Y and Liang, X and Wu, Z and Wu, Y and Xie, Y and Chen, H and Yang, A}, title = {Genistein Pretreatment Attenuates Ovalbumin-Induced Food Allergy in Mice with Intestinal Barrier Preservation and Modulation of Gut Microbiota and Metabolites.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/foods15111995}, pmid = {42279781}, issn = {2304-8158}, support = {No. 20225BCJ22022//Funding for Academic and Technical Leaders in Major Disciplines, Jiangxi Province, China/ ; No. 32260595//National Natural Science Foundation of China/ ; }, abstract = {Food allergy (FA) is an increasing public health concern, highlighting the urgent need for safe, bioactive-based preventive strategies. This study evaluated genistein, a plant-derived isoflavone, in an ovalbumin (OVA)-induced murine FA model. Genistein was administered before sensitization and throughout allergy induction. Clinical symptoms, rectal temperature, diarrhea, OVA-specific antibodies, mast cell responses, intestinal barrier markers, gut microbiota, short-chain fatty acids (SCFAs), and fecal metabolites were assessed using immunological, histological, microbiome, and metabolomic analyses. Genistein pretreatment prevented OVA-induced clinical symptom scores, rectal temperature decline, diarrhea occurrence, OVA-specific antibody responses, and mast cell responses. These changes were accompanied by preservation of jejunal tight junction-related markers and modulation of T-cell-associated immune responses. In vitro, genistein modulated antigen uptake, maturation-associated features of bone marrow-derived dendritic cells (BMDCs), and BMDC-driven CD4[+] T-cell polarization. In parallel, genistein-pretreated mice showed altered gut microbial structure, higher relative abundances of selected SCFA-associated taxa, increased fecal butyrate, and fecal metabolomic alterations involving purine metabolism, bile-acid-related metabolism, and tryptophan-related microbial metabolites. Consistently, correlation analyses indicated associations among microbial taxa, metabolites, immune indicators, and intestinal barrier markers. Together, these findings provide preliminary mechanistic insight into genistein in experimental FA and support further investigation of genistein as a dietary bioactive candidate for FA prevention.}, }
@article {pmid42279791, year = {2026}, author = {Jiang, S and Sun, H and Zhang, C and Zhang, Y}, title = {Deep Learning and Microbiome Analysis Reveal the Preservation Mechanism of Cinnamomum cassia for Strawberry.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/foods15112005}, pmid = {42279791}, issn = {2304-8158}, support = {52300027//National Natural Science Foundation of China/ ; KM202310011004//Beijing Municipal Education Commission/ ; }, abstract = {Strawberry preservation remains a critical challenge due to rapid postharvest microbial spoilage. This study investigated the preservative efficacy of Cinnamomum cassia and Punica granatum peel aqueous extracts, prepared via spray drying, on strawberries over 5 days of storage, with a specific focus on their regulatory impact on the fruit surface microbiome. Preservation tests demonstrated that the C. cassia extract was more effective in reducing visible mold development. High-throughput sequencing revealed that the C. cassia treatment reshaped microbial community structures, decreasing the relative abundance of spoilage-associated bacteria and the primary pathogenic fungus Botrytis (94.37%), while enriching potentially beneficial or antagonistic genera such as Sphingobium (28.72%), Sphingomonas (9.52%), and Cladosporium (0.62%). Using a probability threshold of 0.7, 121 compounds were identified as potential active candidates from a library of 675 C. cassia constituents. These compounds predominantly have a molecular weight between 100 and 250 and are characterized by prevalent functional groups including alkene (49.60%), hydroxyl (38.80%), and benzene rings (36.40%). In vitro antibacterial assays confirmed the inhibitory activity of vanillin and its isomers, validating the reliability of the computational predictions. These findings suggest that the preservative mechanism of C. cassia is likely mediated by the collective action of a multi-component matrix that modulates the microecological balance on the fruit surface, rather than the isolated effect of a single compound. This integrated approach provides an effective framework for developing plant-derived preservation strategies by combining microbiome dynamics with machine learning.}, }
@article {pmid42279801, year = {2026}, author = {Guo, W and Li, Y and Han, J and Liu, X and Ni, L}, title = {Integrated Microbiome and Metabolomics Analysis Reveals That Ganoderma lucidum Triterpenoids Ameliorate Colitis Associated with the Modulation of the Gut Microbiota and Metabolic Profiles.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/foods15112016}, pmid = {42279801}, issn = {2304-8158}, support = {XRC-25053//Research Project of Fuzhou University/ ; 2025M772970//China Postdoctoral Science Foundation under Grant/ ; }, abstract = {Colitis is a global health challenge that severely impairs quality of life, necessitating effective dietary interventions. This study investigated the protective effects of Ganoderma lucidum triterpenoids (GLTs) on pathological symptoms, inflammatory responses, and gut microbiota dysbiosis in a dextran sulfate sodium (DSS)-induced murine model. Our results demonstrated that GLT intervention significantly attenuated the disease activity index (DAI), prevented colon shortening, and fortified gut barrier integrity through upregulating the transcription of tight junction proteins. GLT inhibited the secretion of pro-inflammatory cytokines (TNF-α, IL-1β, and IL-6) and bolstered antioxidant defenses (CAT) by controlling the TLR4/NF-κB pathway and upregulating the Nrf2 pathway. Furthermore, 16S rRNA sequencing and non-targeted metabolomics revealed that GLT reshaped the gut microbial landscape (enriching Enterorhabdus and Lachnospiraceae NK4A136 group) and reconfigured amino acid metabolism to restore colonic homeostasis. Collectively, these findings highlight the potential of GLT as a functional food ingredient to prevent colitis, potentially linked to the modulation of the microbiota-metabolite-immune interplay, offering a novel nutritional strategy for inflammatory bowel disease management.}, }
@article {pmid42279810, year = {2026}, author = {Alhaj, OA and Elsahoryi, NA and Jahrami, HA}, title = {Dairy Bioactive Compounds as Precision Modulators of Gut Microbiota: From Molecular Mechanisms to Personalized Immunometabolic Health.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/foods15112024}, pmid = {42279810}, issn = {2304-8158}, abstract = {The gut microbiota (GM) has become a key mediator of host health, with dietary manipulations promising ways of modulating the microbiome. This review focuses on the role of dairy bioactive (DB) compounds as precision modulators of intestinal microecology, including the whey proteins (WPs), including lactoferrin (LF), α-lactalbumin (LA), β-lactoglobulin, lysozyme (LZ), lactoperoxidase, glycomacropeptide (GMP), milk oligosaccharides (MOs), and bioactive peptides (BPs). This review compiles the existing evidence illustrating their dual-action mechanism through direct prebiotic activity and the promotion of beneficial taxa (Bifidobacterium, Lactobacillus, Faecalibacterium), along with selective antimicrobial activity and pathogen suppression. These compounds improve intestinal barrier integrity through tight junction (TJ) protein regulation, regulating short-chain fatty acid production, and modulating immune signaling pathways. Clinical evidence shows significant benefits in metabolism and inflammation among various populations. However, individual responses vary according to host factors such as enterotypes, FUT2 genotype, and baseline microbiota composition, suggesting the need for personalized intervention strategies. This review addresses critical knowledge gaps in dose-response relationships, long-term efficacy, and mechanistic pathways and suggests future directions for precision nutrition. By modifying molecular mechanisms in clinical applications, we have identified DB compounds as promising candidates for targeted modulation of the microbiota to optimize health and disease management. The review also brings together molecular mechanistic and clinically implementable, personalized dietary strategies, which have not been fully captured by previous reviews. It pinpoints gaps in knowledge related to dose-response characterization, long-term trial design, and multi-omics stratification that collectively define a new precision nutrition framework. In this approach, dairy-based intervention is planned for each person based on their microbial, genetic, and metabolic characteristics.}, }
@article {pmid42280315, year = {2026}, author = {Jia, L and Lu, H and Jiang, C and Hu, W and Yu, G and Xiang, X and Shen, G and Tao, J and Chen, L and Miao, W}, title = {Torreya grandis Diester Oil Attenuates High-Fat Diet-Induced Pulmonary Inflammation with Superior Efficacy to Natural Torreya grandis Oil.}, journal = {Nutrients}, volume = {18}, number = {11}, pages = {}, doi = {10.3390/nu18111671}, pmid = {42280315}, issn = {2072-6643}, support = {2026C02A1023//Department of Science and Technology of Zhejiang Province/ ; }, mesh = {Animals ; *Diet, High-Fat/adverse effects ; *Plant Oils/pharmacology ; Oxidative Stress/drug effects ; Male ; Mice ; Lung/drug effects/metabolism/microbiology ; *Pneumonia/etiology/drug therapy/prevention &amp; control/metabolism ; NF-kappa B/metabolism ; Mice, Inbred C57BL ; Cytokines/metabolism ; Seeds/chemistry ; PPAR gamma/metabolism ; Signal Transduction/drug effects ; Nitric Oxide/metabolism ; }, abstract = {BACKGROUND/OBJECTIVES: A high-fat diet (HFD) not only induces metabolic disorders but also causes oxidative damage to the lung tissue, triggering inflammatory responses. However, the detailed mechanisms by which HFD induces pulmonary oxidative stress and inflammation, particularly involving NF-κB/PPAR-γ signaling and lung microbiota, remain poorly understood, and effective dietary intervention strategies are still lacking. This study investigated the effects of HFD on lung tissue injury in mice and systematically evaluated the protective effects and potential mechanisms of Torreya grandis seed oil (TGO) and Torreya grandis seed diester oil (TGO-DG).<br><br>METHODS: After 12 weeks of HFD feeding, HFD group mice exhibited a marked increase in body weight (90.36%) compared with the control group, whereas body weight gain was significantly attenuated in the TGO (57.95%) and TGO-DG (55.78%) groups.<br><br>RESULTS: Biochemical analyses revealed that the levels of malondialdehyde (MDA), nitric oxide (NO), and pro-inflammatory cytokines (TNF-&#x3b1;, IL-6, IL-1&#x3b2;) were significantly elevated in the HFD group, indicating pronounced oxidative stress and inflammatory responses in lung tissue. These symptoms were significantly attenuated by TGO and TGO-DG, with TGO-DG showing a more marked effect. Western blot (WB) results showed that both TGO and TGO-DG suppressed IL-6 expression and altered the expression of proteins in the NF-&#x3ba;B and PPAR-&#x3b3; signaling pathways, which may contribute to the alleviation of pulmonary inflammation. Lung microbiota analysis revealed that TGO was associated with an increased proportion of Lactobacillus species, which correlated with the restoration of pulmonary microbial homeostasis.<br><br>CONCLUSIONS: Overall, these results suggest that TGO and TGO-DG effectively alleviate HFD-induced oxidative stress and inflammation in lung tissue through regulation of inflammatory signaling pathways and lung microbiota composition. Notably, TGO-DG exhibited superior protective effects, highlighting its potential as a lipid ingredient.}, }
@article {pmid42034994, year = {2026}, author = {Chen, Y and Bao, R and Jin, W and Yin, X and Qin, L and Pan, J and Yao, Y and Shen, J and Fang, T and Ma, Y and Zhou, C and Miao, Q and Hu, B}, title = {Metagenomic and genomic characterization of extrapulmonary Mycobacterium abscessus infections: a comparative cohort study.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {}, pmid = {42034994}, issn = {1471-2334}, support = {SHDC22024315//Shanghai Shen Kang Hospital Development Center/ ; }, abstract = {INTRODUCTION: The incidence of Mycobacterium abscessus complex (MABC) infections is rising, becoming a major pathogen of nontuberculous mycobacteria responsible for pulmonary disease (PD) and extrapulmonary disease (ED). However, studies on the clinical characteristics of MABC-ED remain limited.<br><br>METHODS: A 7-year retrospective analysis was conducted on MABC-ED cases at Zhongshan Hospital in Shanghai, China. We analyzed predisposing factors, clinical features, metagenomic sequencing (MS) results, drug susceptibility testing (DST), and genomic characteristics of MABC-ED patients, comparing the data with those of PD cases.<br><br>RESULTS: Among 17 MABC-ED patients, 15 had predisposing risk factors and underlying conditions, with 2 of 3 patients with rheumatic disease showing poor prognosis. The diagnostic performance of metagenomic sequencing for MABC-ED was comparable to that for MABC-PD. However, MABC-ED samples exhibited distinct microbiome features and a more diverse mycobacterial community structure compared to PD. Resistance rates among extrapulmonary MABC isolates were observed as follows: 0% (amikacin), 20% (macrolides), 30% (linezolid), and 40% (cefoxitin). One case showed paradoxical results between erm (41) T28 sequevar and susceptibility phenotype. Genomic analysis revealed no specific dominant circulating clones (DCC) for MABC-ED isolates.<br><br>CONCLUSION: MABC-ED patients commonly present with risk factors and underlying diseases. Metagenomic sequencing diagnosis of MABC-ED poses challenges, and DST and whole genome sequencing data indicate diversity among MABC-ED isolates. Our study provides detailed data on MABC-ED, contributing to a better understanding of its disease characteristics.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-026-13117-9.}, }
@article {pmid42046020, year = {2026}, author = {Zhou, Q and Huang, P and Zhou, R and Zeng, F and Jiang, J and Zhao, B and Zhao, B and Xu, H and Wei, W and Li, X}, title = {Multi-omics profiling of gut microbiota and host transcriptome identifies diagnostic signatures and mechanistic links in moyamoya disease.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42046020}, issn = {1471-2180}, support = {82171517; 82271556//National Natural Science Foundation of China/ ; ZNJC202245//Translational Medicine and Interdisciplinary Research Joint Fund of Zhongnan Hospital of Wuhan University/ ; PDJH202201//Climbing Project for Medical Talent of Zhongnan Hospital, Wuhan University/ ; }, abstract = {BACKGROUND: Moyamoya disease (MMD) features progressive intracranial artery stenosis and collateralization. Growing evidence implicates a dysregulated gut–brain axis in cerebrovascular pathology. We aimed to identify MMD-associated gut microbes and delineate the molecular mechanisms linking intestinal signals to vascular inflammation in MMD.<br><br>RESULTS: We profiled fecal microbiota using full-length 16S rRNA sequencing from 24 MMD patients and 20 matched controls, prioritizing taxa with LEfSe, LASSO, and random forest algorithms. A species-level diagnostic model showed robust discrimination in our cohort (ROC AUC&#x2009;=&#x2009;0.9146), and DCA supported its clinical utility. To connect gut signals to host vascular responses, we integrated peripheral and vascular transcriptomes from GEO and a cross-disease cerebrovascular cohort. Differential expression, WGCNA, and LASSO analyses identified key MMD genes and their immune modules. We then intersected these with microbiome-derived, gut-related genes to nominate candidate mediators of gut&#x2013;immune&#x2013;vessel crosstalk. This multi-omics pipeline identified Fusobacterium nucleatum, Lachnoanaerobaculum cf. saburreum C27KA, and NK4A214_group as MMD-specific microbial markers. Crucially, these markers were associated with immune infiltration signatures and inflammatory pathway activation in diseased vessels. Further integration pinpointed QRFPR and HCAR2 as key mediators of gut-derived cerebrovascular inflammation, suggesting a potential microbiota&#x2013;immune&#x2013;vascular pathway along the gut&#x2013;brain axis.<br><br>CONCLUSION: We characterized an MMD-associated microbiota profile and proposed QRFPR and HCAR2 as candidate genes linking intestinal microbes to vascular immune activation. By mapping the gut&#x2013;brain axis from microbial taxa to host receptors and vessel-wall transcriptional programs, this study uncovers potential disease mechanisms and highlights new avenues for microbiome-informed biomarkers and therapeutic targeting in MMD.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-05084-7.}, }
@article {pmid42269619, year = {2026}, author = {Guo, Y and Wang, Z and Li, D and Wang, L and Lan, H and Guo, F and Zhao, Z and Liu, Z and Meng, L and Shen, X and Wang, M and Zhao, W and Zhang, W and Kong, C and Shi, L and Sun, Y and Seim, I and Jiang, A and Ma, K and Su, Z and Zhang, N and Ji, Q and Chen, J and Chen, K and Qi, C and Li, B and He, B and Liu, Y and Zhou, J and Zheng, Y and Zhang, H and Wang, Y and Han, M and Yang, T and Tong, J and Zhang, Y and Wang, Z and Xu, X and Chen, J and Liu, Y and Chen, H and Zeng, T and Wei, X and Li, C and Yang, H and Wang, B and Liu, X and Shao, C and Zhang, W and Gu, Y and Xiao, X and Xu, X and Wang, J and Mock, T and Fan, G and Li, Y and Liu, S and Dong, Y}, title = {The genetic repertoire of deep-sea microbiome: From sequence to structure and function.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.05.009}, pmid = {42269619}, issn = {1934-6069}, abstract = {The deep sea, as the largest and maybe most hostile environment on Earth, is still underexplored, especially regarding its genetic repertoire. Yet, previous work has revealed significant habitat-specific deep-sea biodiversity. Here, we present an integrated deep-sea microbial genetic dataset comprising 502 million nonredundant genes from 2,138 samples and 2.4 million predicted structures and use it to link specific protein structures with genetic variants associated with life in the deep sea and to assess their biotechnology potential. Combining global sequence analysis with biophysical and biochemical measurements revealed unprecedented sequence diversity and substantial structural conservation of proteins. Especially, proteins involved in replication, recombination, and repair were identified as being under rapid evolution and with specialized properties. Among these, a structurally divergent helicase exhibited advantages in controlling nanopore sequencing speed. Thus, our work positions the deep sea as an evolutionary engine that generates and hosts genetic diversity and bridges genetic knowledge with biotechnology.}, }
@article {pmid42269666, year = {2026}, author = {Dewey, CW and Rojas, CA and Pomeroy, C and Gerardi, J and Ganz, HH}, title = {Fecal microbiota transplantation shows promise in slowing or reducing cognitive impairment in aging dogs.}, journal = {Journal of the American Veterinary Medical Association}, volume = {}, number = {}, pages = {1-6}, doi = {10.2460/javma.26.03.0231}, pmid = {42269666}, issn = {1943-569X}, abstract = {OBJECTIVE: To investigate potential effects of fecal microbiota transplantation (FMT) on cognitive scores and bacterial microbiota composition in dogs with suspected canine cognitive dysfunction (CCD).<br><br>METHODS: The study was conducted from September 19, 2024, to September 11, 2025. Dogs with presumptive CCD were given oral FMT capsules daily for 90 days. Each dog received 1 FMT capsule every 12 hours. Fecal samples and cognitive (disorientation, impaired social interactions, sleep disturbance, house soiling, learning and memory loss, activity changes, and anxiety and fear [DISHAA]) assessments were completed at baseline and on days 30, 60, and 90. Fecal samples were submitted for 16S rRNA gene sequencing.<br><br>RESULTS: 11 dogs were enrolled; 10 dogs had no adverse events from FMT treatment, and 1 dog developed gastrointestinal signs and was removed from the study. All 10 remaining dogs had complete microbiome data; however, owners of 4 dogs did not report final (90-day) DISHAA scores. Of the 6 dogs with complete data, cognition improved in 4 (mean, -8.25 points) but worsened in 2 (mean, +7 points) according to owner-reported DISHAA scores. Microbiome richness and diversity increased in 4 of the 6 dogs. Several dogs also showed positive modulation of microbiome composition including reductions in Streptococcus spp and increases in Peptacetobacter hiranonis, Prevotella copri, and Bacteroides spp.<br><br>CONCLUSIONS: These findings provided preliminary evidence that FMT may help improve cognitive function in dogs with CCD. However, the study sample size was small and ideal FMT dosing level and treatment duration remain undefined. A larger study with longer follow-up is warranted, based on our results.<br><br>CLINICAL RELEVANCE: FMT showed promise in slowing or reducing cognitive impairment in aging dogs and may be considered as adjunct therapy in these cases.}, }
@article {pmid42269934, year = {2026}, author = {Zhao, Y and Wang, X and Ma, Q and Liu, E and Zhang, D and Liu, H and Cai, L and Wang, J and Feng, T and Schroyen, M and Chen, M}, title = {Persistent Benefits of Early Gestational Chenodeoxycholic Acid Supplementation on Late Pregnancy in Sows via Sustained Modulation of the Gut-Metabolism Axis.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {101664}, doi = {10.1016/j.tjnut.2026.101664}, pmid = {42269934}, issn = {1541-6100}, abstract = {BACKGROUND: Our previous studies in pigs have identified chenodeoxycholic acid (CDCA) as a potent metabolic regulator during early gestation, capable of enhancing embryo implantation by optimizing maternal metabolic status and gut microbiota-host interactions, while the long-term impacts of early gestational CDCA on late pregnancy remain largely unexplored.<br><br>OBJECTIVE: This study investigated whether supplementation with CDCA during early gestation (gestational day 0-28) exerts a sustained metabolic modulation effect on maternal health and reproductive outcomes in late gestation in a sow model.<br><br>METHODS: Multiparous sows (n = 24) were randomly assigned to receive either a control diet or a diet supplemented with 0.15% CDCA during early gestation. The reproductive performance, oxidative stress, inflammatory status, gut microbiome, and serum metabolome in late gestation were subsequently evaluated.<br><br>RESULTS: Results showed that early CDCA intervention significantly increased the total and live litter sizes (P < 0.05). Furthermore, CDCA treatment alleviated maternal oxidative stress and systemic inflammation, and improved insulin sensitivity in late gestation (P < 0.05). Untargeted metabolomics revealed a distinct metabolic remodeling, characterized by the enrichment of beneficial metabolites, such as L-ornithine, and the depletion of proinflammatory and oxidative markers, including 1-palmitoylphosphatidylcholine, 2-lysophosphatidylcholine, 3-hydroxyanthranilic acid, and N-carboxymethyllysine. 16S rRNA sequencing indicated that CDCA exerted a targeted modulation rather than a global reconstruction of the gut microbiota. Specifically, CDCA suppressed potential harmful bacteria, including NK4A214_group, Clostridium_sensu_stricto_1, and Turicibacter, while enriching beneficial genera like Subdoligranulum. Multi-omics integration identified NK4A214_group as a key driver associated with exacerbated inflammatory status and unfavorable metabolic profiles.<br><br>CONCLUSIONS: Collectively, these findings demonstrate that early-gestational CDCA supplementation elicits a long-term protective effect on maternal metabolism via optimizing specific gut microbe-metabolite interactions, thereby ensuring optimal gestational outcomes.}, }
@article {pmid42270015, year = {2026}, author = {Wang, S and Liu, Z and Jiang, C and Wei, Y and Liu, G and Pan, Y}, title = {The intratumoral microbiota: Orchestrating metabolic-immune crosstalk and shaping the therapeutic landscape in cancer.}, journal = {Biochimica et biophysica acta. Molecular basis of disease}, volume = {}, number = {}, pages = {168316}, doi = {10.1016/j.bbadis.2026.168316}, pmid = {42270015}, issn = {1879-260X}, abstract = {The intratumoral microbiota is now recognized as a key component of the tumor microenvironment, where it influences tumor metabolism, shapes immune activity, and modulates treatment responses. Microbial metabolites such as short-chain fatty acids regulate pathways that control energy use in cancer cells and modify immune signaling within tumors. Microbial imbalance disrupts metabolic homeostasis and promotes immune escape, contributing to cancer progression and resistance to therapy. Specific taxa including Fusobacterium nucleatum drive distinct protumorigenic effects through metabolic and immunologic routes. Spatial heterogeneity of microbial colonization further defines metabolic gradients and immune niches that influence treatment efficacy. Advances in sequencing, multi-omics, and spatial profiling have clarified these interactions and identified microbial signatures with diagnostic and prognostic potential. Therapeutic strategies such as precision probiotics, engineered bacteria, and nanotechnology-based delivery systems offer avenues to target microbial metabolic pathways and enhance treatment response. Continued integration of microbiology, oncology, and bioinformatics will support translation of these findings into personalized cancer therapies.}, }
@article {pmid42270094, year = {2026}, author = {Deng, L and Gao, X and Guo, C and Hu, X and Qi, J and Wang, J and Huang, X and Zhang, Y and Hu, Z and Wang, H and Hong, B}, title = {Structural and Functional Alterations of Microbiome in Upper and Lower Respiratory Tract in Patients With NSCLC.}, journal = {Cancer control : journal of the Moffitt Cancer Center}, volume = {33}, number = {}, pages = {10732748261460118}, pmid = {42270094}, issn = {1526-2359}, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/microbiology/pathology ; *Microbiota ; *Lung Neoplasms/microbiology/pathology ; Bronchoalveolar Lavage Fluid/microbiology ; Female ; Case-Control Studies ; Male ; Sputum/microbiology ; Prospective Studies ; Middle Aged ; *Respiratory System/microbiology ; Bacteria/isolation &amp; purification/genetics ; Aged ; Fungi/isolation &amp; purification ; }, abstract = {IntroductionThe airway microbiome plays a pivotal role in lung cancer development, but the microbiome characteristics in upper and lower respiratory tract of non-small cell lung cancer (NSCLC) patients remains unclear.MethodsThis was a prospective case-control study. The study included 60 samples from NSCLC patients and non-cancer controls: 23 sputum (SP) samples (14 NSCLC, 9 controls) and 37 bronchoalveolar lavage fluid (BALF) samples (21 NSCLC, 16 controls). Metagenomic sequencing was performed to characterize microbial composition and diversity, differential taxa, inter-kingdom networks, and functional profiles for bacteria and fungi.ResultsFor bacterial community, BALF samples from NSCLC tend to show higher alpha diversity than that of non-cancer controls (Shannon p = 0.046, Simpson p = 0.089), whereas SP samples from NSCLC show a trend toward lower alpha diversity (Shannon p = 0.053, Simpson p = 0.033). For fungal community, alpha diversity shows no significant difference between NSCLC and non-cancer groups in either SP (Shannon p = 0.250, Simpson p = 0.480) or BALF (Shannon p = 0.800, Simpson p = 0.700) samples. Beta diversity exhibits differences in bacterial community composition between NSCLC and non-cancer controls in both SP (p = 0.018) and BALF samples (p = 0.015), while fungal communities appear relatively stable (p = 0.611 for SP; p = 0.611 for BALF). LEfSe and Random Forest analyses identify bacterium Porphyromonas SGB2015 and fungus Psilocybe cubensis significantly enriched in BALF samples from NSCLC, whereas no species is enriched in SP samples. Cross-kingdom network indicates increased complexity and connectivity in NSCLC-associated microbial communities. Functional analysis shows the enrichment of biosynthetic pathways in SP samples and metabolic pathways in BALF samples from NSCLC.ConclusionThese findings suggest that NSCLC may be associated with compositional, structural, and functional alterations of the airway microbiome, with potentially distinct patterns between upper and lower respiratory tract.}, }
@article {pmid42270217, year = {2026}, author = {An, X and Cao, Y and Zhang, Y and Zhuo, Y and Li, X and Qiu, B and Segal, E and Achmon, Y}, title = {Elucidating the effect of surface disinfection methods on strawberry microbiome composition and volatile organic compounds.}, journal = {Food research international (Ottawa, Ont.)}, volume = {239}, number = {}, pages = {119482}, doi = {10.1016/j.foodres.2026.119482}, pmid = {42270217}, issn = {1873-7145}, mesh = {*Fragaria/microbiology ; *Volatile Organic Compounds/analysis ; *Disinfection/methods ; *Microbiota/drug effects ; *Food Microbiology/methods ; *Fruit/microbiology ; Temperature ; Fungi ; Ultraviolet Rays ; }, abstract = {Strawberries are highly perishable, with a shelf life of only a few days at room temperature. It is mostly ascribed to their susceptibility to spoilage, leading to significant postharvest losses. This study employed a unique system to examine the spoilage of strawberries through the combined perspectives of volatilomics and microbiome analysis. Three surface disinfection techniques: UV irradiation, washing with NaClO and ethanol, or with tea waste extract, were compared to untreated samples at temperatures of 4 °C, 10 °C, and 25 °C, respectively. The results indicate that certain volatile organic compounds (VOCs) were affected by the surface disinfection methods and could be correlated with the spoilage severity over time. For each experimental condition, five putative compounds were tentatively identified as key VOCs by statistical analysis, supporting the feasibility of establishing a multidimensional VOC fingerprint matrix for strawberry spoilage monitoring. The fungal microbiota's succession was strongly influenced by temperature, with key spoilage genera like Penicillium, Alternaria, and Cladosporium identified by sequencing, revealing temperature-modulated microbial dynamics. Relationships between identified potential indicators and spoilage microorganisms were elucidated by correlation analysis. The results suggested surface treatments may affect the occurrence of microbial communities, highlighting the complexity of microbial-chemical dynamics during spoilage processes, where VOC profiles appear to function both as metabolic fingerprints and ecological regulators within the spoilage microbiome. These findings provide new insights into the largely unknown metabolic processes involved in strawberry spoilage, offering new opportunities for more effective prevention strategies to reduce spoilage and waste.}, }
@article {pmid42270218, year = {2026}, author = {Li, F and Wang, S and Chen, B and He, M and Zhou, J and Duan, G and Zhu, Y and Liu, W and Tu, H}, title = {The phyllosphere as a potential microbial habitat sharing taxa with the Jiang-flavor Baijiu fermentation system: A preliminary study.}, journal = {Food research international (Ottawa, Ont.)}, volume = {239}, number = {}, pages = {119488}, doi = {10.1016/j.foodres.2026.119488}, pmid = {42270218}, issn = {1873-7145}, mesh = {*Fermentation ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; *Microbiota ; *Food Microbiology ; Biodiversity ; *Plant Leaves/microbiology ; Edible Grain/microbiology ; }, abstract = {Open spontaneous fermentation, a hallmark of many traditional food systems globally, relies heavily on the surrounding environment for microbial assembly. However, the role of the phyllosphere as a potential microbial habitat within the green spaces adjacent to fermentation facilities remains poorly understood. In this preliminary study, we characterized the epiphytic microbial communities of 11 dominant plant species in the vicinity of a traditional Jiang-flavor Baijiu facility. We identified a rich biodiversity comprising 5495 bacterial and 1678 fungal amplicon sequence variants (ASVs). The phyllosphere exhibited significantly higher bacterial alpha-diversity than fermented grains (Jiupei), positioning it as a highly diverse microbial habitat within the external environment. Notably, we observed extensive taxonomic sharing: 100% of the abundant and always moderate bacterial and fungal ASVs detected in Jiupei were also present on plant surfaces. Furthermore, 70.71% of conditionally rare bacterial ASVs and 68.94% of conditionally rare fungal ASVs from Jiupei were shared with the phyllosphere. These findings demonstrate that multiple microbial taxa co-occur in the phyllosphere and the fermentation system, indicating significant taxonomic sharing across the facility environment. While this exploratory survey does not establish direct microbial transfer, it highlights the phyllosphere as a potential microbial habitat that mirrors the taxonomic composition of the fermentation ecosystem, thereby informing the micro-environmental management of open fermentation systems globally.}, }
@article {pmid42270336, year = {2026}, author = {Ito, T}, title = {Professional Dyeing Work Enriches Dye-decolorizing Bacteria in the Fingertip Microbiome.}, journal = {Microbes and environments}, volume = {41}, number = {2}, pages = {}, doi = {10.1264/jsme2.ME26026}, pmid = {42270336}, issn = {1347-4405}, mesh = {*Bacteria/metabolism/classification/isolation &amp; purification/genetics ; *Coloring Agents/metabolism ; Humans ; *Microbiota ; *Fingers/microbiology ; *Occupational Exposure/analysis ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Biodegradation, Environmental ; DNA, Bacterial/genetics ; }, abstract = {Individuals who regularly handle specific chemicals may harbor microorganisms capable of metabolizing those compounds. Such hands may therefore provide a practical route for obtaining functional microorganisms from easily accessible human-associated environments. In this study, we found that nearly 90% of professional dyers harbored dye-decolorizing bacteria, which were efficiently isolated from their fingertips, with 20% of isolates exhibiting decolorizing activity. These strains showed distinct genus-level profiles. These findings indicate that occupational exposure to dyes strongly enriches dye-decolorizing bacteria, suggesting that the hands of textile workers may serve as a source for isolating microorganisms with potential applications in dye bioremediation.}, }
@article {pmid42270509, year = {2026}, author = {Samuel, TM and Samuel, SM and Varghese, E and Sreenesh, B and Büsselberg, D}, title = {Defying inflammation-driven early-onset colorectal cancer: predict, prevent, and personalize.}, journal = {Trends in cancer}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.trecan.2026.05.005}, pmid = {42270509}, issn = {2405-8025}, abstract = {Early-life exposure to both modifiable and nonmodifiable risk factors may induce chronic low-grade inflammation (CLGI), a silent threat potentially driving the rising incidence of early-onset colorectal cancer (EOCRC). Notably, CLGI could promote EOCRC by altering the proinflammatory and immune microenvironment that supports tumor growth and cancer development. In this review, we examine how risk factors disrupt immune homeostasis and contribute to CLGI in young individuals, thereby promoting the development of EOCRC. Additionally, identifying CLGI-specific biomarkers could aid in early detection and diagnosis, while targeting specific molecular pathways may enable personalized therapeutic interventions for EOCRC by reducing the chronic inflammatory threat. We also highlight the importance of lifestyle changes and interventions to reduce CLGI and address the growing health concern of EOCRC.}, }
@article {pmid42270548, year = {2026}, author = {Carlson, N and Jurmu, JD and Dearing, MD}, title = {Gut microbes compensate for protein-deficient diets.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2026.05.013}, pmid = {42270548}, issn = {1878-4380}, abstract = {By coupling natural variation in carbon stable isotope signatures with amino acid-specific analysis, Mertz et al. demonstrate the substantive contribution of the gut microbiome in improving diet quality through the production of essential amino acids that are absorbed by the host (deer mouse) and incorporated into muscle tissue.}, }
@article {pmid42270571, year = {2026}, author = {Tang, X and Shen, Z and Li, B and Yuan, J}, title = {A pilot study investigating the bacterial and fungal community shifts in facial skin in rosacea.}, journal = {The Journal of international medical research}, volume = {54}, number = {6}, pages = {3000605261454625}, pmid = {42270571}, issn = {1473-2300}, mesh = {Humans ; *Rosacea/microbiology/pathology ; Skin Microbiome ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; Female ; *Skin/microbiology ; Prospective Studies ; *Face/microbiology ; Middle Aged ; *Fungi/genetics/isolation &amp; purification/classification ; Male ; Adult ; Case-Control Studies ; Microbiota ; }, abstract = {ObjectiveThis study aimed to characterize the bacterial and fungal communities in the facial skin of patients with rosacea versus healthy controls and assess their association with skin oil content.MethodsIn this prospective observational study, facial skin samples from eight individuals (six patients with rosacea and two healthy controls) across three skin oil types were analyzed using 16S rRNA and internal transcribed spacer sequencing. Analyses included alpha/beta diversity, compositional profiling, and cross-kingdom correlations.ResultsPatients with rosacea exhibited higher bacterial diversity (Shannon index: 2.26 ± 1.12) than controls (0.71 ± 0.07). Fungal communities underwent extreme restructuring with near-complete species replacement between individuals (Bray-Curtis ∼1.0). Skin oil content was a key determinant of microbial diversity. Cross-kingdom bacteria-fungi correlations were weak and nonsignificant.ConclusionsRosacea is associated with distinctive cross-kingdom microbiome alterations, featuring increased bacterial diversity and profound fungal reorganization. These findings challenge prevailing dysbiosis paradigms and highlight the potential for therapeutic strategies targeting both bacterial and fungal elements.}, }
@article {pmid42270638, year = {2026}, author = {Hauptmann, M and Gottschick, C and Muthukumarasamy, U and Klee, B and Strowig, T and Mikolajczyk, R and Schaible, UE}, title = {High early-life gut Bacteroides links to microbiome stability, resilience, and risk for childhood infections.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {42270638}, issn = {2055-5008}, mesh = {Humans ; *Bacteroides/isolation &amp; purification/classification/drug effects/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; Anti-Bacterial Agents/therapeutic use ; Infant ; Child, Preschool ; Female ; Male ; Longitudinal Studies ; Disease Susceptibility ; Germany ; Biodiversity ; }, abstract = {Early childhood events, up to the age of two, are critical for the development of the microbiome and balanced immunity later in life. We investigated whether susceptibility to infections and microbiome resilience after antibiotic treatment are associated with key taxa in the early childhood microbiota. Therefore, we performed longitudinal microbiota analysis from stool samples of children within the German LoewenKIDS intensified subcohort. According to the exposure to antibiotic treatment, sample groups were defined as never-treated controls, 45-225 days pre-treatment (pre45-225), 0-30 days pre-treatment (pre0-30), 0-30 days post-treatment (post0-30), or >90 days post-treatment and age >540 days (post>90). 1176 stool samples of 162 children were included in our analysis, of which 49 children received antibiotics. Using generalized linear mixed models adjusted for age, we show that high abundance of Bacteroides was associated with receiving antibiotic treatment 45-225 days later, while low Bacteroides abundance before treatment was associated with low alpha diversity and increased beta diversity post treatment. Our data suggest a key role of the genus Bacteroides for the susceptibility to infections requiring antibiotic treatment and for microbiome stability and resilience in early childhood.}, }
@article {pmid42270686, year = {2026}, author = {Lee, S and Lee, H and Kim, JW and Kim, HJ and Lee, KJ}, title = {Quantitative evaluation of microbiome sequencing resolution under varying experimental conditions using defined mock communities.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-53382-x}, pmid = {42270686}, issn = {2045-2322}, abstract = {Objective evaluation of sequencing resolution is crucial for comparing technologies and ensuring reproducibility in microbiome analysis. Specifically, a systematic approach is necessary to quantitatively assess the effect of various platforms and experimental conditions on species-level resolution. Therefore, this study quantitatively evaluated multiple strategies, including 16S V3-V4 (16P), full-length 16S rRNA gene (16F), and whole metagenome shotgun sequencing (WMS), using a commercial DNA-based mock community (MC) and a domestically developed whole-cell MC (Korea MC [KMC]). The WMS strategy included 12 combinations of input DNA concentrations and sequencing output levels. A total of 64 WMS libraries were constructed for KMC samples, and 112 sequencing datasets were analysed. Taxonomic resolution was assessed using an adjusted F1-score integrating detection sensitivity and abundance-level reproducibility. Qualitatively examining the detected species against the expected species across platforms, WMS showed a true positive abundance ratio of over 90%, 16F was observed to have an average of 60%, and 16P was observed to have an average of less than 10%. The combination of 10 ng input and 10 gigabases output consistently yielded the highest species-level resolution. However, reduced performance was observed in some MCs under 1 ng or 100 ng DNA input conditions. Detection sensitivity varied by taxon and condition. Specifically, Streptococcus pneumoniae and Cryptococcus neoformans were detected only under high-input or -output conditions, whereas Escherichia coli exhibited optimal accuracy at intermediate inputs. Acinetobacter species demonstrated reduced resolution as input DNA increased. KMC samples showed species- and format-specific variability in DNA extraction efficiency. This study presents a quantitative evaluation of species-level resolution across sequencing conditions using defined mock communities. The results highlight how sequencing configuration and taxon-specific characteristics can influence detection performance and provide insights for interpreting microbiome sequencing results under different experimental conditions.}, }
@article {pmid42271018, year = {2026}, author = {Mohssen, M and Zayed, AA and Kigerl, KA and Du, J and Smith, GJ and Schwab, JM and Sullivan, MB and Popovich, PG}, title = {Disruption of the spinal cord-gut axis alters microbial dynamics and carbohydrate cross-feeding in the gut.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-10447-x}, pmid = {42271018}, issn = {2399-3642}, support = {890085//Craig H. Neilsen Foundation (Neilsen Foundation)/ ; ABI#2149505//National Science Foundation (NSF)/ ; DBI#2022070//National Science Foundation (NSF)/ ; }, abstract = {Spinal cord-gut communication regulates gut bacteria, yet the underlying mechanisms remain poorly understood. Previous studies relied primarily on gene markers with limited functional analysis or genome-resolved snapshots from small cohorts. Here, we assessed microbiome dynamics via genome-resolved metagenomics on 333 samples from male and female C57BL/6 mice collected before and up to six months after surgical disruption of the spinal cord-gut axis. This resulted in 6,635 microbial draft genomes as a foundation for a new "Mouse B6 Gut Catalog" that significantly expands species and strain representation for this widely used laboratory mouse strain. Sampling revealed that disrupted spinal cord-gut signaling causes persistent, lesion-severity-, sex-, and time-specific shifts in microbial community composition, with consistent depletion of Lactobacillus johnsonii. Feeding purified L. johnsonii to spinal cord-injured mice prevented metabolic defects and systemic inflammation caused by disruption of the spinal cord-gut axis. Analyses using genome-resolved and community-based metabolic profiling indicated altered carbohydrate sharing and utilization of gut microbes, potentially depleting L. johnsonii, providing a genome-inferred mechanism for future hypothesis testing. This study improves murine microbiome catalogs, illustrates how metagenome-informed microbial interventions can provide a mechanistic understanding to improve host health, and underscores the vital role of a healthy spinal cord in regulating gut ecosystem function.}, }
@article {pmid42271159, year = {2026}, author = {Liang, X and Zhang, Y and Xie, W and Xiong, J and Lin, S and Wen, Y and Cao, Y and Yu, S and Wang, K and Deng, J and Zhao, J and Xu, J and Hu, Y and Liu, Y and Feng, Q and Zhong, Y and Gonzalez, FJ and Xie, C}, title = {Dietary fat alters goblet cell function and microbial bile acid metabolism to promote intestinal lipid absorption in mice.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {42271159}, issn = {2058-5276}, support = {92557304//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82530024//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82521004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82570954//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Dietary fat reshapes host-microbiota interactions, yet the upstream events that mediate overnutrition-driven microbiome alterations and metabolic dysfunction remain unclear. Here we compared mouse models of diet-induced and genetic obesity using multi-omics to identify the colonic mucus niche as an early, diet-sensitive driver of metabolic dysfunction. Excessive dietary lipids impaired glutamine metabolism and redox homeostasis in goblet cells, thinning the mucus layer and depleting the mucus-adapted symbiont Akkermansia muciniphila while expanding the bile-acid-transforming bacterium Clostridium scindens. Altered bile acid composition along the enterohepatic axis activates FXR-PLIN2 signalling in the small intestine and increases fat absorption. In parallel, enterocytes upregulate the PPARα-dependent uptake pathway that supports luminal lipid entry. Supplementation with glutamine restored goblet cell function and the gut microbiota-derived bile acid pool, thereby reducing intestinal FXR activation and lipid uptake. These findings reveal that dietary fat impairs colonic goblet cell function and reshapes microbial bile acid metabolism, influencing small-intestinal fat absorption.}, }
@article {pmid42271189, year = {2026}, author = {Ojeh, N and Mohapatra, BR and O'Shea, M and Springer, D and Ward, J and Sallu, M and Paquette, N and Gooding, K and Springer, A and Peter Adams, O}, title = {Phylogenetic Profiling of the Diabetic Foot Ulcer Microbiome of an Afro-Caribbean Population.}, journal = {MicrobiologyOpen}, volume = {15}, number = {3}, pages = {e70329}, pmid = {42271189}, issn = {2045-8827}, support = {//University of the West indies/ ; }, mesh = {Humans ; *Diabetic Foot/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Fungi/classification/genetics/isolation &amp; purification ; *Phylogeny ; Male ; Female ; Middle Aged ; Pilot Projects ; Skin Microbiome ; Barbados ; Diabetes Mellitus, Type 2/complications ; Caribbean People ; Aged ; DNA, Bacterial/genetics/chemistry ; DNA, Ribosomal Spacer/genetics/chemistry ; }, abstract = {Diabetic foot ulcers (DFUs) are associated with high morbidity, amputation rates, and healthcare costs in Barbados. This pilot study compares the microbiome diversity of chronic DFUs and paired normal skin (controls) from biopsies in Afro-Caribbean patients with type 2 diabetes using Illumina amplicon sequencing targeting the 16S ribosomal RNA (rRNA) gene and the internal transcribed spacer 2 (ITS2) region. Both DFUs and controls harbored diverse bacterial and fungal communities, with differences in taxonomic composition and relative abundance profiles. The dominant bacterial genera were Corynebacterium (18.3% in DFUs, 24.3% in controls) and Staphylococcus (14.9% in DFUs, 14.1% in controls). The dominant bacterial species was Corynebacterium striatum (17.3% in DFUs, 23.8% in controls) followed by Pseudomonas aeruginosa in DFUs (8.9%) and Staphylococcus aureus in controls (13.3%). The dominant fungal genera was Densospora (12% in DFUs, 12.6% in controls). The dominant fungal species was Rhodotorula graminis in DFUs (6.18%) and Paracamarosporium leucadendri in controls (3.85%). Candida duobushaemulonii, with intrinsic resistance to antifungal agents, was detected with higher relative abundance in DFUs than in controls (4.44% vs. 2.36%). Fungal Shannon alpha diversity was significantly reduced in DFUs (p = 0.039), while beta diversity did not differ between groups for bacteria (p = 0.982) or fungi (p = 0.975). The differences in taxonomic composition and relative abundance profiles, and co-occurrence of clinically relevant bacterial and fungal taxa, highlight the potential role of polymicrobial communities in DFU chronicity in the Afro-Caribbean cohort studied, and supports future studies to evaluate implications for antimicrobial stewardship.}, }
@article {pmid42271199, year = {2026}, author = {Steinert, RE and Van den Abbeele, P and Schaefer, C and Poppe, J and Vu, LD and Bajic, D}, title = {Carotenoids modulate fermentation of inulin ex vivo in IBS and overweight adult gut microbiota.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05271-6}, pmid = {42271199}, issn = {1471-2180}, abstract = {BACKGROUND: Carotenoids have direct antioxidant and anti-inflammatory health benefits. Owing to their low bioavailability, they also reach the colon, yet their microbiome interactions remain poorly characterized.<br><br>METHODS: We investigated how &#x3b2;-carotene (BC), lutein (LU), lycopene (LY) and zeaxanthin (ZE), at biological relevant doses (between 1 and 60&#xa0;mg/d), impact composition and metabolite production of irritable bowel syndrome (IBS) and overweight (OW) adult gut microbiota using the ex vivo SIFR[&#xae;] fermentation system (systemic intestinal fermentation research). Fresh fecal samples were collected from 12 donors (n&#x2009;=&#x2009;6 per cohort) and incubated for 24&#xa0;h under anaerobic conditions, with carotenoids administered alone or in combination with prebiotic inulin (IN, tested at 2.5&#xa0;g/day).<br><br>RESULTS: We observed phenotype-specific microbiota characteristics for each cohort at baseline. Carotenoids alone had only minor effects but in combination with prebiotic inulin significantly altered community composition (Bray-Curtis dissimilarity, P&#x2009;<&#x2009;0.05) and enhanced short-chain fatty acid (SCFA) production. Most carotenoids increased butyrate production vs. inulin alone with ZE (at 2&#xa0;mg/d) in IBS (+&#x2009;7.6%) and LU (at 60&#xa0;mg/d) in OW (+&#x2009;8.0%) showing the strongest effects (padjusted<0.10). In contrast, LY (at 45&#xa0;mg/d) uniquely increased acetate (+&#x2009;3.5%) and propionate (+&#x2009;8.0%) at the expense of butyrate (-7.5%, padjusted<0.10) when compared vs. inulin only. Changes in SCFA correlated with carotenoid- and cohort-specific shifts in the abundance of Bifidobacterium, Alistipes, Akkermansia, Faecalibacterium and Coprococcus. ZE also enhanced the effect of inulin on the health-related metabolites 3-phenyllactic acid (PLA) and 2-hydroxyisocaproic acid (HICA), particularly IBS subjects (padjusted<0.20).<br><br>CONCLUSIONS: Antioxidant carotenoids may support anaerobic gut microbes including dominant butyrate producers and counteract phenotype-specific dysbiosis, potentially offering novel dietary approaches for IBS and obesity-associated dysbiosis. As these effects were observed when carotenoids were combined with inulin, carotenoids may have greater impacts when consumed as part of a fiber-rich diet, reflecting their natural occurrence in plant-based foods.}, }
@article {pmid42271362, year = {2026}, author = {Zhang, Z and Lu, T and Dong, B and Liu, J and Zhang, Y and Li, S and Liu, H and Li, X and Guan, T and Guo, H and Yan, Q and Lei, Z and Yu, X and Wang, L and Kang, J and Li, L and Zhao, D}, title = {Gut fungal signatures in colorectal cancer and their potential for supporting diagnosis: a multi-cohort metagenomic analysis.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-08403-8}, pmid = {42271362}, issn = {1479-5876}, support = {82370563//National Natural Science Foundation of China/ ; 2024RJ018//Outstanding Young Scientific and Technological Talents Project of Dalian/ ; 2023-MSLH-032//Joint Funds of the National Natural Science Foundation of Liaoning Province/ ; }, abstract = {BACKGROUND: Colorectal cancer (CRC) is influenced by host factors and environmental exposures that shape gut microbial ecosystems. Although bacterial and viral alterations in CRC have been widely investigated, the role of gut fungi remains underexplored, partly because of their low biomass and the limited availability of well-curated fungal reference genomes.<br><br>METHODS: We conducted a large-scale metagenomic analysis across 9 publicly available cohorts comprising 1,433 fecal samples to characterize CRC-associated fungal alterations and fungal-bacterial co-abundance patterns. The predictive value of microbial signatures was assessed using LASSO and random forest models, with external validation performed in 6 independent cohorts comprising 272 samples.<br><br>RESULTS: Multi-cohort analysis revealed CRC-associated alterations in gut fungal community structure and selected diversity measures. Differential abundance analysis identified 15 fungal species with recurrent changes across cohorts. Among them, Saccharomyces cerevisiae c86 and Trichophyton rubrum c61 showed predominant enrichment in healthy controls, whereas Barnettozyma c122 and Pseudopithomyces c302 showed predominant enrichment in CRC. Fungal-only models exhibited limited standalone predictive capacity. However, integrating fungal features with bacterial biomarkers modestly improved CRC prediction performance compared with bacterial-only models. In external validation, the random forest-based fungal-bacterial model increased the mean AUC from 0.722 to 0.762, with improved AUCs in 5 of the 6 validation cohorts.<br><br>CONCLUSIONS: This study suggests that CRC is associated with gut fungal dysbiosis and supports the exploratory value of gut fungal signatures as adjunctive features in microbiome-based CRC prediction models. These findings highlight the importance of incorporating fungal communities into CRC microbiome research while emphasizing the need for prospective and mechanistic validation.}, }
@article {pmid42271469, year = {2026}, author = {Xing, J and Jiang, Z and Jing, X and Li, Y and Guo, F and Liu, P and Liu, Z and Sun, N}, title = {Analysis of gut microbiota and intestinal mucosal neurotransmitter changes and their correlation in adolescent depression mice.}, journal = {Annals of general psychiatry}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12991-026-00686-x}, pmid = {42271469}, issn = {1744-859X}, abstract = {BACKGROUND: Adolescent depression is a major mental health disorder with increasing prevalence and substantial long-term consequences. Although growing evidence suggests that the gut-brain axis is involved in depression, the relationships among gut microbiota, intestinal mucosal neurotransmitters, and adolescent depression remain insufficiently understood. This knowledge gap limits a better understanding of the pathophysiological mechanisms underlying adolescent depression and the identification of potential microbiota-related targets. Therefore, this study aimed to investigate alterations in gut microbiota and intestinal mucosal neurotransmitters, as well as their correlations, in an adolescent mouse model of depression.<br><br>METHODS: We established an adolescent depression mouse model using chronic unpredictable mild stress (CUMS), and collected data with the Smart video tracking system. We collected intestinal contents and mucosal tissues from mice. We analyzed gut microbial composition using metagenomic sequencing and quantified mucosal neurotransmitters with liquid chromatography-tandem mass spectrometry (LC-MS/MS). We analyzed correlations among gut microbiota, intestinal mucosal neurotransmitters, and behavioral indicators.<br><br>RESULTS: Mice in the CUMS group exhibited a significantly reduced sucrose preference rate in the sucrose preference test (P&#x2009;<&#x2009;0.001); a significantly prolonged immobility time in the forced swim test (P&#x2009;<&#x2009;0.01); and a significantly decreased total movement distance in the open field test (P&#x2009;<&#x2009;0.01). No significant intergroup difference was observed in the tail suspension test. Regarding the gut microbiome, the CUMS group showed significantly lower Simpson index (P&#x2009;=&#x2009;0.018) and Pielou's evenness index (P&#x2009;=&#x2009;0.022). Beta diversity analysis indicated a statistically significant but modest between-group difference in community structure (ANOSIM R&#x2009;=&#x2009;0.145, P&#x2009;=&#x2009;0.03); this finding was supported by PERMANOVA (Bray-Curtis; pseudo-F&#x2009;=&#x2009;1.675, R&#xb2; = 0.0897, P&#x2009;=&#x2009;0.033). LEfSe (Linear discriminant analysis Effect Size) analysis suggested 27 candidate taxa with discriminatory signals between groups (nominal P&#x2009;<&#x2009;0.05; exploratory). Neurotransmitter analysis demonstrated that levels of 5-HIAA (5-hydroxyindoleacetic acid), 5-HT (serotonin), 5-HTP (5-hydroxytryptophan), and Kyn (kynurenine) in the colon were significantly decreased in the CUMS group, whereas levels of PA (phenylethylamine) and NE (norepinephrine) were significantly elevated (P&#x2009;<&#x2009;0.05). Spearman correlation analysis found that Lactobacillus and Lactobacillus acidophilus correlated positively with sucrose preference and negatively with immobility in the forced swim test. Lactobacillus acidophilus also showed a positive correlation with 5-HT pathway metabolites: 5-HIAA, 5-HT, 5-HTP, and Kyn.<br><br>CONCLUSION: Adolescent mice exposed to CUMS showed depression-relevant behavioral alterations, shifts in gut microbiota composition, and changes in 5-HT pathway metabolites. Gut microbiota dysbiosis was significantly associated with alterations in 5-HT pathway metabolites. Because this study is correlational, causal relationships require validation in future interventional studies.}, }
@article {pmid42271554, year = {2026}, author = {Pons, A and Aspillaga, E and Catalán, IA and Viver, T and Arlinghaus, R and Martorell-Barceló, M and Barcelo-Serra, M and Alós, J}, title = {Social organization and habitat use shape the gut microbiome of a marine fish.}, journal = {The Journal of animal ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1365-2656.70286}, pmid = {42271554}, issn = {1365-2656}, support = {FPI/2269/2019//FPI Predoctoral Fellowship Direcci&#xf3; General de Innovaci&#xf3; i Recerca of the Balearic Islands Government/ ; PID2019&#x2011;104940GA&#x2011;I00//CLOCKS Project/ ; PID2022-139349OB-I00//METARAOR Project/ ; #033W024A//German Federal Ministry of Education and Research/ ; PD/041/2021//University of the Balearic Islands/ ; }, abstract = {The gut microbiome hosts diverse bacterial communities that significantly influence individual spatial behaviour in animal societies. However, this relationship remains understudied in marine fish due to the challenges associated with measuring behavioural traits in free-living fish and simultaneously obtaining gut microbiome composition data. In this study, we conducted a field experiment to explore the relationship between space and habitat use, social organization, and gut microbiome composition in marine fish. We used a novel high-resolution acoustic telemetry system to collect 7930 one-day-long movement trajectories from 232 individuals of Xyrichtys novacula of the same population (153 females, 79 males) near the coastline of Mallorca, Spain. A subset of these individuals was recaptured to analyse the diversity of core and non-core gut microbiome, quantified using operational phylogenetic units (OPUs) based on 16S rRNA gene amplicons through Illumina sequencing. Individuals closer to Posidonia oceanica seagrass meadow had higher non-core microbiome diversity, especially larger individuals. Multivariate analysis showed no significant differences in microbiome composition across the tested variables (i.e. body size, territory size, degree, strength, distance to the seagrass meadow, and sex), but males showed a visually greater, but non-significant, variability in core microbiome composition. Core microbiome composition was weakly associated with social harem structure. These findings indicate that gut microbiome composition is primarily shaped by local habitat conditions, while social organization may contribute weakly and indirectly, pending further experimental validation.}, }
@article {pmid42271557, year = {2026}, author = {Wassel, MA and Makabe-Kobayashi, Y and Iqbal, MM and Huang, C and Amano, M and Shimizu, A and Mandario, MAE and Takatani, T and Sakakura, Y and Hamasaki, K}, title = {Tetrodotoxin (TTX) reshapes the functional potential of the gut microbiome in juvenile tiger pufferfish (Takifugu rubripes) across salinity gradients.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {42271557}, issn = {2524-4671}, support = {22K05822 and 25K09271//JSPS KAKENHI/ ; No. JURCAOSIRG23-08//Interdisciplinary Collaborative Research Program of the Atmosphere and Ocean Research Institute, The University of Tokyo/ ; }, abstract = {BACKGROUND: The gut microbiota of aquatic organisms responds dynamically to environmental stressors such as salinity fluctuations. However, how microbial communities respond to combined environmental and dietary stressors, and how these interactions influence functional potential, remains incompletely understood. Here, we investigated whether dietary administration of tetrodotoxin (TTX), a neurotoxin naturally accumulated by juvenile tiger pufferfish (Takifugu rubripes), alters gut bacterial community composition and functional potential across salinity gradients.<br><br>RESULTS: Juvenile T. rubripes were reared under four salinity conditions (34.0, 17.0, 8.5, and 2.1 ppt) and fed either a control or TTX-containing diet (1.22 MU/g). Integrated 16S rRNA gene amplicon and shotgun metagenomic analyses revealed that salinity was the primary driver of gut microbiota structure, with only 5.1% of amplicon sequence variants (ASVs) shared across salinity levels. In contrast, TTX ingestion induced salinity-dependent shifts in specific bacterial taxa rather than broad community restructuring. Core taxa, including Arcobacteraceae, Mycoplasma, Brevinema, and Vibrio, were consistently detected across treatments but exhibited pronounced changes in relative abundance and functional potential under salinity and toxin stress. Metagenomic profiling indicated that Arcobacteraceae encode genetic modules for amino acid and B vitamin biosynthesis that are absent or incomplete in the host genome, suggesting metabolic complementarity. TTX ingestion reduced the genetic representation of these biosynthetic pathways at specific salinities, particularly those associated with Arcobacteraceae. Conversely, phenylalanine biosynthesis potential enriched in TTX-fed fish, primarily associated with Vibrio spp., indicating a possible microbial functional adaptation to toxin administration. Despite these microbiome and functional shifts, TTX ingestion did not affect host growth.<br><br>CONCLUSIONS: Dietary neurotoxin administration reshaped gut microbiome functional profiles in a salinity-dependent manner, highlighting microbiome plasticity and improving our understanding of host-microbiota-environment interactions relevant to aquaculture health management.}, }
@article {pmid42271576, year = {2026}, author = {Manikandan, DC and Sathiyabama, M}, title = {Agro-nanotechnology: A comprehensive overview of its role in groundnut production.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.70783}, pmid = {42271576}, issn = {1097-0010}, abstract = {Groundnut (Arachis hypogaea L.) is an economically important oilseed crop cultivated worldwide for its nutritional and industrial value. However, its productivity and quality are frequently constrained by several challenges, including abiotic and biotic stresses, post-harvest losses, and aflatoxin contamination. In recent years, agro-nanotechnology has emerged as a promising approach to address these limitations by improving nutrient delivery, enhancing plant defense responses, and supporting advanced agricultural strategies. Nanoparticles have been reported to improve nodulation and rhizosphere interactions by influencing plant-microbiome dynamics, thereby contributing to enhanced crop growth and stress tolerance. However, direct evidence remains limited, and several observations are derived from related crop systems. Recent advances have highlighted the integration of nanotechnology with CRISPR-Cas genome editing systems, enabling targeted and DNA-free delivery of gene-editing components for crop improvement. It has been proposed that such approaches could contribute to improved oleic acid content, reduced allergenicity, and enhanced disease resistance in groundnut. Nano-remediation strategies have also shown potential in mitigating pesticide residues and heavy metal contamination, thereby reducing the risk of aflatoxin accumulation. Key developments in this field include nano-formulations for precise nutrient management, modulation of plant-microbiome interactions, and nanoparticle-mediated delivery systems for genome editing technologies. Nevertheless, several challenges remain, including regulatory uncertainties, potential environmental risks, nanoparticle toxicity, and the lack of standardized field-scale evaluations. Addressing these limitations through interdisciplinary research, robust risk-assessment frameworks, and crop-specific regulatory policies will be essential for the responsible implementation of agro-nanotechnology. Overall, this review highlights the emerging role of agro-nanotechnology in addressing key constraints in groundnut production, while emphasizing the need for further groundnut-specific validation and field scale applicability. © 2026 Society of Chemical Industry.}, }
@article {pmid42271632, year = {2026}, author = {Alessandra, N and Paola, G and Anna, BC and Chiara, C and Cristina, &#xc1;A and Ángeles, BM and Ludovica, R and Isabel, N}, title = {Compost from decentralized composting models used for improving soil quality and plant-rhizosphere microbial community response to salinity stress.}, journal = {Integrated environmental assessment and management}, volume = {}, number = {}, pages = {}, doi = {10.1093/inteam/vjag099}, pmid = {42271632}, issn = {1551-3793}, abstract = {The new EU Soil Monitoring Directive establishes the regulatory framework for assessing soil health and mitigating critical threats like salinity and contamination in degraded soils. While it promotes nature-based solutions-such as compost amendment-for soil restoration, compost efficacy remains strictly dependent on feedstock origin and processing technologies, which influence agronomic performance and potential risks of introducing emerging contaminants into soil. This study evaluated, for the first time within a holistic One Health framework, the efficiency of various composts in mitigating plant salinity stress while considering the possible spread of emerging contaminants, such as antibiotic resistance genes (ARGs) and the mobile genetic element intI1. The salinity tolerance of the Rosmarinus officinalis-microbiome system was assessed in pot experiments using degraded soil amended with four composts from various production systems: community (CC) and decentralized (DUC) urban composts, derived from the organic fraction of municipal solid waste and yard trimmings, and two agro-composts based on cattle manure and barley straw (SA) and on olive mill waste, leaves, poultry manure, and pruning residues (MA). Plant biomass, soil microbial activity and abundance were evaluated, alongside ARG dynamics. A Soil Quality Index was also calculated. Data were analysed using non-parametric ANOVA (p < 0.05). Salt stress significantly reduced plant biomass, while CC and DUC composts mitigated this effect, enhancing plant growth under this stress. Interestingly, the rhizosphere microbial community responded to salinity by increasing its activity, presumably owing to a pre-existent defence osmotic mechanism, not linked to the compost presence. However, compost type influenced microbial abundance and ARG dynamics. Notably, although salinity and composts promoted an ARG presence in soil, CC resulted more effective in improving soil quality and salt plant tolerance, including in a One Health prospective, confirming the importance of the compost production process for the use of these improvers.}, }
@article {pmid42272236, year = {2026}, author = {van der Meulen, LWJ and Bergmans, ME and Assil, S and Klarenbeek, N and de Kam, ML and Tibboel, AJ and Brach, T and Herpers, BL and Frieling, J and de Jong, V and Freyee, B and van Doorn, MBA and Rissmann, R and Niemeyer-van der Kolk, T}, title = {S. aureus colonization and clinical symptoms remain stable upon topical XZ.700 treatment: Results of a double-blind randomized clinical trial in patients with mild to moderate atopic dermatitis.}, journal = {British journal of clinical pharmacology}, volume = {}, number = {}, pages = {}, doi = {10.1002/bcp.70630}, pmid = {42272236}, issn = {1365-2125}, support = {//Micreos Human Health B.V./ ; }, abstract = {AIM: Recovering dysbiosis may improve atopic dermatitis (AD) symptoms. XZ.700 is a recombinant chimeric endolysin that specifically targets Staphylococcus aureus and could be a new treatment option for patients with AD. The aim of this first-in-human study was to evaluate the safety, tolerability and efficacy of topical XZ.700 and explore the pharmacodynamic effects in patients with mild to moderate AD.<br><br>METHOD AND MATERIALS: This study consisted of Part A and Part B. In Part A, subjects were randomized and received XZ.700 10&#xa0;&#x3bc;g/g, XZ.700 30&#x2009;&#x3bc;g/g, XZ.700 100&#x2009;&#x3bc;g/g or vehicle twice daily for 7&#xa0;days on nonlesional skin and on all lesions (1%&#x2009;&#x2264;&#x2009;BSA&#x2009;&#x2264;&#x2009;10%). In Part B, subjects received XZ.700 100&#x2009;&#x3bc;g/g or vehicle on all lesions twice daily for 14&#x2009;days (1%&#x2009;&#x2264;&#x2009;BSA&#x2009;&#x2264;&#x2009;15%). Clinical scores and patient-reported outcomes were recorded. Pharmacodynamic measurements were taken.<br><br>RESULTS: In total, 35 patients completed the study. Tolerability of XZ.700 was acceptable. XZ.700 100&#x2009;&#x3bc;g/g showed no evidence of effect on cultured S. aureus (estimated difference -52.9% CFU/mL; 95% CI -88.4% to 90.8%), oSCORAD (1.03; 95% CI -5.20 to 7.26) or EASI (-0.534; 95% CI -2.48 to 1.41). Furthermore, XZ.700 treatment did not result in a significant reduction in the relative abundance of S. aureus via metagenomics or other pharmacodynamic outcomes.<br><br>CONCLUSION: Tolerability and safety of short-term topical administration of XZ.700 100&#x2009;&#x3bc;g/g for 14&#x2009;days were acceptable in most participants; however, some local application-site events occurred, and one hypersensitivity reaction led to discontinuation. XZ.700 did not demonstrate target engagement or clinical benefit vs. vehicle under the tested conditions.}, }
@article {pmid42272277, year = {2026}, author = {Mantargi, MJS and Alavudeen, SS and Easwaran, V and Goruntla, N and Afzal, M and Khan, NA and Hussein, ATM and Mohammad, AAS}, title = {Obesity-associated carcinogenesis with treatment gaps: A narrative review of updated evidence and natural products strategies.}, journal = {Journal of physiology and pharmacology : an official journal of the Polish Physiological Society}, volume = {77}, number = {2}, pages = {143-154}, doi = {10.26402/jpp.2026.2.01}, pmid = {42272277}, issn = {1899-1505}, mesh = {Humans ; *Obesity/complications/drug therapy/metabolism ; Animals ; *Biological Products/therapeutic use ; *Neoplasms/drug therapy/etiology/metabolism ; *Carcinogenesis/drug effects/metabolism ; Phytochemicals/therapeutic use ; Antineoplastic Agents/therapeutic use ; }, abstract = {Obesity contributes significantly to cancer development due to superfluous adipose tissue interfering with physiologic balance. The current narrative review outlines the molecular and physiological pathways linking obesity and cancer and highlights the role of natural products as preventive and therapeutic agents. Underlying processes intertwining obesity and cancer include chronic low-grade inflammation, insulin resistance, hormonal imbalance, adipokine dysregulation, oxidative stress, and changes in the gut microbiome. All of these are used to facilitate tumor-promoting microblood to increase tumor growth and help cancerous cells proliferate and metastasize. There are specific mediators that are important in the activation of oncogenic signalling pathways, such as tumor necrosis factor-alpha, interleukin 6, insulin-like growth factor-1, estrogen, leptin, and reactive oxygen species. Phytochemicals that have the potential to be used as natural anti-inflammatory, antioxidant, and anticancer agents include, but are not limited to, curcumin, resveratrol, epigallocatechin gallate (EGCG), quercetin, berberine, gingerol, and capsaicin. The compounds regulate major molecular pathways of the obesity-related cancers. A new method of delivery that automatically and involuntarily targets the delivery mechanism by use of nanotechnologies has demonstrated its capacity in increasing bioavailability and therapeutic effects of these bioactive agents. To reduce the burden of this impact of obesity on cancers, a strategy involving a blend of lifestyle changes, pharmacological treatment, and science-based natural solutions is required. We conclude that in order to increase the potential of natural products, there is a need to have clinical studies on oncology and public health, as well as regulatory advancement.}, }
@article {pmid42272345, year = {2026}, author = {Bai, Y and Huang, H and Hang, X and Hu, S and Tong, Q and Xu, J and Jia, J and Bi, H}, title = {Multi-Targeting Carnosic Acid Kills Drug-Resistant Helicobacter pylori With Narrow-Spectrum Activity.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e76080}, doi = {10.1002/advs.76080}, pmid = {42272345}, issn = {2198-3844}, support = {82473974//National Natural Science Foundation of China/ ; 32470188//National Natural Science Foundation of China/ ; GZC20251367//Postdoctoral Fellowship Program of the China Postdoctoral Science Foundation/ ; 2025M782601//China Postdoctoral Science Foundation/ ; 326QN0613//Hainan Provincial Natural Science Foundation of China/ ; 326QN0606//Hainan Provincial Natural Science Foundation of China/ ; 2025NHCTDC12002//National Health Commission Key Laboratory of Tropical Disease Control of China/ ; 2026NHCTDC12004//National Health Commission Key Laboratory of Tropical Disease Control of China/ ; XSTS2026115//Academic Improvement Support Program of Hainan Medical University of China/ ; XSTS2026003//Academic Improvement Support Program of Hainan Medical University of China/ ; }, abstract = {Helicobacter pylori (H. pylori) is a significant global human pathogen intricately linked to gastritis, peptic ulcers, and gastric cancer. The escalating challenge of antimicrobial resistance and the adverse effects of conventional antibiotics on the gut microbiome necessitate the development of novel, targeted therapeutics. In this study, we demonstrate that carnosic acid (CA), a natural compound derived from traditional Chinese medicine, exhibits potent and specific anti-H. pylori activity in vitro, with no detectable resistance observed after prolonged serial passaging. CA also displayed enhanced antibacterial efficacy under physiologically relevant acidic conditions, correlating with its strong inhibition of urease, a key colonization factor for H. pylori. Beyond urease suppression, CA acted through multiple mechanisms, including inhibiting biofilm formation and disrupting mature biofilms, impairing bacterial motility, and compromising cell membrane integrity. In vivo, the combination of CA and omeprazole achieved superior eradication in a mouse model of multidrug-resistant H. pylori infection compared to standard triple therapy. Furthermore, CA treatment showed negligible toxicity to host tissues and minimal disruption to the diversity and composition of the gut microbiota. These findings position CA as a promising lead compound against drug-resistant H. pylori, offering a multi-targeting and microbiota-friendly strategy to combat this pathogen.}, }
@article {pmid42272754, year = {2026}, author = {Wu, H and Shi, L and Wang, C and Liang, Y and Huang, C}, title = {Integrative metagenomic and metabolomic analysis reveals a gut microbiota-metabolite-immune axis in pediatric allergic rhinitis with functional constipation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1779298}, pmid = {42272754}, issn = {2235-2988}, abstract = {OBJECTIVE: This study aimed to delineate the alterations in the gut microbiome and host amino acid metabolism in children with comorbid allergic rhinitis and functional constipation (ARFC), and to explore their links with clinical allergy markers.<br><br>METHODS: We performed shotgun metagenomic sequencing and amino acid-targeted metabolomics on fecal samples from 19 children with ARFC and 16 age-matched healthy controls (HC). Microbial community structure, differentially abundant taxa, and metabolic profiles were analyzed. Integrative analyzes, including correlation networks and machine learning modeling, were employed to investigate microbiota-metabolite-host interactions.<br><br>RESULTS: Significant beta-diversity distinction was found between ARFC and HC gut microbiota (PCoA R[2]=0.228, P&#xa0;=&#xa0;0.001). ARFC children exhibited enrichment of mucin-degrading Bacteroidota (e.g., Bacteroides, Phocaeicola) and depletion of beneficial Bacillota (e.g., Bifidobacterium, Blautia). Metabolomics identified 50 differentially abundant metabolites, with widespread downregulation of immunomodulatory amino acids including L-glutamine and &#x3b3;-aminobutyric acid (GABA). Enriched pathways involved mTOR and FoxO signaling, and neurotransmitter synapses. Integration revealed significant correlations between specific microbial genera (e.g., Bacteroides, Proteus) and metabolites (e.g., kynurenine), and between gut species (e.g., Bacteroides thetaiotaomicron) and serum IgE levels. A machine learning model integrating key microbial and metabolic features, evaluated under a rigorous leave-one-out cross-validation framework, demonstrated robust discriminative performance in this cohort (AUC&#xa0;=&#xa0;0.946).<br><br>CONCLUSION: This multi-omics study unveils a distinct "gut dysbiosis-metabolite dysregulation-immune dysfunction" axis in ARFC children. The synergistic shift towards a mucolytic, pro-inflammatory microbiota alongside deficient immunomodulatory metabolite production, which correlates with clinical allergy markers, provides a novel mechanistic framework for this comorbidity and highlights potential diagnostic biomarkers for future validation.}, }
@article {pmid42272779, year = {2026}, author = {Jain, A and Johnston, C and Zhang, Y and Oh, J and Tsung, C and Kent, E and Zhang, H}, title = {An overview of current research on exercise interventions in aging and aging-related disease.}, journal = {Frontiers in aging}, volume = {7}, number = {}, pages = {1832962}, pmid = {42272779}, issn = {2673-6217}, abstract = {Global declines in physical activity have contributed to an acceleration in immune aging, characterized by systemic inflammation (inflammaging) and impaired immune regulation (immunosenescence). This narrative review provides an overview of the evidence in both preclinical and clinical models supporting exercise as a critical intervention to counteract immune aging and its related diseases. Regular physical activity modulates systemic inflammation, reduces neutrophil extracellular trap (NET) formation, and promotes favorable shifts in immune cell populations, including T cell and natural killer (NK) cell subsets. Exercise interventions have been associated not only with maintaining immune health but also in mitigating autoimmune disease progression, improving metabolic regulation, enhancing tumor immune surveillance, and reducing neuroinflammation. Emerging studies highlight the role of exercise in promoting vascular normalization within the tumor microenvironment, alleviating tumor hypoxia and acidosis, and restoring T and NK cell function. In the elderly, appropriately prescribed multimodal exercise regimens may lower infection risk without clear evidence of immunodepression, supporting exercise as a potentially safe and effective strategy for immune rejuvenation. Furthermore, novel mechanistic insights, including the modulation of NET burden, IGF-1 signaling, kynurenine metabolism, and microbiome composition, suggest that exercise influences key biological pathways underlying age-related immune decline. While exercise offers broad clinical benefits, future research should prioritize mechanistic studies to optimize exercise prescriptions and inform the development of exercise-mimetic therapeutics. Taken together, investigating the exercise regimens employed in these studies remains a promising intervention for promoting healthy immune aging and improving resilience against chronic inflammatory, metabolic, infectious, and malignant diseases.}, }
@article {pmid42272857, year = {2026}, author = {Kerezoudi, EN and McKay, S and Kurt, S and De Kreek, M and De Medts, J and Verstrepen, L and Ghyselinck, J and Meulebroek, LV and Calame, W and Albers, R and Mercenier, A and Brummer, RJ and Rangel, I}, title = {Dietary chicory rhamnogalacturonan-I modulates gut microbiota and immune responses in healthy adults.}, journal = {Microbiome research reports}, volume = {5}, number = {2}, pages = {11}, pmid = {42272857}, issn = {2771-5965}, abstract = {Background: Pectic rhamnogalacturonan-I (RG-I) is a dietary fiber that modulates the gut-immune axis. This study evaluates a novel variant of RG-I from chicory root (chRG-I). Methods: In a randomized, double-blind, placebo-controlled trial, 55 healthy adults were stratified by habitual fiber intake and baseline Bifidobacterium levels before receiving 500 mg/day of chRG-I or placebo for four weeks. Primary endpoints included fecal Bifidobacterium counts. Secondary outcomes assessed fecal metabolites, systemic immune cell activation markers, and gastrointestinal symptoms. To provide mechanistic insights, donor-matched fecal samples were used in in vitro fermentation and Caco-2/peripheral blood mononuclear cell co-culture gut barrier models. Results: Supplementation with chRG-I induced a statistically significant bifidogenic effect, with absolute levels peaking at week three, and lower levels of some fecal short-chain fatty acids (SCFA) compared to placebo. However, donor-matched in vitro fermentations with chRG-I confirmed robust production of SCFA and reduction of branched-chain fatty acids levels (BCFA). Systemically, chRG-I upregulated HLA-DR expression on myeloid dendritic cells. Clinically, chRG-I was well-tolerated and slightly improved stool consistency compared to placebo. In an intestinal barrier challenge model, chRG-I fermentates (a pool of metabolites including SCFA and fragments of chRG-I) protected barrier integrity, modulated the cytokine milieu away from a predominantly pro-inflammatory response, as characterized by increased IL4 and IL22 and reduced IL9, IL17A, and IL21. Conclusion: Supplementation with a low dose of chRG-I is well-tolerated, beneficially modulates the gut microbiome - which can protect the intestinal barrier, and subtly enhances systemic immune readiness, suggesting that chRG-I may have benefits as a functional food ingredient.}, }
@article {pmid42272859, year = {2026}, author = {Fathima, S and Sarkar, T and Sharma, N and Kilgore, PE and Nguyen, HH}, title = {Immunoglobulin Y protects intestinal epithelium and modulates gut microbiota.}, journal = {Microbiome research reports}, volume = {5}, number = {2}, pages = {8}, pmid = {42272859}, issn = {2771-5965}, abstract = {Aim: This study investigated the effects of Muno-IgY®, a multi-pathogen-specific immunoglobulin Y (IgY), on microbial growth, adhesion, fermentation activity, and immune signaling using a multi-tiered in vitro approach. Methods: IgY activity was first evaluated in Caco-2 adhesion and invasion assays using adherent-invasive Escherichia coli (AIEC) at optimized concentrations, followed by assessment in a SHIME® in vitro gut model inoculated with human fecal microbiota enriched in Enterobacteriaceae. Microbial composition, fermentation markers, and metabolite production were analyzed, and downstream effects on epithelial barrier integrity and immune signaling were evaluated using a Caco-2/peripheral blood mononuclear cell (PBMC) co-culture model exposed to SHIME® effluents. Results: Muno-IgY® significantly reduced AIEC adhesion/invasion from 39.76% in controls to 13.08% and 9.13% at 3 and 6 mg/mL, respectively (P < 0.05). In the SHIME® model, IgY significantly increased acetate and propionate production (P < 0.05), alongside a marked increase in ammonium concentration (P < 0.01). Microbial biomass increased modestly, while alpha- and beta-diversity indices were not significantly altered. The compositional shifts indicated enrichment of beneficial and mucin-associated taxa and reduction of opportunistic or pathogenic species in the Muno-IgY® group. In Caco-2/PBMC co-cultures, IgY-treated effluent decreased transepithelial electrical resistance (TEER) indicating reduced barrier integrity (P < 0.05) but significantly decreased pro-inflammatory cytokines Interferon-γ (IFN-γ) and Interleukin-22 (IL-22) (P < 0.05). Conclusions: Muno-IgY® demonstrates the ability to inhibit pathogen adhesion and modulate microbial composition and immune responses in vitro. These findings support its potential as a non-antibiotic approach for microbiome-targeted interventions, although further validation in vivo is required.}, }
@article {pmid42272905, year = {2026}, author = {Maji, M and Mandal, S and Dhali, A and Miller, LJ and Grove, J and Snowden, JA and Chakrabarti, S and Aithal, G}, title = {Role of neutropenic diet in prevention of infection and graft-versus-host disease in haematopoietic stem cell transplant recipients: systematic review and meta-analysis protocol.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1820858}, pmid = {42272905}, issn = {2296-861X}, abstract = {INTRODUCTION: Haematopoietic stem cell transplantation (HSCT) is associated with substantial early infectious risk, neutropenia, immunosuppression, and graft-versus-host disease (GVHD). Many centres continue to use neutropenic, low-microbial, low-bacterial, or protective diets to reduce dietary exposure to potential pathogens, despite variation in diet definitions and concerns regarding nutritional intake, patient experience, cost, and microbiota recovery. This protocol describes a systematic review and meta-analysis evaluating the benefits and harms of neutropenic diets compared with less restrictive, standard, or food-safety-based dietary approaches in HSCT recipients.<br><br>METHODS: We will include randomised and non-randomised comparative studies involving children or adults undergoing HSCT from any graft source and conditioning intensity. Eligible interventions will include neutropenic, low-microbial, low-bacterial, or protective diets; comparators will include unrestricted, less restrictive, standard hospital, or food-safety-based diets. MEDLINE, Embase, CENTRAL, Web of Science, CINAHL, Scopus, ClinicalTrials.gov, and the WHO ICTRP will be searched from inception without language or date restrictions, supplemented by reference screening, expert contact, grey literature, and conference proceedings. Two reviewers will independently screen studies, extract data, and assess risk of bias using RoB 2 for randomised trials and RoBANS for non-randomised studies.<br><br>RESULTS: The primary outcomes will be infection rates, acute GVHD, nutritional status, time to neutrophil recovery, and patient satisfaction or quality of life. Secondary outcomes will include overall survival, relapse, chronic GVHD, length of hospitalisation, antibiotic use to day 100, micronutrient deficiency, and cost outcomes. Where appropriate, pooled estimates will be generated using random-effects models, with subgroup and sensitivity analyses used to explore heterogeneity. Certainty of evidence will be assessed using GRADE.<br><br>DISCUSSION: This review will clarify whether neutropenic diets reduce infectious complications or GVHD after HSCT, and whether any potential benefit is offset by nutritional, patient-centred, microbiome-related, or economic harms. Findings will inform clinical practice, patient counselling, and future policy on dietary restrictions after HSCT.<br><br>https://www.crd.york.ac.uk/PROSPERO/view/CRD420251162724, identifier PROSPERO (CRD420251162724).}, }
@article {pmid42272927, year = {2026}, author = {Sougoufara, S and Bandibabone, J and Chatterley, L and Hughes, I and Taberes, CM and Ball, J and Palliaser, T and Dhokiya, V and Heinz, E and Hughes, G and Walker, T}, title = {The presence of the wAnD strain of Wolbachia is correlated with lower levels of Plasmodium sporozoites and a less diverse microbiome in wild Anopheles demeilloni mosquito cephalothoraxes.}, journal = {Gates open research}, volume = {10}, number = {}, pages = {28}, pmid = {42272927}, issn = {2572-4754}, abstract = {BACKGROUND: The increasing insecticide resistance of malaria vectors is an urgent concern for disease control and novel vector control strategies are needed. Wolbachia are endosymbiotic bacteria that can invade mosquito populations and reduce transmission of human pathogens. Wolbachia strains in wild Anopheles (An.) malaria vectors are rare, with only two known genuine symbioses; An. moucheti with wAnM and An. demeilloni with wAnD. In this study, we set out to determine if there was a correlation between wAnD in different An. demeilloni mosquito body parts, infective stage Plasmodium (Pl.) falciparum malaria sporozoites in cephalothoraxes and the mosquito microbiome.<br><br>METHODS: We undertook a combination of quantitative PCR, 16S rRNA amplicon sequencing and sanger sequencing of the Wolbachia surface protein (wsp) gene after isolating An. demeilloni female body parts from wild caught individuals collected in 2021 and 2024 from the Sud Kivu region of Democratic Republic of Congo. Results Wolbachia prevalence rates were significantly higher in abdomens compared to cephalothoraxes and density was also significantly higher in abdomens (P<0.0001). Overall sporozoite prevalence was 1.3% (9/704) which was not significantly different between Wolbachia-positive and Wolbachia-negative cephalothoraxes (P=0.3630) despite Pl. falciparum only detected in Wolbachia-negative cephalothoraxes. However, Wolbachia-positive abdomens were associated with a lower sporozoites rate compared to Wolbachia-negative abdomens (P=0.0329). 16S rRNA amplicon sequencing revealed no significant difference in alpha/beta diversities between abdomens and cephalothoraxes but the cephalothorax microbiome composition between Wolbachia-positive and Wolbachia-negative was significantly different (P<0.05).<br><br>CONCLUSIONS: Our findings indicate a significant effect of the wAnD strain on the cephalothorax microbiome and potentially the ability of sporozoites to reach Salivary glands in mosquitoes with Wolbachia-infected abdomens. Further studies are needed to determine the mechanisms in which the wAnD strain interacts with Plasmodium sporozoites in An. demeilloni and if this strain could be used for malaria biocontrol through transinfection of major malaria vectors.}, }
@article {pmid42272967, year = {2026}, author = {Frisch, S and Aliyazdi, S and Rehner, J and Schmartz, G and Gevaerd, C and Latta, L and Veldung, B and Becker, SL and Keller, A and Schaefer, UF and Loretz, B and Vogt, T and Lehr, CM}, title = {Staphylococcal proliferation on skin models to investigate novel anti-infective treatments against dysbiosis.}, journal = {Bioengineering &amp; translational medicine}, volume = {11}, number = {3}, pages = {e70124}, pmid = {42272967}, issn = {2380-6761}, abstract = {Inflammatory skin conditions like Acne inversa are characterized by dysbiosis, an imbalance of commensal and pathogenic bacteria, posing challenges for specific treatments. Consequently, we investigated how biofilm formation, low-nutrition skin environments, and air interfaces influence susceptibility to anti-infective treatments in mixed bacterial cultures. To achieve this in a cost-effective and reproducible manner, we developed a simplified substrate made of gelatin, hyaluronic acid, chondroitin sulphate, and alginate (=Gel-Alg). This in vitro model simulates biofilm cultivation on skin surfaces for aerobic bacteria. We selected Staphylococcus aureus and Staphylococcus epidermidis as two clinically relevant strains, which are also abundant in Acne inversa. We tested single and mixed cultures under different conditions: (i) nutrient broth, (ii) Gel-Alg substrate, (iii) EpiDerm™ commercial skin model, and (iv) ex vivo human skin. Proliferation, measured by colony-forming units, was comparable across most conditions, except for human skin. Metabolic activity, assessed via Presto Blue staining, revealed significant differences. Dual-species cultivation and quantification by viability PMA qPCR indicated dominance of S. epidermidis over S. aureus in skin-like environments. Treatments with biofilm-dissolving rhamnolipids, the antibiotic vancomycin, and combinations thereof demonstrated varying efficacy in single and mixed cultures. While the drug combination could almost completely eradicate staphylococcal biofilms in broth, susceptibility varied in skin-like models and moreover strongly depended on temperature (37°C vs. 32°C). In conclusion, this study suggests that reductionistic models, while mimicking key features, could be valuable for early selective antimicrobial drug development for specific applications like Acne inversa therapy.}, }
@article {pmid42273048, year = {2026}, author = {Jiao, Y and Liu, Y and Gao, Q and Song, L and Sun, F and Li, Y and Li, H and Li, S and Li, J and Du, J and Li, C and Tian, X and Liu, R}, title = {Glutamicibacter soli JF_198 stimulates the rhizosphere colonization of indigenous Paenibacillus sp. to suppress cucumber Fusarium.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1843711}, pmid = {42273048}, issn = {1664-302X}, abstract = {INTRODUCTION: Beneficial microorganisms can facilitate the formation of advantageous microbial communities in the plant rhizosphere, thereby promoting plant health. Our research indicates that Glutamicibacter soli JF_198 can mitigate the severity of cucumber Fusarium wilt caused by Fusarium oxysporum f. sp. cucumerinum. This study investigates the tripartite association among Glutamicibacter soli JF_198, the cucumber rhizosphere microbiota, and cucumber Fusarium wilt suppression.<br><br>METHODS: We evaluated JF_198-mediated disease suppression in cucumber pot experiments and analyzed rhizosphere bacterial communities by 16S rRNA amplicon sequencing. Rhizosphere transplantation, bacterial isolation, antagonistic screening, and growth, competition, and root colonization assays were performed to assess the role of candidate Paenibacillus isolates under cucumber root-exudate conditions.<br><br>RESULTS: JF_198 treatment was associated with changes in selected rhizosphere bacterial taxa, particularly an increased trend in Paenibacillus-related taxa. Rhizosphere transplantation experiments showed that JF_198-associated rhizosphere microbiota could partially transfer disease-suppressive effects to sterile soil. We identified Paenibacillus-assigned OTU1077 as a candidate indigenous beneficial taxon showing increased relative abundance under JF_198 treatment. Further investigation suggested that JF_198 treatment was associated with enhanced Paenibacillus sp. colonization under root-exudate conditions.<br><br>DISCUSSION: Our findings suggest that G. soli JF_198-mediated disease suppression under controlled pot conditions is associated with changes in selected rhizosphere bacterial taxa and increased relative abundance of indigenous biocontrol-associated bacteria. This study provides preliminary insights into microbiome-associated disease suppression under controlled pot conditions and may inform future development of microbial consortia, pending further validation under field conditions.}, }
@article {pmid42273240, year = {2026}, author = {Meng, D and Zhang, BB and Zhao, JN}, title = {Letter to the Editor: Deciphering macrophage heterogeneity and optimizing probiotics via spatial multi-omics.}, journal = {World journal of gastrointestinal pharmacology and therapeutics}, volume = {17}, number = {2}, pages = {118195}, pmid = {42273240}, issn = {2150-5349}, abstract = {We read the paper published in World Journal of Gastroenterology by Yang et al on how Bifidobacterium species alleviate colitis by modulating deoxycholic acid (DCA) levels and macrophage polarization, which provides important insights into the microbiome-immune axis. However, the classic M1/M2 polarization model oversimplifies the plasticity of macrophages and fails to account for the spatial heterogeneity of the intestinal microenvironment. Therefore, we propose integrating spatial transcriptomics and spatial metabolomics to resolve the intricate correlations between DCA distribution and specific macrophage subsets. Building upon this, we further discuss the transition from broad-spectrum probiotic supplementation to mechanism-driven precision probiotic strategies, emphasizing the future need to develop engineered strains capable of spatial awareness and metabolic pathway remodeling. This spatial multiomics-guided precision intervention framework holds promise for advancing colitis treatment toward approaches with greater mechanistic depth.}, }
@article {pmid42273247, year = {2026}, author = {Loktionov, A}, title = {Current approaches to disease severity and therapy effectiveness assessment in patients with inflammatory bowel disease.}, journal = {World journal of gastrointestinal pharmacology and therapeutics}, volume = {17}, number = {2}, pages = {116608}, pmid = {42273247}, issn = {2150-5349}, abstract = {Inflammatory bowel disease (IBD) is a group of chronic recurrent disorders, Crohn's disease and ulcerative colitis being its two major types. IBD patients require continuous lifetime monitoring of disease activity and effects of therapeutic interventions, achievement of stable remission being the goal of the current 'treat-to-target' strategy. This review considers a wide range of approaches applied for this purpose. Although ileocolonoscopy combined with histological evaluation and now employing modern endoscopic techniques is still regarded as the gold diagnostic standard, its inability of visualizing small intestine is a limitation. Alternative non-invasive techniques such as capsule endoscopy and, especially, cross-sectional imaging, comprising computed tomography enterography, magnetic resonance enterography, and intestinal ultrasound, are becoming increasingly popular. In addition, the use of molecular biomarkers detectable in human body fluids is a rapidly developing area, and recent rapid progress in gut microbiome research promises to add a new dimension to it. It is also anticipated that new approaches based upon multi-omics can identify new composite biomarkers useful for IBD monitoring. Artificial intelligence-driven integration of abundant information provided by various diagnostic and analytical modalities outlined in this review may help in transforming the current 'one-size-fits-all' treatment paradigm into a truly personalized model of IBD care.}, }
@article {pmid42273259, year = {2026}, author = {Amaral, A and Piotrowska-Tomala, K and Kordowitzki, P}, title = {Editorial: Endometrial health and disease: from molecular insights to clinical advances.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1860973}, doi = {10.3389/fvets.2026.1860973}, pmid = {42273259}, issn = {2297-1769}, }
@article {pmid42273381, year = {2026}, author = {Zhang, Y and Wang, D and Zhuang, B and Zhu, F and Tan, C and Zhang, J and Zhang, Q}, title = {The Multifaceted Roles of Gut Microbiota and Their Metabolites in Metabolic Dysfunction-associated Steatotic Liver Disease: A Literature Review.}, journal = {Journal of clinical and translational hepatology}, volume = {14}, number = {5}, pages = {554-564}, pmid = {42273381}, issn = {2310-8819}, abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) represents a major global health concern and encompasses a spectrum ranging from hepatic steatosis and metabolic dysfunction-associated steatohepatitis to liver fibrosis, cirrhosis, and ultimately hepatocellular carcinoma. Insulin resistance, the pathogenic cornerstone of MASLD, drives enhanced peripheral lipolysis and increased hepatic de novo lipogenesis, thereby overloading the liver with lipids and inducing steatosis. Subsequent lipotoxicity, inflammation, and gut microbiota dysbiosis further exacerbate disease progression. The gut microbiota and their metabolites communicate with the liver via the gut-liver axis, forming a complex signaling network that directly or indirectly modulates hepatic metabolism, systemic immune responses, oxidative stress, and intestinal barrier integrity. In this review, we synthesize evidence for the beneficial and detrimental effects of the major human gut microbial communities and their metabolites during the course of MASLD. We delineate how these gut-derived factors regulate hepatic function through an integrated tripartite "gut-liver axis-oxidative stress-metabolic reprogramming" mechanism. These insights may inform microbiome-based precision interventions and accelerate the development of therapeutic strategies targeting MASLD.}, }
@article {pmid42273689, year = {2026}, author = {Yang, L and Li, Z and Li, Y and Zhang, Q and Zhang, H}, title = {Synergistic antitumor and immunomodulatory effects of Bifidobacterium animalis subsp. lactis V9 combined with anti-PD-1 therapy.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1791276}, pmid = {42273689}, issn = {1664-3224}, mesh = {Animals ; Mice ; Humans ; Female ; *Immune Checkpoint Inhibitors/pharmacology ; *Programmed Cell Death 1 Receptor/antagonists &amp; inhibitors/immunology ; *Bifidobacterium animalis/immunology ; Cytokines/metabolism ; Cell Line, Tumor ; Immunomodulation ; Tumor Microenvironment ; *Neoplasms/therapy/immunology ; *Probiotics ; Gastrointestinal Microbiome/immunology ; }, abstract = {BACKGROUND: Immune checkpoint inhibitors (ICIs) targeting PD-1/PD-L1 have revolutionized cancer immunotherapy but remain limited by low response rates, immune-related adverse events (irAEs), and reduced efficacy following antibiotic exposure. The gut microbiota critically influences ICI responsiveness, and Bifidobacterium species have emerged as potent immunomodulatory commensals. However, the mechanistic contribution of specific live biotherapeutic strains remains unclear.<br><br>METHODS: We systematically characterized Bifidobacterium animalis subsp. lactis V9 (B. lactis V9), through in-vitro cytokine assays and multiple syngeneic tumor models (CT26, MC38, 4T1). Immunophenotyping, microbiota colonization, and toxicological studies were conducted to evaluate efficacy, immune modulation, colonization stability, and safety.<br><br>RESULTS: B. lactis V9 dose-dependently induced TNF-&#x3b1;, IL-6, and IL-10 secretion in THP-1 macrophages, exhibiting a balanced cytokine profile distinct from LPS stimulation. In vivo, B. lactis V9 alone moderately inhibited tumor growth but synergized with &#x3b1;PD-1 to achieve a 50% tumor growth inhibition and extend survival in CT26 models, accompanied by increased IFN-&#x3b3;[+]CD8[+] T cells and activated CD86[+]CD11c[+] dendritic cells. The synergy persisted despite antibiotic pretreatment, indicating colonization stability (8&#xd7;10[8]-10[9] copies/g) and a metabolite-driven mechanism. In 4T1 models, B. lactis V9 co-therapy mitigated &#x3b1;PD-1-induced uterine inflammation and pulmonary hemorrhage by downregulating IL-1&#x3b1;, IL-1&#x3b2;, and IL-17A while maintaining effector cytokines. Toxicology assessments revealed no adverse findings up to 3.52&#xd7;10[12] CFU/kg (acute) or 5.00&#xd7;10[11] CFU/kg (90-day repeated dose), with all genotoxicity tests negative.<br><br>CONCLUSIONS: B. lactis V9 harmonizes pro- and anti-inflammatory responses through TLR2/TLR4-NF-&#x3ba;B/MAPK signaling, remodels the tumor microenvironment, and enhances &#x3b1;PD-1 efficacy without increasing toxicity. Its colonization resilience and favorable safety profile support clinical translation as a microbiome-based adjunct to immunotherapy. These results provide a mechanistic foundation for combining live biotherapeutic products with ICIs to optimize antitumor immunity.}, }
@article {pmid42273701, year = {2026}, author = {Wang, Z and Bian, Q and Chu, Y and Zhu, W and Qin, Y and Zheng, J}, title = {The microbiome-inflammation-immune axis in oral squamous cell carcinoma: from mechanistic insights to therapeutic perspectives.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1842459}, pmid = {42273701}, issn = {1664-3224}, mesh = {Humans ; *Microbiota/immunology ; *Mouth Neoplasms/immunology/microbiology/therapy ; Tumor Microenvironment/immunology ; *Inflammation/immunology/microbiology ; Dysbiosis/immunology ; *Carcinoma, Squamous Cell/immunology/therapy/microbiology ; Animals ; Signal Transduction ; }, abstract = {Oral squamous cell carcinoma, the most prevalent malignancy of the head and neck, presents ongoing challenges regarding its molecular mechanisms and clinical management. Current research largely focuses on isolated signaling pathways or specific immune responses, often overlooking the potential contributing role of the microbiota in tumorigenesis. This review proposes the "microbiome-inflammation-immune axis" as an interpretive working hypothesis to elucidate how dysbiosis and microbial interactions may activate host inflammatory responses, trigger pattern recognition receptors and signaling pathways, and remodel the immune microenvironment, thereby potentially facilitating oral cancer progression. Concurrently, this paper emphasizes clinical translation by critically compiling and evaluating relevant clinical analytical indicators-such as peripheral blood inflammatory markers and salivary microbial markers-from the fields of inflammation and microbiology. This provides multidimensional reference points for future disease diagnosis and treatment.}, }
@article {pmid42273932, year = {2026}, author = {Rezaei, F and Rollin, JA}, title = {A Microbial Formulation Perspective on Probiotic Skincare: Viability, Challenges, and Current Approaches to Maintain Probiotic Viability.}, journal = {Biotechnology and bioengineering}, volume = {}, number = {}, pages = {}, doi = {10.1002/bit.70268}, pmid = {42273932}, issn = {1097-0290}, abstract = {The human body hosts a vast and dynamic microbial ecosystem that plays essential roles in immunity, metabolism, and tissue function. Growing scientific and consumer interest in the human microbiome has accelerated innovation in topical skincare, particularly in the emerging category of probiotic, prebiotic, and postbiotic formulations. However, despite rapid market growth, most commercial products rely on non-viable microbial derivatives rather than live, strain-identified organisms, largely due to formulation, regulatory, and stability challenges. This review provides a microbial formulation perspective on probiotic skincare, beginning with an overview of the human and skin microbiomes, followed by a discussion of how beneficial microorganisms influence skin appearance and barrier function. We clarify the definitions and scientific distinctions among probiotics, prebiotics, and postbiotics and evaluate current cosmetic applications. We then explore the technical and regulatory hurdles associated with incorporating live microbes into cosmetic products, including preservative compatibility, viability, packaging, and activation requirements. Finally, we present some available strategies and technologies in an effort to keep probiotic viable until use and outline future research considerations needed to advance authentic, evidence-based probiotic skincare.}, }
@article {pmid42274211, year = {2026}, author = {Yarkosky, EJ and Udensi, CG and Ferreira, RBR and Collins, KJR and Hotze, EM}, title = {MicrobioME: a CURE model for diverse microbiology laboratory classrooms.}, journal = {Journal of microbiology &amp; biology education}, volume = {}, number = {}, pages = {e0029825}, doi = {10.1128/jmbe.00298-25}, pmid = {42274211}, issn = {1935-7877}, abstract = {Undergraduate research experience (URE) positively contributes to student success, STEM identity, and STEM post-graduate careers. Despite these benefits, traditional UREs are limited, and many students encounter barriers to gaining access to these opportunities. Course-based Undergraduate Research Experiences (CUREs) increase access to UREs by incorporating authentic research projects into the course curriculum. Despite the recognized benefits of CUREs, few have been developed for introductory or upper-level microbiology courses. This scarcity largely reflects the substantial planning and financial investment required of faculty to create effective CUREs that are affordable, relevant, and align with course learning objectives. These combined demands present significant challenges to widespread adoption of CUREs in microbiology education. We considered these limitations when developing the "MicrobioME" CURE for implementation in pathogenic microbiology laboratory courses. Students participating in the MicrobioME CURE isolate and identify bacterial isolates from their own skin microbiome and investigate the impact of isolate-produced small molecules on Staphylococcus aureus biofilm production. We studied MicrobioME CURE implementation in two laboratory courses at the University of Kansas (KU) and West Virginia University (WVU) in cohorts differing in class size, research experience, meeting times, and faculty expertise in microbiome research, providing an opportunity to compare student outcomes in varied environments. Here, we report student outcomes of and provide tools for implementing the MicrobioME CURE in microbiology laboratory courses at other universities. Our results suggest that the MicrobioME CURE is scalable, affordable, and modular, making it an accessible and practical solution to increasing access to authentic research experience.}, }
@article {pmid42274249, year = {2026}, author = {Villafuerte, NM and Stevens, EN and Sheikh, MA and Rodriguez, VH and Lin, J and Zhang, F}, title = {Natural commensal microbes induce internal hatching in C. elegans.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0403425}, doi = {10.1128/spectrum.04034-25}, pmid = {42274249}, issn = {2165-0497}, abstract = {The microbiome is increasingly recognized as a key factor of the plasticity of host life-history traits. Using the Caenorhabditis elegans model system, we examined how naturally associated bacterial strains affect internal egg hatching, a stress-adaptive reproductive strategy in this species. Among the bacterial strains tested, four strains (Ochrobactrum BH3, Lelliottia JUb66, Pantoea BIGb0393, and Enterobacter CEent1) induced high levels of internal hatching (28-57%) in C. elegans during late adulthood, compared to <5% in animals grown on E. coli OP50. These effects were accompanied by extending the reproductive window while showing a trend toward reduced total progeny and lifespan. Genetic analyses revealed that these effects are mediated through various components of the insulin signaling pathway: the α-proteobacterial strain BH3 acts via DAF-16/FOXO, whereas the three γ-proteobacterial strains act independently of DAF-16, suggesting differences in pathway dependence. Our findings demonstrate that naturally associated microbiome members can differentially interact with host endocrine signaling to shape reproductive outcomes. These results underscore the role of microbial cues in shaping life-history plasticity in animals.IMPORTANCEMicrobiome members profoundly influence host physiology, including reproductive strategies. Using the Caenorhabditis elegans natural microbiome model, we show that commensal bacteria can induce internal egg hatching, a facultative vivipary phenotype previously linked primarily to early-life starvation or pathogen exposure that severely reduces reproductive output. In contrast, commensal strains trigger this shift mainly in late adulthood, extending the reproductive window with minimal impact on overall fecundity. We further demonstrate that bacterial strains act through distinct components of the host insulin signaling pathway. More broadly, these findings highlight diverse avenues within conserved endocrine networks that are susceptible to microbial modulation and underscore the potential to leverage microbiomes to influence host life-history traits.}, }
@article {pmid42274262, year = {2026}, author = {Guan, M and Guo, X and Kong, M and Qin, Y and Xu, H and Su, X and Wang, P and Wang, X}, title = {Potential mechanisms underlying Enterococcus faecalis-driven pancreatic cancer cell proliferation.}, journal = {mBio}, volume = {}, number = {}, pages = {e0396325}, doi = {10.1128/mbio.03963-25}, pmid = {42274262}, issn = {2150-7511}, abstract = {The development of various cancers is intricately linked with the human microbiome. Recent studies have highlighted a substantial association between pancreatic cancer and gut microbiota. However, the specific roles and underlying regulatory mechanisms of individual gut microbial species in pancreatic cancer progression remain poorly understood. Enterococcus faecalis, a common member of the human commensal microbiota, has been found to be enriched in the tumor tissues of pancreatic cancer patients. However, its functional contribution has not been clearly defined. In this study, we established a co-culture system involving E. faecalis and pancreatic cancer cells. Our results show that E. faecalis promoted the proliferation, migration, and invasion of pancreatic cancer cells. Following pre-treatment with E. faecalis, the phosphorylation level of epidermal growth factor receptor (EGFR) was markedly elevated. Inhibition of EGFR effectively suppressed the pro-proliferative effects induced by E. faecalis. Further investigation revealed that E. faecalis stimulated the production of reactive oxygen species (ROS) in pancreatic cancer cells. This ROS production might be sensed by Toll-like receptors (TLRs), leading to the activation of the EGFR signaling pathway. When cells were incubated with TLR inhibitors or ROS scavengers, both EGFR expression and its downstream pro-proliferative effects were significantly attenuated. Collectively, this study provides mechanistic insights into how E. faecalis contributes to pancreatic cancer progression and offers new perspectives for the development of diagnostic and therapeutic strategies targeting this microbial signaling pathway.IMPORTANCEA diverse microbiome is closely associated with cancer, as bacterial presence has been detected in the majority of solid tumors. However, the composition, abundance, and functional profiles of the microbiota vary significantly across different tumor types, thereby exerting distinct effects on tumorigenesis and disease progression. Recent studies have shown that pancreatic cancer hosts a variety of bacterial populations, including gut-derived bacteria that may translocate to pancreatic tissue via mesenteric venous or lymphatic drainage pathways. For example, Enterococcus and Enterobacter species have been identified in the cyst fluid of patients with pancreatic cystic neoplasms. Moreover, antibodies against Enterococcus faecalis capsular polysaccharide have been detected in the sera of patients with pancreatitis and pancreatic cancer, and E. faecalis has been observed in pancreatic ducts. Despite these observations, the precise mechanisms through which E. faecalis influences pancreatic cancer remain unclear. Our study demonstrates that E. faecalis promotes pancreatic cancer cell proliferation through the activation of the Toll-like receptor-reactive oxygen species-epidermal growth factor receptor signaling pathway.}, }
@article {pmid42274451, year = {2026}, author = {Calvão, J and Iselin, C and Wasmayr, J and Furtmüller, C and Zeng, Z and Vadivel, CK and Gluud, M and Bataiosu-Zimmer, E and Buus, TB and Ødum, N and Gonçalo, M and Guenova, E}, title = {Pathogenesis of cutaneous T-cell lymphoma: Malignant inflammation, immune reprogramming, and microenvironmental drivers.}, journal = {The Journal of investigative dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jid.2026.03.035}, pmid = {42274451}, issn = {1523-1747}, abstract = {Cutaneous T-cell lymphomas, namely mycosis fungoides and Sézary syndrome, arise through a complex interplay of genetic alterations, epigenetic deregulation, immune imbalance, and tumor-microenvironment interactions. A progressive T helper 1-to-T helper 2 shift and chemokine-directed trafficking promote immune evasion and sustained malignant T-cell activity, whereas emerging data show subclonal diversity enabling adaptation to microenvironmental and therapeutic pressures. Skin-resident immune cells further shape disease behavior, and Staphylococcus aureus superantigens act as microenvironmental amplifiers that enhance malignant signaling and contribute to treatment resistance. A deeper understanding of how these molecular, immunological, and microbiome factors converge is essential to develop more precise, biomarker-informed therapeutic strategies.}, }
@article {pmid42274459, year = {2026}, author = {King, D and Kalogeromitros, M and Gutama, B and Slutsky, HL and Mubang, R and Wagner, A and Kitko, CL and Lineaweaver, WC}, title = {Skin Lesion Reconstruction in Graft Versus Host Disease Using Autograft From the Bone Marrow Donor Panniculectomy Tissue.}, journal = {Annals of plastic surgery}, volume = {}, number = {}, pages = {}, pmid = {42274459}, issn = {1536-3708}, abstract = {Chronic graft-versus-host disease (cGVHD) is a common complication following hematopoietic stem cell transplant, with the skin being the most frequently affected organ. The cutaneous manifestations may be refractory to conventional wound care and skin autografts due to the complex underlying immunology. In this case report, a pediatric patient with a history of Ph-like B-cell acute lymphoblastic leukemia underwent a haploidentical bone marrow transplant from his mother. His course was complicated by cutaneous cGVHD, which failed multiple lines of immunosuppression and conservative wound management. In addition, he developed multidrug-resistant wound infections. He underwent split-thickness skin allograft transplantation from his mother's pannus, and his wounds were largely resolved within 3 months postoperatively. This report provides a review of the literature to discuss the biology behind cutaneous cGVHD, including the role of the microbiome, and the proposed mechanism for the success of this treatment. It also highlights the unique benefits of utilizing the pannus and leveraging the immunologic tolerance established by prior bone marrow transplant from the same donor. This case presents donor skin allografting in the setting of donor tolerance as a viable option for refractory cutaneous cGVHD.}, }
@article {pmid42274490, year = {2026}, author = {Guo, Q and Niu, M and Wang, Y and Yang, S and Cai, Q and Ma, Y and Li, Y and Chen, X}, title = {Regulatory Effects of Two Ionic Liquids ([Omim]Br, [Opy]Br) on the Growth and Root Microecology of Maize Seedlings.}, journal = {Biology}, volume = {15}, number = {11}, pages = {}, pmid = {42274490}, issn = {2079-7737}, support = {No. 32272018//National Natural Science Foundation of China/ ; }, abstract = {Accumulation of ionic liquids (ILs) in soil may alter its physicochemical and biological properties. However, the current understanding of their effects on the rhizosphere microenvironment of crop plants remains limited. We examined the effects of two ILs-[Opy]Br and [Omim]Br-which differ in cation structure but share the bromide anion, on maize rhizosphere microbial communities and metabolites at a concentration of 0.6 g/kg soil. Exposure to [Opy]Br and [Omim]Br significantly impaired maize seedling development, with [Opy]Br inducing more severe growth suppression. These phytotoxic effects were also reflected in changes in rhizosphere soil properties. In bacterial communities, [Omim]Br more strongly inhibited membrane transport (e.g., ATP-binding cassette transporters), lipid synthesis, and carbon metabolism, thereby impairing bacterial nutrient uptake and energy metabolism. In fungal communities, saprophytic fungi were activated under both treatments, accelerating organic matter decomposition, whereas pathogens were suppressed, particularly under [Omim]Br treatment. Metabolomic analysis revealed widespread accumulation of amino acids in maize roots following exposure to both ILs, accompanied by significant depletion of the antioxidant glutathione. Carbohydrate metabolism was broadly suppressed, with [Omim]Br exerting a more pronounced inhibitory effect. Hormone levels were generally reduced, with [Opy]Br causing more severe depletion. Overall, both ILs induced oxidative stress, hormonal disruption, and metabolic imbalance in maize. This study provides a reference for evaluating the risks and regulatory potential of ILs in agricultural environments.}, }
@article {pmid42274506, year = {2026}, author = {Yu, Y and Zhao, Y and He, W and Yu, Z and Yang, Y and Wang, J}, title = {Integrated 16S rRNA Sequencing and Metabolomic Analyses Reveal Gut Microbiota Dysbiosis and Metabolic Perturbations in Neonatal Dairy Calves with Bovine Rotavirus-Induced Diarrhea.}, journal = {Biology}, volume = {15}, number = {11}, pages = {}, pmid = {42274506}, issn = {2079-7737}, abstract = {Bovine rotavirus (BRV) is a major pathogen causing diarrhea in neonatal dairy calves, yet its impact on the gut microbiome and host metabolism remains incompletely understood. This study integrated 16S rRNA gene sequencing and untargeted metabolomics to characterize the fecal microbial and metabolic profiles of BRV-infected diarrheic calves compared to healthy controls. Fecal samples were collected from 16 Holstein calves (<30 days old), equally divided into a BRV-infected group (confirmed by RT-qPCR) and a healthy control group. Alpha diversity analysis revealed a significant reduction in microbial richness (Chao1, p = 0.012) in the BRV group. Beta diversity (Jaccard distance) showed distinct clustering between groups (PERMANOVA, p < 0.05). Linear discriminant analysis effect size (LEfSe) identified a significant enrichment of Escherichia (Proteobacteria) and Enterococcus (Firmicutes) in BRV calves, whereas healthy controls were enriched in Blautia and Faecalibacterium (both Firmicutes, with Faecalibacterium also commonly associated with healthy gut communities). Metabolomic analysis via UHPLC-MS/MS demonstrated a clear separation of metabolic profiles. BRV infection was associated with significant alterations in lipid metabolism pathways, notably elevated levels of lysophosphatidylcholines (LPCs) and lysophosphatidylethanolamines (LPEs). Integrated Spearman correlation analysis revealed extensive and significant associations (|ρ| > 0.6, FDR-adjusted p < 0.05) between differential bacterial genera (e.g., Enterococcus, Escherichia) and differential metabolites (e.g., glycerolipids, amino acid derivatives), suggesting a close linkage between gut microbial dysbiosis and metabolic remodeling during BRV infection. These findings provide a multi-omics perspective on the interplay between the gut microbiota and host metabolism in BRV-induced diarrhea, offering potential insights for developing microbiota-based diagnostic or therapeutic strategies.}, }
@article {pmid42274550, year = {2026}, author = {Edkaidek, H and Dahiya, D and Nigam, PS}, title = {Epigenetic Modulators: Role of Gut Microbiome in Transformation of Nutrient Bioactives and Host Gene Regulation.}, journal = {Cells}, volume = {15}, number = {11}, pages = {}, pmid = {42274550}, issn = {2073-4409}, mesh = {Humans ; *Epigenesis, Genetic ; *Gastrointestinal Microbiome/genetics ; Animals ; DNA Methylation ; *Nutrients/metabolism ; *Gene Expression Regulation ; Polyphenols/metabolism ; }, abstract = {Biological activity of diets consisting of dietary fibers, peptides and polyphenols is largely mediated by the gut microbiota, which converts these compounds into bioactive metabolites. This review examines the microbiota-epigenome axis, highlighting gut microbiota-derived metabolites, including short-chain fatty acids (SCFAs), urolithins, and phenolic acids, that modulate host gene expression through DNA methylation, histone modifications, and non-coding RNA regulation. Current evidence from molecular and microbiome studies indicates that these metabolites influence key metabolic and inflammatory pathways, including lipid absorption via CD36, SIRT1 activation, and one-carbon metabolism involving folate and S-adenosylmethionine (SAM). Inter-individual variability in metabolic responses is associated with differences in microbial composition and metabotypes, which determine the magnitude of epigenetic regulation. Furthermore, dietary polyphenols derived from pomegranate, berries, tea, cocoa, and grapes are shown to modulate gut microbiota composition and enhance epigenetic effects. A "butyrate-polyphenol synergy" model is proposed, in which combined microbial metabolites optimize host epigenetic programming. Overall, agri-food by-products are suggested to function as modulators of the host epigenetic landscape, providing a framework for microbiome-targeted dietary strategies to improve metabolic and inflammatory health.}, }
@article {pmid42274565, year = {2026}, author = {Khan, MS and Faizan, M and Yang, G and Kang, KS}, title = {Gut Dysbiosis-Mediated Major Depressive Disorder: A Review of Pathogenic Mechanisms and Potential Therapeutic Strategies.}, journal = {Cells}, volume = {15}, number = {11}, pages = {}, pmid = {42274565}, issn = {2073-4409}, support = {RS-2025-02263193//Bio &amp; Medical Technology Development Program of the National Research Foundation/ ; RS-2026-25474823//National Research Foundation/ ; }, mesh = {Humans ; *Major Depressive Disorder/therapy/microbiology/etiology ; *Dysbiosis/complications/microbiology/therapy ; *Gastrointestinal Microbiome ; Animals ; }, abstract = {Major depressive disorder (MDD) is a mental illness with high mortality, suicide, and relapse rates that could become the leading cause of health problems worldwide by 2030. The microbiota-gut-brain axis involves bidirectional communication between the human gut microbiota and the central nervous system (CNS). The gut microbiome is a complex ecosystem of approximately 100 trillion microorganisms, including viruses, bacteria, and fungi. The gut microbiota has recently been recognized for its impact on various diseases and health concerns. Several factors influence the composition and structure of gut microbes, ultimately affecting human physiology, with the nervous system being particularly vulnerable. The gut-brain-microbiota axis influences several important brain functions through numerous pathways, including vagus nerve signaling, gut microbial synthesis of metabolites, and immune-related chemicals. These factors can influence neurotransmitter activity, neuroinflammation, behavior, and mental health. Despite increased interest, the possibility of modifying the gut microbiota as a therapeutic approach remains unclear. Although numerous studies suggest that microbiota play an important role in many illnesses, the precise mechanisms are yet to be elucidated, and there are currently no evidence-based, microbiota-focused treatments for these illnesses. Recent research indicates that gut dysbiosis (GD) causes increased intestinal permeability (leaky gut), initiates systemic inflammation, and contaminates the blood. Opportunistic microbial metabolites cross the blood-brain barrier, triggering a neuroinflammatory cascade and apoptotic pathways while affecting neurogenesis and neurotransmitters, ultimately resulting in the development of MDD and anxiety. This review examined the factors influencing normal gut microbiota and GD-mediated MDD, as well as possible therapeutic options. The study outlines its objectives and methodological approaches, including the screening and filtering of research on GD-induced depression. Furthermore, it explored the daily use of dietary supplements, revealing new paths for clinical and preclinical research.}, }
@article {pmid42274631, year = {2026}, author = {Cittadini, C and Iessi, E and Vona, R and Matarrese, P}, title = {Exploring Risk Factors and Sex Differences in Colorectal Cancer: Insights from Current Evidence.}, journal = {Cells}, volume = {15}, number = {11}, pages = {}, pmid = {42274631}, issn = {2073-4409}, support = {PNRR-MAD-2022-12375679//Ministry of Health/ ; }, abstract = {Colorectal cancer (CRC) is the third most diagnosed malignancy and the second leading cause of cancer-related mortality worldwide. A consistent and epidemiologically well-documented feature of CRC is its sexual dimorphism: age-standardized incidence rates are 33-45% higher in men than in women, and mortality rates differ by 43-50%. Beyond epidemiology, biological sex influences tumor location, molecular subtype, and clinical outcome. Women more frequently develop right-sided, microsatellite-unstable tumors driven by the CpG island methylator phenotype pathway, whereas men predominantly present with left-sided, chromosomally unstable tumors harboring APC, KRAS, and TP53 mutations. Sex steroid hormones play a central modulatory role: estrogens, primarily via estrogen receptor β (ERβ), exert tumor-suppressive effects on colonic epithelium, whereas androgens promote pro-inflammatory and pro-tumorigenic signaling through androgen receptor (AR)-dependent pathways. The gut microbiome displays sex-specific compositional profiles ('microgenderome') and contributes to sex-specific CRC susceptibility through bidirectional interactions with sex hormones, shaping distinct immunological and metabolic microenvironments. Finally, sex influences the pharmacokinetics of fluoropyrimidines, the toxicity of targeted agents, and the response to immune checkpoint inhibitors. This review summarizes current evidence on sex-related differences in CRC epidemiology, molecular pathology, hormonal regulation, gut microbiota composition, and treatment outcomes, highlighting the need to systematically incorporate sex as a biological variable in CRC research and clinical practice.}, }
@article {pmid42274817, year = {2026}, author = {Mehdizadeh, M and Omidi, A and Abideen, Z and Morya, S and Al-Taey, DKA}, title = {Impacts of microplastics on rhizosphere microbiome structure and function: a systematic review.}, journal = {Environmental monitoring and assessment}, volume = {198}, number = {7}, pages = {}, pmid = {42274817}, issn = {1573-2959}, abstract = {The pervasive contamination of agricultural soils by microplastics (MPs) represents a significant environmental stressor with potential repercussions for the rhizosphere microbiome, a critical interface for plant health and soil fertility. This systematic review synthesizes findings from 32 primary studies to evaluate MP-induced stress and its impacts on rhizosphere microbial communities. The evidence consistently demonstrates that microplastics significantly alter microbial community structure, with the majority of studies reporting substantial shifts in beta diversity. The effects on alpha diversity were context-dependent, varying with factors such as polymer type, concentration, and the presence of co-stressors; studies reported both significant decreases (a 9-10% reduction in bacterial richness with 100,000 mg kg[-1] polylactic acid (PLA) MPs) and increases. A critical finding was the marked reduction in beneficial microbial guilds; for instance, specific plant growth-promoting rhizobacteria (PGPR) genera declined significantly (p < 0.05) under combined MP and antibiotic stress. Furthermore, biodegradable microplastics (BMPs; e.g., PLA, poly(butylene adipate-co-terephthalate (PBAT)) induced equally potent or more severe disruptions than conventional polymers, often enriching copiotrophic bacteria and altering functional gene profiles for nutrient cycling. Under the high‑dose, short‑term experimental conditions reviewed, these perturbations compromise plant nutrient acquisition and stress resilience; however, whether such effects scale to environmentally realistic microplastic concentrations remains an open question, necessitating caution when extrapolating to long‑term agricultural sustainability. The review underscores the urgent need for field-relevant, long-term studies to fully understand the ecological risks posed by MPs in terrestrial ecosystems.}, }
@article {pmid42275074, year = {2026}, author = {Yang, B and Yuen-Simović, B and Yuan, H and Degnan, BM and Degnan, SM}, title = {Early transcription factor activation distinguishes symbiotic from non-symbiotic bacteria during microbiome processing in a sponge.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag150}, pmid = {42275074}, issn = {1751-7370}, abstract = {Animals that filter-feed on environmental microbes must rapidly discriminate among captured bacteria to maintain beneficial associations while avoiding inappropriate immune activation. In innate immunity, this discrimination is executed through transcription factors (TFs), whose activation and nuclear translocation initiate effector gene expression and shape the nature of the host response. In sponges, bacteria are first physically captured by choanocytes, but the timing and cellular context in which TF-mediated immune discrimination becomes evident remains unclear. Here, we investigate the earliest detectable regulatory responses associated with discrimination between symbiotic and non-symbiotic bacteria in the marine sponge Amphimedon queenslandica. Using a feeding-based design to model post-metamorphic microbiome restructuring, we exposed juvenile sponges that already harbour vertically inherited symbionts to native (symbiont) or foreign (non-symbiont) bacterial communities and assessed early cellular processing and transcriptional responses to bacterial uptake. Symbiotic bacteria were rapidly transported across the epithelium and induced a strong, transient activation of conserved innate immune TFs, including IRF, NF-κB, and STAT, together with associated signalling pathways. IRF and NF-κB translocated to the nuclei of amoebocytes that had engulfed symbionts, indicating that discrimination becomes evident shortly after uptake and precedes downstream effector responses. In contrast, foreign bacteria were internalized more slowly, failed to induce coordinated immune TF activation or nuclear translocation, and instead elicited a xenobiotic-dominated transcriptional program. Together, these findings identify TF activation as an early regulatory checkpoint in sponge-microbe interactions and reveal key mechanisms that underpin the initial stages of symbiont discrimination.}, }
@article {pmid42275092, year = {2026}, author = {Marsh, G and Bourquin, M and Leale, A and Bröder, L and Altshuler, I}, title = {Soil microbial diversity, succession, and greenhouse gas cycling across a Greenlandic glacial chronosequence.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag054}, pmid = {42275092}, issn = {1574-6941}, abstract = {Accelerated glacial retreat in Greenland drives increased development of glacial outwash plains. These newly exposed landscapes provide an opportunity to study microbial dynamics during soil development. We explore soil microbial diversity, community assembly, and biogeochemical cycling across the Kiattuut Sermiat glacial chronosequence (southern Greenland) via 16S rRNA gene amplicon analysis paired with microbial abundance, soil physicochemical parameters, and gas flux data. Microbial diversity varied with soil depth, with more acidic topsoils abundant in Cyanobacteriota and Armatimonadota taxa. While aerobic lower soils likely contained relatively more anoxic pore spaces, hosting aerobic nitrifiers such as Nitrospirota, low oxygen associated Planctomycetota taxa, and less characterised Gemmatimonadota. Microbial diversity varied across the chronosequence following distance-decay principles, as communities were predominately dispersal limited and shaped by heterogenous selection, with greater heterogeneous conditions further from the glacier terminus. Soil CO2 fluxes increased with distance from the glacier, following a shift from autotrophic sulfur- and iron-oxidising taxa towards heterotrophic members. CH4 fluxes demonstrated greater uptake further from the glacier and CH4-oxidation was associated with the methanotroph Methylocapsa. Considering the climatic relevancy of Greenlandic proglacial environments, we describe the largely unexplored microbial diversity and biogeochemical cycling of greenhouse gases in these developing soils.}, }
@article {pmid42275109, year = {2026}, author = {Reich, HG and Cunningham, NR and Abramenko, AP and Adler, J and Budavari, P and Charendoff, I and Coleman, T and Crooke, S and Flint, A and Goeler-Slough, N and Houssein, A and Kwakye, B and Langer, M and Langer, M and Lennertz, H and Lin, S and McAllister, J and Mohammed, S and Morales, C and Ngochanthra, M and Noppenberger, J and Osbaldeston, R and Palacios, K and Shin, E and Sicher, E and Hillaire, TS and Sun, X and Totah, F and Villafañe, K and Wood, A and Zhao, B and Smith, M and Yoshida, O and Allen, C and Dvorak, J and Matthews, MC and Wink, HR and Richard, C and Stadtfeld, C and Smith, S and Dallmeyer-Drennen, G and Harvey, EL and Whalen, KE}, title = {Widespread siderophore production among Symbiodiniaceae-associated bacteria.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnag069}, pmid = {42275109}, issn = {1574-6968}, abstract = {Nutritional exchanges fuel the evolutionary and ecological dominance of multi-partner symbioses among reef-building corals and microbial associates in oligotrophic tropical marine ecosystems. Mutualistic relationships with endosymbiotic dinoflagellates (Family Symbiodiniaceae) are central to coral holobiont metabolism, yet their metabolic contributions are sensitive to nutrient availability. Symbiodiniaceae may compensate for oligotrophic environments via metabolic exchanges with prokaryotic partners. Bacterial production of ligands with affinities for otherwise insoluble elements promotes uptake and exchanges. Bacterial secretion of small molecules with high Ferric (Fe3+) iron affinities, herein referred to as siderophore production, presents one example of microbial metabolic cooperation. We isolated 78 pure bacterial culture lines from 14 Symbiodiniaceae cultures to screen for siderophore production using a Chrome Azurol S (CAS) overlay assay. Colorimetric changes observed on CAS overlays indicated ubiquitous siderophore production across 22 bacterial genera. Many of the isolated bacterial cultures corresponded to known 'core' Symbiodiniaceae microbiome. These results suggest an avenue of bacterial metabolism may facilitate biotic iron exchange among coral holobiont partners. Future characterization of the identity siderophores secreted will inform predictions on their impacts on iron exchange within the coral holobiont. Ultimately, a greater ability to acquire iron via siderophore production may improve the coral holobiont's tolerance to environmental stressors.}, }
@article {pmid42275114, year = {2026}, author = {Lu, TT and Isip, M and Han, CJ and Shih, HJ and Syukur, S and Trinh, LL and Perin, S and Lin, YC and Lin, PA and Ma, KW}, title = {Upregulated jasmonate signaling shifts Arabidopsis microbiota interactions and stress adaptations through a positive feedback loop.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag146}, pmid = {42275114}, issn = {1751-7370}, abstract = {The model plant Arabidopsis thaliana hosts diverse microbial communities collectively known as the microbiota. The plant microbiota is generally taxonomically structured and, in many cases, confers benefits to the plant host including plant growth promotion and enhanced stress tolerance. However, microbial imbalance can also result in deleterious effects, a phenomenon termed dysbiosis that was first coined in the gut microbiome field. To uncover the regulatory mechanism maintaining healthy plant homeostatic interactions with microbiota, we conducted screening using defined synthetic bacterial communities. We identified an Arabidopsis mutant displaying altered microbial profiles with an overall increase of microbial load and microbiota-dependent growth defects. Transcriptomic analyses combined with phytohormone quantification revealed that these phenotypes are attributed to an upregulation of the jasmonic acid (JA) signaling pathway in this mutant upon microbiota colonization. Furthermore, chemical treatment with different JA inducers reproduced similar phenotypes in wild-type plants, suggesting regulation through a positive feedback loop. Although activation of the JA pathway is typically associated with enhanced plant stress responses, our mutant exhibited reduced pathogen load at the expense of reduced plant growth and impaired salt tolerance. Together, our findings demonstrate that JA signaling not only orchestrates plant growth and defense but also plays a pivotal role in shaping plant-microbiota interactions. Controlled regulation of the JA signaling pathway is therefore essential to maintain balanced plant response to multiple environmental stressors.}, }
@article {pmid42275128, year = {2026}, author = {Takahashi, K and Yoshikawa, Y and Chaki, T and Yamakage, M}, title = {Gut Microbiota Modulation Attenuates Myocardial Ischemia-Reperfusion Injury in Diabetic Mice.}, journal = {Shock (Augusta, Ga.)}, volume = {}, number = {}, pages = {}, doi = {10.1097/SHK.0000000000002882}, pmid = {42275128}, issn = {1540-0514}, abstract = {BACKGROUND: The gut microbiome is increasingly being recognized as a regulator of cardiometabolic health; however, whether microbiome interventions can attenuate myocardial ischemia-reperfusion injury (IRI) in diabetic hearts remains unclear. Therefore, we tested whether fecal microbiota transplantation (FMT) from lean non-diabetic donors could mitigate myocardial IRI in type 2 diabetes mellitus (T2DM) db/db mice and explored candidate taxa associated with protection.<br><br>METHODS: Male db/db mice (T2DM model) received a 14-day course of FMT from lean db/m donors or a vehicle after antibiotic pretreatment. Myocardial IRI was induced, and infarct size was quantified. The gut microbiota was evaluated by 16S rRNA gene sequencing.<br><br>RESULTS: FMT significantly reduced the infarct size as a percentage of the area at risk compared to the IRI group (38.7 &#xb1; 13.4% vs. 58.7 &#xb1; 4.3%, P = 0.003). Microbiome analysis revealed that among alpha-diversity metrics only the Simpson index differed between the donor and diabetic groups. In beta-diversity analyses, diabetic mice clustered separately from donor mice, and the microbiome intervention induced a modest but significant shift detected by the presence or absence of Unweighted UniFrac. Differential abundance analysis and exploratory LEfSe further suggested Akkermansia, particularly Akkermansia muciniphila, as a candidate taxon reduced in diabetic mice and partially restored after the FMT intervention.<br><br>CONCLUSION: A donor-derived microbiome intervention attenuated myocardial IRI in db/db mice and was accompanied by partial remodeling of the gut microbiota. Akkermansia muciniphila emerged as a candidate taxon associated with a reduced susceptibility to IRI in diabetic hearts.}, }
@article {pmid42275228, year = {2026}, author = {Harsonowati, W and Sanjaya, LL and Krismawati, A and Rembang, JHW and Rawung, JBM and Widiyono, W and Doni, F and Iqbal, R and Ullah, S}, title = {Endophyte function in climate-stressed crops: integrating molecular regulation, metabolic trade-offs, and ecological constraints.}, journal = {Plant signaling &amp; behavior}, volume = {21}, number = {1}, pages = {2687952}, doi = {10.1080/15592324.2026.2687952}, pmid = {42275228}, issn = {1559-2324}, mesh = {*Endophytes/physiology/metabolism ; *Stress, Physiological ; *Crops, Agricultural/microbiology/metabolism ; *Climate Change ; Reactive Oxygen Species/metabolism ; }, abstract = {Climate change increasingly exposes crops to simultaneous abiotic and biotic stresses, disrupting physiological stability and reducing agricultural productivity. Although endophytes are widely recognized for improving plant stress tolerance, their effectiveness remains inconsistent across environmental conditions. This review develops an integrative framework to explain how endophyte-mediated responses are regulated at the molecular, metabolic, and ecological levels under climate stress. We examine multi-level interactions to inform predictive deployment in varied agricultural environments. We critically synthesize recent studies on ROS-hormone signaling, carbon allocation trade-offs, metabolic reprogramming, microbiome interactions, ecological filtering, and host genotype-dependent responses. We aim to identify mechanisms that govern the stability or destabilization of plant-endophyte associations under stress conditions. The analysis indicates that endophyte-mediated beneficial traits remain effective only when redox regulation, metabolic balance, and ecological compatibility are maintained within functional physiological limits. Under severe or prolonged stress, disruption of ROS homeostasis, carbon limitation, and ecological instability progressively reduce symbiotic effectiveness, physiological stability, and plant growth performance. Potential predictive variables in this framework include ROS accumulation thresholds, antioxidant capacity, photosynthetic stability, carbon allocation balance, and ecological persistence of endophytes under fluctuating environmental conditions. These variables may enable the prediction of endophyte functional stability, stress adaptation, and growth promotion under heterogeneous climate stress conditions. Collectively, this framework advances current understanding from descriptive interpretation toward a context-dependent perspective that may support future prediction and validation of endophyte performance in climate-resilient agriculture.}, }
@article {pmid42275298, year = {2026}, author = {Majumder, A and Majumder, S and Bano, S and Sen, K and Nayak, KB}, title = {Significance of GSH and H2S regulation for cancer: an intricate interplay between diet, microbiota, metabolic reprogramming, and immune health.}, journal = {Redox report : communications in free radical research}, volume = {31}, number = {1}, pages = {2687238}, doi = {10.1080/13510002.2026.2687238}, pmid = {42275298}, issn = {1743-2928}, abstract = {Due to the proliferative nature of cancer cells, they utilize more dietary extracellular nutrients via one-carbon metabolism for the various metabolic processes, including the synthesis of antioxidants such as glutathione (GSH) and hydrogen sulfide (H2S). Indeed, several studies have found that specific cancer types produce significantly higher levels of GSH and H2S than normal healthy cells, which may serve as a protective mechanism, allowing them to resist stress, survive, and grow. This metabolic heterogeneity, driven by intrinsic and extrinsic factors, contributes to the distinct metabolic characteristics and vulnerabilities of tumor subtypes, which can be exploited to develop anticancer strategies. In this review, we summarize the fundamental roles and regulation of GSH and H2S in normal physiological systems and in the genesis and progression of cancer, their effects on the tumor microenvironment (TME), and their contribution to drug resistance. We also discuss the influences of diet and the gut microbiome on GSH and H2S production, and how cancer cells reprogram their metabolism to grow and survive in a stressful environment by overproducing GSH and H2S.}, }
@article {pmid42275736, year = {2026}, author = {Barcan, RA and Carradori, S and Samsing, F and Nguyen, NL and He, L and Wang, Y and Barcan, AS}, title = {Machine learning in applied microbiology, from data quality to model validation and implementation.}, journal = {Microbiological research}, volume = {311}, number = {}, pages = {128588}, doi = {10.1016/j.micres.2026.128588}, pmid = {42275736}, issn = {1618-0623}, abstract = {Machine learning (ML) is now widely applied in microbiology, but its reliability varies markedly across domains. In this review, we analysed data from 254 scientific articles that evaluates ML through three linked dimensions including data readiness, model suitability, and deployment readiness across diagnostics and pathogen identification, virology, microbiome research, industrial and environmental microbial biotechnology. This framework helps distinguish robust progress from performance inflated by methodological limitations. Our review shows that pathogen identification and antimicrobial resistance prediction consistently achieve strong performance when supported by curated datasets, reliable labels, and comprehensive reference databases. However, their practical value remains limited by internal validation, lineage confounding, and uneven transfer across strains, institutions, and regions. In virological studies, predictive stability is further challenged by incomplete reference databases, changing taxonomy, and temporal drift during outbreaks. In microbiome research, ML classifiers can detect disease and environmental signals, but their generalization across cohorts remains weak because of compositional data structure, technical bias, and incomplete metadata. Industrial bioprocessing and environmental applications show promise when process data are rich and controlled, but deployment beyond laboratory or site-specific settings remains limited. Across structured microbiological datasets, classical supervised models often remain competitive with deep learning while being easier to interpret and validate. Detailed quantitative benchmarks supporting these comparisons are synthesized in the main text and summary tables. Overall, progress will depend less on algorithmic novelty than on interoperable and well-annotated datasets, representative sampling, standardized benchmarking, reproducible workflows, and prospective multi-site validation.}, }
@article {pmid42276012, year = {2026}, author = {Budzinski, L and Beenken, AE and Sempert, T and Kang, GU and Abbas, A and Lietz, L and Maier, R and Mashreghi, MF and Chang, HD and Alexander, T}, title = {IgG4-related disease has a specific intestinal microbiota signature.}, journal = {EBioMedicine}, volume = {129}, number = {}, pages = {106326}, doi = {10.1016/j.ebiom.2026.106326}, pmid = {42276012}, issn = {2352-3964}, abstract = {BACKGROUND: While the intestinal microbiome has been implicated in Immunoglobulin-4 related disease (IgG4-RD), it remains poorly characterised. Therefore, we performed a comprehensive microbiome characterisation to identify disease-specific alterations.<br><br>METHODS: In this cross-sectional study, cryopreserved stool samples from 28 patients with IgG4-RD were characterised by 16S rRNA gene sequencing and by multiparameter microbiota flow-cytometry to determine their taxonomic composition and phenotype at the single cell level. These data were evaluated in comparison with 24 healthy controls (HC) and assessed for their potential to classify IgG4-RD using random forest classification, with an independent validation cohort (12 IgG4-RD, 12 HC).<br><br>FINDINGS: Patients with IgG4-RD exhibited reduced taxonomic diversity and disease-specific alterations in the microbiome compared to HC, characterised by significantly elevated levels of several species within the Bacillota phylum. These taxonomic alterations classified patients and HC with an AUROC of 0.87 (95% CI: 0.77-0.97) but showed reduced performance in the validation cohort (AUROC 0.58, 95% CI: 0.29-0.87). Flow cytometry revealed distinct phenotypic microbiota alterations, robustly distinguishing patients with IgG4-RD from HC in both the training (AUROC 0.9, 95% CI: 0.81-0.99) and validation cohort (AUROC 0.78, 95% CI: 0.59-0.97). The IgG4-RD microbiota were predominantly DNA-low and showed no enhanced endogenous IgG4 coating, neither natively nor after in vitro incubation with autologous serum.<br><br>INTERPRETATION: Our study revealed specific alterations in the intestinal microbiota on taxonomic and phenotypic level in IgG4-RD, which potentially reflect different mechanisms of adaptations of the gut microbiota to immune disturbances specific to IgG4-RD. We provide proof-of-concept that this "microbiota fingerprint" may be suitable to identify IgG4-RD in a machine-learning approach and may provide important insights into the complexity of intestinal microbiota alterations in IgG4-RD.<br><br>FUNDING: This work was supported by grants from Rolf M. Schwiete Foundation, DFG (German Research Foundation), Innovative Medicines Initiative 2 Joint Undertaking (3 TR), and EFRE-Project.}, }
@article {pmid42276199, year = {2026}, author = {Bertollo, AG and Puntel, CF and Scaini, G and Quevedo, J and Barichello, T and Ignácio, ZM and Réus, GZ}, title = {The interplay between microbiota and the gut-brain axis in treatment-resistant depression.}, journal = {Progress in neuro-psychopharmacology &amp; biological psychiatry}, volume = {}, number = {}, pages = {111782}, doi = {10.1016/j.pnpbp.2026.111782}, pmid = {42276199}, issn = {1878-4216}, abstract = {Major depressive disorder (MDD) is a common psychiatric condition, and many patients do not respond to standard antidepressant treatments, developing what is known as treatment-resistant depression (TRD). The microbiota-gut-brain axis (MGBA) encompasses the biological processes underlying MDD and TRD. This two-way communication system connects the gut microbiome, the immune system, the central nervous system, and hormone signaling. Changes in the composition and diversity of gut microorganisms can affect neurotransmitter production, blood-brain barrier (BBB) function, immune function, and metabolic processes. These changes may contribute to the development and persistence of TRD. This review describes how the MGBA may influence TRD through mechanisms including BBB function, changes in the kynurenine pathway, variations in short-chain fatty acid (SCFA) production, immune and inflammatory responses, imbalances in the hypothalamic-pituitary-adrenal (HPA) axis, and disruptions in neurotransmitter signaling. The review discusses treatment strategies, focusing on the gut microbiome, including modifications, probiotics, and other approaches.}, }
@article {pmid42276495, year = {2026}, author = {Benedetti, F and Rahman, T and Uversky, VN and Zella, D}, title = {DnaK unmasked: Potential contributions of intrinsic disorder to the hijacking of human proteostasis by a bacterial chaperone.}, journal = {International journal of biological macromolecules}, volume = {371}, number = {}, pages = {153019}, doi = {10.1016/j.ijbiomac.2026.153019}, pmid = {42276495}, issn = {1879-0003}, abstract = {Bacteria are abundantly present through the body, and the proteins they secrete into the cellular microenvironment both interact with surface receptors and are internalized and interact with internal proteins responsible for important pathways and functions. One of these proteins is DnaK, a moonlighting bacterial chaperone interacting with many human proteins. Intrinsically disordered regions (IDRs) enable structural flexibility essential for multifunctionality, yet their role in DnaK and its interactors remains unclear. Analyzing data from our previous studies of Mycoplasma DnaK and human protein interactions, this study is the first to employ computational analysis to assess disorder in bacterial DnaK, bacterial proteomes, and human interactors, aiming to elucidate novel disorder-mediated mechanisms of bacterial pathogenesis. Results indicate that bacterial chaperones, including DnaK, are expected to be significantly more disordered than the proteome averages (∼27-42% chaperones are highly disordered vs. ∼7-10% proteome-wide highly disordered proteins). Human proteins interacting with bacterial DnaK cluster in chromatin organization and RNA processing networks. DnaK interactors are significantly more disordered than human HSP70/HSC70 interactors, as well as average human proteins, nuclear proteins, and proteins involved in RNA processing and DNA repair. Confirmed interactors, such as XRCC1 and USP10, feature long IDRs with many PTMs, have multiple disorder-based binding regions, and show high LLPS propensity, suggesting that disorder facilitates cellular pathways subversion. These findings are consistent with a model, in which DnaK, by virtue of its structural flexibility, may preferentially engage disordered host proteins, potentially influencing cellular pathways, paving the way for a hypothesis that warrants direct experimental validation.}, }
@article {pmid42276549, year = {2026}, author = {Camus, J and Freeman, CD and Hu, X and Komnik, A and Casey, RL and Brewer, DT and Yang, S and Hines, KM and Tchoupa, AK}, title = {Extracellular wax ester biosynthesis by staphylococcal lipases detoxifies skin fatty acids and shapes interspecies competition.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag148}, pmid = {42276549}, issn = {1751-7370}, abstract = {To maintain its barrier function, human skin requires lipids, including cholesterol, ceramides, free fatty acids, and wax esters. In contrast to other skin lipids, wax esters remain largely unexplored as metabolites of the skin microbiome. Recently, we discovered that Staphylococcus aureus utilizes its lipase Lip2 to detoxify antimicrobial fatty acids (AFAs) by esterification with cholesterol. The observed promiscuity of Lip2 and the presence of similar lipases among skin staphylococci prompted the search for novel substrates and products. Here, we identify S. aureus Lip2 and Lip1, Staphylococcus simulans SsL, and Staphylococcus epidermidis GehD and GehC as lipases capable of metabolising wax esters. These lipases degraded wax esters into AFAs and fatty alcohols, and, except for GehC, shared the ability to esterify AFAs with fatty alcohols thereby generating wax esters. In monocultures of bacteria heterologously expressing staphylococcal lipases, synthesis of wax esters mirrored protection from AFAs by fatty alcohols in planktonic or biofilm settings. In pairwise cocultures, lipases secreted by lipase-proficient Staphylococcus aureus, Staphylococcus simulans, and Staphylococcus epidermidis functioned as public goods, rescuing lipase-deficient mutants. In absence of detoxifying substrates/lipases, Staphylococcus simulans or Staphylococcus epidermidis outcompeted Staphylococcus aureus when exposed to AFAs. A skin-mimicking high-salt environment increased the resistance of Staphylococcus aureus, but not Staphylococcus simulans, to AFAs, enabling Staphylococcus aureus to match or outcompete Staphylococcus simulans in the presence of AFAs or AFAs plus fatty alcohols, respectively. Collectively, our findings suggest that commensal modulation of skin lipids determines whether niche-specific communities are resilient or permissive to pathogenic invasion by Staphylococcus aureus.}, }
@article {pmid42276619, year = {2026}, author = {Upadhyay, R and Santhosh, S and Malathi, R and Kumari, PS and Vijayanand, S and Sevanan, M}, title = {Starved synapses: Gut microbiome dysbiosis and its role in Alzheimer's glucose impairment.}, journal = {International review of neurobiology}, volume = {186}, number = {}, pages = {241-264}, doi = {10.1016/bs.irn.2026.01.010}, pmid = {42276619}, issn = {2162-5514}, mesh = {Humans ; *Alzheimer Disease/metabolism/microbiology ; Animals ; *Glucose/metabolism ; *Dysbiosis/metabolism ; *Gastrointestinal Microbiome/physiology ; *Blood-Brain Barrier/metabolism ; *Brain/metabolism ; }, abstract = {Alzheimer's disease (AD) is increasingly recognised as a multifactorial disorder driven by metabolic, microbial, and neuroinflammatory imbalances. The study of the research results proposes that gut dysbiosis and impaired brain glucose metabolism are closely interrelated through the gut-brain metabolism axis. Changes in the intestinal microbiome may disrupt insulin sensitivity, cause systemic inflammation, and disrupt the blood-brain barrier, worsening neuronal glucose deficits and facilitating amyloid-β (Aβ) aggregation and tau phosphorylation. Alongside, neurodegenerative cascades are further enhanced by neuronal metabolic reprogramming, characterised by decreased glucose uptake, dysfunctional glycolytic enzymes, and oxidative stress. Short-chain fatty acids (SCFAs) are mainly butyrate, which have a neuroprotective effect in regulating inflammation and gut integrity, and dysbiosis causes increased pro-inflammatory cytokines and endotoxin leakage. This two-way communication network provides new therapeutic opportunities, such as probiotics, prebiotics, nutritional control, and metabolic reprogramming interventions, to regain homeostasis and prevent the advancement of AD.}, }
@article {pmid42276744, year = {2026}, author = {Thornton, CS and Schaupp, L and Tunney, MM and Mall, MA}, title = {Bridging the airway microbiome and targeted therapy in bronchiectasis: multi-omics insights, endotypes and emerging therapies.}, journal = {The European respiratory journal}, volume = {}, number = {}, pages = {}, doi = {10.1183/13993003.00239-2026}, pmid = {42276744}, issn = {1399-3003}, abstract = {Bronchiectasis is a heterogeneous chronic airway disease primarily driven by persistent infection, microbial dysbiosis and dysregulated host immunity. While culture-based microbiology has historically informed clinical management, advances in high-throughput sequencing and multi-omic technologies have transformed our understanding of the airway ecosystem, revealing that disease activity is shaped, not only by individual pathogens, but by complex and dynamic host-microbe interactions. Despite the breadth of descriptive microbiome data, translation into clinically actionable diagnostics or therapies has been limited. Importantly, cross-sectional correlations between microbiota and inflammation do not establish cause and effect, underscoring the need to embed host-microbiome profiling within both longitudinal and interventional therapeutic trials. In this review, we critically appraise current microbial and host multi-omics research in bronchiectasis, integrating microbiome studies with host inflammatory, proteomic and immunophenotyping data. We highlight themes emerging across cohorts, including low microbial diversity, pathogen dominance, loss of commensal networks and neutrophil-driven inflammation and discuss how these features align with biological endotypes associated with exacerbations and treatment response. Drawing on lessons from host-directed therapeutic successes, we examine translational roadblocks limiting microbiome-guided care. We further review emerging microbiome-modulating strategies such as pathogen-specific biologics, bacteriophage therapy, live biotherapeutic products, biofilm-targeting adjuncts and precision antibiotic stewardship. Finally, we propose a roadmap toward microbiome-informed precision medicine through harmonized methodologies, integration of host and microbial biomarkers into clinical trials and embedding multi-omics pipelines within large international registries. Collectively, these advances have the potential to shift bronchiectasis research and clinical management towards rationally designed, precision medicine-driven therapeutic strategies.}, }
@article {pmid42276769, year = {2026}, author = {Fang, F and Lau, HC and Yu, J}, title = {Microbiota and metabolites modulation of cancer stem cells and chemotherapy sensitivity.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2026-338801}, pmid = {42276769}, issn = {1468-3288}, abstract = {Cancer stem cells (CSCs) drive tumour initiation, metastasis and therapeutic resistance through metabolic and microenvironmental adaptability. The microbiota critically modulates cancer development and treatment response, with increasing evidence linking commensal microbes and their metabolites to aberrant CSC function. In this review, we summarise the mechanistic roles of microbiota and metabolites (eg, short-chain fatty acids, bile acids) in CSC regulation, including their effects on the CSC niche via stromal cell modulation, extracellular matrix remodelling and soluble factor networks. Given the central roles of CSCs in chemoresistance, we further discuss how microbes and metabolites influence CSC-associated chemotherapy resistance and highlight microbiota-targeting and metabolite-targeting strategies including probiotics, metabolite formulations, antibiotics and nanomedicine to disrupt CSCs and enhance chemosensitivity. In summary, deeper insights into CSC-microbiota-metabolites crosstalk promise novel therapeutic targets to overcome resistance and improve patient outcomes.}, }
@article {pmid42276771, year = {2026}, author = {Kang, G and Lam, WKJ}, title = {Beyond the virus: rethinking nasopharyngeal carcinoma through the gut microbiome.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2026-339135}, pmid = {42276771}, issn = {1468-3288}, }
@article {pmid42276790, year = {2026}, author = {Gonen-Colak, B and Turan-Demirci, B and Buyuktuncer, Z}, title = {Modification of Gut Microbiome by Cereal and Pseudocereal Consumption: A Systematic Review.}, journal = {Nutrition reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/nutrit/nuag078}, pmid = {42276790}, issn = {1753-4887}, support = {20780//Hacettepe University Scientific Research Projects Coordination Unit/ ; }, abstract = {CONTEXT: Diet profoundly shapes the composition and function of the gut microbiome. Cereals and pseudocereals, as part of a healthy diet, may have significant potential in the modulation of the gut microbiome.<br><br>OBJECTIVE: This review aimed to systematically analyze the evidence from human intervention studies that examine the effects of cereal and pseudocereal consumption on the gut microbiome composition, diversity, and metabolites.<br><br>DATA SOURCES: Three electronic databases were searched from database inception to May 2025: PubMed/Medline, the Web of Science, and Cochrane. This review included randomized controlled trials with parallel and crossover designs, controlled nonrandomized intervention studies, and single-arm pre-post intervention studies. In addition, only English-language articles reporting changes in the gut microbiome and bacterial fermentation metabolites associated with dietary intake of cereal and pseudocereals in adult individuals (>18&#x2009;years) were included.<br><br>DATA EXTRACTION: Basic information regarding the methodological characteristics of the included studies and the outcome measures was recorded.<br><br>DATA ANALYSIS: A total of 9670 articles were analyzed, of which 48 articles were ultimately included. The majority of the included studies (41/48) showed that cereal consumption was associated with significant changes in the gut microbiome composition. In terms of microbial diversity, only 4 of 29 studies showed significant increases in the &#x3b1;-diversity of the gut microbiome. Among the 28 studies analyzing short-chain fatty acid levels, 12 studies reported significant changes in the levels of short-chain fatty acids.<br><br>CONCLUSIONS: Although the importance of daily cereal consumption in modulating the gut microbiome is recognized, well-designed new studies are needed to identify the most effective types of cereal or pseudocereals, and the amount that is adequate to achieve the desired modulation.}, }
@article {pmid42276807, year = {2026}, author = {Souza, MCDCD and de Jármy-Di Bella, ZIK and Bianchi-Ferraro, AMHM and Souza, SDL and Amanda Rafaelly Honório, M and Sobral, APT and Ribeiro, CDPV and Bussadori, SK and Fernandes, KPS and Chavantes, MC and Zamuner, SR}, title = {Effects of Erbium:YAG laser combined with vaginal estriol therapy in postmenopausal women with Genitourinary Syndrome of Menopause: protocol for a randomised, double-blind, controlled trial.}, journal = {BMJ open}, volume = {16}, number = {6}, pages = {e117269}, doi = {10.1136/bmjopen-2026-117269}, pmid = {42276807}, issn = {2044-6055}, mesh = {Humans ; Female ; *Estriol/administration &amp; dosage/therapeutic use ; Double-Blind Method ; Middle Aged ; *Lasers, Solid-State/therapeutic use ; *Postmenopause ; *Female Urogenital Diseases/therapy/drug therapy ; Vagina ; Aged ; Syndrome ; Combined Modality Therapy ; Administration, Intravaginal ; Treatment Outcome ; Research Design ; }, abstract = {INTRODUCTION: Genitourinary syndrome of menopause (GSM) is a chronic, oestrogen-deficient condition that is frequently underdiagnosed and undertreated. Although low-dose vaginal estriol improves epithelial trophism and microbial balance, a substantial proportion of women report persistent symptoms. High-quality randomised evidence evaluating combined therapeutic strategies remains scarce. Energy-based modalities, including the erbium:YAG (Er:YAG) laser (λ=2940 nm), have been proposed as adjunctive treatments. This trial aims to assess the efficacy of Er:YAG laser therapy combined with vaginal estriol compared with estriol alone in postmenopausal women with GSM.<br><br>METHODS AND ANALYSIS: This is a single-centre, randomised, double-blind, controlled clinical trial. Postmenopausal women aged 45-70 years with vaginal pH &#x2265;5.0&#x2009;and at least one moderate GSM symptom (Visual Analogue Scale &#x2265;4) will be eligible. Exclusion criteria include current systemic or local hormone therapy, previous vaginal energy-based treatment, abnormal cervical cytology and body mass index &#x2265;35&#x2009;kg/m[2]. All participants will receive vaginal estriol cream (0.5&#x2009;mg per dose) daily for 14 days, followed by twice-weekly administration for 16 weeks. Participants will be randomised (1:1) to receive either estriol plus sham Er:YAG laser or estriol plus active Er:YAG laser. Three laser sessions will be delivered at approximately 4-week intervals. Assessments will occur at baseline, monthly during treatment and 4&#x2009;months after the final session. The primary outcome is the Vulvovaginal Health Index, with the primary endpoint defined as the change from baseline to 4&#x2009;months post-treatment, reflecting sustained effect. Secondary outcomes include GSM symptom severity, vaginal microbiome composition (16S rRNA sequencing), quality of life (Menopause Rating Scale) and sexual function (Female Sexual Function Index). Data will be analysed using repeated-measures analysis of variance or appropriate non-parametric tests, with significance set at p<0.05.<br><br>ETHICS AND DISSEMINATION: Ethical approval has been obtained from the Human Research Ethics Committee of UNINOVE. Written informed consent will be obtained. Findings will be disseminated via peer-reviewed journals and scientific meetings.<br><br>TRIAL REGISTRATION NUMBER: NCT06873971.}, }
@article {pmid42276920, year = {2026}, author = {Guldan, M and Shah, E and Al-Shiab, R and Ozbek, L and Covic, A and Kanbay, M}, title = {Linking the exposome to frailty: pathways, mechanisms, clinical implications, and prevention.}, journal = {European journal of internal medicine}, volume = {}, number = {}, pages = {107006}, doi = {10.1016/j.ejim.2026.107006}, pmid = {42276920}, issn = {1879-0828}, abstract = {BACKGROUND: Frailty is a state of vulnerability that emerges from cumulative, non-genetic influences acting across the life course. This review applies an exposome lens, integrating general external exposures, specific external exposures, and internal biologic processes. We aimed to synthesize how social, environmental, behavioural, clinical, and biological exposures contribute to frailty and identify clinically actionable prevention targets.<br><br>METHODS: This structured narrative review synthesized epidemiological, clinical, environmental, and mechanistic evidence linking exposome-related exposures to frailty in older adults. Literature was identified through targeted searches of PubMed/MEDLINE, Scopus, Web of Science, and Google Scholar, supplemented by reference screening. Evidence was organized across exposome domains and narratively appraised according to study design, temporality, consistency, biological plausibility, and clinical relevance.<br><br>RESULTS: Socioeconomic disadvantages, loneliness, and social isolation are consistently associated with higher frailty risk, whereas green and walkable environments may support healthier aging through mobility and social participation. Protective factors include specific high-quality dietary patterns and physical activity, whereas ultra-processed foods, sedentary behaviour, air pollution, climate stressors, infections, and selected chemical exposures are linked to adverse outcomes. Cardiometabolic, cardiorespiratory, and neurological vulnerability further connect external exposures with frailty progression. Internal pathways, including chronic inflammation, mitochondrial dysfunction, endocrine-metabolic dysregulation, gut microbiome dysbiosis, and epigenetic aging support plausible mechanistic pathways through which exposures may contribute to frailty.<br><br>CONCLUSION: Exposome-informed frailty care should combine validated frailty assessment with brief screening for actionable risks, including social connection, diet, physical activity, pollution and temperature vulnerability, infection history, vaccination status, and chronic disease burden. Practical strategies include social prescribing, healthier dietary patterns (e.g., Mediterranean-style diets), physical activity in green and low-pollution spaces, seasonal health planning, vaccination, and cardiometabolic optimization.}, }
@article {pmid42277050, year = {2026}, author = {Xu, J and Han, Z and Xue, Q and Wang, H and Li, Y and Song, J and Li, L and Hu, M and Wang, D}, title = {Gut commensal Odoribacter splanchnicus attenuates hyperlipidemic periodontitis via gut-oral metabolic transmission of β-GPA.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01033-4}, pmid = {42277050}, issn = {2055-5008}, support = {82470987//National Natural Science Foundation of China/ ; jcsz2025678-2//Science and Technology Project of Jilin Province Department of Finance/ ; 2024JBGS07//"Medicine+X" Interdisciplinary Innovation Project/ ; }, abstract = {Hyperlipidemic periodontitis (HPD) represents a prevalent comorbidity linking systemic metabolic dysregulation with local inflammation, yet the microbial mechanisms driving this gut-oral crosstalk remain elusive. Here, the comorbid state of HPD is linked to hyperlipidemia-associated gut microbiota changes, which are prominently accompanied by the depletion of Odoribacter splanchnicus in both patients and mice. Fecal microbiota transplantation demonstrates that this gut dysbiosis exacerbates periodontal destruction when local inflammation is present. Mechanistically, intragastric administration of live O. splanchnicus ameliorates HPD by remodeling the gut ecosystem and upregulating the metabolite β-guanidinopropionic acid (β-GPA). Notably, direct supplementation with β-GPA reproduces these protective effects. Furthermore, β-GPA is proposed as a systemic effector linking the gut and periodontal tissues, where its protective effect is associated with the suppression of the pro-inflammatory Toll-like receptor 4 (TLR4) signaling cascade. These findings highlight a link involving O. splanchnicus, β-GPA, and the modulation of TLR4 signaling, offering a potential microbiome-based therapeutic strategy for managing complex metabolic-inflammatory comorbidities.}, }
@article {pmid42277130, year = {2026}, author = {González-Stegmaier, R and Ejsmentewicz, T and Podesta, C and Jorquera, R and Lagos, R and Barrientos, C and Aravena, E and Larrain, M and Aguilera, JP and Silva-Moreno, E and Villarroel-Espíndola, F}, title = {Gut microbiome profiles in Chilean participants with colorectal adenomas: an exploratory 16S rRNA sequencing study.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-57417-1}, pmid = {42277130}, issn = {2045-2322}, support = {LMT-2020 &amp; LMT-2021//Fundaci&#xf3;n Arturo L&#xf3;pez P&#xe9;rez (FALP) Cancer Center/ ; LMT-2020 &amp; LMT-2021//Fundaci&#xf3;n Arturo L&#xf3;pez P&#xe9;rez (FALP) Cancer Center/ ; LMT-2020 &amp; LMT-2021//Fundaci&#xf3;n Arturo L&#xf3;pez P&#xe9;rez (FALP) Cancer Center/ ; LMT-2020 &amp; LMT-2021//Fundaci&#xf3;n Arturo L&#xf3;pez P&#xe9;rez (FALP) Cancer Center/ ; LMT-2020 &amp; LMT-2021//Fundaci&#xf3;n Arturo L&#xf3;pez P&#xe9;rez (FALP) Cancer Center/ ; LMT-2020 &amp; LMT-2021//Fundaci&#xf3;n Arturo L&#xf3;pez P&#xe9;rez (FALP) Cancer Center/ ; LMT-2020 &amp; LMT-2021//Fundaci&#xf3;n Arturo L&#xf3;pez P&#xe9;rez (FALP) Cancer Center/ ; LMT-2020 &amp; LMT-2021//Fundaci&#xf3;n Arturo L&#xf3;pez P&#xe9;rez (FALP) Cancer Center/ ; LMT-2020 &amp; LMT-2021//Fundaci&#xf3;n Arturo L&#xf3;pez P&#xe9;rez (FALP) Cancer Center/ ; LMT-2020 &amp; LMT-2021//Fundaci&#xf3;n Arturo L&#xf3;pez P&#xe9;rez (FALP) Cancer Center/ ; LMT-2020 &amp; LMT-2021//Fundaci&#xf3;n Arturo L&#xf3;pez P&#xe9;rez (FALP) Cancer Center/ ; 1221415//ANID-FONDECYT/ ; }, abstract = {Colorectal cancer (CRC) is the third most commonly diagnosed cancer globally and the second leading cause of cancer-related mortality. The disease typically progresses from premalignant adenomatous lesions. Recent studies highlight the pivotal role of the gut microbiota in colorectal carcinogenesis, suggesting a complex interplay between the microbiota and tumor development. This study analyzes gut microbiota profiles in a single-center cohort of Chilean individuals with and without adenomas, using 16S rRNA sequencing to interrogate microbial changes associated with the transition from healthy colon epithelium to precancerous lesions. The results show that the adenoma-associated microbiota is characterized by increased Proteobacteria abundance and decreased Firmicutes abundance compared with healthy controls. Participants with precancerous lesions exhibit increased abundance of Desulfovibrio, a genus of sulfate-reducing bacteria capable of producing hydrogen sulfide (H2S), a microbial metabolite that has been linked to DNA damage and epithelial stress responses. These findings provide a baseline of the microbial landscape in our population and identify biomarkers associated with premalignant lesions, highlighting microbiome analysis as a diagnostic tool for colorectal disease.}, }
@article {pmid42277260, year = {2026}, author = {Jie, Z and Liang, W and Ding, Q and Liu, X and Zhang, Y and Chen, N and Li, S and Tong, X and Gao, H and Lu, R and Huang, X and Guo, R and Chen, J and Zhu, J and Zhang, Z and Liu, N and Xie, Z and Wang, X and Qi, L and Li, Y and Xiao, L and Zhang, S and Jin, X and Xu, X and Yang, H and Wang, J and Zhao, F and Jia, H and Kristiansen, K and Zhang, T and Hao, L and Zhu, L and Chen, C}, title = {Genomic landscape of the human vaginal microbiome is linked to host genetics and population of origin.}, journal = {Nature genetics}, volume = {}, number = {}, pages = {}, pmid = {42277260}, issn = {1546-1718}, abstract = {The vaginal microbiome is essential for women's health, yet its genomic diversity and interaction with the host remain incompletely characterized. Here we present the Global Vaginal Metagenome-assembled Genomes catalog, an extensive repository of vaginal microbial genomes generated by integrating 10,665 in-house Chinese metagenomes, with 2,967 publicly available metagenomes and 1,433 bacterial isolates. The catalog comprises 65,055 genomes from 890 prokaryotes, 11 eukaryotes and 6,590 viral taxonomic units, many not represented in public reference databases. We investigate virus-bacteria interactions, revealing conserved phages-host associations. We then identify substantial intraspecies genomic and functional variations displaying population-specific patterns. A metagenome-genome-wide association study identifies seven host genetic loci associated with vaginal species at study-wide significance and replicated in at least one independent cohort, notably connecting the gene OPRK1 with the potential pathogen Ureaplasma urealyticum. In summary, our research provides a comprehensive reference for future studies on genotype-phenotype interplay within the human vaginal microbiome.}, }
@article {pmid42277392, year = {2026}, author = {Bugelli, V and Calabrò, F and Camatti, J and Cecchi, R and Di Paolo, M and Franceschetti, L}, title = {Artificial intelligence in forensic science: a systematic review. Part II: long-range postmortem interval estimation.}, journal = {International journal of legal medicine}, volume = {}, number = {}, pages = {}, pmid = {42277392}, issn = {1437-1596}, abstract = {Postmortem interval (PMI) estimation remains a major challenge in forensic medicine due to the complex and multifactorial nature of decomposition processes. In recent years, artificial intelligence (AI) and machine learning techniques have been increasingly applied to improve PMI prediction. This systematic review aimed to evaluate the current evidence on AI-based models developed for PMI estimation. A systematic literature search was conducted in PubMed/MEDLINE and Scopus from database inception to 1 March 2026, following PRISMA 2020 guidelines. Studies were included if they applied AI, machine learning, or deep learning methods to estimate PMI using real postmortem datasets. Data extraction included study characteristics, data modality, AI model architecture, validation strategy, and reported performance metrics. A total of 64 studies met the inclusion criteria. The most common approach involved microbiome-based models (n = 29), followed by metabolomics and proteomics approaches (n = 11) and imaging-based AI models (n = 11). Random Forest algorithms were the most frequently used machine learning method, particularly in microbiome studies. Reported predictive performance varied widely across studies, with several models achieving high accuracy or low prediction errors depending on the data modality and PMI range investigated. AI represents a promising tool for improving the accuracy and objectivity of PMI estimation by enabling the integration of complex forensic datasets. However, current evidence is limited by heterogeneous methodologies, small datasets, and a lack of external validation. Future research should focus on large multicenter datasets, standardized validation protocols, and multimodal AI models integrating diverse forensic data sources.}, }
@article {pmid42277393, year = {2026}, author = {Babar, P and Babar, S and Ghate, M}, title = {Recent advances in the identification of vaginal fluid for forensic applications.}, journal = {International journal of legal medicine}, volume = {}, number = {}, pages = {}, pmid = {42277393}, issn = {1437-1596}, abstract = {Identification of body fluids in forensic investigations is important for three main reasons: first, the type of body fluid present at the crime scene may indicate the nature and context of the crime; second, one may predict the likelihood of getting quality DNA; and third, it may help to verify or discredit the statements from the victim or suspect. Vaginal fluid (VF) is a common body fluid found at the crime scene in sexual assault cases and is usually found mixed with other body fluids like semen, saliva, and blood. Methods for identifying VF are limited compared to those for blood, semen, and saliva. The existing cytochemical methods for VF detection are destructive and have low sensitivity and specificity. Examination of VF samples using spectroscopic techniques such as Fourier-transform infrared spectroscopy, fluorescence spectroscopy, and Raman spectroscopy has revealed unique spectral properties. However, identifying VF with these techniques is complicated, especially when it is mixed with other body fluids. Specific proteins unique to VF have been identified through proteomic studies. New methods to detect microbiome, DNA methylation, and RNA profiles specific to VF are being developed. Although these methods hold promise for correctly identifying VF traces at crime scenes, challenges such as high cost, complex data interpretation, and limited robustness remain. Further research to integrate chemometric algorithms, simplify workflows and develop robust methods is extremely important. Developing methods to identify and detect VF traces that are quick, reliable, non-destructive, and adaptable to existing forensic workflows is the need of the hour.}, }
@article {pmid42277400, year = {2026}, author = {Fu, Y and Long, N and Sourn, P and Zhang, M and Tan, W and Yu, H and Yuan, J and Chen, Y and Wang, J and Zhang, X and Li, X and Wang, S and Feng, L and Wu, J and Wang, Z and Ding, W}, title = {Gardnerella enrichment in the vaginal microbiome of women with gestational diabetes mellitus is associated with lower fetal birthweight percentiles.}, journal = {Diabetologia}, volume = {}, number = {}, pages = {}, pmid = {42277400}, issn = {1432-0428}, support = {2024ZD0532100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 2023BCA004//Hubei Province's Major Scientific and Technological Project/ ; }, abstract = {AIMS/HYPOTHESIS: We aimed to characterise alterations in the late-pregnancy vaginal microbiota in women with gestational diabetes mellitus (GDM), and to examine their associations with maternal glycaemic status and fetal growth.<br><br>METHODS: In this observational case-control study, women with newly diagnosed, diet-managed GDM (n=60) and healthy pregnant control participants (n=119) were recruited at a single tertiary centre. Vaginal swabs were collected in the third trimester and analysed by full-length 16S rRNA gene sequencing. Associations between vaginal microbiota composition, maternal glycaemic measures, and fetal birthweight percentile (FBW%ile) were evaluated.<br><br>RESULTS: The overall vaginal microbial composition differed between groups despite similar alpha diversity. Beta diversity analyses showed significant separation between the women with GDM and the control group (R=0.068, p=0.011 by ANOSIM). Lactobacillus-dominated communities were less frequent in women with GDM than in control participants (73.3% vs 86.6%, p=0.029), with reduced Lactobacillus abundance (79.8% vs 87.4%, nominal p=0.020) and increased Gardnerella abundance (9.7% vs 1.4%, nominal p=0.011). Within the GDM group, Gardnerella abundance correlated positively with fasting glucose levels (r=0.3617, nominal p=0.007) and inversely with FBW%ile (r=-0.2774, nominal p=0.032). Stratification by FBW%ile (<50% vs &#x2265;50%) showed a higher proportion of non-Lactobacillus-dominated communities (44.4% vs 12.1%, p=0.001) and higher Gardnerella abundance (15.0% vs 3.2%, nominal p=0.020) in the low FBW%ile subgroup. Associations with Gardnerella were attenuated in sensitivity analyses that excluded samples with extreme Gardnerella abundance.<br><br>CONCLUSIONS/INTERPRETATION: Late-pregnancy GDM was associated with modest shifts in vaginal microbial structure, characterised by reduced Lactobacillus dominance and relative enrichment of Gardnerella. Exploratory analyses of associations of Gardnerella with maternal fasting glucose levels and fetal growth suggest that variation in the vaginal microbial environment may contribute to metabolic and fetal growth heterogeneity in women with GDM.}, }
@article {pmid42277415, year = {2026}, author = {Prada, J and Pereira-Dias, L and Santos, JA and Santos, C}, title = {Influence of Environment and Rootstock On the Rhizosphere Bacterial Communities in Four Vineyards of the Douro Demarcated Region.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02798-z}, pmid = {42277415}, issn = {1432-184X}, abstract = {The Douro Demarcated Region (DDR) is a worldwide acknowledged winemaking region. Climate change is threatening the sector, as climatic shifts are expected. This work analyzed environmental and genetic traits modulating the rhizobiome of four vineyards in the DDR, focusing on understanding the hierarchy of ecological conductors for these communities. These vineyards' terroir was environmentally, genetically, and culturally characterized. Rhizosphere bacterial community composition was analyzed using 16S metabarcoding from soil samples collected between July 2022 and January 2024. Results support the hypothesis of an ecological profiling hierarchy. The soil physicochemical properties likely acted as a primary environmental modulator, determining the composition of the bacterial microbiome and contributing to the diversity and richness of the bacterial communities. The major drivers among the soil's physiochemistry were organic/inorganic profile, mainly influenced by organic matter content and pH. Rootstock genotype appears to exert a secondary selection on the microbiome, focusing on the microorganisms' functional traits. The 1103-P rootstock positively influenced the abundance of copiotrophic bacteria, compared to the R110, demonstrating that the first recruits a more versatile, exploratory, and expansionist microbiome, whilst the second focuses on attracting a highly specialized community, more focused on maximizing energy gathering and optimizing resource use. This work demonstrates that the microbial terroir is a result of multiple factors, promoting abiotic modulation and host-mediated selection, which establishes a very specific community for each scenario. The assessment of these holistic dynamics is fundamental to establishing a baseline for future precision viticulture strategies, namely bio-inoculants, to support and promote a better grapevine adaptation to climate change.}, }
@article {pmid42277556, year = {2026}, author = {Yuan, G and Zhou, M and Xiong, C and Bai, R and Cao, F and Yuan, Y and Zhang, WH and Bai, W}, title = {Root anatomical traits modulate the assembly and nitrogen-transformation potential of root-associated microbiomes in a temperate steppe.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71342}, pmid = {42277556}, issn = {1469-8137}, support = {U2571209//National Natural Science Foundation of China/ ; 32371722//National Natural Science Foundation of China/ ; 32030075//National Natural Science Foundation of China/ ; }, abstract = {Plants have evolved numerous belowground strategies to capture nutrients. While root functional differentiation between absorption and transportation has been inferred from order-based traits, the role of microbiomes in mediating this differentiation remains unclear. We measured traits (anatomical, chemical, and morphological) of lower order (absorption-dominated) and higher order (transportation-dominated) roots of 37 herbaceous species (13 monocots and 24 dicots) in a temperate grassland. Furthermore, we employed high-throughput quantitative polymerase chain reaction and 16S rRNA gene sequencing to investigate bacterial nitrogen-transformation gene abundance, diversity, and community assembly along the soil-root continuum (rhizosphere, rhizoplane, and endosphere) and analyzed their relationships with root traits. Monocot roots exhibited greater bacterial diversity and nitrogen-transformation gene abundances than dicots. Within dicots, lower order roots showed higher bacterial diversity and nitrogen-transformation gene abundances than higher order roots, a pattern not observed in monocots. Lower order roots, characterized by higher cortex proportion, facilitated the enrichment of diverse bacteria and recruitment of nitrogen-transformation microorganisms. These patterns were associated with a decrease in homogeneous selection from lower order to higher order roots. This study reveals the mechanisms of functional differences among herbaceous root orders from a microbiome perspective, offering further insights into how root-microbe interactions underpin nitrogen-transformation potential in terrestrial ecosystems.}, }
@article {pmid42277753, year = {2026}, author = {Pan, Y and Wang, XT and Li, Y and Wang, W and Sonne, C and Tong, YW and Ren, N and Ok, YS}, title = {Microbial communication in saline environments: quorum sensing and the future of anaerobic wastewater treatment.}, journal = {BMC biology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12915-026-02651-2}, pmid = {42277753}, issn = {1741-7007}, support = {No. 52300155, No. 52400025//the National Natural Science Foundation of China/ ; No. 2023M740917, 2024M754204//China Postdoctoral Science Foundation/ ; No. LBH-Z23177//Heilongjiang Province Postdoctoral Science Foundation funded project/ ; No. LH2024E042//Natural Science Foundation of Heilongjiang Province/ ; No. Z2024B010//Science Foundation of National Engineering Research Center for Safe Disposal and Resources Recovery of Sludge, Harbin Institute of Technology/ ; No. QA202322//Open Project of State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology/ ; RS-2025-00555967//National Research Foundation of Korea(NRF) grant funded by the Korea government(MSIT)/ ; RS-2021-NR060142//Basic Science Research Program through the National Research Foundation of Korea(NRF) funded by the Ministry of Education/ ; }, abstract = {Anaerobic treatment of industrial wastewater offers a sustainable and cost-effective approach to reducing environmental contamination while recovering biogas. High-salinity wastewater poses ecological risks and remains difficult to treat due to salt-induced sludge disintegration, volatile fatty acid accumulation, and reduced methane production. Quorum sensing is emerging as a key regulator of microbial activity and system stability under salt stress. This review summarizes salinity-stress inhibition mechanisms, evaluates quorum sensing-based mitigation strategies, and proposes a stage- and performance-based framework for quorum sensing application to advance resilient and efficient anaerobic treatment systems.}, }
@article {pmid42277802, year = {2026}, author = {Guo, N and Shi, J and Zhang, X and Xu, H and Ji, T and Qiu, F and Li, K and Wu, Z and Ma, J and Weng, Q and Qiu, R and Shu, G and Chen, Z and Chen, J and Wang, X}, title = {Mesoporous catechin hydrogel for enhanced astaxanthin-based inflammatory bowel disease therapy.}, journal = {Journal of nanobiotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12951-026-04665-y}, pmid = {42277802}, issn = {1477-3155}, support = {2025KY1929//Medical and Health Science and Technology Program of Zhejiang Province (China)/ ; 2023RC309//Medical and Health Science and Technology Program of Zhejiang Province (China)/ ; }, abstract = {Inflammatory bowel disease (IBD) is a persistent intestinal inflammation driven by epithelial barrier dysfunction, immunological imbalance, and microbial dysbiosis. The restoration of gut homeostasis through biomaterial-based strategies offers a potential avenue for alleviating inflammation in IBD. Herein, an alginate-based hydrogel incorporating astaxanthin-loaded mesoporous catechin nanoparticles (AST@MCN-Gel) was designed to relieve inflammation and rebalance gut homeostasis. The mesoporous framework of MCN enabled effective encapsulation of the hydrophobic AST, thereby increasing its water solubility and bioavailability. In lipopolysaccharide-induced macrophages, AST@MCN exhibited superior ROS-scavenging capacity and anti-inflammatory activity relative to either AST or MCN. Mechanistically, AST@MCN modulated macrophage phenotype from pro-inflammatory (M1) to anti-inflammatory (M2) state through regulation of the MAPK/NF-κB pathway. On the other hand, the alginate-based hydrogel effectively enhanced the intestinal retention of AST@MCN, resulting in a marked improvement in oral therapeutic efficacy. In a DSS-induced IBD mouse model, oral administration of AST@MCN-Gel significantly alleviated the clinical symptoms and restored intestinal barrier integrity. Analysis of the gut microbiome further indicated that AST@MCN-Gel ameliorated gut dysbiosis by restoring microbial diversity and suppressing the proliferation of pathogenic species. Collectively, these underscore the potential of AST@MCN-Gel as an effective biomaterial-based therapeutic approach for restoring intestinal homeostasis and improving IBD therapy.}, }
@article {pmid42277887, year = {2026}, author = {Mamjoud, A and Zirah, S and Rebuffat, S and Biron, &#xc9; and Fliss, I}, title = {Uncovering how selected potent bacteriocins reshape the broiler chicken gut microbiome in a PolyFermS continuous in vitro model.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42277887}, issn = {1674-9782}, support = {IRCPJ 499946-15//NSERC/ ; 2014-022-C12//CRIBIQ/ ; 109048-001//IDRC-Innovet-Initiative/ ; }, abstract = {BACKGROUND: Bacteriocins are promising alternatives to antibiotics in poultry production, offering pathogen control with minimal disruption to gut microbiota and reduced risk of resistance dissemination. This study compared the impact of three bacteriocins-microcin J25, nisin Z, and pediocin PA-1-against bacitracin as a positive control, specifically evaluating their effects on gut microbiota composition and metabolic activity. The study utilized the PolyFermS continuous fermentation model to simulate chicken caecal conditions.<br><br>RESULTS: 16S rRNA sequencing revealed that bacitracin and nisin Z significantly altered the microbiota composition, reducing key families such as Lactobacillaceae and Ruminococcaceae, while microcin J25 and pediocin PA-1 had negligible effects. Short-chain fatty acid analysis revealed a significant time-dependent decrease in butyrate levels following nisin Z and bacitracin treatments, with the most pronounced reduction observed at 48&#xa0;h post-injection. Conversely, microcin J25 and pediocin PA-1 maintained stable profiles. Untargeted LC-MS metabolomics indicated a marked metabolic shift under nisin Z treatment, including increased amino acids and cyclic dipeptide levels, while microcin J25 had minimal impact. Stability assays confirmed that microcin J25 remained active up to 24&#xa0;h, whereas nisin Z and pediocin PA-1 lost antimicrobial activity rapidly.<br><br>CONCLUSIONS: These findings support the selective use of bacteriocins as alternatives to antibiotics in poultry farming, with microcin J25 demonstrating the most favorable profile for microbiota preservation and metabolic stability. Future research will focus on in vivo trials in broiler chickens to confirm these findings and evaluate the practical application of microcin J25 in a production environment.}, }
@article {pmid42277889, year = {2026}, author = {Klimešová, B and Volfová, K and Hammerbauerová, I and Dulavová, K and Pajer, P and Bundilová, K and Modrý, D and Adamík, P and Votýpka, J}, title = {Bartonella transmission and gut microbiome dynamics in Ceratophyllus sciurorum fleas and their edible dormouse hosts (Glis glis).}, journal = {Parasites &amp; vectors}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13071-026-07494-y}, pmid = {42277889}, issn = {1756-3305}, support = {284423//Grantov&#xe1; Agentura, Univerzita Karlova/ ; NU2305-00511//Ministerstvo Zdravotnictv&#xed; Cesk&#xe9; Republiky/ ; }, abstract = {BACKGROUND: The genus Bartonella comprises facultative intraerythrocytic bacteria capable of causing long-lasting bacteremia in their natural hosts, with zoonotic potential across multiple species. Rodents serve as important reservoirs for a broad diversity of Bartonella spp., with blood-feeding arthropods, particularly fleas, mediating transmission. Despite their frequent association with humans, the role of edible dormice (Glis glis) and their fleas (Ceratophyllus sciurorum) in Bartonella ecology remains poorly understood.<br><br>METHODS: We combined long-term ecological and epidemiological data with gut and body microbiome analyses of C. sciurorum to investigate the prevalence, diversity, host specificity, and transmission of Bartonella across flea life stages. The study was conducted over 6&#xa0;years in a natural dormouse population. Bartonella detection and characterization were performed using multilocus PCR targeting gltA, rpoB, ftsZ, and ITS loci, bacterial cultivation on selective media, and long-read nanopore sequencing. Flea gut microbiomes were assessed in pooled and individual samples to determine the impact of Bartonella infection on microbial community structure. Transmission across flea life stages was evaluated by analyzing larvae, newly emerged adult fleas, and adults directly collected from dormice.<br><br>RESULTS: We observed a consistently high prevalence of Bartonella in both dormice and their fleas. Four species were identified: B. gliris and B. grahamii subsp. shimonis dominated, each represented by multiple genotypes, whereas B. washoensis and B. bilalgolemii were each detected in a single flea. Moreover, mixed infections of B. gliris and B. grahamii subsp. shimonis were frequent in both dormice and their fleas. Detection of Bartonella DNA in flea larvae and newly emerged adults indicates possible transstadial perpetuation. Flea gut microbiomes were highly variable but consistently dominated by Bartonella in infected fleas. In contrast, uninfected fleas exhibited more diverse communities, often enriched with Staphylococcus and other environmental or host-associated taxa. We, therefore, suggest that flea populations can maintain Bartonella over extended periods, even in the absence of continuous contact with vertebrate hosts.<br><br>CONCLUSIONS: The dormouse-flea-Bartonella system represents a valuable natural model for studying flea-borne zoonoses. The high prevalence and persistent bacteremia in dormice of different ages indicate their role as suitable reservoirs for at least two Bartonella species. Flea populations are capable of sustaining Bartonella over long periods, and detections in immature life stages suggest continuity of infection across flea generations. Therefore, C. sciurorum appears to play an important role in maintaining B. grahamii subsp. shimonis and B. gliris in nature. Infection is consistently associated with pronounced restructuring of the flea gut microbiome, highlighting the ecological and microbial dimensions of vector-borne pathogen transmission. These findings underscore the importance of considering vector-associated microbial communities when evaluating disease dynamics and zoonotic risk in natural host-vector systems.}, }
@article {pmid42277905, year = {2026}, author = {Serrano-Gómez, G and Zaida, S and Pons-Tarín, M and Mayorga, L and Maria, TC and Natalia, B and Francisco, G and Manichanh, C}, title = {Microbial, functional, and virulence biomarkers associated with familial risk of Crohn's disease and ulcerative colitis.}, journal = {Biomarker research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40364-026-00950-y}, pmid = {42277905}, issn = {2050-7771}, support = {PI20/00130//Instituto de Salud Carlos III/ ; PID23-147387OB-100//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; SGR 00459//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca/ ; }, abstract = {BACKGROUND: First-degree relatives of patients with inflammatory bowel disease (IBD) carry elevated disease risk and offer a unique window into preclinical gut microbiome alterations. We investigated whether familial IBD risk is associated with intermediate, disease-specific, or shared gut microbiome configurations in both Crohn's disease (CD) and ulcerative colitis (UC), the two main form of IBD.<br><br>METHODS: Using shotgun metagenomics, we analysed fecal samples from CD (n&#x2009;=&#x2009;68) and UC (n&#x2009;=&#x2009;77) patients, their healthy first-degree relatives (CD-HFDRs, n&#x2009;=&#x2009;37; UC-HFDRs, n&#x2009;=&#x2009;30), and unrelated healthy controls (HCs, n&#x2009;=&#x2009;497), integrated species-level taxonomy, MetaCyc functional pathways, and virulence factor gene (VFG) profiling, with differential abundance analyses adjusted for relevant covariates.<br><br>RESULTS: HFDRs exhibited preserved alpha diversity but intermediate dysbiosis relative to patients and HCs. CD-HFDRs shared CD-associated taxonomic alterations, including depletion of Faecalibacterium prausnitzii, and enrichment of adherence- and invasion-associated VFGs, with 16 of 18 HFDR-enriched VFGs also elevated in CD patients. CD-HFDR functional pathway profiles nonetheless closely resembled those of HCs, revealing a dissociation between taxonomic and functional dysbiosis. Random forest classifiers distinguished HFDRs from HCs with strong performance: species- and VFG-based models achieved an AUCs of 0.966 in CD, and 0.946 in UC. Top predictive features were depletion of F. prausnitzii and enrichment of the E. coli adhesin gene fdeC. UC-HFDRs showed subtler alterations but comparable classifier performance.<br><br>CONCLUSIONS: IBD first-degree relatives harbour a transitional gut microbiome between health and disease, more pronounced in CD, with F. prausnitzii depletion and pathobiont virulence genes emerging as robust microbiome-based risk indicators.}, }
@article {pmid42278088, year = {2026}, author = {Jeon, H and Kim, H and Yoon, S and Lee, S and Rahman, MH and Bai, SC and Lee, SJ and Lee, EW and Min, T and Moniruzzaman, M and Lee, S}, title = {Effects of Dietary Host-Derived Bacillus-Fructo-Oligosaccharide Formulations on Growth Performance and Thermal Challenge Responses in Juvenile Olive Flounder (Paralichthys olivaceus).}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {11}, pages = {}, doi = {10.3390/ani16111655}, pmid = {42278088}, issn = {2076-2615}, support = {2025//Pukyong National University/ ; }, abstract = {This study evaluated the effects of dietary host-derived Bacillus strains combined with fructo-oligosaccharide (FOS) on growth performance, basal physiological status, intestinal morphology, and thermal stress responses in juvenile olive flounder (Paralichthys olivaceus). A total of 486 fish with an initial body weight of 7.26 ± 0.04 g were randomly distributed into 27 tanks and fed nine experimental diets for nine weeks. The diets consisted of a basal control, an FOS-only diet, three single-strain synbiotic diets containing FOS and one host-derived Bacillus strain (B. sonorensis, B. subtilis, or B. velezensis), and four multi-strain synbiotic diets containing FOS and combinations of two or three strains. Probiotics were included at 1 × 10[7] CFU g[-1] diet, and FOS was supplemented at 5 g kg[-1] diet. After the feeding trial, no significant dietary effects were observed on growth performance, somatic indices, whole-body proximate composition, plasma biochemical parameters, antioxidant enzyme activities, immune-related indicators, stress-related biomarkers, or intestinal morphology. Fish were subsequently subjected to lethal and acute high-temperature challenges to evaluate thermal stress tolerance and associated physiological responses. In the lethal temperature challenge, fish fed the multi-strain diets FOS + B. sonorensis + B. velezensis and FOS + B. sonorensis + B. subtilis + B. velezensis showed numerically higher survival than the other groups; however, these differences were not statistically significant. Following acute heat exposure, dietary treatments did not significantly affect plasma metabolites, and most heat-shock- and energy-metabolism-related genes were not differentially expressed among treatments. Hepatic AMPKβ expression showed a significant dietary treatment effect, with higher expression in the BCF and ACF groups than in the ABF group. Overall, host-derived synbiotic supplementation did not significantly enhance growth performance or basal physiological responses under the present experimental conditions. However, some multi-strain combinations showed a non-significant tendency toward higher survival under lethal thermal stress. Further studies incorporating gut microbiome profiling, metabolomic analysis, and alternative dietary conditions are required to clarify whether host-derived Bacillus-FOS synbiotic formulations can influence thermal stress resilience in olive flounder.}, }
@article {pmid42278115, year = {2026}, author = {Naing, YP and Kim, SH}, title = {Alterations in Blood Markers, Rumen Fermentation, and Microbiota Due to Heat Stress in Holstein Cows During the Dry Period and Early Lactation.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {11}, pages = {}, doi = {10.3390/ani16111682}, pmid = {42278115}, issn = {2076-2615}, support = {project number: RS-2023-00231583//Rural Development Administration/ ; }, abstract = {In this study, physiological and microbial responses under heat stress conditions were evaluated by analyzing blood biochemical parameters, rumen fermentation characteristics, and rumen microbiome (bacterial community composition) in Holstein dairy cows during the dry period and early lactation under summer conditions in Korea. Fourteen cows were observed during the hot summer month (from the first to the third week of August), with the temperature-humidity index (THI) recorded in the barns during the dry and early lactation periods being 80.80 and 81.66, respectively. Blood and rumen fluid samples were collected to evaluate physiological responses and changes in blood parameters, rumen fermentation, and rumen microbial composition. Blood analysis revealed significant variations between the two stages. Early lactating cows exhibited lower glucose, blood urea nitrogen, and cholesterol levels but higher ketone and aspartate aminotransferase levels, indicating increased energy demands and protein metabolism. A complete blood count showed reduced red blood cell count, hematocrit, and hemoglobin levels during the early lactation period, whereas white blood cell counts increased. The levels of heat shock proteins (HSPs), such as HSP27, HSP70, and HSP90, also differed significantly. Rumen fermentation analysis revealed lower ammonia nitrogen concentrations but significantly higher propionate and total volatile fatty acid concentrations during the early lactation period, indicating adaptive changes in rumen function. Rumen microbial analysis revealed significant differences in bacterial diversity and composition. Early lactation cows exhibited relatively high abundances of Bacteroidota and Prevotella, whereas the dry period was dominated by Clostridia and Eubacteriales. Network analysis highlighted shifts in microbial interactions, with specific keystone species identified at each stage. These findings suggest distinct physiological and rumen microbial adaptations in response to HS, with early lactation characterized by heightened metabolic demands and significant shifts in rumen bacterial communities. Such insights could inform tailored management strategies to mitigate the impact of HS on dairy cows during their critical production stages.}, }
@article {pmid42278131, year = {2026}, author = {Liu, C and Zhang, J and Dong, Y and Ju, H and Haoren, T and He, L and Suritu,  and Ma, H and Liu, J and Hu, D and Zhang, D and Yan, L and Zhang, S and Gao, Y}, title = {Phenological Changes in the Fecal Microbiota of Elaphurus davidianus in Inner Mongolia Daqingshan National Nature Reserve.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {11}, pages = {}, doi = {10.3390/ani16111698}, pmid = {42278131}, issn = {2076-2615}, support = {No. BLX202253//the Fundamental Research Funds for the Central Universities/ ; No. 25CD009//the Financial Program of BJAST/ ; No. JCYJ202511//the Fundamental Research Funds for the Central Universities/ ; }, abstract = {Given the ongoing global decline in biodiversity, species reintroduction has become an important strategy for the conservation of endangered wildlife. Père David's deer (Elaphurus davidianus), a historically extinct-in-the-wild species successfully reintroduced in China, represents a useful model for evaluating ecological responses following reintroduction into different habitats. Increasing evidence suggests that fecal microbiota can serve as a non-invasive indicator of host-associated microbial communities and their variation under different conditions. In this study, we investigated the fecal microbiota of a reintroduced population in the Daqingshan National Nature Reserve (Inner Mongolia). A total of 90 fresh fecal samples were collected between December 2021 and October 2023 across different seasonal periods. High-throughput 16S rRNA gene sequencing was used to characterize microbial community structure, and comparative analyses were conducted alongside published datasets from populations in Beijing and Shishou. The results revealed significant seasonal variation in microbial community composition and diversity, with distinct clustering of rainy, dry, and transitional (October) samples. Several taxa exhibited differential enrichment between seasons, suggesting temporal shifts in microbial community structure. A comparative analysis with other populations (Beijing and Shishou) revealed differences in microbial composition at broad taxonomic levels, suggesting potential variations related to regional environmental conditions, diet, and management practices. Overall, the observed patterns are consistent with seasonal variation in plant resource availability and highlight the potential influence of geographic context on microbial community structure. This study provides baseline data on the fecal microbiota of Père David's deer in a semi-arid steppe environment and the potential indication of host suitability from the perspective of the microbiome.}, }
@article {pmid42278142, year = {2026}, author = {Yuan, Z and Xie, F and Ding, Y and Li, X and Ghonaim, AH and Jiang, C and Ren, M and Li, S}, title = {Dietary Fiber Levels Modulate Intestinal Mucosal Architecture and the Microbiome-Metabolome Axis to Support Immune Homeostasis in Brooding Wanxi White Geese.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {11}, pages = {}, doi = {10.3390/ani16111709}, pmid = {42278142}, issn = {2076-2615}, abstract = {Dietary fiber is a critical determinant of intestinal health, yet its optimal inclusion level for WWG during the critical brooding period remains undefined. This study aimed to evaluate the effects of varying dietary CF levels (approximately 3%, 5%, and 9%) on the intestinal morphology, immune function, and microbiome-metabolome axis of brooding WWG. A total of 120 one-day-old goslings were randomly assigned to the three dietary treatments for a 28-day trial. Histological analysis revealed that the 9% CF diet significantly improved gut morphology, yielding superior villus-to-crypt ratios in the jejunum and ileum. Molecular assays indicated that higher fiber levels (5-9%) upregulated the expression of nutrient transporters (SGLT1 and GLUT2). Concurrently, the 9% CF diet effectively suppressed the potent pro-inflammatory cytokine TNF-α in the jejunum while appropriately upregulating IL-6 and NF-κB, indicating enhanced mucosal immune vigilance and structural maturation. Multi-omics integration (shotgun metagenomics and LC-MS metabolomics) demonstrated that specific fiber levels significantly shifted microbial abundances, specifically enriching Bacteroidetes and Actinobacteria. These microbial shifts were strongly correlated with enriched metabolic pathways, notably lysine biosynthesis and purine metabolism, which synergistically support mucosal homeostasis. Collectively, these findings demonstrate that a 9% dietary CF inclusion is an effective nutritional strategy to optimize intestinal architecture and microbial-metabolic profiles in brooding WWG.}, }
@article {pmid42278182, year = {2026}, author = {Li, Z and Hu, X and Feng, H and Sun, H and Tan, J and Yu, T and Lin, Z and Cheng, G and Chen, P}, title = {Effects of Dietary Deoxynivalenol on Growth Performance, Immunity, Reproductive Hormones, and Microbiome-Metabolome Responses in Immature Gilts.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {11}, pages = {}, doi = {10.3390/ani16111751}, pmid = {42278182}, issn = {2076-2615}, support = {2023YFD1301902//National Program on Key Research Project of China/ ; }, abstract = {We evaluated the effects of different levels of DON (LD 441 and HD 1223 μg DON/kg in diet) on the growth performance, immunity, reproductive hormones, and intestinal health of immature gilts. No significant differences were observed in average daily gain, average daily feed intake, or feed to gain ratio between the LD group and the HD group (p > 0.05). The red blood cell count and hematocrit were higher in the LD group compared with the HD group on d 21 (p < 0.05). The gamma-glutamyl transferase activity in the LD group on d 1, 21, 28, 35, and 42 was higher (p < 0.05) compared with the HD group. The aspartate aminotransferase, total antioxidant capacity, and lactic dehydrogenase levels on d 35 were higher in the LD group than those in the HD group (p < 0.05). On d 35, the levels of interleukin 1β, interleukin-4, interleukin-10, tumor necrosis factor-α, and interferon-γ in LD were higher than those in the HD group (p < 0.05). The levels of immunoglobulin A, immunoglobulin M, immunoglobulin G, and complement 4 on d 35 were higher in the LD group compared with those in the HD group (p < 0.05). The gonadotrophin-releasing hormone, luteotrophic hormone, follicle-stimulating hormone, or estradiol did not differ between LD and HD groups throughout the experiment (p > 0.05). For fecal microbiota, Streptococcus in the HD group was reduced compared with the LD group (p < 0.05). In summary, feeding diets contaminated with 1223 μg DON/kg exerted adverse effects on serum profiles of gilts but did not affect their growth performance or reproductive hormones in the present study.}, }
@article {pmid42278192, year = {2026}, author = {Soares Ferreira Junior, A and Linares Silva, N and Alvarez, DAN and da Silva Souza, L and Machado, LD and Rodrigues da Silva, BF and Yoshio Hirai, W and Mesquita Ciconelli, R and Piccolo Feliciano, JV and Colturato, I and Maurício Navarro Barros, G and Scheinberg, P and de Oliveira, GLV}, title = {Unraveling the Role of Zonulin in Allogeneic Hematopoietic Stem Cell Transplantation: A Multicenter Study.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27114659}, pmid = {42278192}, issn = {1422-0067}, support = {2023/08142-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2024/02936-8//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2022/12989-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2023/12271-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 313190/2021-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; Finance Code 001//Coordena&#xe7;&#xe3;o de Aperfeicoamento de Pessoal de N&#xed;vel Superior/ ; }, abstract = {The role of zonulin as a biomarker of intestinal permeability in the allogeneic hematopoietic stem cell transplantation (allo-HSCT) setting remains poorly understood. In this study, we aimed to evaluate serum zonulin dynamics, identify its predictors, and assess its prognostic significance in patients undergoing allo-HSCT. This multicenter, prospective cohort study was conducted across four Brazilian hospitals. Eligible participants were patients aged ≥12 years who provided at least one blood sample during the allo-HSCT course. A control group of 15 healthy adult individuals was also included. Serum zonulin levels were quantified using enzyme-linked immunosorbent assay multiple times over the allo-HSCT course. Outcomes included acute graft-versus-host disease, overall survival, and bloodstream infections. A total of 477 blood samples were collected from 140 patients. Compared with the control group, zonulin levels were persistently elevated at all evaluated time points throughout the allo-HSCT course. However, no significant differences were observed among the different time points assessed during transplantation. No clinical or transplantation-related characteristics were identified as significant predictors of elevated zonulin levels. Finally, zonulin did not demonstrate prognostic value for allo-HSCT-related outcomes. Future studies should investigate whether other intestinal permeability biomarkers have prognostic relevance in the allo-HSCT setting.}, }
@article {pmid42278195, year = {2026}, author = {Gama de Souza Silva, MC and De Pietro, L and Cataldo, CRS and Bisaccia, A and Nuccio, F and Li Pomi, F and Gangemi, S}, title = {Beyond Inflammation: The Role of Oxidative Stress and Gut-Skin Axis Dysbiosis in the Pathogenesis of Immune-Mediated Skin Disorders and Potential Therapeutic Implications.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27114656}, pmid = {42278195}, issn = {1422-0067}, mesh = {Humans ; *Oxidative Stress ; *Dysbiosis/immunology ; *Skin Diseases/immunology/etiology/metabolism/pathology/microbiology/therapy ; Animals ; *Gastrointestinal Microbiome/immunology ; *Skin/microbiology/immunology/metabolism/pathology ; *Inflammation/immunology ; Reactive Oxygen Species/metabolism ; Skin Microbiome ; }, abstract = {The skin is a complex immunological organ in which reactive oxygen species (ROS)-related pathways and host-microbe interactions synergically maintain immune homeostasis. Dysregulation of several oxidative mechanisms, including lipid peroxidation, mitochondrial dysfunction, ferroptosis, and impaired antioxidant defenses, alongside gut microbiome imbalance, is increasingly recognized as a key modulator of the immune response involved in disease onset and progression. However, their role in immune-mediated dermatoses remains incompletely defined. This narrative review aims to provide a comprehensive overview of the contribution of these altered pathways to the pathogenesis and prognosis of the major immune-mediated skin diseases. Across all conditions examined, elevated oxidative biomarkers, such as malondialdehyde (MDA), advanced glycation end-products (AGEs), advanced oxidation protein products (AOPPs), 8-hydroxydeoxyguanosine (8-OHdG), and reduced antioxidant capacity are consistently reported. Ferroptosis, driven by iron-dependent lipid peroxidation and dysfunction of Glutathione peroxidase 4 (GPX4), emerges as a relevant cell death pathway, particularly in psoriasis and atopic dermatitis (AD). In parallel, dysbiosis of the gut and skin microbiomes, characterized by depletion of short-chain fatty acid (SCFA)-producing taxa such as Faecalibacterium prausnitzii, Bifidobacterium, and Akkermansia muciniphila, has been reported across multiple diseases. Particular attention is given to shared molecular axes, such as the disruption of epithelial barrier integrity, activation of innate and adaptive immune responses, and the role of microbial-derived metabolites in modulating redox signaling, unraveling a bidirectional crosstalk. Emerging therapeutic strategies targeting these bidirectional crosstalks show biological plausibility and promising preliminary results. Integrating redox and microbial profiling into clinical practice may improve patient stratification and foster the development of more personalized therapeutic approaches beyond conventional immunological treatments.}, }
@article {pmid42278203, year = {2026}, author = {Krstić Tomić, T and Nedeljković, M and Mesaroš, A and Todorović, J and Pešaković, M and Stanković, S and Lozo, J}, title = {Comparative Biocontrol Efficacy and Mechanisms of Indirect and Direct Application Methods Against Leaf Spot Caused by Pseudomonas syringae pv. aptata in Sugar Beet.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27114672}, pmid = {42278203}, issn = {1422-0067}, support = {451-03-34/2026-03/200178, 451-03-33/2026-03/200178, and 451-03-33/2026-03/200215//Ministry of Science, Technological Development and Innovation of the Republic of Serbia/ ; }, abstract = {Using beneficial bacteria from the plant microbiome to combat pathogens is an environmentally friendly strategy for biological control. Although significant progress has been made in characterizing microorganisms with biocontrol potential, the optimal methods for applying such biological preparations to achieve maximum effectiveness against plant pathogens remain insufficiently defined. Our goal was to select rhizobacteria from the sugar beet microbiome and analyze their biocontrol capacity in both indirect and direct applications to protect the plant from Pseudomonas syringae pv. aptata P21. The methodological approach differed: indirect application involved seed priming with selected strains, Bacillus safensis MRh275, B. pseudomycoides JRh226, Stenotrophomonas maltophilia JRh266, or the T2 consortium (MRh275 and JRh266), while direct application involved simultaneous treatment of both the pathogen and the biocontrol strain. Although the direct approach resulted in a greater reduction in lesions and a lower concentration of H2O2, the indirect approach showed higher activity of peroxidase and superoxide dismutase as antioxidant enzymes, as well as phenylalanine ammonia-lyase, which is involved in the phenylpropanoid pathway and plant defense mechanisms. Infected plants showed higher expression of NPR1, MYC2, and LOX defense-related genes only under indirect biocontrol with all three strains, except in the T2 application. The T2 consortium performed best in direct biocontrol, where it most effectively reduced lesions. Since encounters between plants and pathogens cannot be accurately predicted, and the application of biological preparations should be easy and accessible for farmers, this study highlights the use of indirect biocontrol through seed priming to enhance the plant's intrinsic defense capacity.}, }
@article {pmid42278234, year = {2026}, author = {Meduri, GU}, title = {Inter-Organ Communication Networks in Systemic Physiology: Glucocorticoid Receptor α as a Central Integrator of Homeostasis.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27114702}, pmid = {42278234}, issn = {1422-0067}, abstract = {The survival of complex multicellular organisms depends on continuous inter-organ communication networks that coordinate organism-wide responses across physiological conditions and stress states, including adaptation to environmental challenges, infection, and injury. Rather than operating as isolated units, organ systems are integrated through interconnected signaling networks that transmit biological information across tissues. Building on prior work examining individual physiological pathways, this review introduces a unified systems-level framework that integrates inter-organ communication into a coherent model of organism-wide regulation. This review proposes a systems-level framework in which homeostasis is maintained through eight principal communication systems: neural, endocrine, immune-inflammatory, vascular, lymphatic, metabolic, microbiome-gut, and mechanical-structural. Epithelial barriers function as dynamic signaling interfaces within multiple systems, while extracellular vesicles act as cross-system mediators of information transfer rather than as independent communication networks. These systems operate across distinct temporal scales to coordinate host defense, metabolic adaptation, vascular regulation, and tissue repair. The framework further introduces a temporal hierarchy of signaling dynamics that links communication systems to phase-specific responses during physiological stress. Within this integrated network, glucocorticoid receptor α (GRα) is proposed to function as a systems-level regulator of inter-organ communication, supported by converging mechanistic, experimental, and clinical evidence, with variability in the strength of evidence across domains. In contrast to prior reviews, which addressed GRα function within individual systems, this work conceptualizes GRα as a central rheostat coordinating cross-system signaling and temporal transitions in homeostatic correction. Evidence was identified through hypothesis-driven searches using the Consensus AI platform and verified through manual review of primary biomedical literature. GRα, a ligand-activated transcription factor expressed in most nucleated cells, enables hormonal stress signals to coordinate gene-expression programs across tissues, modulating neuroendocrine responses, endothelial function, inflammatory signaling, metabolic regulation, microbiome-host interactions, and tissue remodeling. Systemic responses to stress progress through three phases of homeostatic correction-Priming, Modulatory, and Restorative-within which GRα supports integrated organism-wide adaptation. This integrative framework provides a mechanistic basis for understanding the emergence and temporal evolution of biological responses in health and critical illness.}, }
@article {pmid42278252, year = {2026}, author = {Mechri, S and Najjari, A and Croze, S and Ouzari, HI and Le Roes-Hill, M and Tounsi, S and Lachuer, J and Jaouadi, B}, title = {Unraveling the Taxonomic Diversity and Functional Potential of the Tunisian Salterns, Abbassia and Thyna, via Integrated 16S-18S Amplicons and Shotgun Metagenomics.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27114714}, pmid = {42278252}, issn = {1422-0067}, support = {101079425//Centre of Biotechnologie of Sfax/ ; }, mesh = {*Metagenomics/methods ; Tunisia ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Archaea/genetics/classification ; Shotgun Sequencing ; Phylogeny ; *Bacteria/genetics/classification ; Metagenome ; }, abstract = {Hypersaline environments are unique ecosystems harboring specialized microbial communities with significant biotechnological potential. This study provides a comprehensive characterization of the taxonomic diversity and functional potential of two Tunisian salterns, Abbassia (Kerkennah) and Thyna (Sfax), using an integrated approach that combines 16S/18S rRNA gene amplicons (Illumina and full-length Nanopore) with shotgun metagenomics. Taxonomic profiling revealed a high species richness (S ≈ 1250 taxa); however, the Abbassia site was characterized by extreme taxonomic polarization, with over 95% of the community dominated by specialized halophilic Bacillota (Salinicoccus and Jeotgalicoccus). In contrast, Thyna exhibited a more even distribution dominated by Pseudomonadota and methanogenic Archaea. Beyond taxonomy, functional annotation via the HUMAnN 3.0 pipeline identified site-specific metabolic specializations. Abbassia was enriched in biosynthetic pathways and robust stress-response mechanisms, including ectoine biosynthesis and ppGpp-mediated stringent response, reflecting adaptation to stable hypersaline conditions. Conversely, Thyna's microbiome prioritized energy extraction and nutrient recycling, with a high abundance of fermentation and glyoxylate cycle pathways. These findings demonstrate that environmental filtering shapes not only the microbial structure but also the metabolic landscape, highlighting the ecological plasticity of microbial life in extreme Tunisian salterns.}, }
@article {pmid42278256, year = {2026}, author = {Al-Ansari, MM and Mahmood, SM and Al-Alwan, M}, title = {The Human Breast Microbiome: From Homeostasis to Malignancy, Mechanistic Insights and Therapeutic Perspectives.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27114723}, pmid = {42278256}, issn = {1422-0067}, support = {RAC# 2240005//King Faisal Specialist Hospital &amp; Research Centre/ ; }, abstract = {Although human mammary glands were traditionally considered sterile, accumulating evidence has established the presence of distinct microbial communities that may have colonized breast tissue primarily via retrograde nipple flow or via hematogenous or lymphatic translocation from other body sites. Comparative studies reveal differences in the microbiota of healthy and diseased breast tissues, with variations in microbial signatures across breast cancer subtypes and in comparison with adjacent normal tissues. This review synthesizes current evidence on the composition of the breast microbiome, the factors shaping its development, and alterations it undergoes in inflammatory and malignant breast diseases. Furthermore, the article discusses mechanistic insights, methodological challenges, and future therapeutic perspectives based on published studies employing culture-independent approaches, such as 16S rRNA gene sequencing and metagenomic analyses. Key host-related factors influencing breast-associated microbial communities, including hormonal regulation, environmental exposure, diet, and therapeutic interventions, are explored. The existing literature is assessed to identify key associations between the breast microbiome and host signaling pathways, as well as the significant challenges that remain unresolved, including low biomass contamination, inter-study variability, limited longitudinal data, and an incomplete understanding of causality. Addressing these limitations is critical for advancing microbiome-based diagnostic and therapeutic strategies for breast disease.}, }
@article {pmid42278312, year = {2026}, author = {Bayliss, E and Shope, L and Woodfin, S and Mair, G and Becker, MH and Moore, W}, title = {The Triangular Interaction Between Dietary Polyphenols, Gut Microbiota and Type 2 Diabetes.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27114782}, pmid = {42278312}, issn = {1422-0067}, mesh = {Humans ; *Polyphenols/metabolism/pharmacology ; *Diabetes Mellitus, Type 2/metabolism/microbiology ; Animals ; *Gastrointestinal Microbiome/drug effects ; Insulin Resistance ; Diet ; Dysbiosis ; }, abstract = {Type 2 diabetes (T2D) is a growing global health concern characterized by peripheral insulin resistance and impaired insulin secretion from pancreatic β-cells. Emerging evidence suggests that the gut microbiome, specifically gut dysbiosis, defined as an imbalance in the gut microbial composition and function, is a critical modulator of the pathophysiology of T2D. Dietary polyphenols, a diverse group of bioactive compounds that are abundant in plant-based foods, have gained increasing attention for their potential to attenuate metabolic disorders through their antioxidant and anti-inflammatory properties. These compounds work through the modulation of gut microbial composition and activity. This process effectively ameliorates dysbiosis. However, the diabetic state itself may influence polyphenol metabolism, absorption, and bioavailability, potentially limiting their therapeutic efficacy. This review examines the complex interrelationships between T2D, dietary polyphenols, and the gut microbiota and proposes a dynamic triangular interaction between these factors that might inform novel strategies for the prevention and management of metabolic disease.}, }
@article {pmid42278324, year = {2026}, author = {Ilinskaya, O and Vagin, K and Kurdy, W and Yakovleva, G and Karamova, N and Zelenikhin, P and Kolpakov, A and Zuev, Y}, title = {Biomineral Complex with Probiotic and Detoxifying Properties for Recovery After Radiotherapy.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27114794}, pmid = {42278324}, issn = {1422-0067}, support = {24-14-00059//Russian Science Foundation/ ; }, abstract = {Radiotherapy is a highly effective, safe cancer treatment, and about half of all cancer treatments involve lifesaving radiotherapy. Despite huge advances in technology that have made it safer and more effective, it is still not without side effects. They differ from patient to patient and can include fatigue, nausea, skin reactions, and hair loss, but dysbiosis is the most common complication associated with radiotherapy. Probiotics aimed at restoring the microbiome have found widespread use, but the problem of their rapid inactivation in the gastrointestinal tract has not yet been solved. Our study aims to confirm the effectiveness of a novel biomineral complex, based on a powdered clinoptilolite containing a rock loaded with lactobacilli for restoring the intestinal microbiome of mice exposed to radiation. Based on the 16S rRNA gene analysis, alpha-diversity and dynamics of changes in the fecal metagenome, as well as the functional potential of mice exposed to radiation, were studied, and the prospects of administering the biomineral complex to achieve positive effects were assessed. NMR analysis of the mineral carrier was carried out, and its safety was confirmed. Moreover, per os administration of the complex following irradiation led to a reduction in the level of chromosomal aberrations induced by irradiation. Thus, the biomineral complex has a microbiome-restoring effect and reduces radiation-induced clastogenesis.}, }
@article {pmid42278332, year = {2026}, author = {Wiszpolski, PS and Stolarski, MJ}, title = {The Role of the Rhizosphere, Endophytes, and the Influence of Plant-Growth-Promoting Bacteria: Take the Cannabis Microbiome as an Example.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27114802}, pmid = {42278332}, issn = {1422-0067}, support = {30.610.007-110//University of Warmia and Mazury in Olsztyn/ ; RID/SP/0025/2024/01//Ministry of Science and Higher Education/ ; }, mesh = {*Rhizosphere ; *Cannabis/microbiology/growth &amp; development ; *Microbiota ; Plant Growth Regulators/metabolism ; *Bacteria/metabolism ; *Endophytes/physiology ; Plant Development ; Soil Microbiology ; Plant Roots/microbiology/growth &amp; development ; }, abstract = {Cannabis sativa L. is a multipurpose crop of increasing agricultural and medical relevance, whose productivity and phytocannabinoid profile are influenced not only by genotype and environmental factors but also by the composition of its microbiota. This review synthesizes current knowledge (2020-2026) on the rhizosphere and endophytic microbiota of hemp, with particular emphasis on plant growth-promoting bacteria (PGPB) and their mechanisms of action. Molecular studies indicate that hemp-associated bacterial communities are dominated by Proteobacteria, Actinobacteriota, Firmicutes and Bacteroidota, with genotype-, tissue- and developmental-stage-dependent variation. PGPB influence plant performance through direct mechanisms, including biological nitrogen fixation, phosphate solubilization, siderophore production and phytohormone synthesis (indole-3-acetic acid (IAA), gibberellins, cytokinins, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase), as well as indirect mechanisms such as antibiosis, enzyme-mediated pathogen inhibition and induction of systemic tolerance to abiotic stress. Experimental studies demonstrate that inoculation with selected strains or consortia can enhance biomass accumulation, improve germination and root architecture, increase resistance to Fusarium oxysporum and modulate cannabinoid and terpene profiles. Importantly, plant responses are cultivar-specific, highlighting the need for genotype-tailored microbial formulations.}, }
@article {pmid42278360, year = {2026}, author = {Mardnaybin, H and Demirci, M and Kirkoyun Uysal, H}, title = {The Gut Microbiome in HIV Pathogenesis: Interconnections Between Dysbiosis, Immune Dysfunction, and Viral Persistence.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27114830}, pmid = {42278360}, issn = {1422-0067}, abstract = {The human gut microbiome is essential for immune regulation and mucosal homeostasis, functions that are profoundly disrupted during HIV infection. Early viral replication in the gut-associated lymphoid tissue (GALT) triggers a self-reinforcing cycle of CD4[+] T-cell depletion, epithelial barrier breakdown, and increased microbial translocation. This persistent immune activation continues even under effective antiretroviral therapy (ART). A growing body of evidence indicates that HIV infection is consistently associated with alterations in gut microbial communities. This dysbiosis is typically characterized by fewer beneficial butyrate-producing commensal bacteria and an enrichment of pro-inflammatory microbial taxa. It also involves disturbances in key microbial metabolites, including short-chain fatty acids (SCFAs) and tryptophan catabolites. Such changes not only exacerbate systemic inflammation but may also contribute to incomplete immune reconstitution and the persistence of latent viral reservoirs despite long-term ART. In this review, we summarize current knowledge of microbiome-HIV interactions, with particular emphasis on the mechanisms through which gut dysbiosis contributes to immune dysfunction and viral persistence. We discuss recent advances in multi-omics technologies, as well as experimental systems such as gnotobiotic and humanized mouse models and intestinal organoid platforms that are helping to elucidate these complex interactions. Furthermore, we evaluate emerging microbiome-targeted interventions-including probiotics, prebiotics, fecal microbiota transplantation, and engineered bacterial therapeutics-and consider their potential role as adjunctive strategies in HIV treatment and cure research. By integrating microbiological, immunological, and clinical perspectives, this review highlights key knowledge gaps and outlines future research directions aimed at harnessing the gut microbiome as a novel therapeutic avenue in HIV management and eradication.}, }
@article {pmid42278409, year = {2026}, author = {Danso Ofori, A and Nasimi, Z and Ahmed, MI and Yan, Y and Li, W and Kandro, AG and Okada, K and Mochida, K and Noutoshi, Y and Zheng, A}, title = {Rice Genotype-Dependent Phyllosphere Microbiome Assembly and Isolation of Antagonistic Burkholderia for Sheath Blight Biocontrol.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27114879}, pmid = {42278409}, issn = {1422-0067}, support = {2024YFHZ0299//Sichuan Province International Science and Technology Cooperation Project/ ; }, abstract = {Rice sheath blight (RSB), caused by Rhizoctonia solani, causes 10-50% yield losses globally. Using 16S rRNA sequencing of 100 rice cultivars, we found that resistant varieties harbor significantly more diverse bacterial communities (3230 OTUs; 2064 unique) than susceptible cultivars (599 OTUs; 36 unique). Resistant varieties were enriched in beneficial Burkholderiaceae, Bacillaceae, and Pseudomonadaceae, while Sphingobacteriaceae and Enterobacteriaceae were predominant in the susceptible rice varieties. From the 260 bacterial isolates, Burkholderia vietnamiensis J14EPLEAF2 presented potent antifungal activity (77% inhibition), suppressed lesion development, and abolished sclerotia formation. This strain displayed multiple plant growth-promoting traits, enhanced seed germination, and primed defense responses by upregulating PR5 and PR10. Hypersensitive response assays confirmed B. vietnamiensis as non-pathogenic, unlike B. gladioli and B. cepacia. This study identifies B. vietnamiensis J14EPLEAF2 as a promising, safe biocontrol agent for sustainable rice disease management.}, }
@article {pmid42278410, year = {2026}, author = {Nemeti, G and Crăciun, AE and Măgureanu, DC and Militaru, FC and Bocsan, IC and Crăciun, CI and Rusu, A and Melincovici, CS and Buzoianu, AD and Mureșan, D and Neag, MA}, title = {The Microbiota-Endometriosis Axis: An Immune-Endocrine Integration Model and Emerging Therapeutic Targets.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27114883}, pmid = {42278410}, issn = {1422-0067}, abstract = {Endometriosis is a chronic, estrogen-dependent inflammatory disorder characterized by the ectopic implantation and persistence of endometrial-like tissue outside the uterine cavity. Despite its high prevalence and significant impact on quality of life, the pathogenesis of endometriosis remains incompletely understood and involves a complex interplay between hormonal dysregulation, immune dysfunction, and chronic inflammation. In recent years, growing evidence has highlighted the role of the microbiota as a potential modulator of these interconnected pathways. This review proposes an integrative framework in which the microbiota acts as a central modulator of immune-endocrine interactions in endometriosis, while synthesizing current evidence on underlying biological mechanisms. We discuss how alterations in the gut, vaginal, and endometrial microbiota contribute to disease pathophysiology through multiple mechanisms, including disruption of intestinal barrier integrity, activation of pro-inflammatory signaling pathways, immune dysregulation, and modulation of estrogen metabolism via the estrobolome. Microbial β-glucuronidase activity and enterohepatic recirculation of estrogens are explored as key processes linking gut dysbiosis to the hyperestrogenic environment characteristic of endometriosis. Furthermore, we review current pharmacological treatments and highlight their limitations, emphasizing the need for novel therapeutic strategies targeting upstream disease mechanisms. Emerging approaches, including probiotics, postbiotics, short-chain fatty acids, and dietary interventions, are discussed as promising adjunctive therapies capable of modulating inflammation, immune responses, and metabolic pathways. Although current evidence remains heterogeneous and largely derived from preclinical and observational studies, the microbiota emerges not only as a potential therapeutic target but as a key integrative node linking endocrine, immune, and metabolic pathways in endometriosis. Future research should focus on well-designed clinical trials to validate microbiome-based interventions and to define their role in personalized management strategies for endometriosis.}, }
@article {pmid42278419, year = {2026}, author = {Salido-Guadarrama, I and Cruz-Orozco, O and Camacho-Arroyo, I and Quintero, JC and Silvestri-Tomassoni, JR and Sánchez-Ramírez, B and Rodriguez-Dorantes, M}, title = {Translational Assessment of Omics Approaches in Endometriosis: Bridging Molecular Discovery with Clinical Utility.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27114888}, pmid = {42278419}, issn = {1422-0067}, support = {CF-2023-G-234//Ministry of Sciences, Humanities, Technology and Innovation/ ; }, mesh = {Humans ; *Endometriosis/metabolism/diagnosis/genetics/therapy ; Female ; Multiomics ; Biomarkers/metabolism ; *Genomics/methods ; Proteomics/methods ; *Translational Research, Biomedical/methods ; Metabolomics/methods ; }, abstract = {Endometriosis affects an estimated 5-10% of women of reproductive age and presents with substantial clinical and biological heterogeneity. Recent clinical guidelines have shifted toward symptom-guided diagnosis supported by expert imaging, moving away from mandatory diagnostic laparoscopy and redefining the evidentiary standards for evaluating new diagnostic technologies. Advances across omics domains, including genomics, epigenomics, transcriptomics, proteomics, metabolomics, extracellular vesicle profiling, microbiome research, and multi-omics integration, have deepened understanding of lesion biology, immune dysregulation, metabolic alterations, and progesterone resistance. However, translation of these molecular insights into clinically actionable tools remains limited. Most candidate biomarkers remain at discovery or internal/developer-led validation stages, constrained by small sample sizes, heterogeneous analytical platforms, incomplete control of confounding variables, and limited independent multicenter validation. In this review, we apply a four-tier evidence-maturity framework, spanning discovery, internal or developer-led validation, independent external validation, and demonstrated clinical utility, to classify omics-based diagnostic, prognostic, and treatment-response applications in endometriosis. We also distinguish potential clinical roles, including triage, adjunctive testing, and replacement-test evaluation, each requiring different validation standards and performance thresholds. Salivary microRNA currently represents the most clinically advanced diagnostic omics candidate, but the available evidence remains developer-led and is best classified as advanced Tier 2/Tier 2+ rather than independent Tier 3 validation. Prognostic and treatment-response applications are less mature and remain discovery-stage because prospective patient-level longitudinal validation and biomarker-stratified treatment trials are lacking. Overall, no omics-derived biomarker has yet achieved independent Tier 3 validation or Tier 4 readiness for routine clinical implementation. At present, omics approaches should be regarded primarily as research and translational prioritization tools rather than determinants of routine clinical decision-making.}, }
@article {pmid42278475, year = {2026}, author = {Ermakov, VS and Falah, K and Nigam, SK}, title = {A Kidney-Microbiome Short- and Medium-Chain Fatty Acid Loop Mediated by OAT1: Implications for the Remote Sensing and Signaling Theory.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27114942}, pmid = {42278475}, issn = {1422-0067}, support = {R01 DK109392/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Organic Anion Transport Protein 1/metabolism/genetics ; Signal Transduction ; Mice ; *Kidney/metabolism/microbiology ; *Fatty Acids, Volatile/metabolism ; Mice, Knockout ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {Short-chain fatty acids (SCFAs) and medium-chain fatty acids (MCFAs) include small organic anions derived from the gut microbiome that interact with organic anion transporters of the SLC22 family, many of which are expressed in the kidney proximal tubule. According to the Remote Sensing and Signaling Theory (RSST), crosstalk between organs (e.g., gut-liver-kidney axis, gut-brain axis) and the gut microbiome is mediated by metabolites and signaling molecules transported by multi-specific "drug" transporters. The renal drug transporter OAT1 (SLC22A6) is also a major transporter of gut-microbiome products and uremic toxins (e.g., indoxyl sulfate); it has been shown to act as part of a regulatory feedback loop involving the gut microbiome. SCFAs, especially propionate and butyrate, have been shown to play a central role in the transcriptional regulation of OAT1 through HDAC inhibition. By fecal metagenomics analyses of Oat1 knockout mice, we now find that propionate synthesis is among the most altered pathways in the gut microbiome. In contrast, these pathways were only minimally altered in the Oat3 (Slc22a8) knockout. Metabolomics analyses indicate that serum propionate derivatives (e.g., propionyl glycine) and 3-hydroxybutyrate are dependent on OAT1 in the knockout mice and in humans treated with probenecid, an OAT1 inhibitor. The gut microbiome of the Oat1 knockout mice also exhibited greater fatty acid synthesis, which generates odd-chain-length fatty acids (e.g. heptanoate) when propionate is available. Overall, the data, especially when considered in light of in vitro experiments of others, indicates the in vivo existence of a feedback loop connecting gut-microbiome-derived SCFAs and MCFAs to kidney proximal tubule uptake via OAT1. This bidirectional feedback loop in turn regulates OAT1 expression through HDAC inhibition. The feedback loop is clearly consistent with the Remote Sensing and Signaling Theory-in particular, the centrality of multi-specific "drug" transporters in organ crosstalk and host-microbiome interactions via small molecules with "high information content." The key role of OAT1 function in maintaining tubular secretion in CKD supports the importance of this RSST loop in renal pathophysiology. Modulating this RSST loop could have therapeutic value in chronic kidney disease and other contexts.}, }
@article {pmid42278484, year = {2026}, author = {Shemfe, DP and Mvubu, NE and Naidoo, P and Giandhari, J and Byrd, DA and Kader, SS and Mkhize-Kwitshana, ZL}, title = {The Hidden Link Between Intestinal Helminthiasis, Gut Microbiome Alterations, and Colorectal Cancer Risk: A Systematic Review.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27114957}, pmid = {42278484}, issn = {1422-0067}, support = {HDID5149/KR/202//South African Medical Research Council/ ; PMDS22070734338//National Research Foundation/ ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology/etiology/parasitology ; *Gastrointestinal Microbiome ; *Helminthiasis/complications/microbiology/parasitology ; Animals ; *Intestinal Diseases, Parasitic/microbiology/complications ; Dysbiosis ; Helminths ; Risk Factors ; Bacteria ; }, abstract = {Colorectal cancer (CRC) is an increasing health concern in low- and middle-income countries (LMICs), especially in Africa, driven by dietary shifts, urbanisation, infections, and limited treatment access. The gut microbiome plays a central role in CRC, while soil-transmitted helminths (STHs) exert complex effects that can promote or mitigate risk depending on species, infection intensity, and host context. This systematic review synthesised 17 human studies (2000-2026) examining helminth impacts on gut microbial diversity, revealing a dualistic pattern. Several studies reported that chronic or moderate helminth infections, such as Ascaris lumbricoides and Trichuris trichiura, were associated with increased bacterial richness and the expansion of beneficial taxa, including Paraprevotellaceae, Parabacteroides, Agathobacter, Ruminococcaceae, and Lactobacillus. These taxa are associated with the production of short-chain fatty acids (SCFAs), protection of the epithelial barrier, and regulation of the immune system, suggesting a potential buffering effect against inflammation-driven carcinogenesis. On the contrary, other studies demonstrated helminth-associated dysbiosis characterised by reduced diversity and enrichment of pro-inflammatory and oncogenic taxa. T. trichiura and Strongyloides stercoralis infections were associated with the expansion of Treponema succinifaciens, Streptococcus gallolyticus, Enterobacteriaceae, and Ruminococcus torques, which are linked to reduced gut microbiome diversity, pro-inflammatory states, and oncogenic processes. Furthermore, A. lumbricoides infections altered the host microbiome at the phylum level, with increased Proteobacteria and reduced Firmicutes and Bacteroidetes, alongside metabolome shifts in amino acid and lipid pathways that have been associated with tumourigenic processes. Collectively, the evidence shows that helminthiasis may either enrich potentially protective microbes or be associated with pro-tumourigenic dysbiosis, with outcomes shaped by species, infection intensity, and host context. Notably, none of the included studies directly assessed CRC, underscoring the fact that current evidence is indirect and mechanistic. Overall, helminths are associated with gut microbiome shifts in both potentially protective and potentially harmful directions. This systematic synthesis of human evidence provides an integrated understanding of how helminth-associated microbiome shifts may influence colorectal carcinogenesis and highlights the need for longitudinal mechanistic studies to clarify causality and inform biomarker discovery and prevention in endemic regions.}, }
@article {pmid42278495, year = {2026}, author = {Zielińska, E and Kycia, K and Mikołajczuk-Szczyrba, A and Piłka, N and Juszczuk-Kubiak, E}, title = {GABA-Producing Bacteria as Potential Psychobiotics in Gut-Brain Axis Regulation.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27114969}, pmid = {42278495}, issn = {1422-0067}, support = {NdS-II/SN/0238/2023/01"//Ministry of Science and Higher Education/ ; }, mesh = {Humans ; *gamma-Aminobutyric Acid/metabolism/biosynthesis ; *Brain/metabolism/physiology ; Animals ; *Probiotics ; *Gastrointestinal Microbiome/physiology ; *Bacteria/metabolism ; *Brain-Gut Axis ; }, abstract = {γ-Aminobutyric acid (GABA) is the main inhibitory neurotransmitter in the central nervous system (CNS) and plays a vital role in maintaining neural balance, regulating mood, and reducing stress responses. Recent metagenomic studies of the gut microbiome have shown that various bacterial species, especially those in the genera Lactobacillus, Bifidobacterium, and Bacteroides, isolated from the human gut and environmental sources such as fermented foods, contain glutamate decarboxylase (GAD) systems that enable GABA production. Microbially produced GABA can influence the microbiota-gut-brain (MGB) axis by activating neural, endocrine, and immune signalling pathways that are crucial for maintaining gut and brain homeostasis. Emerging evidence suggests that supplementation with GABA-producing bacteria, known as psychobiotics, may improve neurotransmitter balance, modulate cytokine production, strengthen the integrity of the intestinal barrier, and alleviate anxiety- and depression-related behaviours. This review summarises current knowledge of GABA-producing bacterial strains derived from the human gut and food environments and explores their potential as emerging psychobiotics in modulating gut-brain communication and mental health.}, }
@article {pmid42278525, year = {2026}, author = {Caragea, ME and Caragea, DC and Assani, MZ and Siloși, I and Boldeanu, MV and Radu, L and Boldeanu, L and Vere, CC}, title = {Mechanisms Linking Recurrent Bacterial Urinary Tract Infections to Chronic Kidney Disease Progression.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27114999}, pmid = {42278525}, issn = {1422-0067}, support = {//the University of Medicine and Pharmacy of Craiova, Romania./ ; }, abstract = {Urinary tract infections (UTIs) are among the most common bacterial infections worldwide and are traditionally considered acute and self-limited conditions. However, growing evidence suggests that recurrent or persistent UTIs may contribute to chronic kidney disease (CKD) progression through complex interactions between uropathogens and host responses. This review examines the pathophysiological links of UTIs caused by uropathogenic Escherichia coli, Klebsiella spp., and Enterococcus spp. and the development of chronic renal injury. Pathogen-specific persistence mechanisms, including intracellular survival, biofilm formation, and chronic colonization, may promote sustained inflammation, oxidative stress, and maladaptive repair responses. These processes are associated with tubular injury and progressive fibrotic remodeling. In addition, host-related factors such as diabetes, immune dysfunction, and antimicrobial resistance may further influence disease progression. Emerging biomarkers of inflammation, tubular injury, and fibrosis may improve early detection and risk stratification in patients with recurrent or complicated UTIs. Collectively, these findings support the concept that recurrent UTIs may represent potential contributors to CKD progression in susceptible individuals and highlight the importance of early recognition, pathogen-oriented management, and improved diagnostic strategies.}, }
@article {pmid42278532, year = {2026}, author = {Ali, B and Khan, Z and Imin, N and Janda, T and Gholizadeh, F}, title = {Multi-Omics Dissection of Drought Stress Responses in Crops: From Molecular Regulatory Networks to Climate-Resilient Breeding Applications.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27115008}, pmid = {42278532}, issn = {1422-0067}, support = {TKP2021-NKTA-06//National Research, Development and Innovation Office/ ; }, mesh = {Drought Resistance ; Multiomics ; *Crops, Agricultural/genetics/metabolism/physiology ; *Plant Breeding/methods ; *Stress, Physiological/genetics ; Droughts ; *Gene Regulatory Networks ; Genomics/methods ; Gene Expression Regulation, Plant ; Climate Change ; }, abstract = {Drought stress is the most pervasive abiotic constraint on global crop productivity, with projected intensification under climate change threatening the yields of staple crops including wheat, rice, maize, and legumes. Conventional breeding approaches have delivered limited gains against drought tolerance, constrained by the polygenic and multifactorial nature of stress adaptation, the complexity of genotype-by-environment interactions, and the inadequacy of field-based phenotyping under variable stress conditions. Omics technologies, including genomics, transcriptomics, proteomics, metabolomics, epigenomics, and phenomics, have substantially advanced the molecular dissection of drought tolerance by enabling high-resolution characterization of stress-responsive genes, regulatory networks, adaptive proteins, and metabolic reprogramming pathways. Specific traits targeted include root system architecture and depth, osmotic adjustment capacity through proline and glycine betaine accumulation, antioxidant defense mechanisms, ABA-mediated stomatal regulation, LEA protein accumulation, epigenetic stress memory, and yield stability under water deficit. This review systematically examines omics-based strategies for drought stress mitigation across major crops, highlighting individual omics contributions, multi-omics integration frameworks, computational tools including machine learning and AI-driven predictive modelling, and translational breeding applications. Case studies in wheat, rice, maize, and legumes illustrate how omics-driven approaches accelerate precision breeding for drought resilience through marker-assisted selection, genomic selection, and CRISPR-based gene editing. Challenges including data integration complexity, high implementation costs, limited cross-species transferability, and the need for field-scale validation of microbiome-based strategies are critically addressed. Future perspectives encompassing single-cell and spatial omics, AI-driven predictive breeding, digital agriculture integration, and international data governance frameworks are discussed. By aligning with climate-smart agriculture principles, multi-omics approaches provide a robust and transformative foundation for developing drought-resilient crop cultivars suitable for water-limited production systems worldwide.}, }
@article {pmid42278533, year = {2026}, author = {Ramadan, YN and Bukhari, SQ and Alatawi, Z and Oriquat, G and Ellah, NHA and Mohamedosman, EHA and Ahmed, R and Hetta, HF}, title = {Evolutionary Genomics of Human Gut Bacteria: Ecological Plasticity Across the Mutualism-Pathogenicity Spectrum.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27115009}, pmid = {42278533}, issn = {1422-0067}, abstract = {The human gut microbiome comprises a diverse community of bacteria whose interactions with the host range from beneficial mutualism to opportunistic pathogenicity. These interactions are shaped by genomic plasticity and ecological pressures that influence whether microbes support host health, remain conditionally harmless, or contribute to disease. Understanding the mechanisms underlying these shifts is essential for clarifying the balance between cooperation and pathogenicity within the gut ecosystem. This review explores the genomic and evolutionary mechanisms that shape microbial adaptation across the mutualism-pathogenicity spectrum in the human gut. Key processes, including horizontal gene transfer (HGT), host-mediated selection, and niche specialization, enable microbes to acquire, regulate, or retain traits that influence colonization, metabolic function, and virulence. These adaptive mechanisms allow gut bacteria to respond dynamically to ecological pressures such as inflammation, antibiotic exposure, and dietary change, resulting in context-dependent microbial behaviors. The review also considers how concepts from insect endosymbiosis may provide insight into gut microbial adaptation. While both systems exhibit host specialization, major differences in transmission mode, ecological flexibility, and genome evolution limit direct comparisons. Rather than following a fixed progression toward parasitism, gut microbes exhibit flexible adaptive strategies shaped by host and environmental conditions. By integrating ecological and evolutionary perspectives, this review presents a balanced framework for understanding how genomic adaptation influences microbial behavior in the gut. This perspective improves our understanding of dysbiosis and microbial pathogenesis and may support the development of microbiome-informed therapeutic strategies for maintaining host health.}, }
@article {pmid42278559, year = {2026}, author = {Li, CC and Sun, DS and Lien, TS and Lin, GL and Cheng, CF and Tsai, KW and Wu, WS and Hu, CT and Lin, MD and Lin, WY and Yang, CH and Liou, JW and Chang, HH}, title = {TiO2 Nanoparticles Trigger Gut-to-Gill Bacterial Translocation and Dysbiosis in Zebrafish.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27115036}, pmid = {42278559}, issn = {1422-0067}, support = {111-2320-B320-006-MY3, 112-2320-B-320-007, 114-2320-B-320-004//National Science and Technology Council/ ; TCMMP114-01, TCAS111-02, TCAS112-02, TCAS113-04, TCRD112-033, TCRD113-041, TCRD114-029, TCRD115-030//Tzu Chi Foundation/ ; }, mesh = {Animals ; *Titanium/toxicity/chemistry ; *Zebrafish/microbiology ; *Dysbiosis/microbiology/chemically induced ; *Gills/microbiology/drug effects ; *Bacterial Translocation/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Nanoparticles/toxicity ; RNA, Ribosomal, 16S/genetics ; *Metal Nanoparticles/toxicity/chemistry ; }, abstract = {Titanium dioxide nanoparticles (TiO2-NPs) are widely produced and persist in aquatic ecosystems, yet their indirect effects on host-microbe interactions remain poorly defined. By using zebrafish (Danio rerio) as a sentinel species, this study investigated the effects of subchronic 5 mg/L TiO2-NP exposure. Dynamic light scattering was utilized to characterize the bimodal aggregates (peaks at 917 and 46,841 nm; surface charge: +22.08 mV) that define the environmental state of TiO2-NPs. Parallel 16S rRNA metagenomic profiling on Day 6, prior to mortality, revealed profound gut dysbiosis. A marked increase in Chao1 richness (p < 0.01), alongside a catastrophic 333-fold reduction in beneficial Cetobacterium and an 856-fold enrichment of pathogenic Mycobacterium, was observed. Beta-diversity and hierarchical clustering analyses revealed a striking convergence between gut and gill microbial signatures, supporting a gut-to-gill translocation model. These results suggest that TiO2-NPs exposure induces intestinal dysbiosis, facilitating opportunistic bacterial migration via internal (gut-blood-gill) or external (fecal-water-gill) pathways. This study identifies dysbiosis-driven secondary infection as a novel, overlooked mechanism of nanoparticle toxicity, necessitating a shift in ecological risk assessments toward host-microbe interactions.}, }
@article {pmid42259341, year = {2026}, author = {Lim, LL and Jenkins, A and Prabhakaran, D and Sookoian, S and Bannuru, RR and Khunti, K}, title = {Biological and mechanistic pathways of cardiometabolic multiple long-term conditions.}, journal = {Lancet (London, England)}, volume = {}, number = {}, pages = {}, doi = {10.1016/S0140-6736(26)00607-0}, pmid = {42259341}, issn = {1474-547X}, abstract = {Cardiometabolic multiple long-term conditions (MLTC) arise from the complex interplay of biological, sociodemographic, environmental, and behavioural factors across the life course. Shared risk factors and mechanisms, including insulin resistance, adiposity, and chronic inflammation, underpin its development. Growing evidence also implicates that even low-level, long-term exposure to fine particulate matter, nitrogen dioxide, and related pollutants can accelerate the trajectory of cardiometabolic MLTC. Early-life exposures, including undernutrition and overnutrition, altered gut microbiome, and endocrine-disrupting chemicals, interact with social determinants of health to aggravate inflammatory and metabolic dysregulation. These mechanisms, together with genetic susceptibility, epigenetic modifications, and multiomics perturbations, shape disease progression, heterogeneity, and the clustering of cardiometabolic MLTC. Yet, fundamental gaps persist, whereby most mechanistic insights are derived from single-disease studies, leaving the temporal hierarchy, causal pathways, and population-level heterogeneity largely unresolved. Addressing these challenges will require life-course research, integrative systems approaches, and translational studies that link mechanistic insights to precision prevention and therapeutic strategies. By bridging discovery with actions, such efforts can enhance care for cardiometabolic MLTC and promote equitable health outcomes globally.}, }
@article {pmid42259432, year = {2026}, author = {Hao, L and Li, ZF and Qu, YN and Zhao, FY and Lu, SY and Li, BQ and Zhang, HY and Wang, HQ}, title = {IUPHAR review. Gut microbial metabolites as remote regulators of behavior and neuropsychiatric disease.}, journal = {Pharmacological research}, volume = {230}, number = {}, pages = {108284}, doi = {10.1016/j.phrs.2026.108284}, pmid = {42259432}, issn = {1096-1186}, abstract = {The gut-brain axis has emerged as a fundamental pathway through which gut-derived microbial metabolites exert remote control over brain development, neural circuit function and behavior. This Review synthesizes evidence that key microbial metabolites including short-chain fatty acids, tryptophan derivatives, bile acids and trimethylamine N-oxide modulate neuroimmune, neuroendocrine and synaptic signaling in a context-dependent manner, influencing whether the brain maintains homeostasis or progresses toward pathology. We critically evaluate how these metabolites contribute to the etiology and symptomatology of neurodevelopmental and psychiatric disorders such as autism spectrum disorder, major depressive disorder, anxiety and post-traumatic stress disorder. Causal insights are highlighted by studies demonstrating that fecal microbiota transplantation from affected individuals to rodents transfers core behavioral phenotypes. It is important to note, however, that while FMT and gnotobiotic studies establish causality in animal models, evidence from human studies remains predominantly correlative, and we have explicitly distinguished these evidence tiers throughout. We also explore the translational potential of microbiome-derived biomarkers for diagnosis and the challenges in developing targeted therapeutics, including probiotics, postbiotics and metabolite-sequestering agents. Moving forward, the field should prioritize decoding the contextual determinants of microbial influence and adopt personalized, function-based strategies to effectively modulate the gut-brain metabolic axis for brain health.}, }
@article {pmid42259440, year = {2026}, author = {Lee, HS and Ibarra, LE and Zuo, B and Zhao, J and Fox, R and Read, QD and Gurung, M and Yeruva, L and Chen, C and Trudo, SP}, title = {Protective effect of apiaceous vegetables against Total Western Diet- and dextran sulfate sodium-induced colitis in mice.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {101652}, doi = {10.1016/j.tjnut.2026.101652}, pmid = {42259440}, issn = {1541-6100}, abstract = {BACKGROUND: Western-style dietary patterns are associated with colitis and colon cancer. Existing data indicate intake of apiaceous vegetables (API; e.g., celery, parsnip) may prevent inflammation-associated diseases.<br><br>OBJECTIVE: We investigated in mice the effect of API supplementation to the Total Western Diet (TWD) against dextran sulfate sodium (DSS)-induced colitis.<br><br>METHODS: Male C57BL/6J mice (8-week-old; 15/group) were fed TWD supplemented with 21% or 42% fresh API (w/w) and given 2% DSS to induce colitis. Diet intake, body weight, and disease activity index (DAI) were monitored. Serum was collected for cytokine/chemokine analysis and colonic tissues for histology and Western blot. Fecal samples were analyzed by 16S rRNA gene sequencing and targeted/untargeted metabolomics. Phenotypic data were analyzed by ANOVA with Tukey's test. Microbiome data were Centered-Log Ratio (CLR) transformed and analyzed using linear mixed models with adjusted pairwise comparisons.<br><br>RESULTS: API supplementation attenuated colitis phenotypes including weight loss (44% recovery; P < 0.001), colon shortening (57% recovery; P < 0.01), disease activity (59% lower; P < 0.001), cytokine/chemokine release (35-73% reductions; P < 0.05), and mucosal F4/80+ cells infiltration (80% reduction; P < 0.001). API also improved gut microbiota diversity and composition, increasing alpha diversity metrics (4.4%-13.8%; P <0.05), suppressing pathogenic bacteria (Paraclostridium, Enterococcus, Eubacterium; estimated CLR difference: -1.8 to -6.7; P < 0.001), and enriching beneficial bacteria (Lachnospiraceae and Blautia; estimated CLR difference: +1.6 to +3.0; P < 0.05). Furthermore, metabolomics indicated TWD consumption increased arachidonic acid and aliphatic aldehydes (by 109%-510%; P < 0.001), and decreased short-chain and unsaturated fatty acids (by 30%-91%; P < 0.001). API supplementation also mitigated TWD-derived functional metabolites (including bile acids; P < 0.05).<br><br>CONCLUSIONS: These data indicate that API intake is beneficial for risk reduction of diseases associated with Western diets. However, further investigations are warranted to determine the mechanism behind these beneficial effects.}, }
@article {pmid42259836, year = {2026}, author = {Galal, L and Eltokhy, MA and Abostate, HM and Omran, ME and Radwan, SMR}, title = {Comparative analysis of the sputum microbiota in different COPD clinical states.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42259836}, issn = {2045-2322}, abstract = {Chronic obstructive pulmonary disease (COPD) is a well-known respiratory illness. COPD patients oscillate between a stable state and an exacerbated state that leads to disease deterioration. Studies suggest that respiratory microbiome dysbiosis plays a vital role in COPD pathogenesis. However, the exact microbial composition among different clinical states of COPD is still elusive. To determine and compare the respiratory microbiota composition in different COPD clinical states, namely, the stable state (S-COPD) and the acute exacerbated state (AE-COPD). In this prospective study, 74 samples were collected from COPD patients. The sputum microbiota was analyzed via 16 S rRNA gene sequencing, and only 35 samples were included due to bad reads or not in accordance with inclusion criteria: S-COPD patients (n = 18), and AE-COPD patients (n = 17). Bioinformatics analysis was used to determine changes in the microbiota among the comparison groups. The most abundant phyla among all the samples were Proteobacteria, Fusobacteria, Firmicutes, and Actinobacteria, with Paracoccus, Streptomyces Leptotrichia Fusobacterium and Ruminococcaceae being the most prevalent genera. Dissimilarity in abundance across the studied COPD states was observed, with significantly greater abundance of Proteobacteria and Fusobacteria in S-COPD patients and greater abundance of Firmicutes in AE-COPD patients at the phylum level. At the genus level, Paracoccus, Fusobacterium, Streptococcus, Haemophilus, and Moraxella were significantly different between the two groups and were more prevalent in S-COPD, whereas Cellulosilyticum, Streptomyces, Leptotrichia, Ruminococcaceae_UCG_014, and Atopobium were more prevalent in exacerbated individuals. Alpha diversity revealed greater diversity in stable versus exacerbated patients, and a PCoA plot of Bray‒Curtis and weighted UniFrac distances revealed that stable patients were highly clustered, whereas exacerbated patients were more disseminated. At the genus level, LEfSe analysis revealed the dominance of Cellulosilytic, Liptotrichia, and Streptomyces in the AE-COPD group, whereas the S-COPD group microbiome was dominated by the genera Paracoccus, Fusobacterium, Streptococcus Haemophilus, and Moraxella (p < 0.05). The results of the present study suggest that COPD patients have unique microbial profiles that differ across different states, with increased abundances of Proteobacteria, chiefly Paracoccus. These findings need more research to clarify the definite role of microbiome dysbiosis in COPD pathogenesis.}, }
@article {pmid42259841, year = {2026}, author = {Deng, F and Fan, Y and Yan, J and Zhang, X and Guo, Y and Li, M and Peng, Y and Zhao, L and Liu, F and Zheng, Y and Deng, B and Deng, J and Chen, S and Jiang, H and Chai, J and Zhao, J and Li, Y}, title = {Genome-resolved and culture-based atlas of the feline gut microbiome enables host-adapted probiotic development.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01038-z}, pmid = {42259841}, issn = {2055-5008}, abstract = {Domestic cats (Felis catus) depend on their gut microbiome for metabolism, immunity, and pathogen defense, yet its genomic characterization remains limited. We combined large-scale metagenomics and culturomics to define the feline gut microbiome and identify indigenous probiotic candidates. Analysis of 412 feline fecal metagenomes produced 2852 strain-resolved metagenome-assembled genomes (MAGs) grouped into 514 species-level genome bins, including 106 putative novel taxa. This catalog revealed 24 core species and two enterotypes: ET-P, deaminated by Prevotella, and ET-CB, enriched for Collinsella, Blautia, Bifidobacterium, Ligilactobacillus, MAG-based screening prioritized 113 candidate probiotic species. Culturomics recovered 2904 isolates representing 110 species-level taxa, including 75 putative novel species and a candidate novel genus. Six feline-derived isolates were selected for downstream testing, and five exhibited favorable probiotic traits in vitro, including acid and bile tolerance, anti-Escherichia coli activity, and favorable cytokine responses. In a pathogenic Escherichia coli-induced dirrhea model in cats, a five-strain indigenous consortium improved fecal scores and reduced IL-2, IL-1β, and IL-6, with TNF-α suppression superior to antibiotics or a commercial probiotic. These results establish FelMGDB as a resource for feline microbiome research and highlights indigenous probiotics as promising interventions for feline gut health.}, }
@article {pmid42259846, year = {2026}, author = {Kakuk, B and Dörmő, &#xc1; and Taifi, A and Járay, T and Kurucsai, G and Gulyás, G and Prazsák, I and Boldogkői, Z and Tombácz, D}, title = {Canine Fecal Microbiome Dataset: Ultra-deep Multi-platform Sequencing Across Extraction and Library Protocols.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07594-5}, pmid = {42259846}, issn = {2052-4463}, support = {LP2020-8/2020//Magyar Tudom&#xe1;nyos Akad&#xe9;mia (Hungarian Academy of Sciences)/ ; FK 142676//Nemzeti Kutat&#xe1;si, Fejleszt&#xe9;si &#xe9;s Innov&#xe1;ci&#xf3;s Hivatal (NKFI Office)/ ; }, abstract = {The canine gut microbiome is an important model for microbiome research, yet methodological variation in DNA isolation, library preparation, and sequencing complicates cross-study comparisons. Here we present a three-component dataset to evaluate methodological effects. First, an ultra-deep sequencing dataset was generated from a single dog fecal sample using both short- (Illumina NovaSeq) and long-read (Oxford Nanopore MinION) platforms. Second, fecal samples from eight co-housed dogs were collected over one year to compare two DNA extraction workflows across 40 samples. Third, three full-length 16S rRNA primer sets were evaluated using synthetic microbial community standards and human and canine fecal samples, all sequenced on the MinION platform. The dataset comprises 75.2 GB of raw sequencing data and quality control and taxonomic classification outputs. The single-sample multi-platform dataset contributes 9.19 GB, the longitudinal cohort 43.45 GB, and the primer comparison dataset 22.61 GB across two accessions. Together, these data provide a multi-platform resource for evaluating extraction, sequencing, and primer-associated methodological effects in canine fecal microbiome profiling.}, }
@article {pmid42259906, year = {2026}, author = {Ling, X and Zhang, Y and Bui, CHT and Chan, HN and Peng, Y and Zhang, XJ and Yim, CC and Yau, JW and Kam, KW and Ip, P and Young, AL and Hon, KL and Tham, CC and Pang, CP and Chen, LJ and Yam, JC}, title = {Profiling of ocular surface microbiome and its ocular types in children and adolescents.}, journal = {Communications medicine}, volume = {}, number = {}, pages = {}, doi = {10.1038/s43856-026-01667-7}, pmid = {42259906}, issn = {2730-664X}, support = {82425017 &amp; 82171089//National Natural Science Foundation of China (National Science Foundation of China)/ ; 11220206//Food and Health Bureau of the Government of the Hong Kong Special Administrative Region | Health and Medical Research Fund (HMRF)/ ; }, abstract = {BACKGROUND: The ocular surface microbiome is increasingly recognized for its role in eye health, but the complexity of its composition complicates personalized characterization. This study aims to define the ocular surface microbiome profile and identify distinct microbial community clusters, or Ocular Types, in a population of children and adolescents.<br><br>METHODS: In this population-based, cross-sectional study, conjunctival swabs from children and adolescents were processed with 16S ribosomal RNA gene amplicon sequencing. Microbial clusters were determined using a partitioning around medoids clustering approach, validated through internal cross-comparison and external datasets. Functional profiles of the clusters were predicted from the sequencing data.<br><br>RESULTS: Here we show that in 1246 samples from 1006 individuals aged 3 to 18 years, the predominant bacterial phyla are Proteobacteria (34.1%), Firmicutes (37.4%), and Actinobacteria (25.2%), with Staphylococcus, Corynebacterium, and Streptococcus as core microbiota. Five distinct Ocular Types are identified, characterized by the dominance of Staphylococcus, Corynebacterium, Streptococcus, uncultured Neisseriaceae, or Escherichia-Shigella. These Ocular Types demonstrate associations with host factors including age, ethnicity and ocular parameter, but not with sex. Functional prediction reveals considerable overlap in the metabolic pathways among the Ocular Types.<br><br>CONCLUSIONS: This study characterizes five distinct ocular surface microbiome types in pediatric population and establishes their association with host factors. These findings provide a structured framework for investigating microbial community dynamics and their potential implications for ocular health.}, }
@article {pmid42259958, year = {2026}, author = {Yu, D and Zhang, L and Zhang, L and Damu, A and Gao, N and Xu, J and Hao, J and Xiao, Y and Zhang, J and Yan, J}, title = {A dual-marker approach for forensic age prediction: integrating the salivary microbiome and antibiotic resistome.}, journal = {International journal of legal medicine}, volume = {}, number = {}, pages = {}, pmid = {42259958}, issn = {1437-1596}, support = {82030058//National Natural Science Foundation of China/ ; 82101977//National Natural Science Foundation of China/ ; 202503021211157//Natural Science Foundation of Shanxi Province/ ; }, abstract = {Age prediction is a critical challenge in forensic science. Current mainstream approaches, such as DNA methylation analysis, often involve complex sample processing (e.g., bisulfite conversion), which can be costly and time-consuming and may compromise DNA integrity, thereby limiting multi-analyte recovery from trace evidence. Recent studies have highlighted the potential of the human microbiome as a source of forensic biomarkers, including for age estimation. Notably, the profile of antibiotic resistance genes (ARGs) in the microbiome has been reported to vary with host age, yet their utility as forensic age biomarkers remains unexplored. To address this, we characterized the salivary microbiome of volunteers via 16S rRNA gene (V3-V4) amplicon sequencing and quantified the abundance of 32 preselected ARGs using high-throughput quantitative PCR (HT-qPCR). Our analysis identified six bacterial genera and seven ARGs whose relative abundances were significantly correlated with chronological age (P < 0.05). We then constructed and compared random forest regression models for age prediction based on (i) microbiome features (Amplicon Sequence Variants, ASVs), (ii) ARG abundances alone, and (iii) an integrated set combining both marker types. Our results showed that the microbiome-only and ARG-only models both yielded higher mean absolute error (MAE) than the integrated model. In contrast, the combined model, built on just 13 features (six bacterial genera and seven ARGs), achieved a test MAE of 6.22 ± 3.75 years (MAE ± SD). This study reveals that ARGs hold promise as novel biomarkers for forensic age estimation. More importantly, the dual‑marker "microbiome‑ARG" strategy achieves effective age prediction using only a small number of features, offering a highly efficient and promising new approach for forensic age estimation.}, }
@article {pmid42260063, year = {2026}, author = {Álvarez-Bobillo, Z and Gracia-Cazaña, T and Gilaberte, Y and Lim, HW}, title = {What's New in Photoprotection?.}, journal = {American journal of clinical dermatology}, volume = {}, number = {}, pages = {}, pmid = {42260063}, issn = {1179-1888}, support = {Research group of Aragon Goverment B59_23D Dermatology//Departamento de Educaci&#xf3;n, Cultura y Deporte, Gobierno de Arag&#xf3;n/ ; Photobiology//Departamento de Educaci&#xf3;n, Cultura y Deporte, Gobierno de Arag&#xf3;n/ ; }, abstract = {It is well established that a complete package of photoprotection includes staying in the shade, wearing photoprotective clothing, hat, and sunglasses, and on otherwise exposed sites, applying sunscreen. Recent advances have modified photoprotection through new active ingredients, innovative formulations, complementary oral strategies, and personalized approaches. This review aims to summarize the latest new developments in photoprotection. A narrative review of the literature was conducted from January 2010 to October 2025 using terms related to photoprotection, sunscreen innovation, visible light, oral photoprotection, microbiome interaction, climate change, and personalized approaches. Articles in English and Spanish were selected based on scientific relevance. Advances in photoprotection include the development of new topical filters targeting UVA1 and visible light, as well as the incorporation of iron oxides and, in some formulations, pigmentary titanium dioxide in tinted sunscreens to enhance protection against visible light. In addition, the use of antioxidants and DNA repair enzymes has been explored to mitigate oxidative stress and address field cancerization. Natural and eco-friendly bioactive ingredients derived from botanical and marine sources show growing potential as photoprotective agents. Additional considerations such as the role of skin microbiome, and personalized photoprotection strategies tailored to skin phototype, lifestyle, diseases, and high-exposure conditions further refine preventive practice. Photoprotection is evolving into a multidimensional approach that integrates advanced topical formulations, oral agents, and individualized recommendations. This paradigm offers improved prevention of photoaging, pigmentary disorders, and photocarcinogenesis while promoting safer and more sustainable photoprotection practices.}, }
@article {pmid42260168, year = {2026}, author = {Smith, J}, title = {Daily briefing: Lung microbiome linked to a mysterious tissue-scarring condition.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/d41586-026-01828-7}, pmid = {42260168}, issn = {1476-4687}, }
@article {pmid42260293, year = {2026}, author = {Kuriyama, Y and Mizuno, F and Yamada, T and Kumagai, M and Tanaka, M and Naka, I and Hirata, K and Mizushima, S and Yonemoto, S and Funahashi, K and Seguchi, N and Sakaue, K and Kanazawa, E and Matsushita, M and Matsushita, T and Saso, A and Nara, T and Sawaura, R and Katagiri, C and Maekawa, T and Kurosaki, K and Saitoh, H and Namiki, S and Ueda, S and Ohashi, J}, title = {Insights into demographic and cultural influences on the oral microbiome from historical Japanese dental calculus.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42260293}, issn = {2045-2322}, support = {24K00163//JSPS KAKENHI/ ; 24K00163//JSPS KAKENHI/ ; 24K00163//JSPS KAKENHI/ ; 24K21381//JSPS KAKENHI/ ; 24K21381//JSPS KAKENHI/ ; 24K21381//JSPS KAKENHI/ ; 24K00163//JSPS KAKENHI/ ; }, abstract = {Recent advances in genomic technologies have enabled detailed analyses of ancient microbiomes using dental calculus. While most studies have focused on European and North American populations, ancient Japanese oral microbiomes remain largely unexplored. Here, we analyzed dental calculus primarily from Edo period individuals (17th-19th centuries) to investigate the compositional, functional, and phylogenetic diversity of ancient oral microbiomes. Our results revealed clear differences between ancient and modern Japanese microbiomes, as well as phylogenetic divergence between the Final Jomon (ca. 1000 BCE) and Edo periods. We also identified regional variation in ancient oral microbiomes and clade-level diversity within the periodontitis-associated archaeon Methanobrevibacter oralis. Interestingly, individuals with traces of tooth blackening (ohaguro), a custom practiced by Edo period women, were all assigned to the same clade, suggesting cultural influences on the oral microbiome. These findings highlight the important role of human culture and demography in shaping the evolutionary dynamics of microbiomes.}, }
@article {pmid42260348, year = {2026}, author = {Gudra, D and Lunge, M and Skinderskis, E and Roga, A and Rubins, S and Fridmanis, D}, title = {Cyanoacrylate glue as an effective skin-decontamination method for hair follicle microbiome sampling: insights from a nonhuman model (Capreolus capreolus).}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05268-1}, pmid = {42260348}, issn = {1471-2180}, support = {LZP-2022/1-0119//Latvijas Zin&#x101;tnes Padome/ ; LZP-2022/1-0119//Latvijas Zin&#x101;tnes Padome/ ; LZP-2022/1-0119//Latvijas Zin&#x101;tnes Padome/ ; LZP-2022/1-0119//Latvijas Zin&#x101;tnes Padome/ ; LZP-2022/1-0119//Latvijas Zin&#x101;tnes Padome/ ; LZP-2022/1-0119//Latvijas Zin&#x101;tnes Padome/ ; }, abstract = {INTRODUCTION: In humans, microorganisms within hair follicles differ from those on the skin surface and may contribute to autoimmune skin diseases such as alopecia areata and vitiligo. Owing to the low biomass of hair follicle microorganisms, precise sample acquisition and strategies to avoid contamination with genetic material are critical. To address this, we developed and evaluated a sampling methodology using a nonhuman wildlife proxy model - the wild roe deer (Capreolus capreolus) - to identify effective approaches for minimizing skin contamination prior to biopsy. Animal was obtained during licenced hunts and frozen at -20°C shortly postmortem. Four sets of biopsy and skin surface swab samples were collected from the right front leg: 1) untreated skin; 2) skin cleaned with isopropyl alcohol (IPA) wipes; 3) skin treated with cyanoacrylate glue (CAG); and 4) skin treated with CAG followed by IPA wipes. Swabs were collected via Copan FLOQSwabs, whereas biopsies were obtained with single-use 1 mm biopsy punches. Nucleic acids were subjected to droplet digital PCR (ddPCR) for 16S rRNA and 18S rRNA gene copy number quantification. Additionally, the swab samples were subjected to 16S rRNA V3-4 region and ITS-1 sequencing.<br><br>RESULTS: ddPCR analysis revealed greater bacterial presence on the skin surface (11,661&#xb1;5,181 copies/&#xb1;L) than fungal presence (87&#xb1;35 copies/&#x3bc;L), and the microbial load was greater in the swab samples (16S: 11,661&#xb1;5,181; 18S: 87&#xb1;35 copies/&#x3bc;L) than in the biopsy samples (16S: 76&#xb1;56; 18S: 8&#xb1;5 copies/&#x3bc;L). Notably, the use of CAG reduced the microbial load in biopsy samples by 3.7-fold. 16S and ITS sequencing analysis revealed slightly greater alpha diversity in swab samples than in biopsy samples, particularly in areas treated with CAG. Beta diversity revealed distinct clustering of swab and biopsy samples, with shorter distances between CAG-treated samples and untreated samples. Fewer bacterial (n = 8) and fungal (n = 1) genera were detected in CAG-treated biopsies compared with untreated (n = 21, n = 9, resp.) and IPA-treated (n = 45, n = 7, resp.) biopsies.<br><br>CONCLUSIONS: These results demonstrate a high probability of biopsy contamination with microbial DNA originating from the skin surface. They also confirmed that CAG effectively reduces such contamination and can serve as a practical decontamination step before biopsy. Although based on a nonhuman wildlife model, this feasibility study provides methodological insights that can inform the design of future human hair follicle microbiome investigations.}, }
@article {pmid42260510, year = {2026}, author = {Babolin, S and Enea, R and Cicala, M and Di Giovanni, D and Mazzone, L and Emberti Gialloreti, L}, title = {Machine learning model to identify gut microbiome-derived metabolites as potential biomarkers of autism spectrum disorder: a pilot study.}, journal = {BMC psychiatry}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12888-026-08178-8}, pmid = {42260510}, issn = {1471-244X}, abstract = {Autism Spectrum Disorder (ASD) arises from complex and not yet completely understood interactions between genetic and environmental factors. Alongside known hallmarks of neurobiological and structural changes in ASD brain, alterations in gut microbiota are frequently observed in ASD and may contribute to its pathophysiology. Identifying reliable biomarkers through multivariate analysis and machine learning offers promising avenues for improving ASD diagnosis and understanding comorbid gastrointestinal symptoms. In this study, a machine learning model was trained to identify ASD and healthy controls based on the theoretical production of metabolites for each gut bacterial species and each individual, combining the data collected from two global databases (GMRepo v2 and Agora2). Random Forest Classification models reach a mean accuracy of 85%, and a subsequent literature analysis of the 5% most significant metabolites showed a 40% correspondence with previously published in vivo studies. Some of the most relevant compounds detected by the theoretical model are amino acid and amino-acidic derivatives, volatile organic compounds, and short-chain fatty acids. Results are coherent with empirical evidence, supporting microbiota's role in ASD pathophysiology by contributing to neurotransmitters' biosynthesis and degradation, intestinal epithelial barrier integrity, immunological modulation. Future work will focus on stratified sampling, empirical validation, and developing personalized metabolic signatures for early diagnosis and precision medicine.}, }
@article {pmid42260597, year = {2026}, author = {Rynikova, M and Gancarcikova, S and Lauko, S and Mudronova, D and Adamkova, P and Janicko, M and Demeckova, V}, title = {Exploring new animal models of ulcerative colitis: evaluating chemical and patient-derived microbial triggers to advance translational relevance.}, journal = {Laboratory animal research}, volume = {42}, number = {1}, pages = {}, pmid = {42260597}, issn = {1738-6055}, abstract = {BACKGROUND: Ulcerative colitis (UC) is a chronic inflammatory disease of the colon with multifactorial aetiology involving genetic, immune, environmental, and microbial factors. Alterations in the gut microbiome are a consistent feature of UC, yet their causal contribution to disease onset and progression remains unresolved. Current animal models rely largely on chemical or genetic induction and fail to capture the complexity of host-microbiome interactions characteristic of human disease. To address this limitation and enhance the translational relevance of preclinical research, this study employed patient-derived microbiota to model UC-associated dysbiosis and investigated its effects alone and in combination with chemical induction.<br><br>RESULTS: We compared three mouse models using different UC-induction triggers: dextran sulphate sodium (DSS), faecal microbiota transplantation (FMT) from a UC patient, and their combination (COMB). DSS and COMB treatments induced marked clinical symptoms, whereas FMT alone caused only mild changes, likely due to the short exposure period. Immunophenotyping revealed distinct immune profiles across all models, with leukocyte and neutrophil infiltration in the colonic mucosa of all groups, demonstrating that the microbiota alone can elicit localized immune activation. Transcriptomic analysis showed that FMT significantly modulated tight junction and mucin gene expression and induced microbiome shifts resembling those observed in human UC. In contrast, DSS triggered a strong pro-inflammatory transcriptional response and reduced microbial diversity, but with compositional changes mostly opposing those seen in UC patients. The COMB model combined features of both approaches - producing clinical symptoms and inflammatory activation similar to DSS and tight junction dysregulation resembling FMT.<br><br>CONCLUSIONS: This study investigated novel experimental models of ulcerative colitis by incorporating patient-derived microbiota as an inducing factor. DSS induced strong clinical and inflammatory responses, FMT primarily altered barrier gene expression and microbiome composition, and their combination merged both inflammatory and epithelial characteristics. These microbiota-based models show promise for more accurately reproducing UC pathophysiology and thereby improving translational relevance. Further optimization is needed, including adjustment of exposure duration and sequence of induction, as well as validation for reproducibility.}, }
@article {pmid42260689, year = {2026}, author = {Wang, K and Peng, Q and Geng, L and Zhang, F and Liu, R and Liu, X and Zhang, J and Shu, C}, title = {Protaetia brevitarsis larvae frass affects substrate microecological systems via two suggestive pathways to enhance cherry tomato growth.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00915-6}, pmid = {42260689}, issn = {2524-6372}, support = {2023YFD1701502//National Key Research and Development Program of China/ ; 32570599//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The identification and development of high-quality humus sources to enhance the productivity and performance of substrate-based vegetable cultivation systems remains a significant challenge in sustainable agriculture. Protaetia brevitarsis larvae (PBL) exhibit exceptional efficiency in decomposing decaying crop straw and produce nutrient-rich frass with high humic acid content and a complex microbial community. However, its impacts on substrate microecological systems and the underlying functional mechanisms remain unclear, limiting its rational application in substrate cultivation. This study aimed to investigate the effects of PBL frass on substrate microecology and elucidate the associated mechanisms using cherry tomato (Lycopersicon esculentum Mill. var. cerasiforme Alef) pot experiments.<br><br>RESULTS: Incorporation of 2% or 4% (w/w) PBL frass into cherry tomato cultivation substrates significantly promoted plant growth, characterized by reduced plant height (indicating more robust, dwarf-type growth) and increased aboveground (stem) and belowground (root) biomass. Furthermore, PBL frass application enhanced substrate microbial diversity through two distinct, complementary pathways: (&#x2170;) Frass-derived microbes, which possess specific colonization capabilities, directly augmented microbial communities in both the rhizoplane and bulk substrate; and (&#x2171;) Organic compounds in PBL frass may have activated a broad range of microbes, enriching the rhizosphere microbiome. This enhanced microbial diversity was associated with an increased abundance of plant-beneficial taxa, which likely contributed to growth promotion and substrate health maintenance.<br><br>CONCLUSIONS: This study uncovers the multifaceted contributions of PBL frass to substrate microbial ecology and reveals its two suggestive regulatory pathways. These results provide a theoretical basis for the sustainable utilization of PBL frass and advance the development of eco-friendly amendments for modern vegetable production.}, }
@article {pmid42260913, year = {2026}, author = {Shahid, M and Ilyas, T and Shafi, Z}, title = {Rhizobacterial Exopolysaccharides in Soil-Plant Systems: Molecular Mechanisms, Engineering Approaches, and Translational Challenges.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.6c02760}, pmid = {42260913}, issn = {1520-5118}, abstract = {Plant productivity has become increasingly affected by various abiotic and biotic factors such as drought, salinity, metal toxicity, heat/cold stresses, and pathogen pressure that disrupt soil-plant interactions. Plant growth-promoting rhizobacteria (PGPR)-secreted exopolysaccharides (EPSs) play a significant role in maintaining rhizosphere stability through promoting soil aggregation, increasing the soil water retention capacity, and proper ion management. In addition, EPSs provide extracellular binding sites for toxic metals and facilitate the formation of stress-tolerant biofilms. Production of EPSs is under the strict control of sophisticated regulatory systems, linking environmental conditions and adaptive mechanisms at the genetic level. Novel advancements in omics and genome editing techniques could be used in the development of improved EPS-secreting strains with enhanced stress-resistance capabilities. Potential applications include PGPR formulations for seed coating, bioinoculants, and soil treatments; however, strain heterogeneity and environmental variability represent important challenges.}, }
@article {pmid42261315, year = {2026}, author = {Setyawan, HY and Widyastuti, E and Sugiarto, Y and Sunyoto, NMS and Ulandari, D and Dewi, J and Choirun, AU and Arwani, M and Okoye, C}, title = {Applications and mechanisms of biochar-mycorrhizal synergies in agriculture based on systematic review.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e21336}, pmid = {42261315}, issn = {2167-8359}, abstract = {Biochar (BC) and arbuscular mycorrhizal fungi (AMF) have emerged as powerful tools for sustainable agriculture, offering significant benefits for soil health, crop productivity, and ecological resilience. Their combined application has shown synergistic effects; however, key gaps in our understanding remain. This systematic review synthesizes findings from recent studies (n = 72) published up to 2025 to examine the synergistic effects of biochar and AMF. A comprehensive search across Scopus, Web of Science, and PubMed employed database-specific Boolean operators combining keywords such as "biochar," "mycorrhizal fungi," "soil health," and "nutrient cycling." This review highlights the role of biochar in improving soil structure, nutrient availability, and microbial diversity, thereby providing favourable habitats for mycorrhizal colonization. Approximately 78% of reviewed studies reported yield or nutrient-uptake improvements ranging between 15-35% under combined BC-AMF treatments, particularly under environmental stresses like drought or salinity. Synergistic interactions also promoted microbiome shifts, notably increasing the dominance of Glomus and Rhizophagus, which were associated with biochar porosity and nutrient composition. However, uncertainties remain regarding the long-term sustainability of these effects, and the influence of biochar properties on AMF functionality. To fully realize the potential of BC-AMF synergies, future research must focus on standardizing biochar production, exploring molecular and soil-plant-microbe mechanisms, and conducting long-term studies. Collaboration among stakeholders is essential to ensure the scalability and adoption of these technologies, positioning BC-AMF systems as ecologically sustainable alternatives that can support resilient agricultural production while reducing dependence on conventional chemical inputs.}, }
@article {pmid42261381, year = {2026}, author = {Sandra, KS and Vithalkar, MP and Beere, V and Bharath, HB and Satyanarayana, B and Rafiq, M and Nayak, Y}, title = {Oligosaccharide prebiotics in functional foods and therapeutics: innovations and challenges.}, journal = {3 Biotech}, volume = {16}, number = {7}, pages = {254}, pmid = {42261381}, issn = {2190-572X}, abstract = {Oligosaccharide prebiotics, such as inulin, fructooligosaccharides (FOS), and galactooligosaccharides (GOS), have demonstrated significant effects on gut microbiota and host health across in vitro, animal, and clinical studies. These studies consistently report an increase in beneficial bacteria, particularly Bifidobacterium and Lactobacillus, leading to higher production of short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate. These metabolic changes are linked to improved integrity of the epithelial barrier, reduced inflammatory signaling, modulation of immune responses, and enhanced metabolic balance. Biotechnological production methods, including enzymatic synthesis, microbial fermentation, and controlled depolymerization of plant polysaccharides, allow for precise control over the degree of polymerization and the types of glycosidic linkages. This control directly affects the fermentability, microbial selectivity, and functional effectiveness of the prebiotics. When incorporated into functional food systems, oligosaccharide prebiotics can enhance physicochemical properties such as texture, sweetness, and stability, all while maintaining their biological performance. Advanced delivery technologies, such as nano- and microencapsulation, improve thermal stability, resistance to gastrointestinal degradation, and targeted colon-specific release. Additionally, synbiotic formulations can further enhance the effectiveness of these prebiotics by promoting microbial colonization and sustained availability of SCFAs. Therapeutic benefits have been observed across various models of gastrointestinal health, metabolism, immune responses, and the gut-brain axis. These benefits involve mechanisms such as GPCR activation, histone deacetylase inhibition, and cytokine regulation. However, several challenges remain, including dose-dependent gastrointestinal intolerance, variability in individual microbiomes, degradation during processing, regulatory hurdles, and high costs of downstream processing. Overall, these findings highlight oligosaccharide prebiotics as versatile and scalable biotechnological ingredients, emphasizing the need for standardized production methods, precise dosing, and long-term clinical validation.}, }
@article {pmid42261608, year = {2026}, author = {Shelat, VG}, title = {Microbial ecology and hepatocellular carcinoma: should a subset be viewed as a microbiome-conditioned malignancy?.}, journal = {Expert review of gastroenterology &amp; hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1080/17474124.2026.2687711}, pmid = {42261608}, issn = {1747-4132}, }
@article {pmid42262083, year = {2026}, author = {Lewin, GR and Khadempour, L}, title = {mGem: Tapping into the language of symbiosis to advance human microbiome research.}, journal = {mBio}, volume = {}, number = {}, pages = {e0366125}, doi = {10.1128/mbio.03661-25}, pmid = {42262083}, issn = {2150-7511}, abstract = {In human microbiome research, the term "commensal" is often used to describe organisms that benefit their hosts. In ecology, in host-microbe symbiosis, a commensal organism has no impact on its host, whereas a mutualist organism benefits its host. While others have recognized this discrepancy in terminology use, old habits are hard to break, and the human microbiome community has continued in this vein. This is our call to action for the human microbiome community to use more precise terminology that appropriately reflects the impact that these microbes have on their hosts. We should use the terms "commensal" and "mutualist" when we know the effect on the host, and "symbiont" when we do not. By using the same terminology as ecologists, we will be able to make use of, and contribute to the vast research in the field of symbiosis.}, }
@article {pmid42262087, year = {2026}, author = {Barrack, KE and Surve, SV and de Sousa Bezerra, AV and Murphy, CE and Soucy, SM and Aguilar Ramos, MA and Valls, RA and Ruff, RD and Balskus, EP and Sanville, JL and Madan, JC and O'Toole, GA}, title = {A genotoxin associated with colorectal cancer linked to gut dysbiosis in children with cystic fibrosis.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {e0019026}, doi = {10.1128/jb.00190-26}, pmid = {42262087}, issn = {1098-5530}, abstract = {Cystic fibrosis (CF) alters the gastrointestinal microbiome from an early age, leading to significant changes in microbial composition and functionality. This study explores the physiological and microbiological factors contributing to dysbiosis in children with cystic fibrosis (cwCF), characterized by an increase in potentially pathogenic Escherichia coli and a decrease in beneficial anaerobes, such as Bacteroides. We employed an in vitro medium representative of the nutritional environment of the CF colon to test the role of factors, including mucin, fat, bile, pH, antibiotics, and features associated with inflammation (e.g., nitrate, sulfate, formate, and reactive oxygen species), on the growth of clinical isolates of E. coli and Bacteroides spp., with a focus on Bacteroides vulgatus. We further examined interactions between these two microbes under CF-like conditions and identified glycerol, a surrogate of increased fat, as a significant driver of altered microbial competition. Finally, we investigated genetic determinants influencing these microbial interactions by performing a transposon mutagenesis screen in E. coli. The results pointed to the role of colibactin, a DNA-damaging genotoxin associated with an increased risk of colorectal cancer (CRC), in mediating this microbial competition. This work enhances our understanding of the mechanisms of microbial competition in the CF gut and potential CRC risk in persons with CF through the identification of early-life microbial biomarkers.IMPORTANCEThe risk of CRC development in CF populations is significantly increased. This in vitro study examines the interplay of altered intestinal physiology in the microbial dysbiosis common in the CF gut, implicating the high-fat/glycerol environment in a competition-mediated depletion of immune-modulating Bacteroides vulgatus. This work identifies candidate features of the young CF intestine and gut microbiome that may contribute to dysbiosis, development of inflammation, and CRC in these populations, informing potential prognostic and therapeutic approaches.}, }
@article {pmid42262089, year = {2026}, author = {Thianheng, P and Schroeter, KL and Larsbrink, J and McKee, LS}, title = {Exploring the native pulp and paper sludge microbiome to inspire new biotechnologies for waste minimization.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0135926}, doi = {10.1128/spectrum.01359-26}, pmid = {42262089}, issn = {2165-0497}, abstract = {Thousands of metric tonnes of diverse sludge wastes are generated annually in the pulp and paper industry. Due to a high moisture content and an abundance of inorganic material, many types of sludge are hard to recycle and instead accumulate in landfills, causing environmental damage. During storage, forestry sludge waste appears recalcitrant to natural attenuation, indicating limited degradation of wood- and process-derived fibers and polymers by environmental microbes. Intentional enzymatic or microbial hydrolysis of carbohydrates within the sludge may, however, be a feasible approach to reduce waste volume and prevent transfer to landfill. Here, we show that a previously validated biomass-degrading enzyme cocktail lacks efficacy on a metal-rich sludge obtained from a Swedish pulp and paper mill, possibly due to enzyme inhibition. Hypothesising that microbes dwelling within sludge may host enzymes better adapted to this complex contaminated substrate, we assessed whether a native sludge microbiome could be identified, and whether it degrades carbohydrates during incubation in microcosms. Marker gene profiling revealed diverse bacterial and fungal communities undergoing genus-level changes over time, and the most abundant species could be enriched via serial cultivation with pulp-derived carbon sources. Complementary chemical analyses showed that biopolymers were largely removed after a 10-week incubation, leading to sludge solubilization and volume reduction. This confirms the capacity for fiber degradation by native microbiomes and suggests the waste as a potential source of microbes and enzymes capable of sludge polymer degradation, the mechanism of which remains to be explored, but which could reduce the need for future landfilling.IMPORTANCEAccording to European and Swedish guidelines, the top priority in waste handling is prevention, followed by reuse, recycling, energy recovery, and, as a last resort, landfill. While effective in municipal contexts, these guidelines are difficult to apply to pulp and paper industries when managing heterogeneous sludge wastes. Process-derived sludges are hugely abundant but have low economic value as their high moisture content prevents combustion, and the complex mixture of organic fibers prevents metal recovery. According to industrial reports, less than 10% of sludge is used for energy, and under 50% is recycled. Our results demonstrate that biological treatment of sludge could be a method of waste reduction to reduce landfilling, specifically targeting hygroscopic carbohydrate-based polymers. Mapping the microorganisms in this under-explored industrial waste material, using combined "omic" technologies and chemical analysis, lays a foundation for discovering robust organisms and enzymes that withstand harsh conditions, such as low water activity and high metal content.}, }
@article {pmid42262103, year = {2026}, author = {Heredia, MY and Knoll, LJ}, title = {Contributions of intestinal protists on the human gut landscape through the lens of Entamoeba spp.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0001126}, doi = {10.1128/msphere.00011-26}, pmid = {42262103}, issn = {2379-5042}, abstract = {Intestinal protists represent an underappreciated yet functionally significant component of the human gut microbiome. Historically dismissed as parasites or transient contaminants, many of these microbial eukaryotes, particularly Entamoeba spp., are now recognized as integral to gut ecosystem function and host immune homeostasis. This review examines the complex roles of Entamoeba spp. in the mammalian gut, positioning them as dynamic microbiome "landscapers" that influence host-pathogen interactions, immune tone, and microbial diversity. We explore the evolutionary adaptation of Entamoeba to the gut's anaerobic and immunologically active environment, highlighting both pathogenic (E. histolytica) and non-pathogenic species (E. dispar, E. coli) and their distinct immunomodulatory strategies. Special attention is given to the host immune responses shaped by E. histolytica, including inflammasome activation, macrophage polarization, and suppression of protective type-2 responses. The review also details Entamoeba's interactions with the gut microbiota, emphasizing their capacity for selective bacterial predation, disruption or enhancement of microbial community structure, and synergistic or antagonistic relationships with commensals and pathogens alike. Methodological challenges in protist detection, genome annotation, and cultivation are discussed, alongside promising advances in sequencing, host DNA depletion, and animal modeling. Taken together, current evidence reframes Entamoeba spp. not as mere pathogens but as key ecological players whose presence can signal resilience or susceptibility within the gut ecosystem. Understanding the context-dependent functions of intestinal protists may offer new insights into microbial therapeutics, immune modulation, and disease prevention strategies.}, }
@article {pmid42262118, year = {2026}, author = {Sommer, AJ and Ferrandis-Vila, M and Mamerow, S and Berens, C and Menge, C and Wei, S and Wang, Q and Aarestrup, FM and Otani, S and Sapountzis, P}, title = {Impact of ceftiofur administration and Escherichia coli inoculation on the calf fecal microbiome.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0050126}, doi = {10.1128/msystems.00501-26}, pmid = {42262118}, issn = {2379-5077}, abstract = {The cattle gastrointestinal tract harbors a diverse community of microorganisms, including pathogenic and commensal strains of Escherichia coli. Antimicrobial use in cattle can disrupt the gut microbiome, leading to shifts in bacterial diversity and abundance. Here, we combined shotgun metagenomics and single-cell sequencing to assess how ceftiofur antibiotic treatment impacted microbial diversity and structure. At the start of the experiment, ceftiofur was administered intramuscularly in parallel with the inoculation of a cocktail of extended-beta-lactamase-producing E. coli strains to simulate environmental exposure and acquisition of resistant strains while animals are under antibiotic treatment. Fecal samples were collected from both the antibiotic-treated (ceftiofur and inoculation) and control (inoculation only) calves over the course of 35 days. Read mapping to genome and gene databases showed substantial differences in microbial richness and beta diversity between treatment groups. Treatment group-enriched taxa included Bacteroidaceae and Fibrobacter, which were more abundant in samples that did not receive ceftiofur, and Akkermansia in ceftiofur-treated calves. In ceftiofur-exposed animals, we observed a gradual loss of virulence factors alongside increased abundances of beta-lactam resistance genes, including cfxA5 and cfxA6, likely encoded by CAG-485 (Muribaculaceae). We further profiled individual cells using single-cell sequencing, which revealed a high number of Clostridium carrying macrolide resistance genes lnu(P) and mph(N) in both ceftiofur-treated and control samples. Overall, our complementary approaches reveal distinct remodeling of the calf microbiome following antibiotic and E. coli administration, tied to key functional genes that can be assigned to specific genera or recurrently detected across diverse taxa.IMPORTANCECattle serve as natural reservoirs of zoonotic strains of Escherichia coli, which can cause severe gastrointestinal infections in humans. Antibiotic usage on cattle farms can drive the emergence of antimicrobial-resistant bacterial strains and alter the underlying cattle gastrointestinal microbiome. Consequently, there is a need to understand how antibiotic administration impacts population dynamics of cattle rumen and intestinal microbes. In this study, we combined both shotgun metagenomics and single-cell genomics on feces from ruminating calves to determine microbiome changes following administration of both ceftiofur and E. coli cocktails. We observed considerable variation in the prevalence and abundance of virulence factors, antimicrobial resistance-related genes, and taxa with key roles in animal nutrition and health between the microbiomes of antibiotic-treated and antibiotic-free calves, with potential implications for their subsequent development and overall well-being.}, }
@article {pmid42262124, year = {2026}, author = {Tanca, A and De Diego, L and Deledda, MA and De Maio, F and Boru, C and Musella, M and Raffaelli, M and Silecchia, G and Delogu, G and Uzzau, S}, title = {Reshaping of the fecal proteome and metaproteome in obese patients 2 years after bariatric surgery.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0176425}, doi = {10.1128/msystems.01764-25}, pmid = {42262124}, issn = {2379-5077}, abstract = {Bariatric surgery provides effective and durable weight loss in patients with severe obesity. Both the surgical procedure and postoperative management, including dietary and behavioral changes, are known to induce long-term alterations in gut microbiota composition. However, their impact on microbial and host proteome profiles remains poorly understood. In this prospective, multicenter cohort study, we compared the fecal metaproteome profile of 45 patients with severe obesity at preoperative baseline (T0) and 2 years after surgery (T1). Patients were randomized to receive either Roux-en-Y gastric bypass or one anastomosis gastric bypass. At T1, the relative abundance of the bacterial genera Akkermansia, Anaerotignum, Desulfovibrio, Streptococcus, and Veillonella significantly increased, whereas that of Faecalibacterium and Romboutsia decreased. Furthermore, we observed a significant increase in the relative abundance of microbial enzymes involved in glycolysis, short-chain fatty acid biosynthesis, amino acid metabolism, and cofactor/vitamin biosynthesis, alongside various outer membrane proteins encoded by Enterobacterales. Conversely, several proteins involved in oxidative phosphorylation and sporulation were reduced. Moreover, 74 human proteins, primarily associated with immune functions, showed a significant increase in relative abundance at T1, while numerous digestive enzymes displayed a downward trend. Our data reveal that a distinct reshaping of the fecal proteome and metaproteome persists 2 years after bariatric surgery. Future studies are needed to elucidate the mechanistic aspects of host-microbiota interaction and to identify associations with long-term clinical outcomes.IMPORTANCEBariatric surgery is widely recognized as the most effective and durable intervention for severe obesity; however, its long-term molecular effects on gut microbiota-host interactions remain poorly understood. By applying shotgun metaproteomics to fecal samples collected before and 2 years after surgery, our study provides novel insights into the functional consequences of bariatric bypass procedures. We demonstrate sustained alterations in both microbial and host protein profiles, including metabolic enzymes, outer membrane proteins, and immune-related factors, revealing a long-lasting remodeling of gut ecosystem functions. These findings underscore the value of metaproteomics in uncovering molecular mechanisms underlying bariatric surgery outcomes and may ultimately guide the development of microbiome- or host-targeted strategies to optimize therapy and long-term patient care.}, }
@article {pmid42262136, year = {2026}, author = {Iacovacci, J and Cannon, N and McCulloch, JA and Rancati, T and Trinchieri, G}, title = {Differential co-occurrence analysis: a method to extract ecological modules from clinical microbiome data.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0028426}, doi = {10.1128/msystems.00284-26}, pmid = {42262136}, issn = {2379-5077}, abstract = {UNLABELLED: The human microbiota plays a pivotal role in health, with widespread alterations implicated in conditions ranging from inflammatory disorders to cancer. While correlation-based network analyses have illuminated ecological interactions within these communities, the host environment uniquely mediates microbial relationships, demanding new methods to capture dynamic, condition-dependent modules of species interactions. Here, we present a statistical framework termed differential co-occurrence analysis, which identifies blocks of taxa whose collective presence is strengthened or weakened under distinct host states. By leveraging recent advances in metagenomics that enable detailed taxonomic profiling and higher-order interaction discovery, our method transcends traditional pairwise correlation constraints. Conceptually akin to associative rule mining, it diverges through the integration of robust statistical modeling, directly extracting interactions that differ significantly between conditions. This approach offers a refined lens to dissect microbiota ecology and could pave the way for new insights into microbiome-associated disease mechanisms.<br><br>IMPORTANCE: The research on the role of the intestinal microbiota in the onset of cancer and as a modulator of anticancer treatments, including chemotherapeutics and immune checkpoint inhibitors, is helping medicine to identify novel strategies for cancer prevention, for the delivery of more effective treatments, and in reducing treatment side effects and complications. Within this context, it is of crucial importance to approach the analysis of clinical microbiome data with an ecology-oriented perspective and to develop bioinformatics tools able to identify functional interactions in bacterial communities of patients from observational cohort studies. Clinical microbiome datasets are typically high dimensional, comprising numerous taxa measured across relatively few samples. This imbalance increases the risk of statistical overfitting and undermines the robustness of analytical findings. However, recent advances in metagenomic bioinformatics pipelines and reference databases have enabled the comprehensive extraction of genetic information from microbiome samples, facilitating the precise characterization of bacterial species presence and absence. In our manuscript, we describe a statistical computational method that we named differential co-occurrence analysis, which focuses on the analysis of the co-presence of microbiota taxa across samples associated with different host conditions. The proposed method can reveal modules of interacting taxa that are strengthened or weakened when the host condition changes (e.g., when passing from a healthy state to a disease state). The method is general and applicable to a broad range of ecological datasets featuring presence/absence data structures. Furthermore, the method accommodates the analysis of higher-order co-occurrence patterns beyond pairwise co-occurrence, thereby enabling the investigation of higher-order interactions, whose detection and identification are a major challenge in ecological network analysis.}, }
@article {pmid42262337, year = {2026}, author = {Kadyan, S and Park, G and Khalili, L and Patoine, C and Mayonu, M and Wang, B and Salazar, G and Yamashiro, Y and Nagpal, R}, title = {Maternal diet shapes neonatal microbiome ontogenesis and neurometabolic resilience.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2684074}, pmid = {42262337}, issn = {1949-0984}, abstract = {Maternal diet high in saturated fatty acids (SFA) promote infant gut dysbiosis and impairs metabolic and neurocognitive outcomes; however, the protective potential of maternal polyunsaturated fatty acids (PUFA), particularly omega-3 (n3), remains unclear. This study examined how maternal diets enriched in SFA (20% milk fat), omega-6 (n6; 20% corn oil), or omega-3 (n3; 19% olive oil + 1% fish oil) influence neonatal metabolism, neurodevelopment, the gut microbiome, the gut-blood-brain metabolomes, and the brain lipidome in C57BL/6 mice. The offspring were exposed to these diets only during gestation and lactation and then maintained on a Western-style diet for 10 weeks. Compared to SFA, maternal PUFA-rich diets induced distinct and persistent microbiome signatures and reshaped the gut and systemic metabolomic profiles into adulthood. The offspring of n3-fed dams displayed higher lean-to-fat mass ratios, improved ileal morphology, and enhanced gut epithelial integrity. Chronic low-grade inflammation (MCP-1) along the gut-blood-brain axis was markedly reduced in n3 offspring. Moreover, maternal n3 intake enhanced synaptic plasticity, suppressed neuroinflammation, and enriched brain lipids and metabolites associated with membrane integrity, neuronal signaling, and anti-inflammatory pathways. Overall, maternal omega-3 intake confers long-term neuroprotective effects by modulating brain lipid remodeling and the gut-brain-immune axis.}, }
@article {pmid42262444, year = {2026}, author = {Hemmatinafar, M and Tajanaki, AS and Jäger, R and Safari, K}, title = {Probiotics and the Gut Microbiome in Combat Sports: A Narrative Review of Performance, Recovery, and Health Pathways.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {42262444}, issn = {1867-1314}, abstract = {Competitive combat athletes are routinely exposed to high training loads, rapid weight-making practices, psychological stress, and frequent injuries-all of which may adversely affect the gut microbiome and, consequently, multiple physiological systems relevant to performance. Growing scientific interest in the role of probiotics and host-microbiome interactions suggests that targeted modulation of gut bacteria may offer functional benefits for athletes. This narrative review synthesizes current evidence on probiotics and microbiome-mediated pathways influencing performance, recovery, and health in combat-sports athletes. A comprehensive literature search was conducted across PubMed, Web of Science, and Google Scholar, with no date limits, including studies published up to October 2025. Search terms covered the gut microbiome, probiotics, athletic performance, combat sports, gastrointestinal barrier function, immune responses, psychological factors, nutrient absorption, hypoxia, weight cutting, and sex-specific considerations. Reference lists of relevant reviews and grey literature were manually screened. Across the available literature, probiotic supplementation has been associated with a range of effects that could be relevant to combat athletes. Evidence, largely from non‑combat and mixed‑population studies, suggests that probiotics may influence several physiological systems, including: (1) inflammatory and oxidative stress responses and injury rehabilitation; (2) immune function and upper respiratory tract infection outcomes; (3) gastrointestinal permeability and nutrient absorption, particularly after rapid weight loss; (4) psychological factors via the gut-brain axis; (5) muscle recovery through inflammatory and metabolic pathways; (6) body composition and weight regulation; (7) oral and skin microbiome composition; and (8) gut microbial changes during hypoxia or hormonal fluctuations. However, most of these findings are indirect, with very few studies conducted specifically in competitive combat‑sport athletes, and the overall evidence base remains heterogeneous. Probiotic and gut microbiome-targeted strategies may serve as potential adjunctive strategies to support health, recovery, and performance in combat athletes. However, because the current evidence is largely derived from non-combat and predominantly male populations, strain-, dose-, and sport-specific recommendations cannot yet be made. There is a clear need for randomized controlled trials in combat-sport athletes-including women-that employ standardized probiotic protocols and sport-specific outcome measures.}, }
@article {pmid42262446, year = {2026}, author = {Cruz Neto, JPR and Godet, M and da Costa, PCT and de Luna Freire, MO and de Albuquerque Lemos, DEC and de Oliveira Coutinho, D and Sampaio, KB and Brasil, JMA and Meugnier, E and Vidal, H and Magnani, M and de Brito Alves, JL}, title = {Combined Probiotics and Phenolics in Western Diet-fed Rats Enhance Parasympathetic Tone in the Gut-Brain Axis by Attenuating Inflammasome Signaling, and Reshaping Gut Microbiome.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {42262446}, issn = {1867-1314}, abstract = {Western dietary patterns are major drivers of cardiometabolic dysfunction, partly mediated by gut microbiome dysbiosis and sustained inflammation along the gut-brain axis. In this study, we investigated whether a synbiotic formulation combining Limosilactobacillus (L.) fermentum strains with polyphenols, quercetin, and resveratrol could mitigate cardiovascular and neuroinflammatory alterations induced by a Western diet. Male Wistar rats were assigned to three groups receiving a standard diet, a Western diet, or a Western diet supplemented with the synbiotic. Arterial pressure and cardiac autonomic function were assessed, alongside gut microbiome diversity and composition, and gene expression analyses of intestinal permeability and inflammatory markers in colonic tissue and in the brainstem. Synbiotic supplementation prevented the Western diet-induced cardiac autonomic imbalance. These functional benefits were accompanied by marked modulation of the gut microbiome, characterized by increased abundance of beneficial bacterial taxa (Gemmiger formicilis, Lactobacillus acidophilus, Flavonifractor plautii, Blautia glucerasea, Blautia stercoris, Roseburia faecis, Marvinbryantia formatexigens, and Romboutsia timonensis) and significant shifts in microbial community structure. In parallel, synbiotic supplementation attenuated pro-inflammatory gene expression in both peripheral and central tissues associated with the gut-brain axis (Nlrp3, Casp1, Il-1β). These findings demonstrate that synbiotic supplementation exerts integrated anti-inflammatory and neuroautonomic protective effects through the gut-brain axis. Our results support the therapeutic potential of combined probiotic-phenolic strategies to counteract cardiometabolic dysfunction induced by Western diets.}, }
@article {pmid42262562, year = {2026}, author = {Wood, CM}, title = {A 30-year retrospective on the respirometric method for measuring instantaneous metabolic fuel use in fish.}, journal = {Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology}, volume = {}, number = {}, pages = {}, pmid = {42262562}, issn = {1432-136X}, support = {RGPIN-2023-03714//NSERC/ ; }, abstract = {In 1996, based on the ideas of Max Kleiber, we proposed a respirometric method in this journal for the quantitative determination of the roles of protein, lipid and carbohydrate as substrates for fueling aerobic metabolism in fish on an instantaneous basis. Here I provide a 30-year retrospective on its performance, explaining how it works, methodological challenges, the applications for which it has been used, its strengths and potential flaws, and the important issues to be addressed going forward. The approach is based on the simultaneous measurement of the rates of O2 consumption (ṀO2), CO2 excretion (ṀCO2) and N-waste excretion (ṀN = Ṁamm + Ṁurea-N) under steady-state conditions in the whole fish when anaerobic metabolism is not occurring. These allow the calculation of the Respiratory Quotient (RQ = ṀCO2/ṀO2) and the Nitrogen Quotient (NQ = ṀN /ṀO2), and from these, the fractional contributions of each of the three fuels. Principal methodological challenges arise from the difficulties of measuring ṀCO2, and to a lesser extent ṀN, in water. To date, the approach has been used mainly to study fuel use during feeding, fasting, starvation, sustainable exercise, and at different temperatures. In general, lipid and carbohydrates have emerged as the major fuels burned in ammoniotelic fish (where ammonia is the predominant N-waste product), while protein is conserved, though protein metabolism may be more important in ureotelic fish (where urea-N is the predominant N-waste product) and air-breathers. Possible unidentified N- products of protein oxidation, the action of the anaerobic gut microbiome in generating ṀN in the absence of ṀO2, and the ability of the gill microbiome to convert N-waste to di-nitrogen (N2) are highlighted as potential flaws.}, }
@article {pmid42263007, year = {2026}, author = {Chen, Y and Liu, Z and Chen, Y and Zhong, J and Li, X and Song, P}, title = {Correlation of hs-CRP and T lymphocyte subsets with severity and prognosis in elderly pulmonary infection.}, journal = {Journal of infection in developing countries}, volume = {20}, number = {5}, pages = {743-749}, doi = {10.3855/jidc.22001}, pmid = {42263007}, issn = {1972-2680}, abstract = {INTRODUCTION: This study aimed to investigate the correlation between high-sensitivity (hs)-CRP, T lymphocyte subset profiles, disease severity, and treatment outcomes in elderly patients with pulmonary infection.<br><br>METHODOLOGY: The study included 85 elderly patients with respiratory infections (46 non-severe, 39 severe) and 79 healthy controls. The levels of hs-CRP, T lymphocyte subsets (CD4+/CD8+, CD4+, CD8+), and clinical pulmonary infection score (CPIS) were measured. Correlations with disease severity and CPIS were analyzed. Additionally, pre- and post-treatment levels of hs-CRP and T lymphocyte subsets were compared in patients with different treatment responses.<br><br>RESULTS: Patients had lower CD4+ counts and CD4+/CD8+ ratios, but higher hs-CRP, CD8+, and CPIS levels (p < 0.05) compared to controls. Severe cases had lower CD4+ and CD4+/CD8+, but higher CD8+, hs-CRP, and CPIS, than non-severe cases (p < 0.05). CD4+ and CD4+/CD8+ were negatively correlated with disease severity and CPIS, while hs-CRP and CD8+ were positively correlated (p < 0.05). The patients who responded to treatment (responders) had higher increases in hs-CRP, CD4+, and CD4+/CD8+ after 7 days of treatment, compared to non-responders; while CD8+ levels were lower (p < 0.05). Receiver operating characteristic (ROC) analysis showed that an hs-CRP difference cutoff of 5.31 had the highest predictive value for treatment outcomes, with 86.67% sensitivity and 68.57% specificity.<br><br>CONCLUSIONS: hs-CRP and T lymphocyte subsets are closely associated with disease severity and treatment response in elderly patients with pulmonary infection, and their dynamic monitoring may aid in clinical prognosis evaluation.}, }
@article {pmid42263027, year = {2026}, author = {Cuevas-Sierraa, A and Tomé-Carneirob, J and Marques da Silva, MM and Tavares da Silva, MI and de Cuevillas, B and Silvestre, MP and Martínez, JA}, title = {Inflammation and Chronic Disease: The Mediterranean Diet in Precision and Personalized Nutrition.}, journal = {Annals of nutrition &amp; metabolism}, volume = {}, number = {}, pages = {1-19}, doi = {10.1159/000551530}, pmid = {42263027}, issn = {1421-9697}, abstract = {Low-grade chronic inflammation (LGCI) is a shared biological pathway for noncommunicable diseases (NCDs) and clinical manifestations, including atherosclerotic cardiovascular disease, type 2 diabetes, obesity-related complications, some cancers, and neurodegenerative conditions. Diet is a powerful modulator of inflammatory status. This summary article synthesizes mechanistic and clinical evidence linking LGCI to NCDs, with emphasis on the role of the Mediterranean dietary pattern (MedDiet) and outlines pragmatic prescription guidelines within precision and personalized nutrition bases. Meta-analytic evidence indicates that MedDiet interventions reduce interleukin(IL)-6 and IL-1β, with a trend toward lower C-reactive protein. The Mediterranean diet promotes beneficial shifts in gut microbiota (gut microbiome) composition, increasing short-chain fatty acid production and supporting epithelial barrier integrity, which contributes to its anti-inflammatory effects. Taken together, these data endorse the Mediterranean Diet as a primary cardiometabolic protective approach, emphasizing the importance of integrating straightforward, equity-focused strategies to translate biological potential into measurable benefits at the population level.}, }
@article {pmid42263077, year = {2026}, author = {Spochacz-Santoro, M and Szeliga, A and Durda-Masny, M and Morańska, K and Englert-Golon, M and Sadowski, W and Bocheńska, M and Doijad, S and Dutilh, BE and Brouns, R and Grabowska, M and Sajdak, S and Męczekalski, B and Szwed, A}, title = {Higher BMI is associated with vaginal microbiome alterations in women with PCOS.}, journal = {Reproduction &amp; fertility}, volume = {}, number = {}, pages = {}, doi = {10.1530/RAF-26-0051}, pmid = {42263077}, issn = {2633-8386}, abstract = {ABSTRACT: Polycystic ovary syndrome (PCOS) is commonly associated with obesity and metabolic disturbances. Although gut and vaginal microbiome changes have been linked to PCOS, the independent role of body mass index in these alterations remains unclear. This study aimed to compare gut and vaginal microbiomes in women with PCOS and healthy controls, emphasizing the impact of body mass index. Seventy-five women were enrolled, including 55 with PCOS and 20 healthy controls. Participants were stratified into normal-weight (<25) and overweight (≥25) groups. Vaginal and anorectal swabs were analyzed using full-length 16S rRNA Nanopore sequencing. Microbial diversity and composition were assessed with alpha diversity indices, principal component analysis, Analysis of Composition of Microbes, PERMANOVA and Vaginal Community State Types classification. Without body mass index stratification, women with PCOS showed differences in several vaginal taxa compared with healthy controls. Within the PCOS cohort, overweight women exhibited higher vaginal alpha diversity, reduced Lactobacillus dominance, and enrichment of anaerobic taxa compared with normal-weight women with PCOS. Differences in vaginal microbial composition were also observed between healthy and PCOS women with normal body mass index. In contrast, gut microbiome alterations were limited and less consistent across analytical approaches. Vaginal community State Types analysis revealed predominance of Class IV communities in both healthy women and women with PCOS. These findings suggest that higher body mass index is associated with vaginal microbiome alterations in women with PCOS, although PCOS-related factors independent of body weight may also contribute to the observed microbial differences.<br><br>LAY SUMMARY: Polycystic ovary syndrome is a common condition that affects hormones, fertility, and metabolism in women. Many women with this condition are also overweight, but it is not fully understood how body weight influences the bacteria living in the body. In this study, we compared bacteria present in vaginal and anorectal samples from women with and without polycystic ovary syndrome, while also considering body weight. We found that women with higher body weight had more noticeable changes in vaginal bacterial composition, including lower amounts of protective Lactobacillus bacteria and higher diversity of anaerobic bacteria. At the same time, some bacterial differences were also observed in women with polycystic ovary syndrome who had normal body weight. Changes in gut bacteria were smaller and less consistent. These findings suggest that both body weight and polycystic ovary syndrome may influence vaginal bacterial composition and should be considered in future studies of women's reproductive health.}, }
@article {pmid42263170, year = {2026}, author = {Sigvardsson, I and Ludvigsson, J and Lerchova, T and Imberg, H and Størdal, K and Mårild, K}, title = {Timing of complementary food introduction is not associated with inflammatory bowel disease risk: A prospective birth cohort study.}, journal = {Inflammatory bowel diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/ibd/izag093}, pmid = {42263170}, issn = {1536-4844}, support = {S20-0007//Birgitta och G&#xf6;ran Karlssons Stiftelse: Swedish Society for Medical Research/ ; 2020-01980//Swedish Research Council/ ; ALFGBG-915661//Swedish Research Council/ ; //Swedish Child Diabetes Foundation/ ; FAS2004-1775//Swedish Council for Working Life and Social Research/ ; FAS2004-1775//Swedish Council for Working Life and Social Research/ ; K2005-72X-11242-11A//Swedish Research Council/ ; K2008-69X-20826-01-4//Swedish Research Council/ ; K2008-69X-20826-01-4//Swedish Research Council/ ; //Medical Research Council of Southeast Sweden (FORSS)/ ; K 98-99D-12813-01A//JDRF Wallenberg Foundation/ ; //Region &#xd6;sterg&#xf6;tland and Link&#xf6;ping university/ ; //Joanna Cocozza Foundation/ ; //Ministry of Health and Care Services/ ; //Norwegian Institute of Public Health/ ; }, abstract = {BACKGROUND: Complementary feeding (ie, food introduction besides formula or breast milk) imprints on the developing gut microbiome and immune system, which may have durable influences on disease risk. This study aimed to prospectively assess the association between the timing of complementary feeding and subsequent inflammatory bowel disease (IBD) risk.<br><br>METHODS: We followed 94&#x200a;238 participants from the All Babies in Southeast Sweden (ABIS) (n&#x2009;=&#x2009;11&#x200a;947) and the Norwegian Mother, Father and Child (MoBa) (n&#x2009;=&#x2009;82&#x200a;291) cohorts from birth (1997-2009) through 2023 (mean age 16.5 [MoBa] to 25.2 [ABIS] years). National patient registers identified IBD diagnoses. The timing of complementary food introduction (<4, 4-5, or&#x2009;&#x2265;6&#x2009;months) was assessed using early-life food diaries and questionnaires. Latent class analyses identified 4 patterns across introductions of major food groups (eg, cereals and dairy). Cox regression estimated hazard ratios (aHRs) for IBD adjusted for socio-demographics and parental IBD. Sensitivity analysis additionally adjusted for breastfeeding duration, formula feeding, and perinatal factors.<br><br>RESULTS: Over 1&#x200a;562&#x200a;350 person-years of follow-up, 400 participants developed IBD (ABIS, n&#x2009;=&#x2009;124; MoBa, n&#x2009;=&#x2009;276). Overall timing of complementary food introduction was not associated with IBD (<4&#x2009;months: aHR, 1.04 [95% CI, 0.67-1.60]; 4-5&#x2009;months: aHR, 0.83 [95% CI, 0.63-1.10] vs &#x2265;6&#x2009;months). Also, aHRs for IBD by latent class analyses-defined introduction patterns approached 1. Results were consistent across cohorts, sensitivity analyses, and Crohn's disease and ulcerative colitis subtypes.<br><br>CONCLUSIONS: The findings from this binational birth cohort study indicate that neither the timing nor the pattern of complementary food introduction is a major risk factor for later development of IBD.}, }
@article {pmid42263421, year = {2026}, author = {Liu, Z and Zhao, X and Guo, Y and Qin, C}, title = {Ontogenetic and spatial variation in the feeding habits of Tripneustes gratilla.}, journal = {Marine environmental research}, volume = {220}, number = {}, pages = {108170}, doi = {10.1016/j.marenvres.2026.108170}, pmid = {42263421}, issn = {1879-0291}, abstract = {As a keystone species in coral reef ecosystems, the collector sea urchin Tripneustes gratilla maintains its ecological balance by regulating algal populations; however, a systematic understanding of its role as a primary consumer in tropical marine environments remains limited. In this study, we investigated T. gratilla populations in coastal waters near Wuzhizhou Island, Sanya city, Hainan Province, China. Using 18S rDNA and 16S rDNA high-throughput sequencing, we analyzed differences in the T. gratilla diet in autumn across different habitats and body size classes. The analysis revealed that Tripneustes gratilla has a diverse diet spanning multiple phyla, including Arthropoda, Rhodophyta, Apicomplexa, and Cyanobacteriota. Distinct spatial dietary patterns were observed across different benthic habitats. In offshore rocky substrates, the gut contents primarily consisted of Rhodophyta (red algae) and Arthropoda (crustaceans), collectively accounting for more than 40% of the ingested material. Conversely, nearshore sandy-gravel substrates showed remarkable dietary specialization, with Arthropoda and Rhodophyta constituting more than 70% of the total dietary composition. Body size influenced the T. gratilla diet: large individuals (500-600 g) consumed specialized diets dominated by Eukaryota and Rhodophyta (>80%), whereas medium and small individuals presented greater dietary diversity. The gut microbiota demonstrated regional universality, with Proteobacteria and Bacteroidetes constituting the core microbiome. Environmental factors (e.g., pH) significantly affect T. gratilla feeding behavior. In this study, we identified habitat heterogeneity and ontogenetic shifts as critical drivers of T. gratilla trophic ecology, providing novel insights into its functional role in ecosystem dynamics.}, }
@article {pmid42263473, year = {2026}, author = {Wu, C and Chen, X and Zhang, Y and Li, X and Yang, D and Dou, E and Zhang, F}, title = {Vertically transmitted seed core endophytes enhance the drought tolerance of Ambrosia artemisiifolia.}, journal = {Microbiological research}, volume = {311}, number = {}, pages = {128575}, doi = {10.1016/j.micres.2026.128575}, pmid = {42263473}, issn = {1618-0623}, abstract = {Seed endophytes play a pivotal role in shaping plant microbiota, with certain species being vertically transmitted throughout the plant's life history. Nevertheless, their transmission patterns and contributions to drought adaptation remain poorly understood. In this study, through comparative analysis of microbial communities in seeds and in vitro plantlets from five geographic populations, Pseudomonas and Bacillus were identified as vertically transmitted core endophytes. Analysis of endophytic communities in leaves and roots of plants grown in a common garden further revealed that these genera not only dominated the microbiota but also served as potential keystone taxa. Moreover, pot experiments demonstrated that these genera remained dominant under drought. Representative culturable isolates associated with core vertically transmitted OTUs, including Pseudomonas benzopyrenica and Bacillus cereus, carried multiple antioxidant-related genes based on whole-genome sequencing, and qRT-PCR analysis further showed that most of these genes were upregulated under drought stress. The pot experiment revealed that both strains enhance plant drought tolerance, with altered NCED expression associated with modulated ABA levels, and changes in GST, SOD2, and CAT expression correlated with reduced accumulation of reactive oxygen species (ROS) and malondialdehyde (MDA) in inoculated plants. These findings advance our understanding of the role of vertically transmitted core endophytes in the adaptation of invasive plants and offer new perspectives for microbiome-based management strategies.}, }
@article {pmid42263474, year = {2026}, author = {Xie, T and Hao, Y and Qin, L}, title = {The skin microbiome as a key regulator of psoriasis: From dysbiotic drivers to host-directed therapeutics.}, journal = {Microbiological research}, volume = {311}, number = {}, pages = {128577}, doi = {10.1016/j.micres.2026.128577}, pmid = {42263474}, issn = {1618-0623}, abstract = {The skin harbors diverse microbial communities. Compared with gut microbiome dysbiosis, perturbations in the skin microbiome may be more directly implicated in the onset and progression of psoriasis (PSO). More than twenty studies reveal microbial dysbiosis within psoriatic lesions, which is manifested by elevated abundances of pro-inflammatory taxa such as Corynebacterium and Staphylococcus aureus, declined levels of commensal microbes including Cutibacterium, increased total bacterial load and decreased microbial community diversity. Such cutaneous microbial dysbiosis accelerates disease progression via multiple biological pathways, involving impairment of the skin barrier, dysregulation of the innate and adaptive immunity, as well as multifaceted biological effects mediated by microbial metabolites. Microbiome-based diagnostic strategies have emerged as novel tools for evaluating disease prognosis, and targeted modulation of the skin microbiome holds promising prospects for clinical translation. In-depth exploration of skin microbial signatures in PSO enables the skin microbiome to serve as clinically valuable biomarkers for predicting subtype transformation and disease progression and fluctuation. Future research priorities lie in the integration of multi-omics strategies to dissect the potential causal mechanisms underlying host-microbe crosstalk, establish optimized bioengineering techniques and further promote the advancement of individualized therapeutic regimens. Collectively, the skin microbiome not only sheds new light on the pathogenic mechanisms of PSO, but also identifies promising candidate targets for auxiliary diagnosis and precise microbiome-based therapeutic interventions.}, }
@article {pmid42263665, year = {2026}, author = {Ueland, K and Elahi, T and Rasmussen, M and Wolfe, AE and Purcell, H and Chakka, SR and Mirimo-Martinez, M and Persinger, H and Johnson, K and Boynton, AM and McMillen, K and Byelykh, M and Biernacki, MA and Yeh, AC and Ali, N and Manjappa, S and Wuliji, N and Fredricks, D and Bleakley, M and Holmberg, LA and Peled, JU and Schenk, J and Raftery, D and Ma, J and Hill, GR and Neuhouser, ML and Lee, SJ and Markey, KA}, title = {Plant-based whole-food diets are feasible during auto-HCT and are associated with dose-dependent microbiome modulation.}, journal = {Blood advances}, volume = {}, number = {}, pages = {}, doi = {10.1182/bloodadvances.2026020270}, pmid = {42263665}, issn = {2473-9537}, abstract = {Plant-based whole foods may represent a tractable approach to mitigating microbiome disruption and improving outcomes in patients undergoing auto-HCT for multiple myeloma, a population in whom intestinal dysbiosis has been linked with inferior survival. We conducted a single-arm clinical trial at our center, in which participants undergoing auto-HCT (n = 22) received fresh, pre-prepared, plant-based meals for 5 weeks spanning conditioning, neutropenia, and early recovery, with the goal of supporting the consumption of nutrient-dense, high-fiber foods. The primary endpoints were feasibility and tolerability, defined by successful enrollment, and patient-reported intake of study meals. Dietary intake was quantified using prospective food diaries and 24‑hour dietary recall surveys. Secondary endpoints included changes in gut microbiome composition and function assessed by shotgun metagenomic sequencing and stool short-chain fatty acid (SCFA) measurements. The intervention was feasible and generally well tolerated, with all participants consuming delivered meals to some degree, with adherence sufficient to support planned dietary and correlative analyses. Greater intake of study meals was associated with more pronounced shifts in gut microbial communities, including enrichment of SCFA-producing taxa and compositional changes consistent with a fiber-responsive microbiome. Stool SCFA concentrations increased from baseline to the end of the intervention, suggesting a functional impact of the dietary strategy on microbial metabolite production during the peri-transplant period. These findings demonstrate that a plant-based meal delivery intervention is implementable during auto-HCT and suggest dose-dependent modulation of the gut microbiome and its metabolic output. The trial is registered at ClinicalTrials.gov (NCT06559709).}, }
@article {pmid42263820, year = {2026}, author = {Rindchen, A and Schneider-Daum, N and Lehr, CM}, title = {Microphysiological ("organ-on-a-chip") models of pulmonary infections for developing novel anti-infectives.}, journal = {Advanced drug delivery reviews}, volume = {}, number = {}, pages = {115917}, doi = {10.1016/j.addr.2026.115917}, pmid = {42263820}, issn = {1872-8294}, abstract = {Infectious diseases are among the leading death causes globally, with the lung being particularly vulnerable due to its continuous exposure to inhaled pathogens. Yet, anti-infective research and drug development are hampered by the lack of models that accurately recapitulate the lung's complex immunological and pathophysiological responses to infections. Microphysiological ("Organ-on-a-chip", OoC) models allow elegant incorporation of multiple cell types, biological barriers, mechanical stress and perfusion, not only in healthy, but also in diseased state. Besides enabling the evaluation of drug efficacy and safety, these models provide a platform to investigate host-pathogen interactions and their modulation by pharmaceutical interventions. This review examines microphysiological systems (MPS) designed to mimic pulmonary infections and highlights how these models capture key hallmarks of such diseases, including disruption of barrier integrity, changes of mucus, mucociliary clearance and surfactant, as well as the recruitment and stimulation of immune cells. Specific design considerations will be explained regarding the challenges of viral and bacterial pulmonary infections. Emphasis is further placed on how MPS may be implemented for repurposing established drugs, as well as for developing new small molecules, biologicals and delivery systems. Remaining challenges, such as incorporation of the microbiome, vaccine development and requirements for standardization and validation, are critically examined. These insights underscore the potential of MPS to bridge preclinical gaps in infection research, accelerate clinical translation, and guide the development of novel anti-infective drugs and delivery systems.}, }
@article {pmid42263891, year = {2026}, author = {Bibi, R and Swayamsiddhi,  and Saishree, S and Sobti, M and Reddy, S and Sarkar, K}, title = {Involvement of immunomodulators in the development of cancer vaccines.}, journal = {Biochimica et biophysica acta. Molecular basis of disease}, volume = {}, number = {}, pages = {168321}, doi = {10.1016/j.bbadis.2026.168321}, pmid = {42263891}, issn = {1879-260X}, abstract = {Previous research shows that cancer vaccines hold great potential as immunotherapeutic agents which activate the body's tumor-cell elimination powers through immune recognition. Cancer vaccines encounter restricted success because of three limiting factors that include immunosuppressive tumor microenvironment (TME) dynamics and deficient antigen presentation and tumor immune evasion methods. Immunomodulators function as vital instruments which help patients overcome vaccination resistance barriers in addition to strengthening vaccine-generated immunity. The review investigates how different immunomodulatory agents such as cytokines and checkpoint inhibitors as well as TLR agonists and STING pathway activators, oncolytic viruses enhance the effectiveness of cancer vaccines. The immune response derives additional advantages from these agents. They enhance antigen presentation, activate T cells, counteract immune suppression, and improve the structural integrity of the tumor microenvironment (TME). The review examines modern treatment developments that include individualized neoantigen vaccines and nanoparticle delivery vehicles alongside microbiome modification strategies as promising methods for customized effective cancer treatments. Although cancer vaccines face obstacles from toxicity and heterogeneous tumors and limitations in manufacturing there is potential to combine them with immunomodulators for creating sustainable and specific cancer treatments. Further research along with innovative work needs to occur to develop clinically effective patient-specific treatments from existing therapeutic breakthroughs.}, }
@article {pmid42263966, year = {2026}, author = {Nazir, MJ and Hussain, MM and Ali, S and Otwil, P and Iddi, AT and Li, T and Wu, Z and Wei, J and Yu, L}, title = {Nucleic acid dynamics at the plant-rhizosphere interface: Regulatory mechanisms, and implications for future food security: A review.}, journal = {International journal of biological macromolecules}, volume = {370}, number = {}, pages = {152977}, doi = {10.1016/j.ijbiomac.2026.152977}, pmid = {42263966}, issn = {1879-0003}, abstract = {Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are no longer regarded solely as carriers of hereditary information or intermediates of gene expression. They are now increasingly recognized as structurally distinct biological macromolecules that regulate plant development, stress adaptation, intercellular communication, and rhizosphere interactions. Recent advances in genome editing, pan-genomics, transcriptomics, epitranscriptomics, and long non-coding RNA (lncRNA) biology have expanded the translational potential of nucleic-acid research for climate-resilient agriculture. Concurrently, the rhizosphere has emerged as a molecular interface in which plant-derived extracellular DNA (exDNA) and extracellular RNA (exRNA) influence microbiome assembly, nutrient signaling, and cross-kingdom communication. Although, these themes are often treated separately in the existing literature, with few reviews integrate intracellular and extracellular nucleic acid functions within a unified plant-soil, particularly rhizosphere, framework. The present review synthesizes current knowledge by linking the macromolecular properties of nucleic acids with their intracellular regulatory functions, extracellular release and fate in soil, roles in rhizosphere communication, and translational relevance for crop improvement and future food security. Particular emphasis is given to biotic and abiotic stresses, including drought, salinity, nutrient limitation, pathogen pressure, and overall climate instability. We propose that plant and rhizosphere nucleic acids constitute a single adaptive continuum connecting intracellular regulation with extracellular ecological function, thereby providing a broader conceptual basis for climate-resilient and resource-efficient agriculture.}, }
@article {pmid42264044, year = {2026}, author = {Han, F and Guo, Y and Lei, J and Zhang, L and Zhao, C and Li, Y and Zhou, W}, title = {Micro-sized aerobic heterotrophic ammonium assimilation granules and microbial community assembly under varying hydraulic shear force.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135139}, doi = {10.1016/j.biortech.2026.135139}, pmid = {42264044}, issn = {1873-2976}, abstract = {Heterotrophic ammonium assimilation (HAA) represents an emerging biological nitrogen removal strategy for saline wastewater treatment. Developing halophilic HAA microbiome into granular form enables simultaneously improve the sludge settleability and robustness. However, the regulatory mechanism of hydraulic shear force (HSF) on granule characteristics and microbial community ecology of the HAA microbiome remain unclear. This study investigated the effects of HSF, controlled by reactor height-to-diameter ratios (H/D = 1, 2.5, 5, and 10), on the nitrogen removal performance, granule morphology, and microbial community assembly. The constructed aerobic HAA granules were uniformly micro-sized (230-280 μm) yet exhibited high density (1030-1115 kg/m[3]) and excellent settleability. Notably, under moderate HSF condition (H/D = 5), the abundance of key HAA-related genes (glnA, gltB, and gdhA) and the enzyme activities of GS, GOGAT, and GDH were maximized, corresponding to highest ammonium removal efficiency. Across all four systems, the constructed aerobic HAA granules strictly performed assimilation function, with no detectable ammonia-oxidizing genes (AMO), nitrifying bacteria, or nitrogen loss. Increasing HSF imposed strong selective pressure on the aerobic HAA granules, resulting in a linear increase in deterministic community assembly while reducing microbial diversity. In system with an H/D of 5, the dominant genera Ponticoccus and Marinobacillus acted as network hubs, maintaining microbial community stability. Overall, this study successfully established micro-sized aerobic HAA granules, and revealed the regulatory effects of HSF on their granule characteristics, microbial community assembly, and nitrogen metabolism. This study provides valuable insights for the design and optimization of stable HAA-based systems for saline wastewater treatment.}, }
@article {pmid42264080, year = {2026}, author = {Abdullah, M and Jayadevan, K and Therayil, A and Kumaraguruparan, N and Kavyasree, PKV and Dilna, P and Faiza, A}, title = {Pharmaco-microdynamics (PMD): Redefining Dose, Exposure, and Control for Living Drug Carriers.}, journal = {Annales pharmaceutiques francaises}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pharma.2026.06.002}, pmid = {42264080}, issn = {2772-803X}, abstract = {Living drug delivery systems including probiotics, engineered microbial therapeutics, and live biotherapeutic products represent a rapidly emerging therapeutic modality whose behavior fundamentally diverges from the assumptions underlying classical pharmacokinetics and pharmacodynamics (PK/PD). Unlike chemically defined, non-replicating drugs, living therapeutics persist, replicate, adapt, and generate bioactive molecules in situ, such that therapeutic exposure is not externally imposed but biologically generated over time. As a result, administered dose functions only as an initiating condition, while realized exposure emerges from population dynamics, ecological establishment, spatial localization, and regulated functional output. These properties render concentration-based PK/PD frameworks insufficient for predicting efficacy, safety, and controllability of living drug carriers. We introduce pharmaco-microdynamics (PMD) as a quantitative delivery-science framework designed to define, measure, and control exposure for living therapeutics. PMD is operationalized through a set of formal metrics including the functional exposure integral (F-AUC), colonization efficiency (CE), residence-time-weighted activity (RTWA), effective functional concentration (EFC50), and the genetic stability index (GSI)that serve as living-system analogues of AUC, bioavailability, mean residence time, EC50, and product-identity specifications. PMD reconceptualizes exposure as a time-integrated biological process governed by four interdependent axes: population kinetics, functional output kinetics, spatial pharmacology, and evolutionary dynamics. By integrating principles from pharmacology, microbial ecology, synthetic biology, biomaterials science, and systems modeling, PMD provides an operational vocabulary for translating adaptive biological agents into predictable and engineerable delivery systems. We further delineate PMD from adjacent frameworks such as quantitative systems pharmacology (QSP) and ecological microbiome modeling, and critically discuss boundary conditions under which classical PK/PD remains applicable to non-replicating or transient microbial interventions. This review critically examines the limitations of classical PK/PD in modeling living drug carriers, formalizes the core principles of PMD, and illustrates them through three quantitative case studies: SYNB1618 for phenylketonuria, synchronized-lysis bacterial tumor therapies, and fecal microbiota transplantation for recurrent Clostridioides difficile infection. Regulatory and clinical implications are addressed, emphasizing the need to shift from dose- and concentration-centric evaluation toward functional biomarkers, persistence metrics, and model-informed assessment of biological activity. Collectively, pharmaco-microdynamics establishes a unifying conceptual and quantitative foundation for the rational development of living medicines.}, }
@article {pmid42264124, year = {2026}, author = {Vandersanden, S and van Leeuwen, J and Vangronsveld, J and Thijs, S}, title = {Integrated physicochemical and microbial analyses reveal redox-driven microbial community structure in a polycyclic aromatic hydrocarbon-polluted subsurface.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128559}, doi = {10.1016/j.envpol.2026.128559}, pmid = {42264124}, issn = {1873-6424}, abstract = {Hydrocarbon-polluted sites are a global environmental concern. Although bioremediation is a cost-effective and sustainable remediation method, its efficiency is often impaired by various environmental and microbial factors. Further advancements in bioremediation require a deeper understanding of the relationship between the soil microbiome and the physicochemical parameters that limit biodegradation. Here, we investigated a 3-meter-deep polycyclic aromatic hydrocarbon (PAH)-polluted soil core from a historically polluted site in The Netherlands. Soil samples were taken from six depths at 50 cm intervals, followed by a physicochemical characterisation, including measurements of PAH, electron acceptors, pH and electrical conductivity. These analyses were complemented by a detailed microbial community analysis. Our findings suggest that microbial communities are primarily shaped by a combination of the availability of electron acceptors and pollution levels. Additionally, groundwater level fluctuations appear to play an important role in the transport and replenishment of electron acceptors. In-depth community analysis further revealed a diversity of metabolic strategies employed by the different communities to cope with the oversupply of electrons. Collectively, these results demonstrate that microbial communities in PAH-polluted soils vary according to habitat-specific redox environments. Therefore, microbial community analysis can serve as an additional diagnostic tool to infer the specific physicochemical constraints that limit efficient biodegradation. Our findings provide a detailed, integrated interpretation of physicochemical and microbial field data, offering insight into the heterogeneous nature of in situ biodegradation. They further highlight the value of comprehensive and integrated microbial community and physicochemical analyses in identifying biodegradation-limiting factors in the field.}, }
@article {pmid42264152, year = {2026}, author = {Gibbons, JA and Nelson, RM and Dabrowski, CN and Narkhede, A and Szalacha, LA and Kneusel, ML and Maru, JS and Huszar, MR and Hoang, LK and Schiavo, V and Eddins, AC and Georgieff, MK and Neu, J and Donovan, SM and Groer, MW and Ho, TTB}, title = {Enteral Iron Dose Effect on Iron Storage, Intestinal Barrier, and Gut Microbiome in Preterm Infants: A Randomized Clinical Trial.}, journal = {The American journal of clinical nutrition}, volume = {}, number = {}, pages = {101389}, doi = {10.1016/j.ajcnut.2026.101389}, pmid = {42264152}, issn = {1938-3207}, abstract = {BACKGROUND: Preterm infants routinely receive enteral iron supplementation to support growth, replace phlebotomy losses, and prevent iron deficiency. However, concerns regarding potential harms, including those on the gut microbiome, have contributed to recommendations for lower dosing.<br><br>OBJECTIVE: To compare the effects of two enteral iron doses on gut health in very-low-birth-weight preterm infants. We hypothesized that higher iron dose would increase abundances of pathogenic bacteria, intestinal inflammation, and barrier dysfunction.<br><br>METHODS: This randomized, double-blind clinical trial assigned preterm infants born <1500 g to receive either the recommended dose, 2 mg/kg/day, or a higher dose of 6 mg/kg/day of total enteral iron. The primary outcome was the fecal microbiome after 2 weeks on iron, assessed by metagenomic sequencing. Secondary outcomes included biomarkers of intestinal inflammation and barrier function (fecal calprotectin, urinary claudin-3, and urinary intestinal fatty acid-binding protein). Iron status, adverse events, and auditory brainstem response latencies at 36 weeks postmenstrual age were also evaluated.<br><br>RESULTS: Among 151 randomized infants who received study iron (77 low-dose; 74 high-dose), bacterial diversity, individual taxa, virulence potential, bacterial overgrowth, and iron-related functional genes were not significantly different between the treatment groups. In subgroup analysis of singletons, treatment groups demonstrated significant differences in temporal shifts in overall bacterial community structure. Infants receiving 2 mg/kg/day had higher post-treatment urinary claudin-3 concentrations, indicating possible differences in intestinal permeability, and a higher prevalence of iron deficiency than those receiving 6 mg/kg/day. Other biomarkers, clinical outcomes, adverse events, and auditory latencies did not differ between groups.<br><br>CONCLUSIONS: Enteral iron supplementation at 6 mg/kg/day was associated with improved iron status and lower intestinal barrier dysfunction, without evidence of harms on gut microbiome compared with the recommended 2 mg/kg/day dose. These findings do not support concerns regarding gut microbiome disruption as a justification for lower iron dosing in preterm infants.<br><br>TRIAL REGISTRATION: Clinicaltrials.gov NCT04497012.}, }
@article {pmid42264215, year = {2026}, author = {Hou, P and Che, Y and Han, J and Deming, C and Amirkhani, A and Kim, CS and Taylor, ME and Velez, D and Cho, E and Holmes, CJ and Suh, G and Castelo-Soccio, L and ,  and McDermott, DH and Murphy, PM and Segre, JA and Kong, HH}, title = {Permissive skin microbiomes in WHIM syndrome: HPV and pathogen expansion.}, journal = {The Journal of investigative dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jid.2026.05.024}, pmid = {42264215}, issn = {1523-1747}, abstract = {Warts, hypogammaglobulinemia, infections, and myelokathexis (WHIM) syndrome is a rare inborn error of immunity (IEI) caused by hyperfunctional pathogenic variants in CXC chemokine receptor 4 (CXCR4), predisposing individuals to recurrent bacterial skin and airway infections and warts. The targeted CXCR4 antagonist plerixafor has shown efficacy in wart regression and potential reduction in bacterial infection frequency. Here, we investigated skin microbiomes of 11 patients with WHIM syndrome using shotgun metagenomics, compared to healthy controls. WHIM skin microbial communities displayed greater inter-individual variability, with highly diverse human papillomavirus profiles and expansion of airway-associated pathogens on the skin. Among patients receiving plerixafor therapy, we observed shifts in the viral composition and a downward trend in viral abundances. Together, these findings demonstrate the distinctive and permissive skin microbiome in WHIM syndrome and highlight the potential microbiome-modulating effects of targeted CXCR4 antagonism.}, }
@article {pmid42264216, year = {2026}, author = {Guo, L and Li, J and An, J and Miao, J and Yi, Y and Zhu, K and Cai, Q and Wang, S and Su, Z and Ye, X and Wang, Y and Pan, M and Lu, Q and Cui, B and Zhang, F and Mao, J and Liu, X and Lu, Y and Ding, D}, title = {Neuroprotective role of Faecalibacterium prausnitzii-derived butyrate in diabetic gastrointestinal autonomic neuropathy.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgg.2026.06.005}, pmid = {42264216}, issn = {1673-8527}, abstract = {Diabetic gastrointestinal autonomic neuropathy (DGAN) is a common yet poorly understood complication of diabetes that is characterized by gastrointestinal dysmotility and enteric neurodegeneration. Here, we investigate whether gut microbiota dysbiosis contributes to DGAN pathogenesis and explore the potential involvement of microbiota-derived metabolites in enteric nervous system (ENS) injury. Gut microbiota profiling reveals disease-associated compositional alterations in patients with DGAN, including depletion of Faecalibacterium-associated signals, with Faecalibacterium prausnitzii identified as a putative species-level annotation and negatively associated with gastrointestinal symptom severity. Fecal microbiota transplantation from patients with DGAN into db/db mice aggravates gut dysmotility and increases apoptosis of ChAT[+] and nNOS[+] myenteric neurons. Further experiments indicate that butyrate, the predominant metabolite produced by F. prausnitzii, attenuates neuronal apoptosis under high-glucose conditions. This biological process is accompanied by enhanced BCL2 expression, downregulation of cleaved caspase-3, and activation of the PI3K/Akt signaling cascade. Collectively, our findings support the presence of a gut microbiota-ENS axis in DGAN and identify butyrate as an important candidate neuroprotective metabolite associated with F. prausnitzii. These results provide a rationale for microbiota-targeted therapeutic strategies for diabetic enteric neuropathy.}, }
@article {pmid42264348, year = {2026}, author = {Zaccaria, E and Honerlagen, H and Šebek, L and Wind, T and Kar, SK and van der Valk, E and van Gastelen, S}, title = {Effects of feeding grass silage- and corn silage-based diets in phenotypically low and high methane emitting Holstein-Friesian dairy cows.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2026-28444}, pmid = {42264348}, issn = {1525-3198}, abstract = {The objectives of this study were to determine (1) whether replacing grass silage with corn silage reduced methane (CH4) emissions equally effectively in dairy cows with a low or high CH4 emission level, (2) whether low or high CH4 emitting cows remained low and high CH4 emitters irrespectively of the diet fed, and (3) whether the diet and CH4 emission level affected lactation performance, feed intake, and rumen microbiome. Emissions of CH4 of 192 lactating dairy cows were measured with the GreenFeed system in a screening phase to select the 12 highest and the 12 lowest CH4 emitting cows (i.e., 15.9 ± 1.49 vs. 24.0 ± 1.43 g CH4/kg DMI). These 24 cows were subsequently enrolled in a crossover design trial with a grass silage-based diet (GS) and a corn silage-based diet (CS). The GS diet consisted of 58.0% grass silage, 19.3% corn silage, and 22.7% concentrate, and CS consisted of 19.3% grass silage, 58.0% corn silage, and 22.7% concentrate (DM basis). Treatment periods lasted 4 weeks and consisted of a 2-week adaptation period followed by a 2-week measurement period. No interaction between diet and CH4 emission level was observed. Hence, the reduction in CH4 emissions by CS compared with GS did not differ between the low (-23%) and high (-18%) CH4 emitting cows. The CH4 emission level of low-emitting cows was 27% lower than that of high-emitting cows, and was persistent irrespective of the type of diet fed. The community structure and diversity of the rumen microbiome responded to diet and CH4 emission level, but no interactions were observed except for 1 low-abundance bacterial genus accounting for less than 0.6% of total bacterial relative abundance. Replacing grass silage with corn silage resulted in increased milk yield and DMI, decreased milk fat content and CH4 emissions, and a shift from acetate to propionate. The latter aligned with the changes in rumen microbiota, shifting from a more fibrolytic, acetate-oriented community with GS toward a more amylolytic, propionate-oriented community with CS. Other than in CH4 emissions, the low and high CH4 emitting cows did not differ from each other in feed intake level, lactation performance, and body measures. Despite these similar production responses, low CH4 emitting cows had distinct ruminal bacterial and archaeal communities compared with high CH4 emitters across both diets. Low CH4 emitters were enriched in Succinivibrionaceae_UCG-001, which was positively associated with ruminal molar proportion of propionate. High CH4 emitters showed higher archaeal diversity and a greater relative abundance of Methanomethylophilaceae. The molar proportions of butyrate and carbon dioxide (CO2) yield were higher in high-emitting cows compared with low-emitting cows. In conclusion, this study shows that replacing grass silage with corn silage effectively reduces CH4 emissions regardless of the cow's CH4 emission level, and that CH4 emission levels in Holstein Friesian cows are persistent regardless of diet fed.}, }
@article {pmid42264710, year = {2026}, author = {Li, Y and Li, M and Meng, Q and Zhang, J and Yang, Z and Zhang, Q and Yan, M}, title = {Coinoculation with Bacillus mojavensis BA23 and Rhizobium indicum RH64 protects red kidney bean from root rot by activating plant systemic defense-related responses and modulating the rhizosphere microbial community.}, journal = {Pesticide biochemistry and physiology}, volume = {221}, number = {}, pages = {107111}, doi = {10.1016/j.pestbp.2026.107111}, pmid = {42264710}, issn = {1095-9939}, abstract = {Root rot is a major threat to red kidney beans (Phaseolus vulgaris), caused mainly by Fusarium oxysporum. This study tested single/combined inoculation of Bacillus mojavensis BA23 and Rhizobium indicum RH64 on disease control, plant growth, and systemic defense in greenhouse pots. Both single strains reduced disease index and improved growth, but coinoculation was better: vs single BA23/RH64, it increased plant biomass by 11.05%/23.81% and reduced disease index by 18.87%/40.27%. BA23 inhibited F. oxysporum (80.54% in vitro) and activated plant defense (e.g., boosted antioxidant enzyme activity), while RH64 had nitrogen-fixing activity (253.22 U·L[-1]) and recruited beneficial rhizobacteria. Coinoculation enriched taxa like Sphingomonadaceae and Vicinamibacteraceae (key for disease suppression and growth promotion) and enhanced rhizosphere microbial network stability (e.g., higher modularity and average degree). Partial least squares path modeling (PLS-PM) showed that bacterial community structure was significantly correlated with reduced disease index and increased plant biomass. In conclusion, coinoculating BA23 and RH64 effectively controls red kidney bean root rot and promotes plant growth by inducing systemic defense-related responses and beneficially reshaping the rhizosphere microbiome.}, }
@article {pmid42265111, year = {2026}, author = {Campese, L and Longo, A and Pelletier, E and Delmont, TO and Ambrosino, L and Miralto, M and Mele, BH and Alberti, A and Labadie, K and Oliveira, PH and Perdereau, A and Wincker, P and ,  and Iudicone, D}, title = {Eukaryotic MAGs from the NEREA observatory: expanding the coastal microbiome dataset.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07571-y}, pmid = {42265111}, issn = {2052-4463}, support = {101082021//MARCO-BOLO/ ; ID: 862923//AtlantECO/ ; 101081642//OBAMA-NEXT/ ; }, abstract = {Marine ecosystems are hotspots of biodiversity and biogeochemical activity, yet much of their complexity remains largely inaccessible without genome-resolved data. Here we present a curated dataset of 52 eukaryotic metagenome-assembled genomes (MAGs) reconstructed from samples collected between April 2019 and January 2020 at three NEREA (Naples Ecological REsearch for Augmented observatories) sites in the Gulf of Naples. NEREA is a coastal observatory integrating physical, chemical and biological measurements with state-of-the-art metagenomics. The eukaryotic MAGs have an average completeness of ~55% and genome size of ~20 Mb. Predicted proteins were functionally annotated against UniProtKB, InterPro, and eggNOG databases, and each MAG was taxonomically classified using a curated RNA polymerase A reference dataset. The recovered MAGs encompass diverse eukaryotic lineages, primarily Ochrophyta, Chlorophyta and Haptophyta. Building on the Tara Oceans eukaryotic MAG legacy, this release represents the first reconstruction of eukaryotic MAGs from a coastal time series, enabling temporal and functional analyses of eukaryotic plankton.}, }
@article {pmid42265593, year = {2026}, author = {Liu, T and Wang, N and Hao, J and Hong, J and Han, Y and Yang, L and Zhang, H and Zhou, J and Tan, Y and Li, L and Yang, R}, title = {Integrated culturomics and 16S rDNA sequencing reveal a functional microbiome signature in endometrial cancer.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05242-x}, pmid = {42265593}, issn = {1471-2180}, support = {2021YFC2301000//National Key Research and Development Program of China/ ; 32394054//National Natural Science Foundation of China/ ; }, abstract = {OBJECTIVE: Endometrial cancer (EC) is a common gynecologic malignancy globally, but the role of the intratumoral microbiome remains poorly defined. While microbial dysbiosis is increasingly linked to cancer, the composition, function, and clinical relevance of the microbiota in EC are underexplored. This study aims to systematically profile the microbiome in EC patients by integrating culturomics and 16S rDNA sequencing, and to evaluate the functional properties of key bacterial strains in relation to tumor progression.<br><br>METHODS: We collected cancerous tissues (CATs), non-cancerous adjacent tissues (NATs), and vaginal swabs from 32 EC patients. Culturomics was performed on 57 samples from 19 patients to isolate and identify bacteria, while 16S rDNA sequencing assessed microbial diversity and composition. Functional assays, including flow cytometry for invasion efficiency and ELISA, were used to evaluate pro-inflammatory capacity.<br><br>RESULTS: Culturomics identified 79 bacterial species, with Staphylococcus, Streptococcus, and Cutibacterium emerging as core genera shared across the vagina, NATs, and CATs. Functional analysis revealed that strains such as Staphylococcus epidermidis and Streptococcus anginosus exhibited high invasion efficiency (up to 84.8%) and significantly upregulated pro-inflammatory responses. 16S rDNA sequencing showed that Lactobacillus dominated the vaginal microbiota, whereas endometrial tissues were enriched with opportunistic pathogens (e.g., Stenotrophomonas). Critically, specific genera were associated with aggressive clinical features: Slackia with poorly differentiated (G3) tumors and Porphyromonas with deep myometrial invasion (&#x2265;&#x2009;50%).<br><br>CONCLUSION: This study uncovers a distinct, translocally disseminated core microbiota in EC, with key strains demonstrating invasive and pro-inflammatory capacities that may play a role in tumor progression. These findings provide a foundation for microbial biomarkers and targeted interventions, highlighting the transformative potential of microbiome research in gynecologic oncology.}, }
@article {pmid42265613, year = {2026}, author = {Hu, Y and Pan, L and Liu, B and Su, C and Zhang, L and Li, W and Fu, T and Gao, T and Lian, H and Wang, L and Zhang, Y and Liu, K}, title = {Eucommia ulmoides leaves improving growth by regulating the rumen microbiome in sheep.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05089-2}, pmid = {42265613}, issn = {1471-2180}, support = {252102110017//Henan Province Science and Technology Research Project (2025)/ ; 2024YFD1300204//Key technologies for efficient utilization of cattle and sheep feed and forage and carbon emission reduction/ ; }, abstract = {BACKGROUND: Ruminants have the ability to convert agricultural byproducts into valuable resources. However, the influence of functional roughage with medicinal value on production performance and rumen function in ruminants remains unclear. This study aimed to examine the role of Eucommia ulmoides leaves (EUL) in the growth performance and rumen microbiome of sheep.<br><br>RESULTS: Twenty-one healthy female sheep were randomly divided into three groups, in which the EUL feeding amounts were 0% (CON), 5% (Diet 1), and 10% (Diet 2) on a dry matter basis. The results revealed that body weight gain, dry matter intake, and feed conversion efficiency were significantly greater in the Diet 1 group than in the CON and Diet 2 group. The metatranscriptome annotation results indicated that feeding EUL to sheep altered the rumen microbial community. Compared with those in the other two groups, the abundances of butyrate-producing bacteria, such as Coprobacillus, significantly increased in the Diet 1 group. Functional enrichment analysis of the metatranscriptome indicated higher metabolic activity in the carbohydrate and amino acid pathways in the Diet 1 group than in the control group, which might be due to improved nutrient utilization in the Diet 1 group.<br><br>CONCLUSIONS: In conclusion, feeding 5% EUL to sheep enhanced production performance, feed conversion efficiency, and microbial metabolism. These findings suggest that EUL plays a critical role in sustainable livestock farming as a promising functional roughage.}, }
@article {pmid42265709, year = {2026}, author = {Li, Y and Zhang, Y and Liu, W and Tao, T}, title = {Bridging gut microbiota and polycystic ovary syndrome: the mediating role of metabolites and immune pathways via Mendelian randomization and mediation analysis.}, journal = {Journal of ovarian research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13048-026-02162-2}, pmid = {42265709}, issn = {1757-2215}, support = {82370797//National Natural Science Foundation of China/ ; J202103E006//Bethune Charitable Foundation/ ; RJTJ23-ZD-005//National Nature Promotion Project, Renji Hospital, Shanghai Jiao Tong University School of Medicine/ ; }, abstract = {BACKGROUND: Polycystic Ovary Syndrome (PCOS) is a common reproductive metabolic disorder impacting women of reproductive age, with its etiology influenced numerous factors. Recent research indicates that the gut microbiota, along with its metabolites and associated immune-inflammatory responses, may contribute to the pathogenesis of PCOS. However, there is finite understanding of the potential intermediate impacts of circulating metabolites, immune cells, and inflammatory proteins on the linkage between intestinal flora and PCOS. This study seeks to explore the interrelationships among the gut microbiome, immune-inflammatory responses, and the metabolome within the context of PCOS.<br><br>METHODS: Aggregated statistics pertaining to individual traits were derived from genome-wide association studies accessible to general public. To elucidate mediation mechanisms, a two-step MR mediation framework was applied. In the first step, univariable MR was used to identify causal effects of gut microbial taxa on circulating metabolites, immune cells, and inflammatory proteins. In the second step, multivariable MR and mediation analyses were employed to estimate indirect effects of these mediators on PCOS. All analyses were performed using the inverse variance weighted (IVW) method as the primary model, complemented by MR-Egger, weighted median, and MR-PRESSO sensitivity tests.<br><br>RESULTS: MR analysis identified the causal impacts of 11 intestinal flora taxa on PCOS, among which 4 taxas (Class Betaproteobacteria, Genus Eubacterium eligens group, Genus Ruminiclostridium6 and Order Burkholderiales) may exert positive effects on PCOS, 7 taxas (Family Bifidobacteriaceae, Genus Bilophila, Genus Holdemania, Genus Hungatella, Genus Ruminococcaceae UCG004, Genus Veillonella, and Order Bifidobacteriales) may act as protective factors on PCOS. Meanwhile, 124 plasma metabolites, 45 circulating immune cell types, and 5 inflammatory proteins exhibited causal effects on PCOS. Notably, the circulating metabolites predominantly involved in PCOS were correlative of androgenic steroids, leucine, isoleucine and valine metabolism, glutathione metabolism, and secondary bile acid metabolism, and other metabolic pathways. Mediation analysis elucidated 34 metabolites-mediated path-ways linking gut microbiota and PCOS, with 13 immune cells/inflammatory proteins-mediated pathways interconnecting gut flora and PCOS.<br><br>CONCLUSIONS: According to MR analysis, circulating metabolites, immune cells, and inflammatory proteins play a role in the correlation between intestinal flora and PCOS. The findings shed new light on the underlying pathophysiological mechanisms of PCOS.}, }
@article {pmid42265811, year = {2026}, author = {Xiang, FM and Tang, XT and Brandón, MG and Henawy, AR and Jiang, S and Xu, X and Chen, X and Zhang, Z}, title = {Dismissing-then-recruiting: a unique mechanism for symbiont recruitment and lignocellulose degradation in gut of black soldier fly larvae.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02441-6}, pmid = {42265811}, issn = {2049-2618}, abstract = {BACKGROUND: Black soldier fly larvae (Hermetia illucens L., BSFL) efficiently degrade lignocellulosic waste despite lacking endogenous lignocellulolytic enzymes, indicating a critical dependence on gut-associated microbiota. However, how BSFL are associated with the enrichment and spatial organization of lignocellulose-degrading symbionts within the gut remains poorly understood.<br><br>RESULTS: We show that BSFL establish a spatially structured microbiome through gut compartment-specific immune regulation. Axenic larvae showed negligible lignocellulose degradation, whereas microbiota-associated larvae achieved&#x2009;~&#x2009;33.3%, confirming microbial dependence. Antimicrobial peptides, including cecropin and defensin, were highly expressed in the anterior midgut, forming a selective barrier. In contrast, the posterior midgut showed reduced immune activity via peptidoglycan recognition proteins (PGRP-LB, PGRP-SC). Concurrently, host glycosylation-related genes (C1galt1, GlcAT-P, FUT8/11) were significantly upregulated in the posterior midgut (17-19 TPM), representing a 4-fivefold increase relative to the anterior region (p&#x2009;<&#x2009;0.01). This region was correspondingly enriched in carbohydrate-active symbionts producing glycoside hydrolases, including galactosidases, fucosidases, and mannosidases, suggesting that upregulated glycan biosynthesis may provide sustained nutrient availability for microbial taxa with corresponding carbohydrate-utilizing capacities. Such compartmentalized immune-metabolic coordination is consistent with a potentially conserved strategy for modulating immune tolerance and fostering symbiont recruitment.<br><br>CONCLUSIONS: Collectively, our findings define a compartmentalized "Dismissing-then-Recruiting" strategy for microbiome assembly in BSFL, which is associated with the structuring of functional symbiont communities for efficient lignocellulose bioconversion, thereby elucidating novel principles for sustainable waste management. Video Abstract.}, }
@article {pmid42265904, year = {2026}, author = {Rashid, SS and Dahchi, M and Jafarian, F}, title = {Combined Antibiotic, Steroid, and Moisturizer Therapy in Eczema Treatment: Balancing Short-Term Relief with Long-Term Risks.}, journal = {Journal of cutaneous medicine and surgery}, volume = {}, number = {}, pages = {12034754261455695}, doi = {10.1177/12034754261455695}, pmid = {42265904}, issn = {1615-7109}, abstract = {Combined antibiotic-corticosteroid-moisturizer therapy, often referred to as the Aron Regimen has gained popularity for managing atopic dermatitis (AD). While this therapy has been shown in some studies to provide short-term improvement in symptoms, evidence for its long-term utility is limited, and its widespread use raises concerns about promoting antibiotic resistance and disrupting the skin microbiome. Studies suggest that topical antibiotics provide limited benefit for most eczema cases, with only modest or context-specific benefits reported in more severe or treatment-resistant situations. Importantly, current clinical guidelines do not recommend the routine use of topical antimicrobials in the absence of clear infection. This review contextualizes the Aron Regimen within current evidence and emphasizes a more cautious, limited role for antibiotic-containing therapies in AD.}, }
@article {pmid42265922, year = {2026}, author = {Uriot, O and Deschamps, C and Etienne-Mesmin, L and Brun, M and Pouget, M and Chalancon, S and Durif, C and Chaudemanche, C and Alric, M and Boirie, Y and Blanquet-Diot, S}, title = {Colonic nutritional and physicochemical parameters drive gut microbiota dysbiosis in obesity: what we learned from the Ob-M-ARCOL model development.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2685908}, doi = {10.1080/19490976.2026.2685908}, pmid = {42265922}, issn = {1949-0984}, abstract = {BACKGROUND: Obesity has reached epidemic proportions worldwide with a substantial burden on both individual health and society. Alterations in gut microbiota are increasingly recognized as a key contributor in disease pathogenesis. However, mechanistic understanding at the ecosystem level remains limited. In line with EU and US regulations, in vitro gut systems can be useful to address these questions, but up to now, there is no validated in vitro model of the obese human colon.<br><br>RESULTS: To address this gap, we performed dietary surveys and conducted an extensive analysis of 250 articles to set-up and validate a unique in vitro colonic model, based on human in vivo data and reproducing obese-specific nutritional, physicochemical, and lumen vs mucus-associated microbial parameters. Then, in an original experimental set-up, we cross-compared data on gut microbiota structure and activities during fermentations performed with fecal microbiota from healthy (n&#x2009;=&#x2009;4) or obese (n&#x2009;=&#x2009;5) donors and operated under healthy or newly designed obese parameters. Interestingly, applying obese parameters on healthy fecal samples resulted in a significant reduction in microbial &#x3b1;-diversity and in taxa associated with health (e.g., Akkermanciaceae, Rikenellaceae, and Archaea), together with a tendency toward increased production of short-chain fatty acids and associated energy, in full agreement with in vivo data. Conversely, applying healthy parameters on obese fecal samples led to gut microbiota resilience.<br><br>CONCLUSIONS: These findings highlight the importance of nutritional and physicochemical environment in shaping colonic bacterial and archaeal populations in obesity. This innovative validated model represents a robust and useful platform for mechanistic investigations on gut microbiome in the absence of the host cells, as well as for preclinical evaluation of food and pharmaceutical strategies aiming to restore microbiota eubiosis in a personalized manner.}, }
@article {pmid42266133, year = {2026}, author = {Duggar, M and Leardini, D and Muratore, E and Margolis, EB and Masetti, R}, title = {Gut Microbiome-Immune Interactions During Pediatric Hematopoietic Cell Transplantation: From Conditioning to GvHD Prevention.}, journal = {Pediatric transplantation}, volume = {30}, number = {6}, pages = {e70371}, doi = {10.1111/petr.70371}, pmid = {42266133}, issn = {1399-3046}, abstract = {Hematopoietic stem cell transplantation (HCT) offers curative potential for children with high-risk hematologic malignancies. However, this treatment carries significant risks, particularly acute graft-versus-host disease (aGvHD), which affects 30%-60% of pediatric recipients and causes 15%-20% of post-transplant deaths. The gut microbiome has emerged as a critical factor in aGvHD development, yet pediatric microbiome dynamics differ substantially from adult patterns. This review seeks to evaluate the current state of knowledge of how the gut microbiome impacts aGvHD pathogenesis and the methods of microbiome modulation that may lead to aGvHD prevention and treatment. Children's microbiomes undergo more rapid compositional shifts and contain distinct bacterial compositions enriched in taxa like Bifidobacterium and Lactobacillus. During transplant, conditioning regimens and antibiotics cause dramatic microbiome disruption in children. This eliminates beneficial bacteria that normally maintain intestinal barrier integrity and produce immunomodulatory metabolites. Consequently, this disruption triggers inflammatory cascades through bacterial translocation, impaired immune education, and altered metabolite production. Unlike adults, where low diversity consistently predicts poor outcomes, pediatric studies show inconsistent diversity-outcome relationships, with only pre-transplant microbiome patterns reliably predicting aGvHD risk. Several promising interventions have emerged from this research. These include enteral nutrition to preserve beneficial bacteria, targeted antibiotic strategies, and fecal microbiota transplantation. Fecal microbiota transplantation has shown remarkable response rates in pediatric steroid-resistant aGvHD cases. Nevertheless, significant knowledge gaps remain regarding pediatric-specific mechanisms, optimal biomarkers, and age-appropriate therapeutic approaches for microbiome-directed aGvHD prevention.}, }
@article {pmid42266457, year = {2026}, author = {Stach, TL and Deep, A and Madge Pimentel, I and Buchner, D and Borton, MA and Soares, AR and Starke, J and Bornemann, TLV and Rehsen, PM and Dreger, KL and Boenigk, J and Vos, M and Leese, F and Beisser, D and Probst, AJ}, title = {Complex compositional and metabolic response of river sediment microbiomes to multiple anthropogenic stressors.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycaf079}, pmid = {42266457}, issn = {2730-6151}, abstract = {Rivers face constant anthropogenic stress, resulting in significant changes in microbial community composition. What remains unclear is whether stream microbiomes exhibit distinct resilience patterns in composition and/or activity upon exposure to different stressors. By subjecting 64 river-connected mesocosms to multiple stressors, we show that sediment microbiomes of small lowland rivers are highly sensitive to low flow velocity. This stress results in altered community compositions incapable of mitigating the applied stressor within a two-week timeframe despite functional stability (inferred via metagenomics). Transcriptomics revealed a systematic heat shock response in the community and a highly active, metabolically versatile, uncharacterized anaerobic keystone species. Increases in temperature (+ 3.5°C) or salinity (+ 0.5 mS/cm) elicited minor responses at community and transcriptomic levels (e.g. upregulation of photosystems). Following a two-week recovery, transcriptomic-inferred stress responses vanished completely, underscoring the river microbiome resilience. Given the complex community responses observed at the activity and compositional levels, we conclude that maintaining natural river flow is vital to preventing energy loss and reduced microbiome activity in river sediments.}, }
@article {pmid42266459, year = {2026}, author = {Van Landuyt, J and Oosterlinck, J and De Vrieze, J}, title = {The anaerobic digestion microbiome is robust toward variation in the waste activated sludge feed.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycaf072}, pmid = {42266459}, issn = {2730-6151}, abstract = {Anaerobic digestion stands out as the foremost technology for maximizing the valorization of waste activated sludge (WAS) to recover energy and recover resources. The physical/chemical and microbial makeup of WAS is susceptible to seasonal fluctuations, due to the open-air nature of wastewater treatment facilities, potentially impacting subsequent digester performance and the quality of the resulting digestate. This study delved into a comprehensive analysis of both the initial WAS and the digestate produced by 12 full-scale digesters during both a summer and winter sampling campaign. A significant influence of seasonal variations was observed on the physical/chemical and microbial composition of WAS. Interestingly, the digestate microbiome exhibited a high resilience with minimal seasonal fluctuations, but instead showed variations between different digesters. In summary, this research demonstrates that while WAS composition manifests in specific physical/chemical attributes, it does not exert a discernible influence on the microbial composition of the resulting digestate.}, }
@article {pmid42266461, year = {2026}, author = {Jang, S and Ryu, CM}, title = {A new role for an old actor: plant small RNAs orchestrate the phytobiome.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycaf060}, pmid = {42266461}, issn = {2730-6151}, }
@article {pmid42266611, year = {2026}, author = {Yang, H and Liu, Y and Zhu, T and Xiao, Z and Wang, H and Zhu, S and Chen, Y}, title = {Gut Microbiome-Metabolite Interactions Contribute to Esophageal Cancer Risk: Evidence From Mendelian Randomization and Multiomics Integration.}, journal = {International journal of genomics}, volume = {2026}, number = {}, pages = {5967802}, pmid = {42266611}, issn = {2314-4378}, abstract = {BACKGROUND: Growing evidence implicates gut microbiota (GM) in the pathogenesis of esophageal cancer (EC). However, the causal nature of this association-particularly the potential mediating role of circulating metabolites-remains insufficiently clarified, especially across EC subtypes.<br><br>METHODS: We applied a two-sample Mendelian randomization (MR) framework to investigate the causal associations of GM and blood metabolites with EC and esophageal adenocarcinoma (EAC). The primary analysis was conducted using the inverse-variance weighted method, with complementary MR approaches and genetic risk score (GRS) validation to ensure robustness. Mediation analyses were further performed to assess whether metabolites mediate the effects of GM on EC and EAC.<br><br>RESULTS: Twenty-five GM taxa showed significant associations with EC, including 11 with risk-promoting and 14 with protective effects. For EAC, 15 taxa were implicated, with 11 increasing and 4 decreasing disease risk. In addition, five metabolites were causally linked to EC (two risk-related and three protective), and six to EAC (five risk-related and one protective). Mediation analyses revealed that specific metabolites partially mediated the effects of GM on both EC and EAC.<br><br>CONCLUSIONS: Our findings provide genetic evidence for a causal GM-metabolite-cancer axis in EC pathogenesis. These results highlight the role of circulating metabolites as potential intermediaries linking GM to EC and EAC, and suggest new avenues for biomarker discovery and microbiome-targeted interventions.}, }
@article {pmid42266650, year = {2026}, author = {Yu, Z and Zhang, S and Lu, Z and Wang, H and Liu, H and Li, Y and Pan, Y}, title = {Crosstalk between iron metabolism dysregulation and the oral microbiome in periodontitis.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2682975}, pmid = {42266650}, issn = {2000-2297}, abstract = {BACKGROUND: Periodontitis is a chronic inflammatory disease caused by periodontal pathogens. The impact of periodontitis is not only limited to the oral cavity, but also related to a variety of systemic diseases. Iron is a kind of redox metal, which may be deleterious to cells by producing damaging free radicals. Iron homeostasis dysregulation, especially ferroptosis, involves in the progression of periodontitis.<br><br>OBJECTIVE: This review aims to systematically summarize the crosstalk between iron metabolism dysregulation and the oral microbiome in periodontitis, focusing on alterations in iron-related biomarkers, iron-mediated tissue damage, the role of ferroptosis, and the potential of iron-targeted therapies.<br><br>DESIGN: A narrative review of recent advances in iron metabolism and ferroptosis, with emphasis on studies investigating molecular mechanisms, clinical correlations, and therapeutic interventions in periodontitis.<br><br>RESULTS: In periodontitis, serum iron and transferrin levels are decreased, while ferritin, hepcidin, and ceruloplasmin are elevated. Dysregulated iron metabolism promotes periodontal pathogen survival, amplifies inflammatory responses, induces ferroptosis in periodontal ligament cells, and contributes to alveolar bone resorption. Iron disorders also link periodontitis to systemic diseases such as anemia of inflammation, type 2 diabetes, and cardiovascular disease. Preclinical studies show that iron chelators (e.g. deferoxamine) and lactoferrin can inhibit bacterial growth, alleviate ferroptosis, and promote periodontal regeneration.<br><br>CONCLUSIONS: Iron metabolism dysregulation and ferroptosis play critical roles in the initiation and progression of periodontitis and its systemic comorbidities. Targeting iron homeostasis represents a promising therapeutic strategy, but further well-designed clinical trials are needed to validate efficacy and safety.}, }
@article {pmid42266651, year = {2026}, author = {Hamada, M and Matsuoka, Y and Ogaya, Y and Kadota, T and Ikeda, S and Akitomo, T and Nomura, R and Nakano, K}, title = {Effects of multiple tongue conditions on the diversity and composition of the oral microbiota.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2684141}, pmid = {42266651}, issn = {2000-2297}, abstract = {OBJECTIVE: The present study examined the effects of multiple tongue conditions on the diversity and composition of the oral microbiota to obtain a more detailed understanding of their potential role in health and disease.<br><br>METHOD: Ninety-three subjects were classified according to tongue conditions, such as a yellow tongue coating, the presence or absence of swelling of the sublingual vein, a red tongue or red tongue tip, a fissured tongue, enlarged tongue, geographic tongue, and tooth marks. The oral microbiota was examined using &#x3b1;- and &#x3b2;-diversity metrics and taxonomic composition analyses.<br><br>RESULTS: &#x3b1;-Diversity was significantly lower in subjects with a fissured tongue than in those without. A &#x3b2;-diversity analysis revealed distinct microbial community structures between these subjects. Taxonomic profiling showed a higher abundance of Firmicutes and sulfur-metabolizing bacteria in subjects with a fissured tongue. However, these differences were not retained after age adjustment. Age-restricted sensitivity analyses identified age-independent microbial signatures associated with a fissured tongue, including a reduced abundance of Veillonella and Granulicatella in saliva samples.<br><br>CONCLUSION: Morphological abnormalities of the tongue are associated with distinct oral microbiome profiles. These features may reflect oral microbial dysbiosis and could be relevant for future studies exploring non-invasive markers of oral health.}, }
@article {pmid42266671, year = {2026}, author = {Zhang, Y and Xue, J and Lin, H and Wang, K and Tan, X and Jiao, X and Jiang, H}, title = {Persistent dysbiosis of intestinal and oral microbiota after neoadjuvant radiotherapy for rectal cancer: Implications for surgery and microbiome intervention.}, journal = {Frontiers in oncology}, volume = {16}, number = {}, pages = {1786044}, pmid = {42266671}, issn = {2234-943X}, abstract = {BACKGROUND: Neoadjuvant radiotherapy represents a conventional approach for managing locally advanced rectal carcinoma. Although this regimen has many benefits, radiation injury is associated with intestinal mucosal injury and gut microbiota dysbiosis. The long-term dynamics of inflammation and microbial recovery, including oral microbiota alterations, remain unclear.<br><br>METHODS: Intestinal mucosal specimens were obtained from patients with rectal cancer who underwent surgical treatment without radiotherapy or at predetermined time intervals (4&#xa0;&#xb1;&#xa0;1 weeks, 8&#xa0;&#xb1;&#xa0;1 weeks and 12&#xa0;&#xb1;&#xa0;1 weeks) after radiotherapy. The levels of TNF-&#x3b1;, IL-4 and IL-6 in the intestinal mucosa were determined using ELISA. Meanwhile, the intestinal mucosa and saliva of 18 recruited rectal cancer patients were subjected to 16S rRNA gene sequencing (radiotherapy group, n=9; non-radiotherapy group, n=9) for analysis of the gut and oral microbial communities.<br><br>RESULTS: Mucosal IL-4 levels were still significantly elevated at 12 weeks post-radiotherapy with respect to the non-radiotherapy group (p<0.05), while TNF-&#x3b1; and IL-6 were back at baseline levels. The gut microbiota composition of radiotherapy patients differed from that of non-radiotherapy patients, with a significant reduction in Chao1 diversity index (p<0.01) and distinct &#x3b2;-diversity clustering (ANOSIM R&#xa0;=&#xa0;0.614, p=0.001). These differences were still present at 12 weeks post radiotherapy. The oral microbiota changes were limited, with only a few taxa that showed significant differences (ANOSIM R&#xa0;=&#xa0;0.38, p=0.009).<br><br>CONCLUSION: Neoadjuvant radiotherapy is associated with persistent intestinal mucosa inflammation and prolonged disruption of gut microbiota and this dysbiosis does not fully normalize within 12 weeks after treatment. Changes in oral microbiota appeared less pronounced. These findings provide the biological context for understanding intestinal recovery after radiotherapy and indicate that more studies are needed to direct future efforts towards the peri-operative manipulation of gut microbiota.}, }
@article {pmid42266678, year = {2026}, author = {Rao, X and Zou, L and Cai, X and Yao, Y and Zhong, L}, title = {Microbiome-orchestrated cross-organ immunity in autoimmunity: from metabolites to therapeutic targets.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1761834}, pmid = {42266678}, issn = {1664-3224}, abstract = {Autoimmune diseases are systemic disorders in which barrier-site immune activation, especially in the gut, can reshape inflammatory programs in distant organs. This review advances a metabolite-centered, cross-organ framework for understanding how gut microbial ecology influences autoimmunity beyond individual gut-organ axes. We synthesize evidence that short-chain fatty acids, bile acid derivatives, tryptophan catabolites, polyamines and related microbial products act as mobile biochemical checkpoints linking intestinal barrier integrity, pattern-recognition signaling, immune-cell metabolism and tissue-specific inflammation in joints, kidneys, skin, lungs and the central nervous system. Across these axes, shared mechanisms include barrier failure, altered microbial metabolite pools, dysregulated MAMP sensing, trafficking or systemic conditioning of lymphoid and myeloid cells, and local stromal imprinting in target organs. We also discuss sex-dependent microbiome-immune interactions, including the microgenderome concept, as a framework for explaining why microbiome composition, hormone metabolism and immune responses may shape autoimmune risk and treatment response differently in females and males. Finally, we evaluate multi-omics, single-cell and spatial profiling, organ-on-chip platforms and causal computational tools, and we outline translational strategies ranging from diet, probiotics, fecal microbiota transplantation and engineered consortia to pharmacologic targeting of metabolite receptors. By treating microbial metabolites as actionable cross-organ immune checkpoints, this review highlights opportunities and limitations for biomarker-guided, metabolite-focused precision therapy in autoimmunity.}, }
@article {pmid42266929, year = {2026}, author = {Stoia, O and Anderco, P and Badiu, T and Todor, SB and Ichim, C}, title = {Artificial intelligence in optimizing antimicrobial therapy for gastro-renal disorders.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1792361}, pmid = {42266929}, issn = {2235-2988}, abstract = {Antimicrobial therapy remains central to the management of gastrointestinal and urinary tract infections, yet its effectiveness is increasingly compromised by antimicrobial resistance and antibiotic-induced microbiome disruption. These challenges are particularly pronounced in gastro-renal settings, where recurrent infections, altered drug absorption and impaired renal clearance generate substantial pharmacokinetic variability and narrow therapeutic margins. Empiric, guideline-based regimens may therefore contribute to treatment failure, resistance selection, and disease recurrence. Artificial intelligence (AI) and machine learning offer novel opportunities to optimize antimicrobial therapy by integrating clinical, microbiological and multi-omics data to predict resistance, guide antibiotic selection and dosing, and support antimicrobial stewardship. However, clinical translation remains limited by data heterogeneity, insufficient prospective validation, regulatory constraints, and the need for continued human oversight. This review synthesizes current AI-driven strategies relevant to gastro-renal infections, highlighting shared pathophysiological challenges, practical clinical applications and key limitations. An integrated framework for AI-assisted antimicrobial optimization is proposed to enhance therapeutic efficacy while mitigating antimicrobial resistance and preserving microbiome integrity.}, }
@article {pmid42266934, year = {2026}, author = {Bautista, J and Lara-Hernández, ME and Hidalgo-De La Cruz, M and Andino-Araque, V and León-Rivera, M and López-Cortés, A}, title = {Host-microbiome interactions in breast cancer progression and treatment response.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1827694}, pmid = {42266934}, issn = {2296-858X}, abstract = {Breast cancer (BC) is a biologically heterogeneous disease in which tumor progression and therapeutic response vary substantially across patients and molecular subtypes. Alongside genetic, endocrine, and immunological determinants, microbial ecosystems have been proposed as components of the host environment that interact with tumor biology. Microorganisms detected in breast tissue, the gastrointestinal tract, and the oral cavity coexist with epithelial and immune compartments and participate in metabolic and inflammatory processes relevant to mammary physiology. Differences in microbial composition have been reported between non-malignant and malignant breast tissue, while intestinal microbial metabolism generates bioactive compounds capable of interacting with immune regulation and systemic endocrine signaling. Microbial enzymatic activity involved in estrogen deconjugation further connects intestinal ecology with hormone-responsive disease. Microbiome-related variation has also been examined in relation to systemic therapies, where differences in microbial composition have been observed alongside variability in therapeutic outcomes. This review examines current knowledge on host-microbiome interactions across breast, gut, and oral environments and discusses how microbial ecology intersects with inflammatory signaling, metabolic regulation, and endocrine pathways relevant to breast cancer progression and treatment response. Methodological challenges and future research directions for microbiome-informed oncology are also considered.}, }
@article {pmid42267107, year = {2026}, author = {Mathyk, BA and Shukla, R and Kumar, V and Mishra, SP and Pandya, S and Patten, N and Gerardi, K and Beatty, HW and Persad, AH and Imudia, AN and Yadav, H and Jain, S}, title = {Parabolic flight induces site specific microbiome changes in women.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1817099}, pmid = {42267107}, issn = {1664-302X}, abstract = {INTRODUCTION: The vaginal microbiome plays a central role in women's health by supporting immune function, maintaining mucosal homeostasis, and preventing infections. Spaceflight and its analogs can induce acute physiological stress, which can alter host microbiome interactions. While other studies have analyzed the microbiome changes at certain body sites, the female-specific microbiome changes have not been explored in depth in space medicine research.<br><br>METHODS: Pre- and post-parabolic flight vaginal and oral microbiome were analyzed via metagenomic shotgun sequencing to assess taxonomic composition and metabolic pathways. Host DNA and bad quality sequences were removed using the KneadData tool. Taxonomic and functional profiles were analyzed with MetaPhlAn and HUMAnN. Microbiome data were integrated with stress response parameters including cortisol, proinflammatory cytokines, and urinary short-chain fatty acids.<br><br>RESULTS: Both alpha- and beta diversity analysis showed minimal impact of parabolic flight on oral microbiome while vaginal microbiome showed significant differences. Taxonomic profiling showed marked restructuring of the vaginal microbiome, characterized by increased Firmicutes dominance and enrichment of Lactobacillus species, particularly Lactobacillus crispatus and Lactobacillus jensenii, whereas oral microbiome stayed relatively stable. Overall, only 2.54% of oral species showed significant postflight changes compared to 57.9% of vaginal species (p&#x202f;<&#x202f;0.0001). Random Forest model identified L. crispatus as a key discriminator of postflight vaginal microbiome composition. Metabolic pathway analysis revealed minimal postflight pathway redistribution in saliva samples but greater number of changes in the vaginal microbiome, with significant postflight enrichment of fatty acid biosynthesis and nucleotide metabolism. Vaginal samples demonstrated a threefold greater proportion of altered metabolic pathways compared to oral samples. In addition, urinary acetate, butyrate, and valeric acid levels were significantly reduced postflight. Salivary cortisol increased postflight and positively correlated with L. jensenii.<br><br>CONCLUSION: Parabolic flight induces body site-specific microbiome changes in reproductive age women, with greater taxonomic and functional metabolic remodeling in the vaginal microbiome than in the oral microbiome. These findings highlight the sensitivity of the vaginal microbial ecosystem to spaceflight stressors and underscore the need for longitudinal and mechanistic studies to determine the persistence, clinical significance, and potential health implications of these changes during longer duration space missions.}, }
@article {pmid42267108, year = {2026}, author = {Seo, JH and Seo, YJ and Ryu, HY and Shin, M and Lee, CY}, title = {Current insights into bacterial secondary infection following influenza A virus infection.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1851115}, pmid = {42267108}, issn = {1664-302X}, abstract = {Influenza A virus (IAV) continues to pose a substantial challenge to global health, not merely through primary viral pneumonia but largely due to lethal secondary bacterial complications. Pathogens such as Streptococcus pneumoniae, Staphylococcus aureus, and Haemophilus influenzae capitalize on the physiological "storm" induced by IAV, leading to significantly exacerbated morbidity. This review provides a comprehensive synthesis of the multifaceted mechanisms that dismantle host antibacterial defenses. Beyond the classical understanding of respiratory epithelial damage and the compensatory upregulation of bacterial adhesion receptors, we delve into the sophisticated dysregulation of innate immune signaling, specifically the collateral damage caused by interferon responses and impaired phagocytic function. Furthermore, we examine the complex roles of direct virus-bacterium synergism and the disruption of the respiratory microbiome (dysbiosis). By integrating these established paradigms, we extend the discussion to the rising clinical concern of nosocomial and multidrug-resistant (MDR) infections in critically ill patients. We conclude by identifying critical knowledge gaps and emphasizing the need for targeted strategies to mitigate the host vulnerabilities that permit opportunistic MDR colonization in the wake of viral insult.}, }
@article {pmid42267126, year = {2026}, author = {Quan, W and Qi, Y and Liu, Y and Sun, X and Wang, H and Zeng, C and Chen, H and Gao, S and Xu, Y and Zhao, Q and Du, T}, title = {Soil-borne diseases in medicinal plants: linking allelopathy and host immunity to microbiome-based interventions.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1797910}, pmid = {42267126}, issn = {1664-462X}, abstract = {The rising global demand for natural medicines has intensified the cultivation of Chinese medicinal herbs, exacerbating continuous cropping obstacles and constraining the sustainable development of Chinese medicinal materials. A defining manifestation is a severe soil-borne disease that limits long-term productivity and stable medicinal quality. Despite progress in understanding individual diseases or host species, integrative syntheses of the coupled "pathogen-environment-host" network remain limited. Here, we synthesize the current understanding of soil-borne disease development under continuous cropping and evaluate ecological management options by integrating evidence on pathogen virulence, continuous-cropping-driven edaphic shifts, host immunometabolism (the coupled reprogramming of immunity and metabolism), and microbiome-based interventions. We summarize the major soil-borne pathogens and their virulence determinants and explain how allelochemical accumulation reshapes the rhizosphere microbiome, weakens the barrier functions, and facilitates pathogen ingress. We further discuss how allelochemical stress reprograms defense hormone networks (notably salicylic acid and jasmonic acid pathways) with downstream consequences for innate immune competence. Building on these insights, we assessed microbiome-guided strategies to restore rhizosphere function, including synthetic community design, recruitment of probiotic taxa, and induction of disease-suppressive soils. By integrating microbiology, chemical ecology, and plant pathology, this review provides a conceptual framework and actionable directions for the precise and sustainable control of soil-borne diseases in Chinese medicinal herb production.}, }
@article {pmid42267128, year = {2026}, author = {Daurova, A and Daurov, D and Sapakhova, Z and Kanat, R and Abilda, Z and Toishimanov, M and Isgandarov, I and Mukhametov, A and Volkov, D and Shamekova, M and Zhambakin, K}, title = {Rhizosphere microbiome dynamics and plant adaptation to abiotic stress in major oilseed crops: a review.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1832403}, pmid = {42267128}, issn = {1664-462X}, abstract = {Abiotic stresses, such as drought, salinity, extreme temperatures, nutrient deficiencies, and heavy metal contamination, severely limit oilseed crop productivity under accelerating climate change. This review synthesizes recent advances in understanding the critical role of soil and plant-associated microbiomes in conferring stress tolerance to major oilseed species, including rapeseed (Brassica napus), sunflower (Helianthus annuus), soybean (Glycine max), and sesame (Sesamum indicum). Beneficial microorganisms, particularly plant growth-promoting rhizobacteria (PGPR), arbuscular mycorrhizal fungi (AMF), and endophytes, enhance plant tolerance through an integrated network of biochemical, physiological, and molecular mechanisms. Biochemically, they modulate phytohormone levels (e.g., IAA and ABA), produce osmoprotectants, and regulate antioxidant systems (e.g., SOD, CAT, POD) to mitigate oxidative damage. Physiologically, these processes contribute to improved root architecture, water-use efficiency, nutrient acquisition, and ion homeostasis under stress conditions. At the molecular level, microorganisms influence gene expression and signaling pathways associated with stress responses, including activation of stress-responsive genes and metabolic adjustments. These interconnected mechanisms collectively strengthen plant resilience by coordinating metabolic regulation, cellular protection, and adaptive responses within the plant-microbiome system. Agroecological practices (soil type, crop rotation, tillage, fertilization) strongly shape microbial community assembly and functional potential, while multi-omics approaches (metagenomics, metatranscriptomics, metabolomics) reveal stress-driven restructuring and adaptive metabolic shifts in the rhizosphere. Emerging tools such as synthetic microbial consortia (SynComs) and targeted microbiome engineering offer promising, sustainable alternatives to conventional breeding and chemical interventions, enhancing soil health, nutrient cycling, and agroecosystem resilience with reduced environmental footprint. This review presents a comprehensive synthesis with a specific focus on oilseed crops, integrating current knowledge on microbiome dynamics under multiple abiotic stress conditions-an area that remains comparatively underrepresented in the literature. It examines key microbial groups driving adaptation, evaluates omics-based insights into plant-microbiome interactions, identifies critical research gaps, and outlines future directions for microbial inoculants and climate-resilient oilseed production systems.}, }
@article {pmid42267559, year = {2026}, author = {Xu, T and Xing, J and Lin, X and Yang, Y and Yang, T and Xu, XS and Yuan, M}, title = {Genus-level oral microbiome composition and Dietary Approaches to Stop Hypertension dietary adherence in relation to hypertension.}, journal = {Journal of hypertension}, volume = {}, number = {}, pages = {}, doi = {10.1097/HJH.0000000000004377}, pmid = {42267559}, issn = {1473-5598}, abstract = {BACKGROUND: Hypertension (HTN) remains a leading global health burden and a key risk factor for cardiovascular disease. While the Dietary Approaches to Stop Hypertension (DASH) diet is an established strategy for blood pressure control, the interplay between dietary patterns and the oral microbiome in the etiology of HTN is not well understood.<br><br>OBJECTIVE: To investigate the independent and joint associations of genus-level oral microbiome composition and adherence to the DASH diet with hypertension in a nationally representative sample of US adults.<br><br>METHODS: We analyzed data from the 2009-2010 and 2011-2012 National Health and Nutrition Examination Survey (NHANES), including 5371 adults with complete oral microbiome, dietary, blood pressure, and covariate data. Genus-level oral microbiome profiles were derived from oral rinse samples using 16S rRNA sequencing and transformed with the centered log-ratio method. DASH adherence was assessed from 24-h dietary recalls using a validated score. Hypertension was defined as self-reported diagnosis, antihypertensive medication use, or measured blood pressure meeting 2017 American College of Cardiology/American Heart Association (ACC/AHA) criteria (systolic &#x2265;130&#x200a;mmHg or diastolic &#x2265;80&#x200a;mmHg). Analyses employed a multistage design: differential abundance testing to identify hypertension-associated genera; survey-weighted multivariable logistic regression to examine independent and joint associations, adjusting for demographic, lifestyle, and clinical covariates; subgroup analyses by sex, age, and microbial characteristics; and sensitivity analyses to assess robustness.<br><br>RESULTS: Greater adherence to the DASH diet was associated with lower odds of hypertension [high vs. low tertile odds ratio (OR) &#x2248;0.62; P&#x200a;<&#x200a;0.005]. Several oral bacterial genera - Actinomyces, Rothia, Lactobacillus, and Veillonella - showed independent associations with increased hypertension risk (OR range: 1.302-1.468; P&#x200a;<&#x200a;0.05). Higher Faith's Phylogenetic Diversity was inversely associated with hypertension (OR&#x200a;=&#x200a;0.742; P&#x200a;=&#x200a;0.037). Stratified analyses suggested effect modification: the protective DASH-hypertension association was strongest among individuals with low Lactobacillus abundance and intermediate microbial diversity and Rothia abundance, more pronounced in women, and attenuated in adults aged at least 60&#x200a;years. Sensitivity analyses confirmed these patterns, highlighting the consistent risk associated with Actinomyces and the stability of joint DASH-microbiome associations.<br><br>CONCLUSION: Genus-level oral microbiome composition and DASH dietary adherence were independently and jointly associated with hypertension risk. These results support a potential oral-dietary axis in cardiovascular risk and underscore the need for integrated microbiome-dietary approaches to hypertension prevention.}, }
@article {pmid42267567, year = {2026}, author = {Liu, BZ and Zhao, XY and Sun, ZW and Wang, J and Zeng, JT and Huang, Y and Cai, KQ and Zhao, JG and Yang, SH and Yuan, JL}, title = {Gut microbiota remodeling in HBB-mutant cynomolgus monkeys reveals blood-gut axis disruption associated with β-thalassemia-related gastrointestinal dysfunction.}, journal = {Zoological research}, volume = {47}, number = {3}, pages = {827-842}, doi = {10.24272/j.issn.2095-8137.2025.141}, pmid = {42267567}, issn = {2095-8137}, abstract = {Gastrointestinal symptoms frequently accompany anemia caused by HBB mutations, such as β-thalassemia; however, the mechanisms linking disordered hemoglobin biology to intestinal dysfunction remain incompletely understood. In this study, HBB-mutant cynomolgus monkeys were generated and analyzed together with wild-type (WT) controls through integrated metabolomic and metagenomic profiling. HBB mutation was associated with a marked shift in gut microbial ecology, characterized by reduced microbial diversity and altered abundances of Lactobacillus and Bacteroides. Metabolic profiling revealed broad perturbation of amino acid, lipid, energy, and immune-related metabolic pathways, with 3-oxooctadecanoic acid (HMDB0254633) emerging as a discriminative metabolite between WT and HBB-mutant animals. Multiomics integration indicated that HBB mutation reshaped microbiota-metabolite interactions and may thereby affect host metabolism and immune responses. To examine the functional relevance of this metabolite, 3-oxooctadecanoic acid was administered to C57BL/6 mice with castor oil-induced diarrhea. High-dose treatment alleviated diarrhea severity, improved stool parameters, limited body weight loss, and partially restored gut microbial composition. These findings provide non-human primate evidence that β-thalassemia-associated HBB mutation disrupts intestinal microbiota homeostasis and metabolic output, identifying 3-oxooctadecanoic acid as a candidate biomarker and potential regulator of gastrointestinal dysfunction. This study provides a valuable framework for understanding how host genetic variation contributes to gut microbiome remodeling and gastrointestinal manifestations in β-thalassemia.}, }
@article {pmid42267822, year = {2026}, author = {Khalil, SB and Kowalski, CH}, title = {The cutaneous microbiome: microbial remodeling of the skin lipid landscape.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0064825}, doi = {10.1128/msphere.00648-25}, pmid = {42267822}, issn = {2379-5042}, abstract = {The human skin microbiome exists within a lipid-rich environment that profoundly shapes microbial colonization, metabolism, and interactions with the host. Resident microbes not only consume host-derived lipids for energy but also transform them into bioactive compounds that influence microbial competition, immune responses, and skin barrier function. In turn, microbially generated lipids become part of the skin lipid landscape, including short-chain fatty acids and cell envelope lipids, and contribute to maintaining homeostasis or, in some cases, influence disease processes such as acne and atopic dermatitis. Despite increased recognition of their importance, the diversity, origins, and bioactivities of microbially derived lipids on skin remain underexplored. Here, we highlight recent advances in understanding how cutaneous microbes shape and are shaped by the skin lipid landscape, emphasizing the potential of microbial lipids as mediators of skin health, disease, and novel therapeutic strategies.}, }
@article {pmid42267833, year = {2026}, author = {Hauza, E and Mutai, IJ and Necel, A and Kamya, D and Śliwka, P and Dusza, I and Węgrzyn, A and Skaradzińska, A}, title = {Bacteriophages in the treatment of cutaneous infections and skin disorders: therapeutic advances and future directions.}, journal = {Clinical microbiology reviews}, volume = {}, number = {}, pages = {e0004826}, doi = {10.1128/cmr.00048-26}, pmid = {42267833}, issn = {1098-6618}, abstract = {SUMMARYSkin and soft tissue infections represent a major clinical challenge. This is particularly true given the rise in antimicrobial resistance, the increasing prevalence of chronic wounds, and the growing number of immunocompromised patients. Conventional antibiotic therapies are frequently compromised by multidrug-resistant pathogens, biofilm formation, and disruption of the skin microbiome, underscoring the urgent need for alternative or adjunctive antibacterial strategies. Bacteriophages, viruses that specifically infect and lyse bacteria, have re-emerged as promising therapeutic agents due to their high specificity, activity against antibiotic-resistant strains, and capacity to target biofilm-associated infections. This review provides a comprehensive overview of current advances in bacteriophage-based approaches for the treatment of cutaneous infections and skin disorders. We discuss the biological principles of phage therapy, its advantages and limitations, and the regulatory and manufacturing challenges associated with clinical translation. Particular emphasis is placed on topical and biomaterial-based phage delivery platforms, including hydrogels, nanocarriers, and adhesive wound dressings, designed to enhance phage stability, local bioavailability, and therapeutic efficacy. Furthermore, we summarize experimental and clinical evidence supporting the use of bacteriophages against the most clinically relevant skin pathogens. By integrating data from in vitro studies, animal models, clinical trials, and compassionate-use cases, this review highlights both the therapeutic potential and current limitations of phage-based interventions in dermatology. Collectively, the available evidence supports the use of bacteriophages as a viable component of future precision antimicrobial therapies for skin infections, while emphasizing the need for well-designed clinical trials, standardized production protocols, and optimized delivery systems to enable broader clinical adoption.}, }
@article {pmid42267859, year = {2026}, author = {Shittu, OE and Enagbonma, BJ and Babalola, OO}, title = {Functional Metagenomics Insights Into the Allium ampeloprasum Rhizosphere Microbiome Under Different Fertilization Regimes.}, journal = {MicrobiologyOpen}, volume = {15}, number = {3}, pages = {e70307}, doi = {10.1002/mbo3.70307}, pmid = {42267859}, issn = {2045-8827}, support = {//International Centre for Genetic Engineering and Biotechnology (ICGEB) through Grant CRP/ZAF22-03 awarded to OOB/ ; }, abstract = {Fertilization practices shape the taxonomy, functional composition, and metabolic functions of the microbiome within the rhizosphere. Nonetheless, the impacts of various fertilization approaches on the functional composition of Allium ampeloprasum rhizosphere microbiomes remain underexplored. This study investigated how biofertilizers and chemical fertilizers impact the microbial functional categories of the A. ampeloprasum rhizosphere, hypothesizing that fertilization systems influence the metabolic profile. The genomic DNA was successfully extracted from the collected soil samples and processed via shotgun metagenomics sequencing. The application of biofertilizers enhanced the rhizosphere microbiome, revealing similar microbial orders across all plots, although plot G2 was uniquely enriched with those belonging to phyla Bacteroidota, Proteobacteria, actinobacteria, Myxococcota, and Verrucomicrobiota. Biofertilizers promoted a broader range of microbial functions, primarily at EggNOG level 1. Notably, the α diversity significantly differed (p < 0.05) among the soil samples. The functional diversity was linked to the soil physicochemical attributes, particularly the carbon and moisture contents, as illustrated by the RDA. Biofertilizer increases microbial diversity, underscoring the need to understand the rhizosphere microbiome to advance sustainable agricultural methods.}, }
@article {pmid42267869, year = {2026}, author = {Wojakowicz, K and Pielech, AK and Kowalińska, JE and Stypka, R and Rabczyński, M}, title = {Gut microbiome in type 2 diabetes mellitus: A literature review.}, journal = {Advances in clinical and experimental medicine : official organ Wroclaw Medical University}, volume = {}, number = {}, pages = {}, doi = {10.17219/acem/218917}, pmid = {42267869}, issn = {1899-5276}, abstract = {Type 2 diabetes mellitus (T2DM) is a complex metabolic disorder influenced by genetic, environmental, and lifestyle factors. Emerging evidence highlights the crucial role of the gut microbiota (GM) in the pathophysiology of T2DM, with alterations in microbial diversity and composition contributing to insulin resistance, systemic inflammation, and metabolic dysregulation. This review explores the current literature on the role of the GM, its metabolites, including short-chain fatty acids (SCFAs), bile acids (BAs), and branched-chain amino acids (BCAAs), as well as the impact of diet and body mass index (BMI) on the progression of T2DM. We examine how dietary patterns, including fiber intake, fat composition, and the use of prebiotics and probiotics, modulate the GM. Furthermore, we analyze evidence regarding the influence of the microbiome on host metabolism, gut permeability, and the pathophysiology of T2DM. Understanding the dynamic interactions among the GM, microbial metabolites, diet, and BMI may provide promising avenues for the development of personalized therapeutic strategies targeting microbiome-mediated mechanisms in the prevention and management of T2DM. Such approaches may facilitate more effective patient-centered interventions.}, }
@article {pmid42268644, year = {2026}, author = {Lieberman, OJ and Nittala, S and Rojas-Valencia, L and Baranzini, SE and Singhal, NS and Hemphill, JC and Amorim, E and Ferguson, AR and Hinson, HE}, title = {Circulating Short-Chain Fatty Acid Profile Predicts Functional Outcome After Moderate-to-Severe Traumatic Brain Injury.}, journal = {Critical care explorations}, volume = {8}, number = {6}, pages = {e1433}, doi = {10.1097/CCE.0000000000001433}, pmid = {42268644}, issn = {2639-8028}, support = {5K23NS110828-05/NS/NINDS NIH HHS/United States ; }, abstract = {OBJECTIVES: Short-chain fatty acids (SCFAs) are immunometabolites produced by the gut microbiome. In animal models, SCFAs affect traumatic brain injury (TBI) severity by modulating the immune response and serving as an energy source. The goal of this study was to assess whether SCFAs are associated with functional outcome in adult patients with moderate-to-severe TBI (msTBI).<br><br>DESIGN: Prospective cohort study.<br><br>SETTING: Urban Trauma Center.<br><br>PATIENTS: Adults (age &#x2265; 15 yr) who had TBI with Glasgow Coma Scale 3-12, intracranial hemorrhage on head CT scan, and at least one reactive pupil. Blood samples had to be collected within 3 hours of trauma.<br><br>INTERVENTIONS: None.<br><br>MEASUREMENTS AND MAIN RESULTS: Univariate and multivariate analyses demonstrated that plasma SCFAs were associated with better functional outcomes at discharge and 6 months, an association driven primarily by differences in plasma acetate and propionate. K-means clustering of acetate and propionate levels identified two patient clusters with distinct discharge and 6-month functional outcomes but similar clinical, biomarker, and radiographic injury severity. Cluster 1 (n = 47) had higher SCFA levels compared with cluster 2 (n = 76) and cluster 1 had more favorable outcomes at discharge (Glasgow Outcome Scale 4-5: 83% vs. 55%; p = 0.003) and 6 months (Extended Glasgow Outcome Scale 4-8: 78% vs. 45%; p = 0.005). Multivariable logistic regression adjusting for the International Mission for Prognosis and Analysis of Clinical Trials in TBI (IMPACT)lab model identified an independent association between the SCFA cluster and functional outcome at discharge (p = 0.001) and 6 months (p = 0.03). Adding the SCFA cluster to the IMPACTlab model improved the area under the receiver operating characteristic curve for the prediction model for a favorable outcome.<br><br>CONCLUSIONS: Our study suggests that SCFA levels are associated with functional outcome after msTBI. Future studies will focus on identifying mechanisms through which SCFAs may improve msTBI outcomes and what drives interpatient variation in their levels, which could position SCFAs as prognostic biomarkers and therapeutic targets in TBI.}, }
@article {pmid42268676, year = {2026}, author = {Viniotis, AF and Jameson, GS and Wertheim, BC and Roe, DJ and Lee, K and Tsai, FY and Gordon, MS and Sharma, S and Guarnieri, CM and Snyder, CE and Thosani, AJ and Amini, A and Sckolnik, SE and Garrick, JM and Korn, RL and Rahmanuddin, S and Evans, RM and Downes, M and Truitt, M and Von Hoff, DD and Borazanci, EH}, title = {A phase II clinical trial of albumin-bound paclitaxel, cisplatin, gemcitabine (NABPLAGEM) and paricalcitol as neoadjuvant therapy in pancreatic cancer.}, journal = {The oncologist}, volume = {}, number = {}, pages = {}, doi = {10.1093/oncolo/oyag232}, pmid = {42268676}, issn = {1549-490X}, abstract = {BACKGROUND: For patients with untreated pancreatic ductal adenocarcinoma (PDAC), chemotherapy before surgery ("neoadjuvant therapy") has shown benefit in reducing recurrence and prolonging survival. Targeting the vitamin D receptor (VDR) with analogs such as paricalcitol may improve chemotherapy effectiveness. This study evaluated the efficacy and safety of neoadjuvant albumin-bound paclitaxel (nab-paclitaxel) plus cisplatin plus gemcitabine (NABPLAGEM) plus paricalcitol (NCT03138720).<br><br>METHODS: Participants were &#x2265;18 years, had stage I-III PDAC without prior chemotherapy or radiation, Karnofsky Performance Status &#x2265;70, and elevated CA 19-9. Study treatment included nab-paclitaxel (125&#x2009;mg/m2), cisplatin (25&#x2009;mg/m2), gemcitabine (1000&#x2009;mg/m2), and paricalcitol (25&#x2009;mcg) on days 1 and 8 of a 21-day cycle for up to six months. The primary outcome was CA 19-9 normalization. Secondary outcomes included margin-negative resection (R0), pathologic complete response (pCR), radiologic response, safety, and survival. Microbiome was analyzed as an exploratory outcome.<br><br>RESULTS: Thirty-two participants were enrolled with median age 69.4 years, 56.2% male, and 93.8% white. Patients had resectable (cohort A, n&#x2009;=&#x2009;10) and borderline resectable/locally advanced (cohort B, n&#x2009;=&#x2009;22) tumors. CA 19-9 normalization occurred in 14 patients (43.8%). Two patients (6.2%) achieved pCR, and 19 (59.4%) achieved R0. Complete or partial radiologic response occurred in 39.3% of patients. Adverse events included grade 3-4 anemia (43.8%) and thrombocytopenia (59.4%). Median (95% CI) overall survival was 43.2 (7.5-upper bound not achieved) and 18.4 (10.9-41.2) months for cohorts A and B, respectively.<br><br>CONCLUSION: Neoadjuvant NABPLAGEM plus paricalcitol demonstrated a high CA 19-9 normalization rate and was fairly well tolerated.}, }
@article {pmid42268809, year = {2026}, author = {Ruschman, GL and Bittor, JA and Charnock-Jones, DS and Day-Walsh, PE}, title = {Toward Microbiome-Informed Strategies for Predicting and Preventing Pregnancy Complications.}, journal = {Reproduction &amp; fertility}, volume = {}, number = {}, pages = {}, doi = {10.1530/RAF-26-0009}, pmid = {42268809}, issn = {2633-8386}, abstract = {ABSTRACT: Despite the prevalence of pregnancy complications, including miscarriage, stillbirth, preeclampsia (PE), fetal growth restriction (FGR), and preterm birth (PTB), current predictive tools remain limited. This underscores an urgent need for novel molecular biomarkers and mechanistic insights. The microbiome regulates host physiology, and its disruption correlates with adverse pregnancy outcomes such as PE, PTB, and gestational diabetes mellitus (GDM), and thus holds promise for predictive insights and therapeutic interventions. However, these associations are largely correlative, based on taxonomic rather than protein or metabolite-based functional changes. Additionally, they are often derived from cross-sectional studies, and the underlying mechanisms remain poorly understood. Given the evidence-based view of a sterile intra-uterine environment, understanding the factors that mediate host-microbial interactions is crucial for improving pregnancy outcomes. Maternal immune and hormonal changes can influence the composition and functional capacity of the microbiome, while the microbiome in turn, modulate immune, neuroendocrine responses, nutrient bioavailability and metabolic processes, impacting placental development and pregnancy physiology. We explore direct and indirect mediators of host-microbiome interactions and discuss how these may be targeted to improve pregnancy outcomes. We briefly consider the potential influence of the paternal microbiome and maternal preconception microbial states on pregnancy physiology and outcomes. Finally, we critically evaluate existing methodologies and databases for studying microbial variation in pregnancy-related disorders and propose strategies to better harness microbiome-based research for clinical application. By integrating current evidence and identifying key knowledge gaps, this review aims to highlight microbiome-informed strategies for improving pregnancy outcomes and lifelong health.<br><br>LAY SUMMARY: Understanding How Microbes Influence Pregnancy Outcomes Pregnancy complications such as miscarriage, stillbirth, preeclampsia (PE), fetal growth restriction (FGR), and preterm birth (PTB) are common, yet we still lack reliable tools to predict who is at risk. This makes it essential to identify new biological markers and better understand the underlying mechanisms. One promising area is the microbiome; the community of microorganisms that live in and on our bodies including bacteria, viruses and fungi. The microbiome plays a major role in regulating health, and changes in its composition have been linked to pregnancy disorders including PE, PTB, and gestational diabetes (GDM). However, most of what we know comes from studies that only identify which microbes are present, rather than what these microbes are doing. Many studies are also cross-sectional, capturing only a single time point, which limits our ability to understand cause and effect. Because the uterus is generally considered a sterile environment, the key question is how the maternal body and microbiome communicate. During pregnancy, the immune system and hormone levels change dramatically, and these shifts can alter the composition and function of the microbiome. In turn, the microbiome can influence maternal immunity, hormone signalling, nutrient availability, and metabolism. These interactions may shape how the placenta develops and how the pregnancy progresses. In this review, we examine how the body and the microbiome interact both directly and indirectly, and how these pathways might be targeted to improve pregnancy outcomes. We also touch on the possible influence of the paternal microbiome and the mother's pre-conception microbiome on fertility, early development, and long-term pregnancy health.}, }
@article {pmid42268876, year = {2026}, author = {Fatima, Z and Surette, MD and Marttala, S and Leto, D and Jayaratne, P and Smaill, F and Smieja, M and Hasan, MR}, title = {Microbiome analysis of bronchoalveolar lavage (BAL) specimens from immunocompromised patients with pneumonia compared to those from healthy volunteers.}, journal = {PloS one}, volume = {21}, number = {6}, pages = {e0351562}, doi = {10.1371/journal.pone.0351562}, pmid = {42268876}, issn = {1932-6203}, abstract = {BACKGROUND: Metagenomic sequencing of bronchoalveolar lavage (BAL) specimens is increasingly being applied for the diagnosis of lower respiratory tract infections, offering agnostic pathogen detection and a faster turnaround time. While metagenomic sequencing of BAL specimens can reveal a wide range of organisms, their clinical relevance is often unclear because of the challenge of distinguishing true pathogens from background taxa. This study compared the BAL microbiomes of immunocompromised patients with pneumonia to those of healthy volunteers, with the aim of assisting clinical interpretation of metagenomics-based approaches for diagnosing pneumonia in this patient population.<br><br>METHODS: BAL specimens from healthy control volunteers (n&#x2009;=&#x2009;20) were collected during a COVID-19 vaccine trial, while residual BAL specimens from immunocompromised patients (n&#x2009;=&#x2009;52) were obtained from the Hamilton Regional Laboratory Medicine Program (HRLMP) after standard culture and PCR testing. 16S rRNA gene amplicon sequencing was performed using Nanopore technology. Reads were classified using Minimap2 in EPI2ME, and microbiome analyses were conducted using the vegan and MaAsLin2 packages in RStudio (v2026.1.1.403).<br><br>RESULTS: Immunocompromised patients showed significantly lower bacterial read counts and reduced alpha diversity (p&#x2009;<&#x2009;0.0001; Wilcoxon Rank-Sum test), along with higher inter-sample heterogeneity. In contrast, BAL samples from healthy controls exhibited a more homogeneous microbial profile dominated by anaerobic Gram-negative genera, including Prevotella, Veillonella, Selenomonas, and Fusobacterium. Beta diversity analyses using Bray-Curtis and Jaccard distance metrics demonstrated significant compositional separation between cohorts (PERMANOVA p&#x2009;=&#x2009;0.001), with tight clustering of healthy controls and marked dispersion among immunocompromised samples. Differential abundance analysis identified 96 significantly altered species (q&#x2009;<&#x2009;0.05), with immunocompromised patients showing depletion of anaerobic commensals and enrichment of clinically relevant pathogens, including Stenotrophomonas maltophilia, Enterococcus spp., Mycoplasma spp., and Nocardia spp.<br><br>CONCLUSION: Immunocompromised patients demonstrated a markedly disrupted and heterogeneous BAL microbiome, characterized by a loss of anaerobic commensals and an enrichment of potentially pathogenic taxa. This study provides a characterization of the dysbiotic state in immunocompromised pneumonia, offering a baseline reference for future longitudinal studies and clinical trials aimed at improving the interpretation of metagenomic findings in this patient population.}, }
@article {pmid42269302, year = {2026}, author = {Zheng, M and Lun, W and Wang, P and Ren, C and He, Y and Huo, M}, title = {The correlation between vaginal microbiome dysbiosis and recurrent spontaneous abortion.}, journal = {Journal of reproductive immunology}, volume = {176}, number = {}, pages = {104918}, doi = {10.1016/j.jri.2026.104918}, pmid = {42269302}, issn = {1872-7603}, abstract = {In recent years, the role of the vaginal microbiota in pregnancy maintenance has garnered increasing attention. Extensive research indicates that vaginal dysbiosis is closely associated with various adverse pregnancy outcomes, including ectopic pregnancy, miscarriage, preterm birth, and premature rupture of membranes. Recurrent spontaneous abortion (RSA) affects approximately 1-5% of women of childbearing age and has a complex etiology, with infection implicated in about 4% of cases. This systematic review examines the compositional characteristics of the vaginal microbiota, its dynamic changes during pregnancy, and the underlying mechanisms linking it to RSA. It focuses on the protective role of lactobacilli, ascending pathogen infection, and local immune regulation, aiming to provide a novel theoretical foundation for the prevention, risk prediction, and personalized treatment of RSA.}, }
@article {pmid42269309, year = {2026}, author = {Barbudo-Lunar, M and Arjona, GL and Trombini, C and Pérez-González, L and Chica, AF and Martín, M&#xc1; and Blasco, J and Michán, C and Siles, J&#xc1; and Alhama, J}, title = {A multidisciplinary approach to risk assessment enables the identification of deteriorated sections within a major waterway: The Guadalquivir River as a case study.}, journal = {Journal of contaminant hydrology}, volume = {282}, number = {}, pages = {105019}, doi = {10.1016/j.jconhyd.2026.105019}, pmid = {42269309}, issn = {1873-6009}, abstract = {To date, few studies have assessed the quality of the Guadalquivir River, the main hydrographic basin of the Southern Iberian Peninsula. Here, we present the first comprehensive study to integrate physico-chemical characterisation, bacterial community assessment, and quality indices along its entire course. The Water Quality Index showed a gradual, progressive deterioration in water quality downstream, with 10% of the stations showing fair quality, signs of eutrophication (∼400 mg/m[3] chlorophyll), and microbiological contamination (Escherichia coli, up to 3000 CFU/100 mL). The lower-middle section showed significant changes in the levels of organic carbon, metals, suspended solids and turbidity, as well as high nitrate (up to 19 mg L[-1]) and ammonia (up to 1.4 mg L[-1]) levels influenced by agricultural activities. Water quality may also be negatively influenced by the impact of tributaries. Since microorganisms are ubiquitous and play indispensable environmental roles, changes in water microbiome composition, structure and functionality were evaluated. Metabarcoding analysis revealed significant alterations, particularly in the upper reaches, despite the prevalence of parameters associated with good quality. In this section, a considerable decrease in α-diversity, very high values of microgAMBI ecological index, and potential functional changes revealed signs of environmental degradation. In addition, the predicted high prevalence of "ABC transporters" and the "two-component system" suggests a response to adverse conditions, driven by a small number of tolerant opportunistic microorganisms, notably the family Comamonadaceae. This area, characterised by extensive olive monoculture, has traditionally been exposed to contamination from biocides. In practical terms, this research confirmed that although widely recognised indices may report high overall water quality, complementary microbiome analyses might help reveal undetected hazards affecting the whole ecosystem. This multidisciplinary study could be used as a model for designing risk maps that identify "hotspots" for action to improve the management of essential water resources.}, }
@article {pmid42269396, year = {2026}, author = {Stylianakis, D and Bertaglia, V and Sangiolo, D and Podda, M and Saba, G and Stylianakis, I and Denaro, N and Pisanu, A and Agelaki, S and Scartozzi, M and Novello, S and Solinas, C}, title = {The antibiotic-immunotherapy interaction in NSCLC: a systematic review and meta-analysis of 54,250 patients across three outcomes.}, journal = {Cancer treatment reviews}, volume = {148}, number = {}, pages = {103162}, doi = {10.1016/j.ctrv.2026.103162}, pmid = {42269396}, issn = {1532-1967}, abstract = {BACKGROUND: Approximately 20-28% of NSCLC patients receiving ICIs also receive systemic antibiotics. Whether this reflects a true microbiome-mediated pharmacological interaction or confounding by indication remains unresolved.<br><br>METHODS: We searched PubMed, Scopus, and CENTRAL (2013-2025) for NSCLC studies reporting OS, PFS, or ORR by antibiotic exposure. Random-effects meta-analysis was performed, with mostly non-pre-specified subgroup analyses by study design, ICI class, antibiotic timing, and line-of-therapy, plus leave-one-out, exposure-window, and adjustment-status sensitivity analyses and meta-regression of heterogeneity sources. Risk of bias was assessed with ROBINS-I and ROB 2, and certainty of evidence was rated with GRADE.<br><br>RESULTS: Forty-one studies including 54,250 patients were analyzed, 27.8% of whom were antibiotic-exposed. Antibiotic exposure was associated with worse OS (HR 1.47, 95% CI 1.30-1.66; p&#xa0;<&#xa0;0.00001; I[2]&#xa0;=&#xa0;79%) and PFS (HR 1.32, 95% CI 1.18-1.47; p&#xa0;<&#xa0;0.00001; I[2]&#xa0;=&#xa0;65%), but not ORR (OR 0.95, 95% CI 0.67-1.35; p&#xa0;=&#xa0;0.77; I[2]&#xa0;=&#xa0;88%). RCT post-hoc estimates were non-significant (OS HR 1.20, p&#xa0;=&#xa0;0.07; PFS HR 1.09, p&#xa0;=&#xa0;0.41; I[2]&#xa0;=&#xa0;0%), whereas observational estimates were larger and driven by less-adjusted cohorts. Subgroup, sensitivity, and meta-regression analyses indicated that heterogeneity was explained mainly by study design and line of therapy. In chemo-free ICI analyses, only mixed ICI regimens remained significant for OS and PFS. GRADE certainty was very low for observational outcomes and low for RCT-based estimates.<br><br>CONCLUSIONS: The strongest available evidence does not support a clear antibiotic-related reduction in ICI efficacy in NSCLC. The observational signal is more compatible with confounding and exposure heterogeneity than with a uniform pharmacological interaction, although a context-specific biological effect cannot be excluded.}, }
@article {pmid42269588, year = {2026}, author = {Massey, WJ and Brown, JM}, title = {The expanding role of the microbiome in GLP-1 pharmacology.}, journal = {Cell host &amp; microbe}, volume = {34}, number = {6}, pages = {989-990}, doi = {10.1016/j.chom.2026.05.006}, pmid = {42269588}, issn = {1934-6069}, abstract = {There is now overwhelming evidence that glucagon-like peptide 1 (GLP-1) receptor agonists have many health benefits. In this issue of Cell Host &amp; Microbe, Bian et al. find that the gut microbiome is implicated in the psychological effects of these drugs. These findings have broad implications for drug-microbe-host interactions.}, }
@article {pmid42269618, year = {2026}, author = {Eriksson, D and Schiller, J and Schickele, A and Priest, T and Mankowski, A and Faucher, E and Ustick, LJ and Kuhn, M and Miravet-Verde, S and Ruscheweyh, HJ and Clerc, C and Gruber, N and Sunagawa, S and Bork, P and Vogt, M}, title = {Variations in the latitudinal diversity gradients of the ocean microbiome.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.05.016}, pmid = {42269618}, issn = {1934-6069}, abstract = {Latitudinal diversity gradients (LDGs), which typically decline from the equator to the poles, are a pervasive macroecological pattern. However, their generality and drivers in the ocean microbiome remain widely unresolved. We integrated global-scale metagenomic data with habitat modeling to study marine microbial LDGs across seasons and depths. Surface mixed-layer microbiomes exhibit diversity peaks at (sub)tropical latitudes and a poleward decline, whereas mesopelagic communities (200-1,000 m) show no latitudinal diversity structuring. Taxonomic resolution reveals that the mixed-layer LDG is underpinned by Alphaproteobacteria and Cyanobacteriia, while other taxa exhibit distinct or contrasting LDGs. Diversity structuring also varies by seasons and regions and is governed by temperature and nutrient availability. Together, these findings highlight that, within the ocean microbiome, LDGs are not universal but reflect lineage-specific ecological strategies and responses to environmental gradients. Our study provides fundamental insights into the structuring of ocean microbiome diversity and lays the foundation for predicting responses to environmental change.}, }
@article {pmid41975402, year = {2026}, author = {Zhu, Y and Xiao, C and Zhang, Z and Zhou, Y and Xu, L and Zhang, L and Qu, K and Yu, B and Yan, H}, title = {Association between oral microbiota and suicidal ideation among vocational high school students in China.}, journal = {BMC oral health}, volume = {26}, number = {1}, pages = {}, pmid = {41975402}, issn = {1472-6831}, support = {82204073//the National Natural Science Foundation of China/ ; 22YJC840037//the Ministry of Education of Humanities and Social Science project/ ; WY22B09//the Wuhan Health Science Research Funding/ ; }, abstract = {OBJECTIVE: To investigate the association between oral microbiome characteristics and suicidal ideation (SI) in vocational high school students.<br><br>METHODS: The oral microbiota composition and abundance of the SI group (N&#x2009;=&#x2009;45) and the matched healthy control group (N&#x2009;=&#x2009;45) were analyzed using 16S rRNA sequencing. Demographic variables and SI assessments (measured by the Columbia Suicide Severity Rating Scale) were obtained. Bioinformatics analyses (e.g., alpha and beta diversity indices, PCoA, NMDS, and LEfSe) were performed to compare oral microbiota characteristics between the SI group and the control group.<br><br>RESULTS: The vocational high school students with SI exhibited significantly lower alpha diversity indices in oral microbiota compared to the control group, including PD whole tree (20.56 [19.45, 21.38] vs. 21.37 [20.17, 23.27]), Chao1 (621.82&#x2009;&#xb1;&#x2009;66.99 vs. 672.24&#x2009;&#xb1;&#x2009;68.52), and observed species (426.91&#x2009;&#xb1;&#x2009;54.59 vs. 466.42&#x2009;&#xb1;&#x2009;69.75) (all p values&#x2009;<&#x2009;0.01). Beta diversity analysis revealed distinct microbial composition between groups (p&#x2009;<&#x2009;0.05), with greater homogeneity in the SI group. LEfSe analysis identified increased abundances of Enterobacter, Escherichia_Shigella, and Parabacteroides in the SI group, while controls showed enrichment of Rikenellaceae and Alistipes.<br><br>CONCLUSION: A decrease in oral microbiota diversity and alterations in the abundance of specific bacterial genera (Enterobacter, Escherichia_Shigella, and Parabacteroides) are associated with SI among vocational high school students. Longitudinal studies are needed to elucidate the underlying mechanisms and potential health impacts.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12903-026-08317-3.}, }
@article {pmid42254517, year = {2026}, author = {Liu, S and Luo, X and Zhou, J and Wang, L and Li, R and Luo, Z and Li, N and Xiao, S and Zhang, P}, title = {A comparative study of the gut microbiome and fecal metabolome in hypertensive patients from middle-temperate and tropical cities of China: Daqing and Haikou.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1801806}, pmid = {42254517}, issn = {1664-302X}, abstract = {BACKGROUND: Geographic variations in climate and lifestyle may be associated with hypertension (HTN) through alterations in the gut microbiota and its metabolites. This study aimed to comparatively analyze the gut microbiome and fecal metabolome of hypertensive patients from two Chinese cities characterized by distinct climatic conditions: Daqing (middle-temperate climate) and Haikou (tropical climate). The objective was to identify gut microbial and metabolic characteristics associated with geographic differences and to provide insights into HTN prevention and management.<br><br>METHODS: A cross-sectional study was conducted between May and December 2024, involving hypertensive patients from Daqing and Haikou. Fecal samples were collected from 28 hypertensive patients in Daqing (DQ group) and 32 in Haikou (HK group), and analyzed using shotgun metagenomic sequencing and untargeted metabolomics.<br><br>RESULTS: Differences in microbial composition and metabolite profiles were observed between the two groups. Using ALDEx2 analysis at the genus level, 34 genera were identified as differentially abundant between the DQ and HK groups. After adjusting for potential confounding variables, including age, body mass index, smoking, and drinking status, 6 genera remained significantly associated with geographic grouping. A logistic regression model based on these genera achieved an area under the curve (AUC) of 0.8069, with Pseudescherichia showing the highest individual discriminatory performance (AUC&#x202f;=&#x202f;0.7925). Functional analysis suggested that pathways such as xylene degradation and biofilm formation were relatively reduced in the DQ group. Metabolomic analysis identified 38 differentially abundant metabolites, including 15-hydroxyeicosatetraenoic acid (15-HETE), 7&#x3b1;,25-dihydroxycholesterol, the putative metabolite (3-hydroxypentadecanoyl) lysine, and ginsenoside Rg3. Dysregulated pathways were mainly involved in glycerophospholipid metabolism, ABC transporters, and choline metabolism. Correlation analysis revealed potential associations between differential microbes and metabolites.<br><br>CONCLUSION: Distinct gut microbiome and metabolome profiles were observed between hypertensive patients from the two geographic regions. These findings suggest potential associations between environmental factors and host-microbiome-metabolite interactions.}, }
@article {pmid42254525, year = {2026}, author = {Chen, J and Zhou, Q and Cao, X and Jin, S and Wu, Y and Ren, T and Xu, C and Chen, H and Zhang, H and Zhang, Y and Liu, J}, title = {The outcome of Infliximab induction in patients with severe ulcerative colitis may be related to intestinal microbiota.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1779143}, pmid = {42254525}, issn = {1664-302X}, abstract = {BACKGROUND AND OBJECTIVE: Although infliximab (IFX) is endorsed for induction therapy in severe ulcerative colitis (SUC), its therapeutic response remains heterogeneous. We conducted a comprehensive analysis of fecal and mucosal microbiota, coupled with targeted metabolomics, to delineate microbial and metabolic signatures predictive of IFX induction efficacy and to explore mechanistic pathways underlying differential treatment responses.<br><br>METHODS: This study was a prospective cohort study (clinical study registration number: ChiCTR2300071816). It enrolled adult patients aged &#x2265; 18 years who were first diagnosed with SUC at the First Affiliated Hospital of Nanjing Medical University and Northern Jiangsu People's Hospital between February 2022 and December 2023. None of these patients had received any medication for UC, including antibiotics. Clinical data, fecal samples, and rectal mucosal samples were collected for analysis. High-throughput sequencing of the 16S rRNA gene and non-targeted metabolomics analysis were performed on both fecal and rectal mucosal samples. All patients underwent IFX (5 mg/kg) induced remission therapy at weeks 0, 2, and 6. Based on their clinical response at week 14, they were categorized into two groups: response and unresponse. Significant differences in bacterial composition between the two groups were identified by screening fecal and mucosal samples. The gut microbiota of feces and intestinal mucosa were combined with clinical data to create four prediction models and conduct comparisons. Furthermore, different metabolites from fecal and mucosal samples of the two groups were screened and compared with KEGG and PubChem databases to identify metabolic pathways associated with the efficacy of IFX-induced therapy.<br><br>RESULTS: Compared with non-responders, IFX responders harbor distinct gut microbiota. Clinical indices alone poorly forecast induction response (AUC 0.6429). Augmenting clinical variables with fecal or mucosal microbiota improves prediction to AUC 0.795 and 0.900, respectively; combining both compartments further elevates performance to AUC 0.964, indicating that integrated microbiome profiling is essential for optimal IFX response prediction. IFX responders and non-responders differ metabolically, with more discriminatory features in mucosa than feces. The most enriched differential pathways in feces included nicotinate and nicotinamide metabolism, butyrate metabolism, biosynthesis of valine, leucine, and isoleucine, pantothenate and coenzyme A biosynthesis, histidine metabolism, and alanine, aspartate, and glutamate metabolism. In mucosa, the most enriched differential pathways included alanine, aspartate, and glutamate metabolism, sphingolipid metabolism, ascorbate and aldarate metabolism, tryptophan metabolism, and D-glutamine and D-glutamate metabolism. The common pathway enriched in both feces and mucosa was alanine, aspartate, and glutamate metabolism.<br><br>CONCLUSION: The intestinal microbiota may be a predictive factor for IFX induction outcome in patients with SUC. The metabolic pathway of alanine, aspartate, and glutamate may be associated with the 14-week clinical response to IFX treatment in SUC.}, }
@article {pmid42254837, year = {2026}, author = {Schmelz, P and Eckensperger, S and Osvatic, J and Séneca, J and Alzubaidy, H and Petersen, JM}, title = {Host depletion kits improve microbiome analyses in environmental samples: seagrass as a test case.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag082}, pmid = {42254837}, issn = {2730-6151}, abstract = {All plants and animals associate with specific communities of symbiotic microorganisms. Characterizing the diversity and functions of these communities is essential for understanding their roles in host health; however, such efforts are often hindered by the dominance of host-derived material in, e.g. DNA extractions. Although various commercial host DNA depletion kits have been developed to overcome these challenges, they have not yet been systematically tested on environmental samples. We used Zostera marina, globally the most widespread seagrass species, as a test case to assess the effectiveness of three different commercially available host DNA depletion kits: QIAamp DNA Microbiome Kit, HostZero Microbial Enrichment Kit, and NEBNext Microbiome DNA Enrichment Kit, when compared to the widely used DNeasy PowerSoil Pro Kit. All three host depletion kits substantially reduced the relative proportion of host DNA, as assessed by 16S rRNA gene amplicon sequencing, and enriched previously identified seagrass-associated bacteria. Furthermore, in metagenomes, only samples processed with host depletion methods allowed for the assembly of metagenome-assembled genomes with high completeness and low contamination. Metagenomic analysis further enabled the recovery of seagrass root core microbiome members, including previously undetected members of the family Sedimenticolaceae, highlighting the value of these techniques for uncovering novel host-associated microbial diversity in environmental samples such as marine plants.}, }
@article {pmid42254838, year = {2026}, author = {Kobayashi, R and Shiba, T and Nagai, T and Komatsu, K and Matsumura, S and Watanabe, T and Nemoto, T and Takada, K and Takeuchi, Y and Iwata, T}, title = {Metatranscriptomic insights into microbial network modulation and pathogen dynamics underlying healing outcomes in non-surgical periodontal treatment.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag092}, pmid = {42254838}, issn = {2730-6151}, abstract = {Gingivitis and periodontitis are caused by oral microbiome dysbiosis. Post-treatment alterations in bacterial community structure are uncharacterized in situ, including how these alterations may differ between resolved and unresolved disease states. Understanding these treatment-induced microbial shifts and identifying prognostic markers in situ associated with favorable or unfavorable outcomes are crucial for developing diagnostic tools and refining therapeutic strategies. Therefore, we performed metatranscriptomic analysis on subgingival plaque samples from the anterior teeth of individuals, including healthy, gingivitis, and periodontitis sites, before and after non-surgical treatment in 28 patients. We revealed a new bacteriological characteristic of periodontitis, where periodontal pathogens emerge within the bacterial network alongside excessive and skewed associations among bacterial taxa, such as those in the Streptococcus and Actinomyces genera. Furthermore, these imbalances were found improvable through non-surgical treatment. However, even in clinically resolved gingivitis or periodontitis, the bacterial networks did not fully revert to the state observed in healthy sites. This was due to the persistence of periodontal pathogens, absent in the networks at healthy sites. By comparing groups in which periodontitis resolved and those in which it did not, specific bacterial taxa, such as Neisseria elongata and Rothia aeria, were suggested to play a role in the periodontitis healing process, while increases in genes related to glycine degradation and bacterial adhesion, including glycine dehydrogenase β-subunit and cleaved adhesin domain were implicated in inhibiting the healing process. These findings provide insights for the development of treatment strategies targeting specific bacteria and functional genes involved in the resolution of periodontitis.}, }
@article {pmid42254885, year = {2026}, author = {Targino, AJM and da Silva Vilarinho, JLP and Carneiro, VMA and Greggianin, BF and Guimarães, MDCM}, title = {Periodontal Ecosystem and Clinical Implications of the Oral Microbiome: A Narrative Review.}, journal = {International journal of dentistry}, volume = {2026}, number = {}, pages = {1479982}, pmid = {42254885}, issn = {1687-8728}, abstract = {BACKGROUND: Periodontal disease, although widely documented, remains one of the leading causes of tooth loss worldwide. This situation can be attributed to patients' difficulty in following treatment protocols and to an incomplete understanding of the disease's mechanisms, which could be explored to develop new therapies.<br><br>OBJECTIVE: The present study aimed to summarize the main advances in understanding the periodontal microbiome, especially concerning the development of genetic sequencing technologies and metabolite analysis, as well as new treatment methods that have emerged from these innovations.<br><br>METHODS: A narrative literature review was conducted through searches in the PubMed, Scopus, Web of Science, and SciELO databases, prioritizing publications from the past 15 years while also including classic and foundational studies relevant to the theoretical framework.<br><br>CONCLUSIONS: Periodontal microbiome results from the synergistic interaction among different microorganisms, rather than just the sum of their individual metabolites. This synergy can create structural microarrangements that resist biofilm disruption, such as fungal barriers surrounding Gram-negative bacteria. Innovative treatments-such as host response modulation with resolvins and oral microbiome modulation, particularly using prebiotics derived from plant extracts (nitrate metabolism)-offer promising prospects. However, limitations remain regarding their clinical use and the challenge of managing refractory cases, highlighting the need for further research to support these findings.}, }
@article {pmid42254896, year = {2026}, author = {Vaggi, C and Vötterl, JC and Lerch, F and Yosi, F and Koger, S and Ricci, S and Verhovsek, D and Metzler-Zebeli, BU}, title = {Characterization of fecal bacterial microbiomes according to fecal color, consistency, and sample type in piglets before and after weaning.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1815748}, pmid = {42254896}, issn = {2297-1769}, abstract = {Fecal samples are widely used as a proxy for the large intestinal microbiota; however, phenotypic characteristics (e.g., color and consistency) may be associated with divergent microbial profiles, especially around weaning, when diet and physiological adaptation rapidly alter gut function. The relationship between fecal phenotype, sample type, and piglet gut microbiota under physiological conditions remains poorly understood. This study investigated the bacterial communities in different fecal phenotypes of piglets shortly before and immediately after weaning. The fecal consistency of 192 piglets across two replicate batches was scored daily from day of life (DoL) 28 to 36, and fecal or rectal swab samples were collected at DoL28 and DoL33. The samples were classified by type (feces/swab), color (brown/yellow), and consistency (balls/liquid). DNA was extracted for quantification of total bacterial gene copies and 16S rRNA gene sequencing, and microbial composition was analyzed using Quantitative Insights Into Microbial Ecology 2 (QIIME2), Statistical Analysis System (SAS), and R. Fecal consistency changed markedly over time, shifting from predominantly ball-shaped on DoL28-32 to softer feces thereafter (p < 0.001). Age strongly influenced microbiota structure, with marked increases in relative abundance of Prevotella and Alloprevotella from DoL28 to DoL33, whereas the abundance of Escherichia, Methanobrevibacter, and Fusobacterium declined. Microbial communities differed between sample types, with swabs potentially reflecting mucosa-associated taxa more closely than fecal samples. Shannon and Simpson indices indicated reduced diversity in yellow and liquid feces on DoL28 (p < 0.001). Swabs and yellow liquid feces on DoL28 showed higher relative abundances of Escherichia, Bacteroides, and Fusobacterium, whereas brown ball-shaped feces were enriched in Lachnospiraceae, Prevotella, and Lactobacillus on both sampling days (p < 0.05). Overall, each fecal phenotype exhibited a distinct bacterial signature, and the sample type influenced the composition of the captured community. Monitoring fecal phenotypes alongside selecting appropriate sample types may enhance the interpretation of microbiome data and offer a practical, non-invasive approach to assess gut health during the critical weaning period.}, }
@article {pmid42254901, year = {2026}, author = {Adegbeye, MJ and Sadarman, S and Poonooru, R and Alvarado-Ramírez, ER and Widiawati, Y}, title = {Editorial: Natural compounds/products and livestock productivity: enhancing antioxidant levels, gut health, mitigating greenhouse gas emissions, and disease control, volume II.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1867705}, pmid = {42254901}, issn = {2297-1769}, }
@article {pmid42254910, year = {2026}, author = {Al-Ardhi, SA and Al-Waeli, SK and Osman, MA and Al-Shahari, EA and Siddig, NH and Ahmed, AE and Hazzazi, Y and Sumayli, M and Al-Rasheed, M and Alanazi, IMM}, title = {Modeling of growth performance, physiological response, and intestinal microbiota shift in growing Japanese quail fed olive leaf powder.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1824857}, pmid = {42254910}, issn = {2297-1769}, abstract = {INTRODUCTION: Due to the anti-inflammatory, antioxidant, and antibacterial properties of olive leaf powder (OLP), it may serve as a beneficial feed supplement for birds. This study aimed to evaluate the effect of adding OLP to feed on growth efficiency, carcass traits, blood parameters, antioxidant activity, and cecal microbial load in growing Japanese quail.<br><br>METHODS: Three hundred and seventy-five one-day-old quail chicks were randomly assigned to five experimental groups, each containing five replicates of 15 birds: a control group fed a basal feed and four experimental groups given 3, 4, 5, and 6% OLP per kg of quail diets for the 6 weeks.<br><br>RESULTS: The results showed a significant (P < 0.05) improvement in growth performance, with increased live body weight (LBW) and an insignificantly improved feed conversion ratio in the 6% OLP group. Carcass yield and total edible meat also substantially improved (P < 0.05). Blood parameters showed improved (P < 0.05) protein and lipid levels and increased liver enzyme activity; moreover, the use of the OLP led to a decrease in TC, TG, LDL, and VLDL levels, as well as an increase in HDL. Additionally, the activity of antioxidant enzymes increased (P < 0.001), along with higher levels of GSH and SOD activity. All meat quality attributes, including cooking loss %, water-holding capacity, PH values, and meat color, improved (P < 0.05) with the use of OLP. Furthermore, intestinal microbiota analysis showed a significant improvement in Lactobacillus count and a decrease in pathogenic bacteria (total bacterial count, coliforms, E. coli, and Salmonella). However, the Bacillus count was not significantly affected by OLP supplementation.<br><br>DISCUSSION: The findings of this study demonstrate that OLP is a promising natural feed additive for growing Japanese quail, enhancing growth performance and the gut microbiome, thereby establishing it as a safe and natural growth promoter.}, }
@article {pmid42255244, year = {2026}, author = {Saadatkhah, A and Nicholson, L and Buchholz, TA and Hong, L}, title = {Beyond the tumor: the role of the gut microbiome in triple-negative breast cancer.}, journal = {Frontiers in oncology}, volume = {16}, number = {}, pages = {1832176}, pmid = {42255244}, issn = {2234-943X}, abstract = {The gut microbiome, a metabolically active community of microorganisms in the gastrointestinal tract, regulates host immunity, metabolism, and inflammation. Dysbiosis, or disruption of this ecosystem, has been linked to cancer initiation, progression, and therapy resistance. Triple-negative breast cancer (TNBC) accounts for 10-15% of breast cancers and is managed primarily with chemotherapy and immune checkpoint inhibitors; however, treatment responses remain variable and these patients are at higher risk of cancer recurrence compared to patients with hormone receptor-positive or HER2-positive breast cancer. Emerging evidence suggests that the gut microbial composition and its diversity can influence outcomes and therapeutic efficacy of systemic treatments in TNBC. We review the current epidemiologic, mechanistic, and clinical evidence on how the gut microbiome influences TNBC biology, with particular attention to the tumor immune microenvironment and response to therapy. We highlight protective and pro-tumorigenic microbial signatures, the impact of antibiotics and obesity, and emerging strategies, such as dietary modulation and microbiome-targeted interventions, that may ultimately be used to optimize TNBC management and improve patient outcomes.}, }
@article {pmid42255295, year = {2026}, author = {Ranjan, P and Das, D and Bundela, V and Ramesh, A and Verma, RK and Nargund, R and Manandhar, U and Drijber, R and Upadhyay, RK and Sharma, MP}, title = {Role of rhizosphere specific microbiome in enhancing soybean productivity across contrasting soil and crop management systems.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1830235}, pmid = {42255295}, issn = {1664-462X}, abstract = {Soybeans are a globally significant legume and oilseed crop with a diverse rhizospheric microbiome that can enhance sustainable agriculture by reducing the need for chemical fertilizers. These microbes can potentially impact plant growth and development through symbiotic (rhizobium and mycorrhizae) and non-symbiotic (plant growth-promoting rhizobacteria and fungi) interactions with soybean roots under optimal crop and soil management practices. During the production of soybeans, practices such as excessive use of fertilizers and pesticides, mono-cropping, and intensive tillage are often employed to achieve higher yields. However, these practices can alter the rhizomicrobiome communities and their interactions with soybean crops. Implementing optimal soil and crop management techniques can create a more favorable environment for rhizomicrobial communication with soybean roots, ultimately enhancing nutrient uptake for the soybean plants. In this review, we address how the soil rhizomicrobiome communicates with soybean roots, its role in promoting plant health and yield, and approaches to enhance soil rhizomicrobiome diversity and function through improved crop and soil management practices. Herein we synthesize current literature on soybean-microbe interactions, including both symbiotic and non-symbiotic relationships with an emphasis on how plant-microbe interactions within soybean cropping systems are influenced by agricultural practices such as crop rotation, intercropping, integrated nutrient management, and no-tillage. Greater understanding of the complexity underlying rhizosphere microbiome relationships will enable design of local cropping systems enhancing soybean yield along with improving soil health.}, }
@article {pmid42255425, year = {2026}, author = {Hu, R and Deng, J and Tu, L and Jiang, T and Xu, J}, title = {Integration of tongue image features and tongue coating microbiome for differentiating dampness patterns in MASLD.}, journal = {Frontiers in endocrinology}, volume = {17}, number = {}, pages = {1851610}, pmid = {42255425}, issn = {1664-2392}, abstract = {BACKGROUND: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a prevalent metabolic disorder that can progress to hepatic fibrosis, cirrhosis, and hepatocellular carcinoma. Traditional Chinese medicine (TCM) has therapeutic effects in MASLD. In TCM, dampness patterns predominate in MASLD and are further classified into damp heat (DH) and cold dampness (CD) subtypes based on distinct pathogenic mechanisms. However, the characteristics of the tongue image and tongue coating microbiome across different dampness patterns and their associations with clinical features remain poorly understood.<br><br>MATERIALS AND METHODS: This study enrolled 320 participants, including 214s dampness patterns patients with MASLD, further classified into DH pattern (n = 110) and CD pattern(n = 104), along with 106 healthy controls. Tongue images and tongue coating samples were collected; tongue image segmentation was performed using a customized Tongue-InSPyReNet framework and extract quantitative features, while tongue coating microbiota were profiled using 16S rRNA gene sequencing. To distinguish between patterns, five machine learning models were developed and evaluated based on integrated tongue image features and microbiome data.<br><br>RESULTS: Significant differences in tongue features and microbial composition were observed between groups. The DH pattern was characterized by a red-crimson tongue with yellow coating and enrichment of Prevotella (P < 0.05). In contrast, the CD pattern more frequently exhibited a pale tongue with petechiae and higher abundances of Streptococcus and Rothia (P < 0.05). Integration of tongue image features and tongue coating microbiome effectively distinguished DH and CD patterns, achieving an AUC of 0.871 and an accuracy of 79.1%.<br><br>CONCLUSION: Our study highlights the contributions of tongue image features and the tongue coating microbiome to differentiating two TCM patterns in MASLD, and may provide the rationale for adopting different treatment strategies for different TCM syndromes of MASLD in the future.}, }
@article {pmid42255437, year = {2026}, author = {Shi, S and Song, W and Wu, Z and Cheng, Y and Liu, H and Tian, F and Li, X}, title = {Multi-omics Mendelian randomization integrating metabolism, microbiome and immunity supports a putative gut-immune-pelvic pathway in deep infiltrating endometriosis.}, journal = {Frontiers in endocrinology}, volume = {17}, number = {}, pages = {1827134}, pmid = {42255437}, issn = {1664-2392}, abstract = {BACKGROUND: Deep infiltrating endometriosis (DIE) is a highly fibrotic and deeply invasive subtype of endometriosis that causes severe pelvic pain, infertility and marked impairment of quality of life. Metabolic, microbial and immune disturbances have been reported in women with endometriosis, but whether these systemic perturbations causally contribute to DIE and which lesion-level molecular mediators connect them to pelvic pathology remains unknown.<br><br>METHODS: We performed two-sample Mendelian randomization (MR) to assess the causal effects of circulating metabolites, gut microbiota (GM) traits and immune cell phenotypes on DIE risk using genome-wide association data from FinnGen and large exposure GWAS. Bayesian colocalization was applied to identify protein-coding genes with shared causal variants between exposures and DIE. Colocalized genes were integrated with RNA-sequencing data from GSE141549 (normal endometrium, n = 43; DIE lesions, n = 88) to evaluate differential expression and immune-cell associations inferred by CIBERSORT-like deconvolution. Machine-learning-based feature selection was used to derive a multigene logistic model, and protein expression of feature genes was validated by immunohistochemistry in independent specimens.<br><br>RESULTS: MR revealed putative causal associations between multiple circulating metabolites, GM taxa and immune phenotypes and DIE susceptibility, including risk-increasing bile acid-related and acylcarnitine species, specific bacterial taxa, and monocytic/dendritic-cell traits, and protective lipid species, short-chain-fatty-acid-linked genera and CD45RA[-]CD4[+] T-cell subsets. Colocalization identified 324 protein-coding genes, of which 42 were differentially expressed between DIE and controls and enriched in inflammatory and extracellular matrix remodeling pathways. A five-gene panel-HDC, GADD45B, CDK5, AHNAK and RASGRP2-was prioritized, showed structured correlations with B-cell, NK-cell and CD4[+] memory T-cell subsets, and showed excellent within-cohort discrimination between DIE lesions and normal endometrium (AUC&#xa0;=&#xa0;0.999). Immunohistochemistry confirmed upregulation of HDC, GADD45B, AHNAK and RASGRP2 and downregulation of CDK5 in DIE lesions.<br><br>CONCLUSION: This multi-omics MR framework supports a putative gut-immune-pelvic pathway in DIE and identifies a biologically plausible five-gene tissue-level signature consistent with lesion-associated fibrotic and immune-inflammatory remodeling.}, }
@article {pmid42255668, year = {2026}, author = {An, Z and Xin, Y and Wang, Y and Wang, T and Niu, J and Hu, X and Li, X and Jin, W}, title = {Lanzhou Lily (Lilium davidii var. unicolor) Extract Alleviates Chronic Stress-Induced Mood Disturbances by Suppressing Neuroinflammation and Modulating the Gut-Brain Axis in Mice.}, journal = {Food science &amp; nutrition}, volume = {14}, number = {6}, pages = {e71914}, pmid = {42255668}, issn = {2048-7177}, abstract = {Chronic stress is a major contributor to mood disturbances through dysregulation of the gut-brain axis and neuroinflammatory responses. Lilium davidii var. unicolor (Lanzhou lily), a traditional medicinal and edible plant, contains bioactive compounds with anti-inflammatory potential. This study investigated the effects of Lanzhou lily extract (LLE) on chronic restraint stress (CRS)-induced behavioral and physiological changes in mice. LLE improved CRS-induced anxiety- and depression-like behaviors, reduced microglial activation in the hippocampus, and suppressed TLR4/MyD88/NF-κB signaling and downstream cytokine release (TNF-α, IL-6, IL-1β). LLE also restored intestinal barrier integrity, decreased serum LPS levels, and modulated gut microbiota composition by enriching Ligilactobacillus murinus and Muribaculum intestinale while reducing Prevotella abundance. Correlation analysis linked microbial restoration with barrier protection and reduced neuroinflammation. UHPLC-Q-Exactive Orbitrap-MS/MS analysis tentatively identified multiple constituents of LLE, including dioscin, matrine, timosaponin AIII, and catechin. Previous studies have suggested that some of these compounds may possess neuroprotective or antidepressant-related activities. These findings suggest that Lanzhou lily extract may modulate the gut-brain axis and exert antidepressant-like effects in a preclinical stress model, warranting further investigation in clinical studies.}, }
@article {pmid42255680, year = {2026}, author = {Luo, T and Zhu, Y and Xu, F and Xie, J and Chen, H and Qin, L and Ren, T}, title = {Hydroxy-α-Sanshools From Zanthoxylum bungeanum Maxim. Alleviate Obesity in Mice via the Regulation of Appetite and Gut Microbiota.}, journal = {Food science &amp; nutrition}, volume = {14}, number = {6}, pages = {e71952}, pmid = {42255680}, issn = {2048-7177}, abstract = {To explore whether hydroxy-alpha-sanshool (HAS) prevents obesity by modulating appetite and the gut microbiome, an obesity model was established using mice fed a high-fat diet. The food intake, body mass, feed efficiency and organ index of the mice were recorded, and the serum levels of GLP-1 and PYY were measured. The mRNA and protein expression of appetite-related genes in the small intestine and brain tissue were detected by real-time quantitative PCR and Western blotting, and the intestinal flora was analyzed by 16S rRNA gene sequencing. The results revealed that the body weight, food intake and feed efficiency of the mice were significantly reduced (4.28%, 14.46%, and 25.33%, respectively) and that the levels of GLP-1 and PYY were significantly increased (p < 0.05) (9.11% and 5.49%, respectively) by the HAS intervention. The relative mRNA expression of NPY and AGRP in the small intestine decreased significantly (39.62%, 21.95%) (p < 0.05); the relative mRNA levels of CART, GLP-1R, NPY2R and GLP-1 in the brain tissue increased significantly; and those of NPY and AGRP decreased significantly (p < 0.05). The protein expression of POMC and GLP-1 increased significantly (p < 0.05), whereas the protein expression of NPY and AGRP decreased significantly (p < 0.05). The diversity of intestinal flora in the cecal contents and the relative abundance of probiotics among the dominant flora increased. In conclusion, HAS could modulate the expression of appetite-related factors and the composition of intestinal microbiota in mice fed with a high-fat diet by regulating food intake and maintaining energy homeostasis, which is consistent with the involvement of the gut-brain axis in this regulatory mechanism.}, }
@article {pmid42255811, year = {2026}, author = {Tiwari, S and Kaur, U and Kaur, N and Alauddin, W and Khairnar, S and Bala, R and Kaushal, V and Mishra, M}, title = {The Gut-Brain-Immune Axis: Role of Microbiota Dysbiosis and Autonomic Nervous System in Infectious Diseases.}, journal = {Cureus}, volume = {18}, number = {5}, pages = {e108276}, pmid = {42255811}, issn = {2168-8184}, abstract = {The human gastrointestinal tract harbors a complex microbial ecosystem that plays a fundamental role in maintaining immune balance and defending against infectious diseases. Disruption of this ecosystem, known as dysbiosis, has been increasingly associated with impaired immune responses and heightened susceptibility to infections. Emerging evidence highlights the importance of the gut-brain-immune axis, particularly the role of the autonomic nervous system (ANS), in regulating these interactions. This systematic review aimed to examine the relationship between gut microbiota dysbiosis and infectious diseases, with specific emphasis on the influence of autonomic dysfunction on disease susceptibility and outcomes. A comprehensive search of PubMed/Medical Literature Analysis and Retrieval System Online (MEDLINE), Scopus, and Google Scholar was conducted to identify relevant observational studies published between 2000 and 2025. Data extraction and quality assessment were performed using standardized tools, including the Newcastle-Ottawa Scale (NOS). A total of 11 studies were included in the qualitative synthesis. The included studies consistently demonstrated that dysbiosis is associated with reduced microbial diversity and loss of beneficial taxa, which in turn were linked to increased infection risk and disease severity. Additionally, autonomic imbalance, reflected by increased sympathetic activity and reduced parasympathetic (vagal) tone, was frequently associated with impaired immune regulation. Reduced heart rate variability was commonly reported, suggesting a potential link between microbial alterations and neuroimmune dysfunction. Overall, the findings suggest that gut microbiota dysbiosis may be associated with infectious disease outcomes, with ANS dysfunction acting as a potential modulatory pathway. These findings should be interpreted with caution, as the included studies are predominantly observational and mechanistic. The results are therefore hypothesis-generating rather than practice-changing, and further high-quality studies are required to establish causal relationships.}, }
@article {pmid42255976, year = {2026}, author = {Lu, Z and Zhang, L and Zhang, Q and Duan, Q and Liu, X and Deng, X and Chen, D and Chen, X}, title = {Genetically Predicted Gut Microbiota in Correlation with the Risk of Head and Neck Cancer.}, journal = {Cancer informatics}, volume = {25}, number = {}, pages = {11769351261457904}, pmid = {42255976}, issn = {1176-9351}, abstract = {BACKGROUND: Existing evidence supports observational associations between the gut microbiome composition and susceptibility to extraintestinal cancers; however, the causal relationship between gut microbiome composition and the risk of developing head and neck cancer (HNC) remains uncertain. Therefore, we conducted a two-sample Mendelian randomization (MR) analysis using publicly available genome-wide association study (GWAS) data to investigate the potential causal link between gut microbiome composition and HNC.<br><br>METHODS AND ANALYSIS: Relevant investigations were conducted to examine the casualties of exposures and outcomes, using inverse variance weighted (IVW), weighted median (WM) and the MR-Egger method. Sensitivity analyses, including the MR-Egger intercept test, Cochran's Q test, and leave-one-out analysis, were used to assess pleiotropy and heterogeneity. In addition, the Steiger directionality test was applied to exclude studies with potential directional biases.<br><br>RESULTS: Our study identified 16 causal relationships between the genetically predicted abundances of gut microbiota and the risk of developing HNC. After sensitivity analysis on these identified relationships, 10 [class (Actinobacteria, Betaproteobacteria), order Bacillales, family (Ruminococcaceae), genus (Eubacterium_ventriosum_group, Coprococcus2, Coprococcus3, Desulfovibrio, Howardella, Subdoligranulum, Veillonella, Victivallis)] out of the initially identified 16 causal relationships were ultimately validated as being associated with HNC tumors. Steiger directionality test indicated that the MR estimate of causal direction was accurate (All p < 0.05).<br><br>CONCLUSION: Our MR analysis revealed that the gut microbiome composition was causally associated with the risk of developing HNC and could serve as a new biomarker for preventive and therapeutic strategies for HNC.}, }
@article {pmid42256174, year = {2026}, author = {Powell, ME and Solomon, SL and Schoepf, V and Castillo, KD}, title = {Stress-Resistant Symbiodiniaceae and Diverse Bacterial Communities Promote Coral Persistence in Variable, Multi-Stressor Environments.}, journal = {Ecology and evolution}, volume = {16}, number = {6}, pages = {e73783}, pmid = {42256174}, issn = {2045-7758}, abstract = {Coral holobionts maintain complex symbioses, which can be influenced by global and local stressors. However, the role of coral-associated bacterial and algal (Symbiodiniaceae) communities in facilitating coral persistence in variable and extreme, multi-stressor environments is not fully understood. Multi-stressor environments, such as semi-enclosed inland bays, provide natural laboratories to study potential coral holobiont responses to future ocean conditions in situ. We investigated the role of Symbiodiniaceae and bacterial communities in coral holobiont persistence across habitats and dry versus wet seasons. We collected three Caribbean coral species (Siderastrea siderea, Siderastrea radians, and branching Porites sp.) from two semi-enclosed inland bays and two nearby fringing reefs in Curaçao across three seasonal timepoints. We show that all coral species hosted high proportions of stress-tolerant Symbiodiniaceae in inland bays, likely facilitating the survival of their coral hosts in these turbid and highly variable and extreme environments. We also observed distinct differences in bacterial community composition across habitats, sites, and seasons in S. siderea and S. radians but not branching Porites sp. Bacterial communities of S. siderea and S. radians contained higher proportions of bacteria with the potential for diverse metabolisms, such as sulfur and nitrogen cycling, in inland bays and during wet seasons. Environmental conditions therefore strongly influence bacterial community composition, and bacterial diversity and metabolic flexibility are likely critical for coral holobiont success across environments and seasons. Our findings show how Caribbean coral holobionts persist in multi-stressor environments and may respond as anthropogenic climate change continues to exacerbate and intensify these stressors.}, }
@article {pmid42256181, year = {2026}, author = {Worsley, SF and Crighton, Z and Lee, CZ and Burke, T and Komdeur, J and Dugdale, HL and Richardson, DS}, title = {Gut Microbiome Communities Vary Across Translocated Populations of the Seychelles Warbler.}, journal = {Ecology and evolution}, volume = {16}, number = {6}, pages = {e73750}, pmid = {42256181}, issn = {2045-7758}, abstract = {Conservation translocations are an increasingly common tool used to help combat species extinction and global biodiversity loss. However, their success is dependent on a wide range of abiotic and biotic factors. To date, the potential role of host-associated microbiomes in translocation success has been overlooked despite their fundamental contribution to host health and fitness. Here, we use faecal samples to evaluate how gut microbiome communities vary across the last remnant (source) population, and all four translocated populations (established between 1988 and 2011), of the Seychelles warbler (Acrocephalus sechellensis). Gut microbiome alpha diversity was lower in all translocated populations compared to the source population on Cousin Island. Gut microbiome composition also varied, with several short-chain fatty acid producing bacterial families being lost from the core microbiome in some translocated populations; such taxa have been shown to play an important role in maintaining host metabolic health. Furthermore, the two translocated populations that were established the longest time ago, and with the fewest individuals, had reduced inter-individual gut microbiome variability compared to the source population. While it was not possible to directly assess the specific drivers of these differences due to samples being collected after the translocation event, it is likely that the size of the founding population, subsequent loss of host genetic variation and environmental factors all contribute to shaping gut microbiome variation amongst these populations. Future work should assess whether taxonomic variation translates into differences in gut microbiome function and the possible consequences for host population health and long-term resilience to environmental change.}, }
@article {pmid42256221, year = {2026}, author = {Giju, JK and John, S and Sivadas, A and Prabhakar, M and K, K and Sunilkumar, D and Nair, BG and Pal, S and Prakash, V}, title = {From dysbiosis to precision medicine: targeting the microbial-metabolic axis in IBD management.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1826972}, pmid = {42256221}, issn = {2235-2988}, abstract = {Inflammatory bowel disease (IBD) is a chronic relapsing inflammatory condition that has a rapidly changing global epidemiology. IBD has been traditionally viewed as a primary immune system dysfunction, but emerging evidence more accurately describes IBD as a perturbance of the intricate balance between host immunity, the intestinal microbiome, and intestinal metabolism. Although genetic and environmental components have long been recognized as contributors, accumulating evidence increasingly highlights the pivotal role of microbial dysbiosis in the pathogenesis of IBD. In patients with IBD, intestinal dysbiosis, which is often characterized by reduced Firmicutes and increased pro-inflammatory bacteria, triggers a cascade of pathogenic events. These pathogenic events include impaired epithelial barrier function, dysregulated immune activation against luminal antigens, and immune reprogramming. Central to these processes are functional changes in microbial metabolism, particularly in pathways involving short-chain fatty acids (SCFAs), bile acids, and redox homeostasis, which critically contribute to the development of chronic mucosal inflammation. The current therapeutic backbone of IBD-including aminosalicylates, biologics, and immunomodulators-largely targets the inflammatory response. However, the challenges such as primary non-response, secondary loss of response, and systemic side effects are often problematic. Consequently, there is an urgent need to develop novel therapeutic and preventive strategies that target the underlying microbial and metabolic causes of the disease rather than modulating immune responses. This review integrates the pathomechanistic implications of the microbiome-metabolic axis in the maintenance of gut homeostasis and its disruption in IBD, with particular emphasis on the global epidemiology of the disease. We further evaluate emerging therapeutic and preventive strategies aimed at restoring the microbiome-metabolic axis, including fecal microbiota transplantation (FMT), probiotic therapy, bacteriophage therapy, and helminth-based therapies. In addition, we explore the potential of advanced approaches such as microbiome engineering and precision genome editing to enable highly personalized therapeutic paradigms. By bridging microbial ecology with clinical pathology, this review highlights the transformative potential of targeting the host-microbiota interface to achieve improved long-term outcomes in IBD.}, }
@article {pmid42256227, year = {2026}, author = {Feng, J and He, X and Li, R and Chen, C and Yu, Z and Zhang, L}, title = {Trends and hotspots in gut microbiota and neonatal necrotizing enterocolitis: a bibliometric analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1684491}, pmid = {42256227}, issn = {2235-2988}, abstract = {BACKGROUND: Neonatal necrotizing enterocolitis (NEC) is one of the most life-threatening gastrointestinal emergencies in preterm infants. Accumulating evidence has identified gut microbiota dysbiosis as a key driver of NEC pathogenesis. Probiotics/prebiotics and bioactive components in breast milk can reduce NEC risk by modulating microbiota balance. With microbial intervention strategies becoming a research hotspot, publications in this field have surged over the past 5 years. However, no studies have yet systematically mapped its knowledge evolution and collaboration networks.<br><br>OBJECTIVE: This study pioneers the use of bibliometric methods to systematically analyze global research trends, core contributors (countries, institutions, authors), and emerging frontiers in gut microbiota and NEC research from 2005 to 2024, aiming to provide strategic guidance for future translational studies.<br><br>METHODS: A total of 1,011 English-language articles were screened from the Web of Science Core Collection. Software tools, including VOSviewer, CiteSpace, and Pajek, were employed to analyze publication trends, country/region and institution collaboration networks, journal co-citations, keyword clustering, and keyword bursts.<br><br>RESULTS: Annual publications increased from 5 in 2005 to a peak of 120 in 2023, with cumulative citations reaching 52,330 and an h-index of 115. The United States led in output (424 publications, 41.9%) and total citations (30,446). China ranked second in publications (158 articles) but exhibited lower average citations per article (22.65). The University of California System (65 publications) and the State University System of Florida (51 publications) were the most productive institutions. Mark A. Underwood (31 publications) focused on multi-omics mechanisms, while Josef Neu achieved the highest average citations per article (107.88) for his work on microbe-host interactions. "Nutrients" published the most articles (49), while "Microbiome" (impact factor 12.7) demonstrated the highest influence. Research hotspots evolved from early-stage microbiota composition analysis to mid-phase mechanism exploration and probiotic intervention evidence synthesis, shifting recently toward clinical translation, intestinal barrier repair, and stem cell therapy.<br><br>CONCLUSION: Research on gut microbiota and NEC shows sustained growth, with trends shifting from microbiota structure description to multi-omics mechanistic exploration and accelerating clinical translation.}, }
@article {pmid42256231, year = {2026}, author = {Gomez-Ramirez, U and De La Torre-González, C and Villamor, P and Huante Guido, M and Contreras-Rodríguez, A and Velázquez-Guadarrama, N}, title = {Recolonization dynamics of the middle ear microbiota following MESNA-assisted dissection in pediatric cholesteatomatous chronic otitis media.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1830192}, pmid = {42256231}, issn = {2235-2988}, abstract = {INTRODUCTION: Cholesteatomatous chronic otitis media (CCOM) remains a clinical challenge due to its high recurrence rates despite surgical intervention. Sodium 2-mercaptoethanesulphonate (MESNA) is used to assist dissection, yet its impact on the middle ear microbiome and ecological recovery remains poorly understood. The aim of this study is to characterize the microbiota of paediatric CCOM and evaluate the ecological shifts induced by MESNA-assisted surgery.<br><br>METHODS: We analyzed 16S rRNA gene sequences (V3-V4) from middle ear tissue of paediatric patients with CCOM (CCOM Before MESNA, n = 13; CCOM After MESNA, n = 13) and healthy controls (n = 11). Bioinformatic processing was performed via QIIME2 and DADA2. We employed a Compositional Data Analysis (CoDA) framework, centering on Aitchison distances, ALDEx2 for differential abundance, and consensus co-occurrence networks (SparCC, SPIEC-EASI, and CLR-Pearson). Functional potential was inferred using PICRUSt2.<br><br>RESULTS: CCOM was associated with a marked reduction in microbial network connectivity, decreasing from 185 edges in healthy controls to only two total edges in the CCOM Before MESNA stage. Cutibacterium emerged as a candidate keystone pathobiont, exhibiting profound ecological isolation and predicted metabolic shifts toward lipid catabolism and biofilm formation in dysbiotic states. MESNA application disrupted the disease-associated community equilibrium, initiating secondary succession. However, post-treatment recovery was marked by taxonomic homogenization and the expansion of Pseudomonas in several patients.<br><br>DISCUSSION: Our findings identify network fragmentation and functional dysbiosis as the ecological signatures of pediatric CCOM. While MESNA disrupts the dysbiotic equilibrium, it does not fully restore a healthy stable climax community within the studied timeframe, as defined in ecological succession theory. These results support a paradigm shift from simple pathogen eradication toward ecological restoration as a strategy to prevent disease recurrence in CCOM patients.}, }
@article {pmid42256254, year = {2026}, author = {Zhang, A and Du, R and Lei, L and Liu, J and Sun, G and Wang, R and Hu, T and Cheng, R}, title = {Fibrinogen was associated with subgingival microbiome in periodontal diseases: a pilot study.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2681264}, pmid = {42256254}, issn = {2000-2297}, abstract = {BACKGROUND: Periodontal diseases are associated with complex interactions among inflammatory responses, microbial dysbiosis, and clinical periodontal parameters. However, the relationships among inflammatory biomarkers, microbial biomarkers, and clinical parameters in gingival crevicular fluid (GCF) remain to be further clarified.<br><br>OBJECTIVE: To explore the interactions among inflammatory biomarkers, microbial biomarkers, and clinical parameters in gingival crevicular fluid in periodontal diseases.<br><br>DESIGN: In this cross-sectional study, GCF and subgingival plaque were collected from healthy, gingivitis, and periodontitis participants. Levels of fibrinogen, fibrin (measured as fibrin degradation products (FDP)), Interleukin (IL)-1&#x3b2;, IL-17, Matrix metallopeptidase (MMP)8, and MMP9 were measured by enzyme-linked immunosorbent assay. The subgingival microbiome was analyzed using 16S rRNA gene sequencing.<br><br>RESULTS: Among all biomarkers, fibrinogen was the most sensitive biomarker detected in GCF. Levels of fibrinogen were higher in the gingivitis (p&#x2009;=&#x2009;0.024) and periodontitis (p&#x2009;=&#x2009;0.002) groups than in the healthy group. Positive correlations were found between fibrinogen and numerous subgingival microorganisms, such as Tannerella forsythia, Treponema denticola, Porphyromonas gingivalis, and Filifactor alocis. Fibrinogen was the only GCF marker that could differentiate between healthy and gingivitis individuals. Fibrinogen and its combination with specific subgingival microorganisms may be potential markers indicating gingivitis and periodontitis.<br><br>CONCLUSIONS: Compared with IL-1&#x3b2;, IL-17, MMP8 and MMP9, fibrinogen in GCF demonstrated distinct associations with clinical parameters and subgingival microbiome in periodontal diseases.}, }
@article {pmid42256255, year = {2026}, author = {Wu, X and Xiao, H and Chen, Y and Wu, C and Xie, Q and Gu, Y and Qin, X}, title = {Blueberry leaf polyphenols suppress biofilm formation and restore oral microbial homeostasis for caries control.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2681284}, pmid = {42256255}, issn = {2000-2297}, abstract = {BACKGROUND: Dental caries is a dysbiotic biofilm-induced disease driven by Streptococcus mutans (S. mutans). Blueberry leaf polyphenols (BLP) are plant-derived polyphenols exhibiting antimicrobial properties. However, their effects on S. mutans remain incompletely understood.<br><br>METHODS: The composition of BLP was determined by ultrahigh-pressure liquid chromatography-triple quadrupole tandem mass spectrometer (UPLC-MS/MS). The minimum inhibitory concentration (MIC) and acid suppression activity were determined. In addition, the effect on biofilm was investigated by adhesion and aggregation assay, crystal violet assay, glycosyltransferases (GTF) activity, extracellular polysaccharides (EPS) quantification, scanning electron microscope (SEM) images and qRT-PCR. Furthermore, we carried out a rat caries model, and microbiome analyzes were performed by 16S rRNA sequencing.<br><br>RESULTS: UPLC-MS/MS analysis identified a range of compounds in BLP, including quercetin and chlorogenic acid. The MIC of BLP was 500&#x2009;&#x3bc;g/mL, and it inhibited the acid production of S. mutans. Importantly, BLP decreased the sucrose-dependent adhesion and its auto-aggregation, inhibited the activity of GTF, resulting in reduced EPS and down-regulated genes like gtfB, comA and gbpB. In addition, it inhibited dental caries in rats and ameliorated the microbiota dysbiosis associated with caries.<br><br>CONCLUSIONS: BLP combats caries by inhibiting S. mutans growth, biofilm formation and restoring the oral microbiota.}, }
@article {pmid42256259, year = {2026}, author = {Dewan, A and Mascellino, MT}, title = {Computational and multi-omics systems biology for precision microbiome therapeutics.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1842701}, pmid = {42256259}, issn = {2813-4338}, abstract = {The human gut microbiome represents a complex and dynamic therapeutic target whose effective interrogation requires system-level analytical approaches beyond single-omics or reductive methods. This mini-review synthesizes recent advances in computational modeling and multi-omics integration relevant to the development of predictive, patient-tailored microbiome therapies. We critically assess the analytical strengths and limitations of genome-scale metabolic models (GEMs); generalized Lotka-Volterra and ODE-based community models; agent-based simulations; and statistical machine-learning frameworks and examine how their integration with metagenomics, metatranscriptomics, metaproteomics, and metabolomics can help bridge microbial functional potential with clinically relevant phenotypes. Representative applications-including MintTea for disease module identification, gNOMO2 for integrative microbiome profiling, and AGORA-based community metabolic modeling-illustrate the translational scope of these frameworks across inflammatory, metabolic, and infectious disease contexts. Hybrid ML-GEM frameworks have not yet been directly applied to FMT outcome prediction; however, the mechanistic principles underlying both approaches - metabolic compatibility modeling and data-driven responder stratification - suggest a compelling direction for future investigation, contingent on prospective validation in adequately powered and independent clinical cohorts. Persistent methodological challenges-such as data heterogeneity, batch effects across sequencing platforms, incomplete multi-omics coverage, and limited interpretability of complex machine-learning models-are being actively addressed through standardized preprocessing pipelines, explainable Artificial intelligence (AI) strategies, and federated analytics. While federated approaches enable privacy-preserving, multi-institutional model training, they introduce additional constraints related to non-identically distributed data, communication overhead, and uneven computational capacity. Overall, the convergence of mechanistic modeling, data-driven learning, and distributed analytical infrastructures may assist in advancing microbiome research from a largely correlational perspective toward mechanistic and ultimately prescriptive frameworks for precision microbiome medicine.}, }
@article {pmid42256281, year = {2026}, author = {Yang, J and Liu, Y and Li, B and Zhang, T and Yan, L and Zhang, K and Xu, F and Wang, Z and Liu, Y and Lin, B and Wang, J and Wei, Y}, title = {A tumor-resident Staphylococcus epidermidis strain exhibits genomic and metabolic traits driving hepatocellular carcinoma progression.}, journal = {iScience}, volume = {29}, number = {6}, pages = {116084}, pmid = {42256281}, issn = {2589-0042}, abstract = {Although bacteria have been detected in hepatocellular carcinoma (HCC), the low microbial biomass has hindered isolation of viable intratumoral strains and evaluation of their functional relevance. Intratumoral microbiota profiling by 5R 16S rRNA sequencing, together with a stringent contamination-controlled workflow, identified enrichment of Staphylococcus in advanced-stage (Barcelona Clinic Liver Cancer [BCLC] C) HCC and enabled isolation of a viable S. epidermidis strain, GX3-2, from HCC tissue. GX3-2 promoted HCC cell proliferation and migration in vitro and was associated with accelerated xenograft growth in a pilot intratumoral inoculation model. Multi-omics analyses linked GX3-2 to distinct metabolic features, including adenosine and 2-phenylethylamine (2-PEA), together with host transcriptional programs related to cell cycle and epithelial-mesenchymal transition. These findings provide proof-of-concept evidence that a tumor-derived S. epidermidis isolate may modulate malignant phenotypes in HCC.}, }
@article {pmid42256599, year = {2026}, author = {Keum, HL and Sul, WJ and Kim, HS}, title = {Comparison of skin microbiota profiles in chronic scratch lesions using tape strip and swab sampling.}, journal = {JAAD international}, volume = {27}, number = {}, pages = {19-20}, pmid = {42256599}, issn = {2666-3287}, }
@article {pmid42257352, year = {2026}, author = {Guiot, J and Gester, F and Frix, AN and Denis, A and Corhay, JL and Louis, R}, title = {[Environmental exposome and interstitial lung diseases].}, journal = {Revue medicale de Liege}, volume = {81}, number = {5-6}, pages = {327-333}, pmid = {42257352}, issn = {0370-629X}, abstract = {Interstitial lung diseases (ILDs) encompass a heterogeneous group of pulmonary disorders whose prevalence is increasing, partly driven by the environmental exposome. Fine particulate matter (PM2.5), air pollutants, bioaerosols, and occupational exposures (such as silica, asbestos, and organic dust) play a major role in the initiation, progression, and exacerbations of ILDs. These agents induce oxidative stress, inflammation, and fibrotic activation. Conditions such as asbestosis, anthracosilicosis, idiopathic pulmonary fibrosis, sarcoidosis, and hypersensitivity pneumonitis illustrate the interaction between individual susceptibility and environmental factors. Infections and the lung microbiome also contribute to pathophysiology and may act as disease triggers in at-risk populations. The exposome concept provides an integrative framework to understand these complex interactions. Despite recent advances, uncertainties remain, particularly regarding the long-term effects of inhaled ultrafine particles.}, }
@article {pmid42257359, year = {2026}, author = {Delahaye, T and Absil, G and Damsin, T and Libon, F and Nikkels, A}, title = {[Climate change and skin].}, journal = {Revue medicale de Liege}, volume = {81}, number = {5-6}, pages = {373-379}, pmid = {42257359}, issn = {0370-629X}, mesh = {Humans ; *Skin Diseases/etiology/epidemiology ; *Climate Change ; Ultraviolet Rays/adverse effects ; }, abstract = {Climate change, pollution, extreme weather events, and ecosystem disruption cause a wide range of consequences for the skin and dermatologic diseases, affecting epidemiology, disease behaviour, and therapeutic response. Some inflammatory dermatoses are worsened by ultraviolet radiation, such as cutaneous lupus and Darier disease. In addition, UV radiation is responsible for most skin cancers. Humidity favours skin infections, particularly fungal infections. Pollution exacerbates atopic dermatitis. Rising temperatures increase sweating, an aggravating factor for fungal infections, Darier disease, and hidradenitis suppurativa. Even some drug-related cutaneous adverse effects are modulated by weather conditions. Several aspects of the dermatological activity contribute to pollution and climate changes, by, for instance, packaging, metabolites and conservatives, UV filters and waste generated by dermatological surgery.}, }
@article {pmid42257498, year = {2026}, author = {Bi, R and Zhang, Y and Zhang, W and Shi, C and Qiao, Z and Quan, R and Sun, Y and Chen, J and Wang, R and Ren, F and Li, Y}, title = {Lactobacillus paracasei L9 Ameliorates Pulmonary Fibrosis in Aged Mice via Gut-Lung Axis-Mediated Regulation of Immune Cell Migration.}, journal = {Aging cell}, volume = {25}, number = {6}, pages = {e70576}, doi = {10.1111/acel.70576}, pmid = {42257498}, issn = {1474-9726}, support = {2022QNRC001//Young Elite Scientist Sponsorship Program by CAST/ ; B18053//111 Project of the Education Ministry of China/ ; }, abstract = {Age-related pulmonary fibrosis (PF) imposes a growing global burden with limited therapies. This study explored the role of Lactobacillus paracasei L9 (L9) in alleviating PF in C57BL/6J mice and its mechanisms. Nine-month oral administration of L9 (4 × 10[9] CFU/mL) suppressed collagen (Col-) I deposition in aged mice, with no significant effect on Col-III. Mechanistically, L9 inhibited the JNK-HSF1 signaling pathway, thereby resulting in a 61% decrease in HSP47 expression, which is crucial for Col-I synthesis. L9 reshaped the gut microbiota by increasing short-chain fatty acid (SCFA)-producing bacteria (e.g., Blautia), leading to a 97% increase in serum propionic acid and 193% increase in butyric acid; notably, the levels of SCFAs in the lungs were below the limit of detection. In L9-treated mice, pulmonary IL-17A levels and Th17 cell populations were reduced. In vitro, SCFAs directly inhibited Th17 cell differentiation and IL-17A secretion, and IL-17A was confirmed to promote Col-I synthesis via the JNK-HSF1 pathway in pulmonary fibroblasts. Consequently, L9 modulates the gut microbiota to produce SCFAs, which regulate naïve CD4[+] T cell differentiation and migration via the gut-lung axis. This reduces pulmonary Th17 cells and IL-17A, thereby suppressing Col-I synthesis in pulmonary fibroblasts and ultimately alleviating age-related PF. In conclusion, this study highlights L9 as a microbiome-targeted precision nutrition strategy for the adjuvant therapy of age-related PF via the novel gut-lung axis mechanism.}, }
@article {pmid42257537, year = {2026}, author = {Yu, J}, title = {Gut microbiome: an emerging player and therapeutic target in cancer.}, journal = {Cancer biology &amp; medicine}, volume = {23}, number = {5}, pages = {}, doi = {10.20892/j.issn.2095-3941.2026.0349}, pmid = {42257537}, issn = {2095-3941}, }
@article {pmid42257577, year = {2026}, author = {Amenta, E and Grigoryan, L and Laytner, L and Olmeda, K and Paasche-Orlow, MK and Trautner, BW}, title = {Lack of knowledge of antibiotic risks among outpatients is associated with intention to use antibiotics without a prescription.}, journal = {Expert review of anti-infective therapy}, volume = {}, number = {}, pages = {1-7}, doi = {10.1080/14787210.2026.2683611}, pmid = {42257577}, issn = {1744-8336}, abstract = {BACKGROUND: Antimicrobial resistance is a major public health issue. Little is known about patients' understanding of the risks associated with antibiotic use or antimicrobial resistance. We conducted a survey in Houston, Texas among ethnically and racially diverse patients to identify factors associated with knowledge of antibiotic risks and to determine whether knowledge of antibiotic risks impacts patients' intention to use antibiotics without a prescription.<br><br>METHODS: A survey was conducted between January 2020 and June 2021 among adult patients in waiting rooms at six public clinics and two private emergency rooms in Houston, Texas. Univariate and multivariate analyses were performed to identify independent risk factors associated with the intention to use non-prescription antibiotics.<br><br>RESULTS: Surveys were collected among 564 individuals, of which 62% knew about any risks (individual or public health) associated with antibiotics, 19% had some knowledge of antibiotic resistance, and 6% had knowledge about microbiome effects. Knowledge gaps, younger age, receiving care in public rather than private healthcare setting were independent predictors of intention to use non-prescription antibiotics in the future.<br><br>CONCLUSIONS: Improving knowledge regarding antibiotic risks may reduce the use of antibiotics without a prescription.}, }
@article {pmid42257587, year = {2026}, author = {Tai, D and Latif, K and Shah, P and Sittambalam, G and Demisse, R and Sekaran, K and Gong, J and Figueiredo, JC and Liu, L}, title = {Ultra-Processed Foods and Gastrointestinal Cancer: Epidemiologic Evidence, Mechanistic Pathways, and Clinical Implications.}, journal = {Cancer epidemiology, biomarkers &amp; prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology}, volume = {}, number = {}, pages = {}, doi = {10.1158/1055-9965.EPI-26-0417}, pmid = {42257587}, issn = {1538-7755}, abstract = {Ultra-processed foods (UPFs), which NOVA classification defines as industrial formulations composed largely of refined ingredients and additives, now account for a majority of caloric intake in many high-income countries. Epidemiologic evidence suggests high UPF consumption may contribute to gastrointestinal (GI) malignancies independent of traditional nutrient-based dietary metrics. This review examines associations between UPF intake and colorectal, gastric, esophageal, and pancreatic cancers, integrating mechanisms supporting biological plausibility. The association between UPF consumption and colorectal cancer is the most consistent, with 10-30% increased risk among individuals with the highest intake. Evidence also suggests associations with non-cardia gastric cancer and esophageal adenocarcinoma, although data remain limited. Findings for pancreatic cancer are inconclusive. Mechanistically, ultra-processing may promote carcinogenesis through multiple pathways. Disruption of the food matrix and rapid glycemic absorption may activate insulin and insulin-like growth factor signaling. Low fiber content and additive exposure may alter the gut microbiome, reduce short-chain fatty acid production, impair intestinal barrier integrity, and promote chronic inflammation. Nitrates, nitrites, and emulsifiers in UPFs demonstrate pro-inflammatory and carcinogenic effects in experimental models. Although observational design limits causal inference, the consistency of epidemiologic associations, dose-response relationships, and supporting mechanistic data suggest UPF reduction may represent a potential GI cancer prevention strategy.}, }
@article {pmid42257736, year = {2026}, author = {Di Nezio, F and Di Cesare, A and García-Cobo, M and Brankovits, D and Sabatino, R and Borgomaneiro, G and Fresno-López, Z and Neunschwander Kurtz, M and Boulamail, S and Cozzoli, F and Fumarola, L and Gonzalez, BC and Roldán, A and Camacho, C and García-Herrero, A and Moro, L and Valdivia, C and Mateo-Mederos, E and García-Gómez, G and Fontaneto, D and Corno, G and Eckert, EM and Martínez, A}, title = {Multilayered Human Activities Shape the Microbial Communities of Groundwater-Dependent Ecosystems on an Arid Oceanic Island.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02797-0}, pmid = {42257736}, issn = {1432-184X}, abstract = {Island coastal aquifers, though spatially limited, sustain key ecosystem functions linked to locally critical provisioning, maintenance and cultural ecosystem services. These functions are largely dependent on the presence of highly adapted biological communities, whose microbial components remain poorly understood. Here, we describe bacterial communities across groundwater-dependent ecosystems on Lanzarote (Canary Islands, Spain), spanning habitats with contrasting environmental conditions and degrees of human influence, using 16 S rRNA gene amplicon sequencing. We then infer the processes shaping community variation by integrating diversity partitioning, indicator species analysis, and machine-learning classification. Bacterial taxonomic diversity varied significantly among habitats, with community composition primarily structured by turnover, consistent with environmental filtering. In contrast, predicted human-associated and potentially pathogenic taxa showed patterns dominated by nestedness, indicating localized enrichment linked to anthropogenic inputs. Caves, enclosed marine bays, and hypersaline systems hosted the most compositionally distinct microbial communities, whereas wells and anchialine pools showed greater overlap in community composition. Together, our results suggest that groundwater microbial communities are influenced by the interplay between environmental filtering and anthropogenic inputs, and that coastal aquifers can act simultaneously as reservoirs of natural biodiversity and sinks of human-associated bacteria. These findings highlight the need for integrative monitoring and conservation strategies that incorporate both hydrological and biological components to safeguard groundwater-dependent ecosystems on oceanic islands.}, }
@article {pmid42257753, year = {2026}, author = {Rajan, H and Devipriya, SP and Bhat, SG}, title = {Integrative frameworks for plastic biodegradation in insect-microbiome systems: mechanistic insights, emerging multi-omics and enzyme engineering perspectives.}, journal = {Biodegradation}, volume = {37}, number = {4}, pages = {}, pmid = {42257753}, issn = {1572-9729}, support = {NTA Ref. No. 211610151053//University Grants Commission/ ; BT/PR48086/BCE/8/1804/2023//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, abstract = {Plastic pollution remains a major global environmental challenge due to the persistence and recalcitrance of synthetic polymers, particularly polyolefins such as polyethylene and polypropylene. Conventional management strategies, including landfilling, incineration, and chemical recycling, are energy-intensive and often fail to achieve complete degradation. Biological approaches offer a promising alternative, yet microbial systems alone are frequently limited by low degradation efficiency, incomplete mineralization, and challenges in scalability. In this context, insect-microbiome systems have emerged as integrated biological platforms in which host physiology and gut microbial communities interact to facilitate polymer transformation. This review synthesizes current knowledge on plastic degradation in insect larvae, with a focus on mechanistic insights into host-microbe interactions. Evidence suggests a multi-step process involving mechanical fragmentation, oxidative modification of polymer chains, microbial depolymerization, and metabolic processing of intermediates. However, the relative contributions of host-derived enzymes and gut microbiota, as well as the extent of true biodegradation versus partial transformation, remain incompletely resolved. Advances in multi-omics approaches have provided important insights into these systems by linking physicochemical changes in polymers to underlying molecular and metabolic processes. At the same time, these data are largely correlative, and direct experimental validation of specific enzymatic roles remains limited. Building on these insights, emerging enzyme engineering and synthetic biology strategies aim to replicate the coordinated, multi-step processes observed in insect systems for improved degradation efficiency. This review highlights insect-microbiome systems as valuable models for understanding complex biodegradation mechanisms and guiding the development of integrated, enzyme-based strategies for sustainable plastic waste management.}, }
@article {pmid42257798, year = {2026}, author = {Zhou, AN and Liu, L and Huang, MM and Yang, S and Fei, H}, title = {The microbiota-gut-immunity axis in teleost fish: dual regulatory mechanisms of viral infections and prospects for microbiome-based antiviral strategies.}, journal = {Fish physiology and biochemistry}, volume = {52}, number = {3}, pages = {}, pmid = {42257798}, issn = {1573-5168}, abstract = {Bacteria and viruses engage in complex synergistic and antagonistic interactions with profound implications for host health, particularly through functional modulation by intestinal and other mucosal (e.g., skin, gill) microbiota. In teleost models, intestinal microbiota demonstrates dual regulatory capacities-either potentiating or suppressing viral infections. However, the mechanistic underpinnings of these interactions remain inadequately explored in aquatic species. This review systematically delineates the dual regulatory pathways (facilitative vs. inhibitory) through which the gut microbiota modulates viral infections in fish. Based on these mechanisms, we propose a novel microbiota-gut-immunity axis framework-defined as the bidirectional communication network linking gut microbial communities, intestinal barrier function, and host systemic immunity-for the development of integrated antiviral interventions. Furthermore, we critically evaluate emerging strategies-including probiotics, prebiotics, postbiotics, synbiotics, fecal microbiota transplantation (FMT), microalgae, seaweed, and phytoactive compounds-to develop preventive and therapeutic countermeasures. Based on mechanistic insights, probiotics and prebiotics emerge as the most promising candidates for large-scale application, as they directly reshape gut microbial composition and enhance host immunity along the microbiota-gut-immunity axis. In contrast, FMT and herbal medicines, while acting on multiple nodes of the axis, currently face safety and standardization challenges, positioning them as adjunctive therapies. Importantly, these mechanistic insights reveal evolutionarily conserved immune pathways with significant translational potential for human virology.}, }
@article {pmid42257872, year = {2026}, author = {Martins, FMT and de Azevedo, CS and Rocha, DG and de Melo, DHA and Ribeiro, MC and de Moura, SAL}, title = {Biases and blind spots in the global research agenda on metallic pollution and bees.}, journal = {Die Naturwissenschaften}, volume = {113}, number = {4}, pages = {}, pmid = {42257872}, issn = {1432-1904}, abstract = {Metallic pollution is an emerging and underappreciated stressor contributing to global bee declines, yet the evidence base remains fragmented across metals, taxa, endpoints, and geographic regions. Here, we provide the first hypothesis-driven scientometric synthesis of the global literature on metallic pollutants and bees. Using Web of Science records, we compiled 154 experimental and field-based studies and quantitatively tested five predictions regarding taxonomic, methodological, and thematic biases. Publication output increased sharply after 2013, with China, the United States, and Brazil leading research activity. Research effort was disproportionately concentrated on managed honey bees (Apis mellifera and Apis cerana), adult workers, and dietary exposure pathways, while larvae, wild bee taxa, and environmentally mediated exposures were less examined. Physiological, behavioural and mortality endpoints dominated the literature, whereas reproductive and microbiome impacts remained major blind spots. Adverse outcomes predominate across metals, although essential elements (Zn, Cu, Se) tended to produce less severe effects than non-essential toxic metals (Cd, Pb, Hg), this difference disappeared when exposure concentration and duration were considered. Experimental concentrations varied significantly among metals in food-based exposure studies, indicating substantial heterogeneity in dosing regimes across the literature. Multi-metal studies were not statistically underrepresented, although only a narrow subset of metal combinations has been repeatedly tested. Overall, this synthesis highlights strong structural biases in current knowledge production and identifies priorities for future research, including broader taxonomic coverage, inclusion of early life stages, standardised field-realistic exposures, and integration of chronic, sublethal, and multi-stressor scenarios. Expanding evidence toward more ecologically representative designs will be essential for robust risk assessment of metallic contamination in pollinator communities.}, }
@article {pmid42258061, year = {2026}, author = {Wu, K and Yang, LX and Chen, ZJ and Du, Y}, title = {Exploring the oral microbiome diversity and genus signatures associated with a novel non-invasive metabolic indicator: a cross-sectional study.}, journal = {The Saudi dental journal}, volume = {38}, number = {6}, pages = {}, pmid = {42258061}, issn = {1013-9052}, abstract = {PURPOSE: To examine the associations between oral microbiome diversity and genus composition with the Zhejiang University Index (ZJU Index) and clinical biomarkers.<br><br>METHODS: We included 2,490 eligible participants from the U.S. National Health and Nutrition Examination Survey (NHANES). Oral microbiome diversity was assessed using alpha and beta diversity, and genus-level analyses were based on abundance transformed using the centered log-ratio (CLR) method to account for compositionality. Weighted logistic regression models were used to assess the corresponding associations. Beta diversity disparities were evaluated through Principal Coordinate Analysis (PCoA) and Permutational Multivariate Analysis of Variance (PERMANOVA).<br><br>RESULTS: Alpha diversity metrics were positively correlated with the ZJU Index in males aged 30-44&#x2009;years (Faith's Phylogenetic Diversity: unadjusted: &#x3b2;&#x2009;=&#x2009;0.05, 95% CI: 0.006 to 0.094, p&#x2009;=&#x2009;0.033; Model 1: &#x3b2;&#x2009;=&#x2009;0.058, 95% CI: 0.011 to 0.104, p&#x2009;=&#x2009;0.026; Model 2: &#x3b2;&#x2009;=&#x2009;0.076, 95% CI: 0.032 to 0.120, p&#x2009;=&#x2009;0.005; Model 3: &#x3b2;&#x2009;=&#x2009;0.081, 95% CI: 0.035 to 0.128, p&#x2009;=&#x2009;0.008) and in females aged 60-69&#x2009;years (Observed ASVs: &#x3b2;&#x2009;=&#x2009;1.242, 95% CI: 0.345 to 2.139, p&#x2009;=&#x2009;0.042; Faith's Phylogenetic Diversity: &#x3b2;&#x2009;=&#x2009;0.097, 95% CI: 0.025 to 0.168, p&#x2009;=&#x2009;0.045). Significant differences in beta diversity metrics were observed among ZJU Index-defined subgroups (p&#x2009;<&#x2009;0.05), confirmed with age- and sex-stratified analyses. Genera including Bulleidia, Senegalimassilia, Fretibacterium, and Hungatella exhibited significant associations with the ZJU Index and with clinical biomarkers (triglycerides, low-density lipoproteins (LDL), high-density lipoproteins (HDL), insulin, and testosterone).<br><br>CONCLUSIONS: Higher oral microbiome alpha diversity was associated with higher ZJU Index in certain populations. Beta diversity demonstrated that ZJU Index-defined subgroups differed in oral microbial composition. Specific genera were identified to be significantly associated with the ZJU Index and clinical biomarkers.}, }
@article {pmid42258064, year = {2026}, author = {Wei, Q and Ding, D and Zhong, J and Liu, R}, title = {MNRS: Multi-Factor Network-Based Ranking Score for Detecting Critical Transitions of Complex Diseases Using Gut Microbial Data.}, journal = {Bulletin of mathematical biology}, volume = {88}, number = {7}, pages = {}, pmid = {42258064}, issn = {1522-9602}, support = {42450084//National Natural Science Foundation of China/ ; T2341022//National Natural Science Foundation of China/ ; 12401630//National Natural Science Foundation of China/ ; }, abstract = {Disease progression is not always gradual and may instead involve abrupt deterioration, with a critical threshold separating pre-deterioration and post-deterioration states. Detecting such pre-disease states is of major importance because they often precede catastrophic transitions. Increasing evidence suggests that the onset and progression of many diseases, including type 1 diabetes, celiac disease, and colorectal cancer, are closely associated with the gut microbiome. Although transcriptome-based approaches, particularly those relying on gene expression data, have been widely used to identify critical states in biological systems, they are often not well suited to gut microbiome data because of its sparsity, compositionality, and substantial noise. Here, we propose a novel computational framework, termed multi-factor network-based ranking score (MNRS), for detecting pre-disease states from gut microbiome data. MNRS infers perturbed microbial networks and quantifies dynamic alterations in species- or genus-level associations, thereby enabling the detection of early-warning signatures of critical transitions. Analyses of both simulated data and multiple real-world datasets show that MNRS accurately identifies pre-disease states and outperforms existing methods in both robustness and detection performance. In addition, MNRS reveals sensitive "dark species" overlooked by conventional differential abundance analyses but potentially important in disease deterioration.}, }
@article {pmid42258075, year = {2026}, author = {Shah, TM and Pandit, R and Bhure, M and Nehra, C and Chavda, P and Patil, NV and Patel, AK and Kachhawaha, S and Kumawat, RN and Bhatt, V and Joshi, M and Joshi, C}, title = {Unravelling the effect of moringa supplemented diet on goat gastrointestinal microbiota and metabolic potential.}, journal = {AMB Express}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13568-026-02079-5}, pmid = {42258075}, issn = {2191-0855}, support = {BT/AQ/1/SP41105/2020//Department of Biotechnology, Ministry of Science and Technology, India/ ; BT/AQ/1/SP41105/2020//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, abstract = {Goat is an important livestock species that contribute significantly to global food supply by converting complex plant biomass into animal protein, depending on the gut commensal microbiota for digestion of complex plant biomass. Gastrointestinal tract (GIT) microbiome manipulation using natural plant-based feed supplement is one of the promising strategies for improving livestock performance and mitigating enteric biogases. Moringa oleifera improves animal performance, yet its effects on microbiota structure and functional remodelling across GIT remain poorly understood. Here, we investigated the impact of moringa supplementation on microbiota structure and functional remodelling across the gut in goats. We show that moringa induces microbiota restructuring associated with metabolic output in terms of body weight gain in goat. The forestomach (FS) and large intestine (LI) showed specific enrichment of efficient fibre utilizing and fermentative microbial community, particularly Ruminococcus flavefaciens, Sodaliphilus sp., Prevotella sp., Treponema bryantii, Faecousia sp., and Phocaeicola sp., whereas small intestine exhibited greater abundance of lactate producing microbes such as Rombustia hominis. These spatial patterns reflect alternative metabolic pathways across the GIT driven by nutrient availability. Moringa supplementation selectively enriched microbial genes involved in the metabolic cascades such as production of butyrate and propionate via succinate pathway in FS, while reductive acetogenesis via Wood-Ljungdahl pathway in LI. Decreased abundance of Entodinium and increased abundance of Prevotella were observed in moringa supplemented diet. Our findings provide mechanistic insight into how diet modulates gut microbial ecosystems, demonstrating that a plant-based feed supplement intervention can restructure microbial composition and functional potential along the GIT.}, }
@article {pmid42258100, year = {2026}, author = {Zahran, E and Elbahnaswy, S and Karam, R and ElBanna, NI and El Sebaei, MG}, title = {The multifaceted challenge of viral nervous necrosis in fish farming: a review of current knowledge and control.}, journal = {Veterinary research communications}, volume = {50}, number = {5}, pages = {}, pmid = {42258100}, issn = {1573-7446}, support = {Grant No. KFU260316.//The Deanship of Scientific Research, Vice Presidency for Graduate Studies and Scientific Research, King Faisal University, Saudi Arabia/ ; }, abstract = {Viral nervous necrosis (VNN), caused by the nervous necrosis virus (NNV) of the genus Betanodavirus, is a significant threat to global aquaculture, resulting in substantial economic losses in both marine and freshwater fish farming. The virus demonstrates considerable genetic diversity, encompassing multiple genotypes and reassortant strains that affect host susceptibility and disease severity across a wide array of fish species. Environmental factors strongly influence viral transmission and outbreak dynamics. Advances in diagnostic methodologies have enhanced the speed and sensitivity of detection. Although commercial vaccines are available for selected host species and production settings, their availability remains limited across fish species, viral genotypes, geographic regions, and early developmental stages. This review summarizes the current knowledge on Betanodavirus virology, host tropism, epidemiology, molecular diagnosis, microbiome, and control. Furthermore, it focuses on advanced disease manipulation via the microbiome and emerging molecular diagnostic platforms.}, }
@article {pmid42258155, year = {2026}, author = {Chapman, O}, title = {Intraspecific Trait Variation in the Mammalian Gastrointestinal Tract: A Digestive Dive and Systematic Literature Review.}, journal = {Integrative and comparative biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/icb/icag070}, pmid = {42258155}, issn = {1557-7023}, abstract = {The gastrointestinal tract (GIT) represents the functional link between food and energy for organisms. It also harbors the gut microbiome, protects against toxins, and eliminates waste, all of which mediate individual health and fitness. The form and function of the GIT can be dynamic, allowing organisms to respond to-and buffer against-rapid changes in their environment and energetic demands. However, knowledge of intraspecific trait variation (ITV) in the GIT is sparse among different taxa and traits (e.g., microstructural traits and physiology). Additionally, the actual mechanics of how these changes occur (e.g., cell proliferation, cellular redistribution) remain largely unknown. This systematic review summarizes the current state of knowledge on mammalian GIT ITV at multiple levels (macroscopic, microstructural, and physiological), speculates as to how global change drivers will affect ITV, and suggests new directions for future work. A comprehensive list of mammal species heretofore examined for GIT morphology and ITV from a total of 260 journal articles or book chapters identified 824 mammal species with quantitative GIT traits available (12% of all mammal species), but only 79 species (1.1%) investigated for GIT ITV. This highlights the increased need to preserve and collect trait data in standardized ways for mammalian GITs, a series of organs typically discarded or unused during specimen preparation. Understanding how wild species utilize GIT ITV to cope with energetic costs will be crucial to predicting how species may fare under rapidly changing environments.}, }
@article {pmid42258310, year = {2026}, author = {Mehboob, AA and Fatima, R and Kanwal, S and Ali, M and Karim, M and Fatima, S}, title = {Exploring the gut-lung axis in post-liver transplant acute lung injury: A multi-omics approach.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {}, number = {}, pages = {}, doi = {10.1556/030.2026.02911}, pmid = {42258310}, issn = {1588-2640}, abstract = {Acute lung injury (ALI) is a significant post-operative complication of liver transplant (LT), with mounting evidence suggesting a role for the gut-lung axis. However, the mechanistic link between gut microbiota dysbiosis and ALI pathogenesis in LT recipients remains poorly understood. This hybrid translational investigation integrates transcriptomic profiling (bulk and single-cell RNA-seq), immune infiltration analysis, fecal microbiota composition (16S rRNA), and predictive functional profiling in ALI vs. non-ALI (NALI) LT patients. Machine learning algorithms (LASSO, SVM-RFE, Random Forest) were used to identify key gene biomarkers. Microbiota-host gene correlations and canonical correspondence analysis (CCA) were performed to evaluate multi-omic relationships. ALI patients exhibited reduced gut microbial diversity and increased abundance of Enterococcus and Escherichia-Shigella, alongside a depletion of beneficial taxa (Faecalibacterium, Bacteroides). CXCL3, CD48, and IRAK3 were identified as robust ALI biomarkers (Area Under the Curve >0.83), validated in both serum and Bronchoalveolar Lavage Fluid. These genes correlated positively with pro-inflammatory microbes and immune cell infiltration. Functional prediction revealed enrichment in lipopolysaccharide biosynthesis, Toll-like receptor signaling, and bacterial chemotaxis. CCA confirmed that microbiota variation significantly explained host transcriptomic variance. Our study uncovers a functional gut-lung immunological axis in post-LT ALI. Gut dysbiosis modulates immune gene expression and lung inflammation, suggesting that the microbiome serves as a potential source of diagnostic biomarkers and therapeutic targets in transplant-associated lung injury.}, }
@article {pmid42258623, year = {2026}, author = {Mosquera, RA and Magana-Ceballos, IG and De Jesus Rojas, W and Huang, X and Koochak, H and Tellez, ME and Castillo-Moguel, JA and Bishehsari, F and Mahdavinia, M and Ramos-Benitez, MJ and Harris, T and Yadav, A and Owens, K and Lemus-Rangel, R and Romero, M and Zuleta, S and Luz, A and Baltazar-Fernandez, A and McBeth, KE and Hashmi, S and Rosario Ortiz, G and Santoyo-Rios, J and Loyo-Rodriguez, JF and Colasurdo, GN}, title = {Multi-Omics Analysis Defines Endotypes and Systemic Inflammation in Primary Ciliary Dyskinesia: A Comparison with Healthy Controls.}, journal = {Annals of the American Thoracic Society}, volume = {}, number = {}, pages = {}, doi = {10.1093/annalsats/aaoag152}, pmid = {42258623}, issn = {2325-6621}, abstract = {INTRODUCTION: Primary ciliary dyskinesia (PCD) is a rare genetic disorder characterized by chronic airway inflammation and progressive lung injury. The inflammatory profile and systemic involvement remain poorly defined. We applied integrated multi omics (transcriptomics, proteomics, and metagenomics) to characterize inflammatory signatures and explore saliva as a noninvasive marker of systemic inflammation. These findings may support improved disease characterization and inform therapy and monitoring.<br><br>METHODS: This cross sectional, multicenter study included participants with PCD and healthy controls from Houston, Texas; Puerto Rico; and Mexico. Demographic and clinical data were collected in the absence of acute infection. Oral swabs underwent a bulk inflammatory transcriptomic profiling of 590-genes using NanoString nCounter&#xae; and microbiome evaluation via metagenomic sequencing. High sensitivity NULISA&#x2122; proteomic profiling of 250-proteins was performed on both saliva and plasma, with results correlated across omic layers. Pathway and gene set analyses were conducted using nSolver Advanced Analysis.<br><br>RESULTS: Seventy-six participants were enrolled: 51 with PCD and 25 healthy controls. PCD patients, especially those older than 10&#x2009;years and those with microtubular defects, showed markedly elevated inflammatory gene and protein expression in saliva and plasma. Five inflammatory endotypes were identified: Neutrophilic protease dominant, Dipeptidyl Peptidase 1(DPP&#x2011;1) profile (78%); neutrophilic recruiting, high&#x2011;Th17 (71%); eosinophilic dominant, high&#x2011;Th2 (51%); Th2/Th17&#x2011;high (47%), and Th2/Th17&#x2011;low (25%). PCD demonstrated increased neutrophil, and CD45&#x2011;related gene expression and activation of ten inflammatory pathways, including NF&#x2011;&#x3ba;B, oxidative stress, T&#x2011;cell-receptor, TREG, Th17, TNF, Th1, Th2, TGF-B signaling, and TLR (P&#x2009;<&#x2009;.01). Saliva and plasma showed strong molecular concordance. Microbiome analysis revealed significant shifts in diversity and abundance linked to inflammatory pathways.<br><br>DISCUSSION: These findings show that PCD is characterized by baseline inflammatory activity with marked endotypic heterogeneity, most frequently involving neutrophilic-immune pathways driven by DPP1-associated protease activity and Th17-mediated neutrophil recruitment, while a distinct subset of patients demonstrates a Th2-predominant inflammatory endotype. Salivary inflammatory profiling, which closely mirrors plasma, may offer a practical, non-invasive approach to capturing this patient-level heterogeneity and monitoring systemic immune activity and treatment response, especially with the new anti-inflammatory medications for bronchiectasis.}, }
@article {pmid42258717, year = {2026}, author = {Wang, Y and Chang, HW and Barratt, MJ and Gordon, JI}, title = {Reply to Wang et al.: Linking microbial metabolites and gut epithelial responses to microbiome-directed therapeutic foods.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {24}, pages = {e2613406123}, doi = {10.1073/pnas.2613406123}, pmid = {42258717}, issn = {1091-6490}, }
@article {pmid42258719, year = {2026}, author = {Wang, Z and Xie, J and Liu, S and Han, M and Wang, L}, title = {Regulation of gut epithelial barrier and tuft/goblet cell responses by microbiome repair: Opportunities and future directions.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {24}, pages = {e2535289123}, doi = {10.1073/pnas.2535289123}, pmid = {42258719}, issn = {1091-6490}, }
@article {pmid42252506, year = {2026}, author = {Galtier, A and Warinner, C and Velsko, IM}, title = {Ancient species diversity and niche adaptation in Tannerella and Porphyromonas revealed through pangenomics.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evag136}, pmid = {42252506}, issn = {1759-6653}, abstract = {De novo assembly of ancient and modern bacterial metagenomes can shed light on evolution and ecology of bacterial species that are challenging to culture. Tannerella and Porphyromonas are bacterial genera linked to periodontal disease, and understanding their evolution may reveal insights into their role in oral disease development. We performed pangenomic and phylogenetic analyses on a global set of isolates and metagenome-assembled genomes of the genera Tannerella (n=238) and Porphyromonas (n=976), including 66 genomes from ancient dental calculus samples (up to 14,800 years old), and modern oral samples from present-day living populations. We identify a novel species of oral Tannerella in modern and ancient humans, which we call Ca. Tannerella abscondita, that is related to and often mistaken for Tannerella forsythia but differs in its virulence repertoire. We reveal distinct niche tropism in Tannerella species and Porphyromonas pasteri, but not Porphyromonas gingivalis. There is limited phylogeographic structuring, and virulence genes are homogeneously distributed across continents and oral niches. Saliva-derived strains of T. forsythia and P. gingivalis from Oceania and T. serpentiformis and P. pasteri from Asia show enrichment of pseudogenes related to ecological niche transitions. A phylogenetic analysis of the P. gingivalis major fimbrial protein gene fimA reveals the genes cluster by genotypes, and that no ancient genes are found in genotypes I and Ib. Using de novo assembly for bacterial pangenomics improves the representation of oral genera found in reference databases and enhances our ability to study the evolutionary history of these taxa.}, }
@article {pmid42252693, year = {2026}, author = {Jourdain, L and Leininger, A and Pacheco, AR and Gu, W}, title = {Environmental selection constrains metabolic network architecture despite taxonomic turnover in anaerobic digestion communities.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag145}, pmid = {42252693}, issn = {1751-7370}, abstract = {Microbial ecosystems often sustain stable metabolic functions despite pronounced taxonomic turnover, yet the mechanisms underlying such reproducible functional states remain poorly understood. Here, we investigated how physicochemical constraints shape functional convergence in anaerobic digestion communities using replicated serial enrichments seeded from four distinct inocula. Across three pH levels and six substrate regimes, replicate communities from different inocula consistently converged toward reproducible metabolite profiles, with pH emerging as the dominant organizing factor. Community composition became progressively environment-driven over time, and after 30 generations, pH explained the largest fraction of compositional variance (PERMANOVA R2 = 0.21, P = 0.001), followed by substrate. Genome-resolved metagenomics revealed that convergence was accompanied by strong pH-dependent structuring of redox-balancing and terminal electron-sink pathways, whereas upstream carbohydrate-entry pathways were conserved. Taxonomic convergence was incomplete and scale-dependent: the ability to correctly assign communities to their inoculum declined from 75% at the genus level to 53% at the phylum level, indicating increasing similarity across inocula at coarser taxonomic resolution despite persistent fine-scale variability. Despite this taxonomic flexibility, communities assembled under identical conditions consistently recruited similar sets of metabolic pathways organized into comparable network architectures. Functional redundancy analyses showed high redundancy and flexible taxonomic implementation for upstream fermentative processes, contrasted with lower redundancy and stronger convergence for terminal methanogenic functions. Together, these results demonstrate that reproducible metabolic function in AD emerges from environmentally constrained assembly of shared metabolic network architectures, rather than deterministic fixation of species composition, highlighting environmental control of metabolic organization as a central principle governing microbiome function.}, }
@article {pmid42252762, year = {2026}, author = {Ahsan, M and Afzoon, S and Nandni,  and Ahmed, A and Mubashirah,  and Priyanka,  and Rahman, HU and Arif, AR and Faiz, A and Mirza, I and Bhatt, N}, title = {Chronic Kidney Disease and the Gut Microbiota: An Expanding Confluence in the Development of the Disease.}, journal = {Comprehensive Physiology}, volume = {16}, number = {3}, pages = {e70192}, doi = {10.1002/cph4.70192}, pmid = {42252762}, issn = {2040-4603}, abstract = {PURPOSE: Chronic kidney disease (CKD) remains a major global health burden despite advances in conventional therapies. This review synthesizes current clinical and experimental evidence on the bidirectional relationship between CKD and gut microbial dysbiosis, emphasizing mechanisms, measurable outcomes, and therapeutic interventions.<br><br>METHODS: A narrative review of recent clinical and experimental studies was conducted to explore alterations in gut microbial composition, generation of uremic toxins, and the impact of CKD therapies on microbial balance. Emerging microbiota-targeted interventions were also examined.<br><br>RESULTS: Studies consistently report reduced microbial diversity, loss of short-chain fatty acid (SCFA)-producing taxa, and enrichment of proteolytic, toxin-producing bacteria in CKD. Gut-derived metabolites such as indoxyl sulfate (IS), p-cresyl sulfate (pCS), and trimethylamine N-oxide (TMAO) are linked to oxidative stress, RAAS activation, and fibrogenesis. In human trials, microbiota-directed therapies show modest biochemical benefits: a meta-analysis of 21 randomized studies reported mean reductions in serum BUN (8.5&#x2009;mg/dL) and CRP (1.4&#x2009;mg/L) with probiotic or synbiotic supplementation, while inulin (10&#x2009;g/day) in stage 3-4 CKD reduced serum pCS by 25% and increased fecal butyrate by 40%. However, most mechanistic data derive from animal and in&#xa0;vitro models, and human evidence remains heterogeneous and underpowered. Stage-specific differences are evident-early CKD shows subtler dysbiosis, while advanced CKD and dialysis populations exhibit profound microbial shifts and variable responsiveness.<br><br>CONCLUSION: The gut microbiota is a promising, modifiable contributor to CKD pathophysiology. Stage-stratified longitudinal studies are needed to establish causality and therapeutic efficacy.}, }
@article {pmid42252802, year = {2026}, author = {Stang, A and Illig, T and Hiller, K and Weilert, H and Schmidt, R and Gronauer, R and Seifert, M}, title = {Lowered Abundance of Gut Bacteriophage Species Is Associated With Human Cancer Cachexia.}, journal = {Journal of cachexia, sarcopenia and muscle}, volume = {17}, number = {3}, pages = {e70324}, doi = {10.1002/jcsm.70324}, pmid = {42252802}, issn = {2190-6009}, support = {3465//Asklepios Proresearch, Asklepios Hospitals Hamburg, Germany/ ; }, abstract = {BACKGROUND: Cancer cachexia exemplifies a high medical need condition without effective treatment. Recent studies implicated bacterial gut microbiome alterations to cancer cachexia. Whether the gut bacteriophage profile, an important microbiome component for health and disease, is also related to cancer cachexia remains unknown. We aimed to profile gut microbiome alterations in human cancer cachexia with attention on bacteriophages.<br><br>METHODS: We performed shotgun metagenomic sequencing in stool samples from 78 cachectic and 42 noncachectic patients (53% male, mean age 67&#x2009;&#xb1;&#x2009;8&#x2009;years) with newly diagnosed, advanced-stage (UICC IV) gastrointestinal cancers. Cachexia was defined according to the main criterion agreed upon international consensus (weight loss [WL] adjusted to body mass index [BMI]). Obtained DNA short-reads were used for k-mers-based, phage-inclusive matching with reference databases, de novo phage assembly and inferring microbiome-encoded functions. We replicated significance-based statistical and prediction-oriented machine-learning analyses in 2022 and 2025 generated metagenome datasets to incorporate the recent change by the International Committee on Taxonomy of Viruses (ICTV) from morphology-based (valid until 2022) to revised genome-based phage taxonomy into microbiome findings of cachexia.<br><br>RESULTS: Cachectic and noncachectic patients differed significantly regarding BMI (mean 20.9 vs. 26.4&#x2009;kg/m2), WL (mean -6.5 vs. -0.2&#x2009;kg), survival (median 5 vs. 13&#x2009;months) and clinical cachexia domains (e.g., C-reactive proteine and appetite loss) (all p&#x2009;<&#x2009;0.001) but not for other clinical covariables (e.g., cancer type) (all p&#x2009;>&#x2009;0.05). Read-based mapping (2022/2025) identified 1.312/1.513 species (74/39 phage species), and de novo assembly resulted in 4.184/4.209 contigs (corresponding to 65/39 phage species). Concordantly, both analyses (2022 and 2025) showed that prevalent cachexia associated significantly with beta-diversity (Bray-Curtis distance, PERMANOVA, p&#x2009;<&#x2009;0.05), but not to alpha-diversity (Shannon-Index, ANOVA, p&#x2009;>&#x2009;0.05), reduced microbiome-encoded detoxification functions (e.g., enriched microbial &#x3b2;-glucuronidase and depleted bacterial efflux pumps) and lowered abundance of bacterial species with false-discovery-rate (FDR)-corrected p&#x2009;<&#x2009;0.05 (2022: Faecalibacterium prausnitzii, Roseburia intestinalis, Streptococcus species and Lachnospiraceae species; 2025: Faecalibacterium species, Ruminococcus gauvreauii and Intestinibacter bartlettii). Further, lowered abundance of bacteriophages associated with cachexia, predominantly affecting double-stranded (2022: Caudovirales, Siphoviridae, FDR-corrected p&#x2009;<&#x2009;0.05; 2025: Myoviridae, Siphoridae, p&#x2009;<&#x2009;0.05) but also single-stranded (2022: Inoviridae, Microviridae, p&#x2009;<&#x2009;0.05; 2025: Inoviridae; p&#x2009;<&#x2009;0.05) DNA phage species. In machine-learning models, bacteriophages were top-ranked cachexia predictors (2022: Caudovirales, Siphoviridae; 2025: Myoviridae, Siphoridae). Accuracy was highest when only phage contigs were taken into account (correctly classified instances: 75.0%-85.8%; AUC: 0.703-0.916).<br><br>CONCLUSIONS: The previously unknown link between gut bacteriophages and human cancer cachexia expands the scope for basic, translational and clinical microbiome-targeted research in an area of significant unmet medical need.<br><br>TRIAL REGISTRATION: Study Box of the German Cancer Society (Registration Number ST-U069, Date: 29 May 2018).}, }
@article {pmid42252976, year = {2026}, author = {Unno, T}, title = {16S-Pipeline: A comprehensive web-based platform for end-to-end 16S rRNA amplicon sequencing analysis.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {64}, number = {5}, pages = {e2603014}, doi = {10.71150/jm.2603014}, pmid = {42252976}, issn = {1976-3794}, support = {RS-2025-02633155//Rural Development Administration/ ; }, abstract = {16S rRNA gene amplicon sequencing is the most widely used approach for characterizing microbial communities, yet analyzing such data requires navigating a fragmented landscape of bioinformatics tools with distinct installation requirements, parameter settings, and data formats. Here we present 16S-Pipeline, an open-source, web-based platform that provides a complete workflow from raw FASTQ files to publication-ready statistical analyses. 16S-Pipeline automatically detects sequencing type (paired-end, single-end, long-read), variable region, and sequencing platform (Illumina, PacBio HiFi, Nanopore), then performs quality filtering, primer trimming, amplicon sequence variant (ASV) inference via DADA2, taxonomy assignment against SILVA v138.1, phylogenetic tree construction, and optional functional prediction via PICRUSt2. Downstream analyses include alpha and beta diversity, taxonomic composition visualization, differential abundance testing using five complementary methods (ALDEx2, DESeq2, ANCOM-BC2, LinDA, MaAsLin2) with consensus reporting, and KEGG pathway mapping. Built-in NCBI SRA integration enables downloading public datasets for re-analysis and generates submission metadata spreadsheets for data deposition. The interactive web interface built on FastAPI and Plotly Dash enables researchers to perform complex microbiome analyses without command-line expertise. 16S-Pipeline is freely available at https://github.com/tatsu1207/16S-Pipeline under the MIT License.}, }
@article {pmid42253015, year = {2026}, author = {Wang, Z and Pu, R and Gao, B and Cai, W and Yang, G}, title = {Oral microbiota associated with tooth loss and cognitive function in older adults: Evidence from NHANES.}, journal = {Journal of periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1002/jper.70154}, pmid = {42253015}, issn = {1943-3670}, support = {82271001//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The aim of this study is to investigate the association between tooth loss and cognitive decline and to explore the potential role of salivary microbial genera in this relationship in a nationally representative population.<br><br>METHODS: Data from 1,413 adults aged &#x2265; 60 years in NHANES 2011-2012 were analyzed. Cognitive function was assessed using the Consortium to Establish a Registry for Alzheimer's Disease (CERAD) Word Learning Tests, the Animal Fluency Test (AFT), and the Digit Symbol Substitution Test (DSST). Salivary microbiome profiles were obtained from a subsample of 661 participants using 16S rRNA sequencing. Complex survey regression, PERMANOVA, and multivariable microbial association analyses were applied. Mediation analyses were conducted as exploratory analyses to evaluate potential microbial pathways linking tooth loss with cognitive outcomes.<br><br>RESULTS: Moderate tooth loss was associated with higher odds of low global cognition (OR&#xa0;=&#xa0;2.91, 95%CI: 2.01-4.23), low AFT (OR&#xa0;=&#xa0;1.57, 95%CI: 1.03-2.39), and low DSST (OR&#xa0;=&#xa0;2.15, 95%CI: 1.47-3.16) after adjustment. Sixteen genera were associated with at least one cognitive metric, including Prevotellaceae_NA, Phocaeicola, and Lactobacillus. In exploratory mediation analyses, three organic acid-producing genera (Lactobacillus, Lachnospiraceae_NA, and Leptotrichiaceae_NA) were identified as potential contributors to the association between tooth loss and cognition.<br><br>CONCLUSION: Tooth loss was associated with cognitive decline in older adults, and both conditions were accompanied by differences in salivary microbial composition. Exploratory mediation analyses suggested that certain organic acid-producing taxa may contribute to the observed association.<br><br>PLAIN LANGUAGE SUMMARY: Tooth loss is common in older adults and has been linked to problems with memory and thinking, but the reasons for this connection are not fully understood. In this study, we used data from a large national health survey of adults aged 60 years and older to examine tooth loss, results from several cognitive tests, and the types of bacteria found in saliva. We found that older adults with more missing teeth were more likely to perform poorly on tests measuring memory, attention, and processing speed. We also observed that some types of oral bacteria were related to both tooth loss and cognitive performance. In exploratory analyses, several groups of bacteria that produce organic acids were linked to the relationship between tooth loss and cognitive outcomes. These findings suggest that differences in the oral microbial community may be one of several biological pathways connecting oral health and cognitive function. Understanding how oral health, diet, and oral bacteria interact may help researchers better understand factors related to cognitive aging and to identify potential targets for future research and prevention strategies.}, }
@article {pmid42253256, year = {2026}, author = {Suchday, P and Dhabuwala, A and Adrejiya, P and Bajpai, P and Shingala, TS and Prajapati, K and Patel, V and Nunna, K and Desai, R}, title = {The Role of Firmicutes in Coronary Artery Disease: A Taxonomic-Level Meta-Analysis of Mendelian Randomization Studies.}, journal = {Current cardiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.2174/011573403X432303260316044935}, pmid = {42253256}, issn = {1875-6557}, abstract = {INTRODUCTION/OBJECTIVE: The Gut Microbiome (GM) plays a critical role in cholesterol metabolism through the production of metabolites such as trimethylamine N-oxide and shortchain fatty acids, contributing to inflammation, endothelial dysfunction, and host gene regulation. This study aims to taxonomically characterize gut microbial profiles, evaluate their association with coronary artery disease, and explore the potential therapeutic implications of microbiome- mediated cardiometabolic pathways.<br><br>METHODS: We pooled data from six Mendelian Randomization studies that utilized the MiBio- Gen consortium and CAD, and cardiovascular risk GWAS data from CARDIoGRAMplusC4D, FinnGen, and UK Biobank databases. Within the phylum Firmicutes, inverse variance weighted analysis was used to estimate the association between: (1) protective effects of Clostridiales vadinBB60 group, Genus Butyricicoccus, Genus Ruminococcus UCG010, Coprococcus 1, Intestinibacter, Ruminiclostridium 6, Anaerotruncus, and Family Acidaminococcaceae; and (2) causative effects of Clostridium innocuum group, Genus Turicibacter, Eisenbergiella, Holdemanella, Eubacterium, Coprostanoligenes group, Ruminococcaceae UCG005, and Genus Catenibacterium on CAD.<br><br>RESULTS: Higher levels of phylum Firmicutes exhibit a statistically significant protective effect on CAD (OR: 0.880, 95% CI: 0.853-0.907), with low heterogeneity (I&#xb2; = 20%, P = 0.857). Conversely, an increased abundance of Firmicutes also correlates with a higher risk of CAD (OR: 1.10, 95% CI: 1.06-1.14), showing low heterogeneity (I&#xb2; = 20%, P = 0.90). Leave-one-out sensitivity analyses confirmed the robustness of these results.<br><br>DISCUSSION: The findings highlight a significant relationship between gut microbiome dysbiosis and adverse cardiometabolic outcomes, potentially mediated through inflammatory pathways, metabolic signaling, and microbial metabolite production. These results support the growing role of microbiome-targeted interventions as emerging strategies for cardiometabolic risk modification.<br><br>CONCLUSION: Firmicutes exhibit both protective and causative effects on CAD. These findings highlight the complexity of the gut microbiome's role in cardiovascular diseases. Further detailed research on the mechanisms by which specific bacteria at the lower taxonomic levels exert this effect is imperative to understand this complex relationship and its clinical implications.}, }
@article {pmid42253936, year = {2026}, author = {Wetzel, S and Kohnert, E and Huber, R and Müller, A and Knott, A and Kousoulas, L and Kreutz, C and Badr, MT and Lederer, AK}, title = {Divergent Resilience of Bacterial and Fungal Gut Microbiota After Colorectal Surgery: Insights From a Prospective Longitudinal Cohort Study.}, journal = {MedComm}, volume = {7}, number = {6}, pages = {e70781}, pmid = {42253936}, issn = {2688-2663}, abstract = {The composition of the gut microbiota changes throughout life and is shaped by various external influences, particularly major physiological stressors such as surgery. The extent of these changes and their impact remain poorly understood. This prospective cohort study aimed to investigate changes in the gut microbiota following colorectal surgery and to identify factors that modify these alterations. Paired pre- and postoperative stool samples from 59 patients at the University Medical Centre Freiburg were analyzed using 16S rRNA and ITS2 gene sequencing. Analyses included alpha and beta diversity, LEfSe differential feature analysis, network analysis with Louvain clustering, KEGG pathway annotation, and correlation with clinical parameters. Bacterial diversity significantly decreased postoperatively (Shannon index: p < 0.001), while fungal diversity remained largely unchanged (p > 0.05). Beta diversity revealed increased inter-patient variability in bacterial communities after surgery (PERMANOVA p = 0.001). Preoperative network analyses identified 18 microbial network clusters and interkingdom associations between bacteria and fungi. KEGG pathway mapping showed cluster-specific metabolic profiles, including enrichment in degradation pathways, antimicrobial resistance mechanisms, and bacterial secretion systems. The contrasting responses of bacterial and fungal communities highlight the importance of considering the entire gut microbiome in perioperative care and suggest a central role for interkingdom interactions in maintaining gut homeostasis during surgical recovery.}, }
@article {pmid42253941, year = {2026}, author = {Yu, R and Zhang, M and Meng, Y and Zhu, C and Zhang, W and Zhang, H and Cao, Z and Du, M and Zhao, Z and Bai, J and Han, Y and Tang, Y and Kang, W and To, KF and Jiao, S and An, L and Zhou, Z}, title = {Gastric Cancer: Pathobiology and Therapeutics.}, journal = {MedComm}, volume = {7}, number = {6}, pages = {e70772}, pmid = {42253941}, issn = {2688-2663}, abstract = {Gastric cancer (GC) remains a formidable global health challenge, characterized by pronounced molecular heterogeneity, late-stage diagnosis, and limited durable responses to existing therapies. This review synthesizes recent advances in GC research through an integrated, multidisciplinary lens, spanning tumor biology, microenvironmental dynamics, and therapeutic innovation. We first consolidate updated histopathological and molecular classification systems, highlighting oncogenic programs that underpin GC development, including Hippo-YAP signaling and emerging neural-stem cell interactions. We then examine the immunosuppressive tumor microenvironment, emphasizing the dynamic crosstalk among tumor-associated macrophages, regulatory T cells, tertiary lymphoid structures, and cancer-associated fibroblasts that collectively drive metastatic dissemination and therapeutic resistance. Emerging biomarker-guided strategies, including CLDN18.2-targeted therapies, dual immune checkpoint blockade, and engineered cellular therapies, are critically discussed alongside rational combination approaches designed to overcome resistance. Beyond canonical paradigms, we highlight transformative frontiers, such as cancer neuroscience, microbiome-driven immune modulation, and spatially resolved multiomics technologies, that enable high-resolution mapping of cellular interactions. Finally, we critically assess translational barriers, including organ-specific metastatic tropism and resistance evolution, and propose that the convergence of deep molecular profiling, neural-immune modulation, and AI-enabled computational oncology will be central to advancing precision medicine for GC. This integrated framework aims to accelerate the development of mechanism-based combination therapies.}, }
@article {pmid42253950, year = {2026}, author = {Han, X and Guo, XL and Qiu, J}, title = {From gut-reproductive microbiota to ferroptosis: a comprehensive insight into the molecular-pathogenicity of endometriosis.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1762013}, pmid = {42253950}, issn = {1664-3224}, abstract = {Endometriosis (EMS) is a highly heterogeneous chronic gynecological disease characterized by pain, infertility, and relapse, with its etiology and pathogenesis not yet fully elucidated. Traditional theories, including "retrograde menstruation," "implantation theory," and "abnormalities in immune tolerance," struggle to adequately explain the complex lesion behavior, diverse phenotypic characteristics, and accompanying immune-metabolic disorders. In recent years, the key roles of imbalances in the gut and reproductive microbiomes, abnormal iron metabolism, and the newly proposed ferroptosis in the occurrence and development of EMS have gradually gained attention, suggesting that this disease may be a systemic condition involving the interplay of microbial ecology, iron metabolism, and cell death. Existing studies indicate that the gut-reproductive microbiome profoundly influences the body's iron homeostasis and iron load by regulating mucosal immunity, systemic inflammatory responses, and metabolic environments. This, in turn, activates the ferroptosis pathway through iron-dependent lipid peroxidation and cell membrane damage, participating in the formation, maintenance, and inflammatory microenvironment shaping of ectopic lesions. Based on these findings, this article systematically reviews the interactions between gut-reproductive microbiome imbalance and iron metabolism disorders, integrating multi-omics evidence such as microbiome analysis, metabolomics, and iron metabolism/ferroptosis-related molecular markers. It proposes a new pathological mechanism framework of "dysbiosis-iron overload-ferroptosis" incorporating microecological imbalance and ferroptosis into a unified picture of the pathogenesis of EMS. Furthermore, this article discusses potential therapeutic strategies and application prospects surrounding microbiome remodeling (such as probiotics, fecal microbiota transplantation, dietary and lifestyle interventions) and pharmacological targeting of key ferroptosis-related molecules. Through a comprehensive and critical analysis of existing evidence, this review aims to provide a more systematic theoretical framework for the mechanistic research of EMS and offer ideas and directions for future clinical translation of precise classification, individualized intervention, and novel treatment plans.}, }
@article {pmid42253968, year = {2026}, author = {Feng, P and Zhang, W and Zhao, Y and Zhao, P and Li, E}, title = {Synthetic microbial communities: a novel emerging models for dissecting gut microbiota-host interactions in neurodegenerative diseases.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1822743}, pmid = {42253968}, issn = {1664-3224}, abstract = {The gut-brain axis (GBA) has emerged as a critical regulatory pathway underlying the pathogenesis of neurodegenerative diseases (NDs) such as Alzheimer's disease and Parkinson's disease. However, the high complexity and individual variability of native gut microbiotas hinder the precise elucidation of causal relationships between specific microbial taxa, their metabolites, and host neuroinflammatory or neurodegenerative processes. Synthetic microbial communities (SynComs), consisting of defined and reproducible bacterial strains, have recently emerged as powerful experimental models to overcome these limitations. This review summarizes the applications of SynComs in dissecting GBA crosstalk in NDs, highlighting their utility in validating key microbial mediators, deciphering molecular signaling pathways (e.g., microbial metabolite-brain barrier interactions, immune cell activation), and evaluating therapeutic strategies targeting the gut microbiota. By reducing community complexity while retaining core functional traits, SynComs enable controlled in vitro and in vivo studies that bridge the gap between observational microbiome profiling and mechanistic insights. Furthermore, the customization of SynComs allows for mimicking disease-specific microbial dysbiosis, facilitating the identification of novel therapeutic targets for NDs. Collectively, SynComs represent an innovative and standardized tool to advance our understanding of gut microbiota-host interactions in neurodegeneration and accelerate the development of microbiome-based interventions.}, }
@article {pmid42254101, year = {2026}, author = {Khan, SA and Qamar, MA and Ali, T and Omer, MH and Tahir, A}, title = {Reconsidering immunotherapy resistance: the emerging role of the tumor microbiome in head and neck and lung cancers.}, journal = {Annals of medicine and surgery (2012)}, volume = {88}, number = {6}, pages = {3812-3814}, pmid = {42254101}, issn = {2049-0801}, abstract = {Immunotherapy with immune checkpoint inhibitors (ICIs) has revolutionized treatment for non-small cell lung cancer (NSCLC) and head and neck squamous cell carcinoma (HNSCC), yet resistance limits durable responses in many patients. Emerging evidence implicates the intratumoral microbiome - comprising bacteria, fungi, and viruses within tumor tissues - as a key modulator of tumor biology, immune infiltration, and ICI sensitivity, beyond traditional tumor-intrinsic and immune factors. In HNSCC, human papillomavirus (HPV)-negative tumors exhibit higher oncobacteria abundance than HPV-positive ones, with elevated levels linked to worse survival in HPV-positive oropharyngeal cases, suggesting an immunosuppressive tumor microenvironment that may influence ICI outcomes. In NSCLC, intratumoral taxa such as Fusobacterium nucleatum and Bacteroides fragilis promote progression and evasion via immune checkpoint modulation (PD-1/PD-L1), pro-inflammatory pathways (toll-like receptors and cytokines like interleukin-6/tumour necrosis factor-alpha), metabolic reprogramming (PI3K/AKT), and recruitment of suppressive cells (neutrophils and myeloid-derived suppressor cells). Pan-cancer studies show microbial enrichments and compositional shifts in responders versus non-responders to ICI, with metabolites (e.g., lactate and succinic acid) driving M2 macrophage polarization, T-cell suppression, and resistance. The gut-tumor axis further exacerbates refractoriness through systemic dysbiosis and immune alterations. Preclinical models indicate that targeted microbiome interventions - such as fecal microbiota transplantation, specific probiotics (e.g., Bifidobacterium spp. and Akkermansia muciniphila), or selective antibiotics - can restore antitumor immunity, enhance ICI efficacy, and minimize broad dysbiosis risks. Integrating intratumoral microbial profiling into HNSCC and NSCLC clinical trials could refine patient stratification, uncover predictive biomarkers, and accelerate microbiome-directed adjunct therapies, advancing precision oncology and expanding immunotherapy benefits.}, }
@article {pmid42254119, year = {2026}, author = {Sanan, A and Bibi, F and Sadat, SH}, title = {Rare co-existence of rodent-borne arenavirus patterns and autoimmune-like systemic flares: novel microbiome markers for public health risk stratification.}, journal = {Annals of medicine and surgery (2012)}, volume = {88}, number = {6}, pages = {3901-3902}, pmid = {42254119}, issn = {2049-0801}, }
@article {pmid42254157, year = {2026}, author = {Arif, L and Abbasi, MM and Raza, AA and Samadi, A}, title = {From microbiome profiling to precision medicine: diagnostic and therapeutic potential in gastrointestinal disorders: current evidence, challenges, and future directions.}, journal = {Annals of medicine and surgery (2012)}, volume = {88}, number = {6}, pages = {3348-3359}, pmid = {42254157}, issn = {2049-0801}, abstract = {Gastrointestinal (GI) disorders, affecting millions globally (approximately 1.5 billion people with IBS alone), impose a significant healthcare burden and remain challenging to diagnose and manage. Current approaches are often invasive or symptom based, highlighting an urgent need for more precise and personalized strategies. The gut microbiome may offer novel diagnostic biomarkers and therapeutic targets, potentially transforming patient care. It supports GI and systemic health via metabolism, immune modulation, and neurochemical signaling. The dysbiosis of the gut microbiota contributes significantly to the pathogenesis of various GI disorders, including inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), colorectal cancer (CRC), and small intestinal bacterial overgrowth. This narrative review critically evaluates the diagnostic potential of microbiome profiling and its clinical applications in developing personalized therapeutic strategies. We examine cutting-edge techniques such as 16S rRNA sequencing, metagenomics, and metabolomics, and discuss how dietary modulation, precision probiotics, and fecal microbiota transplantation are being increasingly used to reshape gut microbial composition. However, it is critical to note that while microbiome alterations show consistent associations with GI diseases, current evidence remains largely observational and associative. To date, no microbiome-based test has achieved regulatory approval or clinical validation as a standalone diagnostic tool for IBD, IBS, or CRC, and therapeutic applications remain investigational with modest clinical benefits in select conditions. Additionally, we highlight the translational challenges of integrating microbiome-based diagnostics into mainstream clinical practice and propose future research imperatives. This review provides a balanced perspective on the promise and challenges of integrating microbiome-based approaches into clinical gastroenterology, while proposing actionable research priorities to guide future investigations toward clinically validated, patient-centered diagnostic, and therapeutic solutions.}, }
@article {pmid42254190, year = {2026}, author = {Wu, X and Cai, S and Bai, Z and Li, P and Jia, Y and Li, J}, title = {Association between the oral microbiota and hyperlipidemia: evidence from a national cross-sectional study.}, journal = {Annals of medicine and surgery (2012)}, volume = {88}, number = {6}, pages = {3129-3141}, pmid = {42254190}, issn = {2049-0801}, abstract = {BACKGROUND: Oral and gut microbiota interact in the pathogenesis of metabolic diseases. However, the associations between the oral microbiome and host lipid metabolism remain unclear. This study aimed to explore the relationship between metabolic syndrome and the oral microbiome.<br><br>METHODS: Participants from the 2009-2012 National Health and Nutrition Examination Survey database were analyzed. Correlations between alpha diversity and hyperlipidemia, as well as blood lipid levels, were examined. Principal coordinate analysis and permutational multivariate analysis of variance were used to determine differences in microbial composition between groups. Linear discriminant analysis effect size (LEfSe) analysis identified key microbial taxa associated with hyperlipidemia. Cox regression and Kaplan&#x2012;Meier methods were applied for survival analyses. Functional Annotation of Prokaryotic Taxa and mediation analyses were used to explore the role of microbial functions in microbiome-mediated hyperlipidemia risk.<br><br>RESULTS: A total of 3104 participants were included, with 2215 diagnosed with hyperlipidemia. Multivariate linear regression revealed significant correlations between alpha diversity and total cholesterol and low-density lipoprotein levels (P < 0.017). Cox regression indicated that higher oral microbial alpha diversity was associated with a lower risk of cardiovascular mortality (P < 0.017). Beta diversity analysis revealed distinct oral microbial profiles between hyperlipidemic and non-hyperlipidemic individuals (P < 0.017). LEfSe analysis identified Prevotella and Parvimonas as key genera enriched in the oral microbiota of hyperlipidemic participants. Sulfur metabolism partially mediated the association between Parvimonas and hyperlipidemia.<br><br>CONCLUSION: The oral microbiota is closely associated with host lipid metabolism. Prevotella and Parvimonas exhibit higher oral abundances in hyperlipidemic individuals, with Parvimonas abundance directly correlated with blood lipids. Parvimonas may increase hyperlipidemia risk via sulfur metabolism. Further studies are needed to elucidate the underlying mechanisms, which could serve as effective targets for hyperlipidemia management.}, }
@article {pmid42254217, year = {2026}, author = {Saad Ibrahim Abdelghany Elbeshbishy, R and Khatak, A}, title = {The skin microbiome: the overlooked axis in modern dermatology.}, journal = {Annals of medicine and surgery (2012)}, volume = {88}, number = {6}, pages = {3045-3047}, pmid = {42254217}, issn = {2049-0801}, abstract = {The skin microbiome plays a critical role in maintaining cutaneous barrier integrity, modulating immune responses, and influencing the expression of dermatologic disease, yet its integration into clinical practice remains limited. Microbial alterations have been described in conditions such as atopic dermatitis, acne vulgaris, psoriasis, and chronic wounds; however, uncertainty regarding causality, interindividual variability, and lack of methodological standardization have hindered clinical translation. Current diagnostic frameworks rarely incorporate microbial metrics, while antimicrobial therapies remain central to management, often without consistent consideration of their ecological impact. Emerging microbiome-directed strategies, including topical probiotics, bacteriophage therapy, and microbiome-preserving approaches, show early promise but lack robust clinical validation. Advancing the role of the skin microbiome in dermatology will require standardized research methodologies, integration of multi-omics approaches, and well-designed clinical trials with clinically meaningful outcomes. This editorial highlights the need for a balanced and evidence-based framework that incorporates microbial perspectives into dermatology without overstating current evidence, advocating for a gradual integration that complements established immunologic and barrier-focused paradigms.}, }
@article {pmid42254258, year = {2026}, author = {Panhwar, H and Panhwar, DM and Mudasir, M and Mahato, AK}, title = {Microbiome-derived metabolites as novel placental functional markers: predictive role in vasa previa.}, journal = {Annals of medicine and surgery (2012)}, volume = {88}, number = {6}, pages = {3859-3860}, pmid = {42254258}, issn = {2049-0801}, }
@article {pmid42254377, year = {2026}, author = {Storck-Thy, C and Krogfelt, KA and Jønsson, R}, title = {The overlooked role of the seminovaginal microbiota in infertility: a narrative mini review.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1784130}, pmid = {42254377}, issn = {2296-858X}, abstract = {Infertility affects up to 15% of couples worldwide and is influenced by complex biological, immunological, and environmental factors. While reproductive microbiome research has expanded rapidly, the majority of published studies remain largely descriptive, focusing on taxonomic profiling rather than functional or mechanistic insight. Findings from vaginal microbiome studies have been heterogeneous and strongly influenced by methodological variation, and the male genital microbiome has received comparatively less attention, particularly in a couple context. This narrative mini review provides a synthesis of studies investigating paired male and female reproductive microbiomes, emphasizing observational evidence of partner- associated microbial patterns in relation to fertility outcomes. The term 'seminovaginal' microbiota is discussed as a hypothesis describing the transient and dynamic interface arising during sexual activity. Current evidence is limited, largely associative, and constrained by insufficient standardization of sampling, sample handling and processing, data analysis, restricting causal interpretation. Addressing these gaps through coupled, longitudinal, and mechanistic study designs is essential for advancing biologically meaningful conclusions in infertility research and reproductive treatments.}, }
@article {pmid42254439, year = {2026}, author = {Rahimah, S and Tallei, TE and Savitri, M and Yamada, C and Kim, HJ and Choi, M and Park, MN and Ophinni, Y and Kim, B}, title = {Nutraceutical Interventions in Stunting: Advances, Challenges, and Prospects.}, journal = {Food science &amp; nutrition}, volume = {14}, number = {5}, pages = {e71910}, pmid = {42254439}, issn = {2048-7177}, abstract = {Childhood stunting remains a major global health challenge, reflecting the cumulative effects of inadequate nutrition, recurrent infection, and chronic intestinal dysfunction during early life. Beyond conventional micronutrient supplementation, nutraceutical interventions have emerged as complementary strategies to address the complex biological pathways underlying impaired linear growth. This review synthesizes current evidence on nutraceutical approaches to stunting, including improvements in macronutrient quality, bioactive food components, and microbiome-targeted strategies such as probiotics, prebiotics, synbiotics, postbiotics, and microbiota-directed foods. Evidence from clinical and preclinical studies indicates that nutraceutical effects on growth are generally modest and heterogeneous, with more consistent effects on weight gain than on height-for-age (HAZ). Variability in efficacy is strongly influenced by baseline nutritional status, environmental enteric dysfunction (EED), infection burden, dietary quality, and water, sanitation, and hygiene (WASH) conditions. Mechanistically, nutraceuticals may act through modulation of gut barrier integrity, inflammatory tone, microbial metabolism, and endocrine signaling pathways, particularly those involving the growth hormone-insulin-like growth factor-1 (GH-IGF-1) axis. Recent microbiota-directed food trials provide proof-of-concept that targeted correction of microbiome immaturity and gut dysfunction can support linear growth. Looking forward, advances in nutrigenomics, microbiome science, and epigenetics support a shift toward precision nutrition strategies that tailor interventions to biological responsiveness and context. Systems biology approaches integrating multi-omics data, network pharmacology, and interpretable artificial intelligence are expected to refine mechanistic understanding and guide intervention design. Effective translation will require rigorous trial designs, regulatory clarity, and integration of nutraceuticals within broader stunting reduction frameworks in low- and middle-income countries.}, }
@article {pmid42254500, year = {2026}, author = {Kubota, A and Zang, L and Shinkai, T and Nakai, M and Tajima, A and Shimada, Y}, title = {Systems-level investigation of the anxiolytic gut-brain interactions induced by paraprobiotic Lactobacillus brevis SBC8803 in zebrafish.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1804536}, pmid = {42254500}, issn = {1664-302X}, abstract = {INTRODUCTION: Anxiety disorders are among the most prevalent mental health conditions worldwide, and interest in psychobiotics-live or inactivated microorganisms that beneficially modulate the microbiota-gut-brain axis-is increasing. Heat killed Lactobacillus brevis SBC8803 enhances serotonin (5 hydroxytryptamine; 5 HT) signaling and ameliorates stress-related phenotypes in mammals, although the gut-brain pathways mediating these effects remain incompletely defined. Here, we investigated the anxiolytic effects and underlying molecular mechanisms of oral SBC8803 administration in adult zebrafish.<br><br>METHODS: Adult male AB-strain zebrafish were fed a diet containing heat killed SBC8803 for 4 weeks, and anxiety-like behavior was evaluated using the novel tank test. To explore the underlying mechanisms, we performed brain RNA sequencing and V3-V4 region of 16S rRNA amplicon sequencing of intestinal contents, followed by integrative multi omics analyses, including Gene Set Variation Analysis (GSVA) combined with DIABLO-based data integration and residual correlation analysis.<br><br>RESULTS: SBC8803-treated fish exhibited a shorter latency to enter the upper half of the tank and more frequent entries into this region, consistent with reduced anxiety-like behavior. Brain transcriptomic profiling identified differentially expressed genes and enrichment of serotonin receptor, CREB, and oxytocin signaling pathways, suggesting enhanced monoaminergic and plasticity-related signaling. Microbiome functional prediction indicated SBC8803-associated shifts in lipid and vitamin metabolism, including pathways related to riboflavin (vitamin B2) and tryptophan. GSVA combined with DIABLO-based data integration revealed coordinated changes between microbial metabolic and brain signaling pathways, consistent with a vitamin B-serotonin-anti-inflammatory axis linking gut metabolism to neural regulation. Furthermore, residual correlation analysis showed innate gut-brain coordination independent of the SBC8803 effect, such as the coupling between brain arachidonic acid and gut histidine metabolism.<br><br>DISCUSSION: These findings support the biological validity of the SBC8803 administration-associated interactions observed in the multi-omics analyses. These findings suggest that the paraprobiotic SBC8803 may exert anxiolytic-like effects in zebrafish and reshape gut-brain network states at behavioral, microbial, and transcriptomic levels, providing a potential mechanistic framework for considering heat killed SBC8803 as a candidate psychobiotic for anxiety-related conditions.}, }
@article {pmid42254513, year = {2026}, author = {Zhang, H and He, R and Xu, L and Zhou, H and Yu, R and Huang, P}, title = {A multi-omics case-control study identifying oropharyngeal microbiome-metabolite patterns that characterize secondary bacterial pneumonia among influenza patients.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1824965}, pmid = {42254513}, issn = {1664-302X}, abstract = {Secondary bacterial pneumonia is a severe complication of influenza;howeve the biological determinants that distinguish progression from uncomplicated infection remain poorly understood. We investigated the oropharyngeal microbiome and plasma metabolome as potential discriminators of pneumonia development. In this study, we report a cross-sectional case-control study conducted during the 2022-2023 influenza season to identify and internally validate a microbiome-metabolite profile that characterizes pneumonia cases from uncomplicated influenza. We enrolled 236 consecutive influenza patients from Jiangsu Province, China (October 2023-December 2024): 59 with secondary pneumonia and 177 uncomplicated controls. Oropharyngeal swabs were subjected to 16S rRNA V3-V4 sequencing; plasma metabolomics was performed by UPLC-MS/MS in both ion modes. Seven machine-learning algorithms were compared; Least Absolute Shrinkage and Selection Operator (LASSO) logistic regression was selected because it yielded the highest cross-validated discrimination. Microbial composition distinguished groups, not richness. Pneumonia cases showed enrichment of Synergistota and Bifidobacteriaceae with depletion of Bacillaceae (β-diversity p = 0.057). Controls exhibited enriched glycolysis and lipid metabolism pathways; pneumonia cases showed elevated degradation pathways (GLUCARDEG and GALLATE-DEGRADATION). Plasma metabolomics revealed a lipid depletion signature: phospholipids PC(O-16:0/0:0) and PS(14:0/18:3(9Z,12Z,15Z)) were significantly reduced (area under the (receiver operating characteristic) curves (AUCs) = 0.69-0.71). Small Molecule Pathway Database (SMPDB) pathway analysis demonstrated suppressed anabolic (tyrosine, steroid, and purine metabolism) and enhanced catabolic (beta-oxidation of very long-chain fatty acids) pathways. Machine learning identified Peptococcus as the top indicator (LASSO AUC = 0.65); Shapley Additive Explanation (SHAP) analysis revealed a monotonic risk increase with abundance. Oropharyngeal dysbiosis and systemic metabolic reprogramming characterize influenza cases that progress to secondary pneumonia. Peptococcus and four metabolites form an internally validated exploratory profile associated with secondary pneumonia; external validation and performance optimization are warranted.}, }
@article {pmid42254515, year = {2026}, author = {Chen, H and Montero-Vale, M and Owusu-Kyei, K and Lara-Muñoz, A and Rubio-Garcia, E and de Pedro-Jové, R and Guiral, E and Chileshe, MN and Williams, J and Bofill, A and Samai, M and Casals-Pascual, C and Vila, J and Menéndez, C}, title = {Early-life carriage and antibiotic resistance of Streptococcus pneumoniae in infants from Sierra Leone.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1822296}, pmid = {42254515}, issn = {1664-302X}, abstract = {Streptococcus pneumoniae remains a major cause of child morbidity and mortality in sub-Saharan Africa, with increasing macrolide resistance mediated by erm(B) and mef(A/E/I). Integrating phenotypic and sequencing-based approaches may improve antimicrobial resistance surveillance accuracy. This study assessed nasopharyngeal carriage and macrolide resistance of S. pneumoniae among young infants in Sierra Leone (November 2022-February 2023), nested within the ICARIA trial (NCT04235816) which evaluated azithromycin for child mortality reduction. Infants aged 6-10 weeks presenting for Penta-1 immunization before trial recruitment were enrolled. Two nasopharyngeal swabs were collected per infant. S. pneumoniae was detected by lytA PCR, azithromycin minimal inhibitory concentrations (MICs) were determined by E-test, and erm(B) and mef(A/E) were identified by PCR in isolates. A subset of paired samples underwent targeted amplicon sequencing for microbiome and resistome profiling. Carriage prevalence was 17.3% (162/936; 95% CI: 14.9-19.9%), with 45.7% (74/162) of isolates resistant to azithromycin (MIC ≥ 2 μg/mL). High-level resistance (MIC ≥ 64 μg/mL) was mainly mediated by erm(B) alone (53.8%) or in combination with mef(A/E) (38.5%), whereas all 22 moderately resistant isolates (MIC 2-48 μg/mL) carried mef(A/E) only. Among susceptible isolates, 3.8% (2/52) harbored mef(A/E) despite low MICs. Microbiome sequencing showed 96% concordance with lytA PCR for S. pneumoniae detection. Normalized resistome read counts for erm(B) and mef(A/E) were significantly higher in PCR-positive samples (p = 1.98 × 10[-9] and p = 8.14 × 10[-7]). These findings provide the first estimates of nasopharyngeal S. pneumoniae carriage and macrolide resistance among infants in Sierra Leone, revealing a high prevalence of resistance. The results underscore the need to strengthen antibiotic stewardship, particularly in child survival programs with azithromycin. Large and longitudinal studies are also needed. Clinical Trial Registration: ClinicalTrials.gov, NCT04235816.}, }
@article {pmid42244577, year = {2026}, author = {Ettinger, CL and Eisen, JA}, title = {Phoronids and their tubes harbor distinct microbiomes compared to surrounding sediment.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.05.28.596327}, pmid = {42244577}, issn = {2692-8205}, abstract = {Phoronids are a phylum of animals with only ∼12 described species, all of which are marine filter feeders that build external tubes for shelter and produce chemical deterrents against predators. Many tube-building invertebrates host distinct microbial communities and even have obligate symbionts for survival in sulfur-rich marine sediments. However, the microbiome of phoronids has only recently begun to be described. To address this, we surveyed the composition of the microbiome of the phoronid, Phoronopsis harmeri , using 16S rRNA gene amplicon and metagenomic sequencing. We found that the phoronid microbiome was dominated by members of the orders Campylobacterales, Desulfobulbales, and Desulfobacterales. We also found that the microbiomes of tubes and phoronids were less diverse than that of surrounding sediment, and that the microbiomes of phoronids, tubes and surrounding sediment were all distinctly structured. Based on analysis of metagenomic data, and even though we were only able to recover low quality MAGs of abundant taxa, we found preliminary evidence that taxa associated with phoronids and their tubes likely participate in sulfur cycling pathways. Future work should perform more robust metagenomic sequencing and chemical analysis to assess if there is a link between known phoronid chemical defenses and microorganisms. Overall, this study provides foundational insight into the microbial communities associated with phoronids and these initial findings suggest that these communities may play an important role in sulfur cycling in marine sediments.}, }
@article {pmid42244628, year = {2026}, author = {Getange, D and Mukaratirwa, S and Chebet, D and Kabii, J and Khogali, R and Villinger, J}, title = {Ehrlichia ruminantium infection is associated with tissue-specific microbial community shifts in Amblyomma gemma ticks from cattle in Kenya.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.26.727963}, pmid = {42244628}, issn = {2692-8205}, abstract = {UNLABELLED: Tick-borne pathogens can reshape vector microbiomes in ways that influence pathogen colonisation and transmission, yet the interplay between Ehrlichia ruminantium and the microbiota of its tick vectors remains uncharacterised. We profiled bacterial communities in haemolymph, midgut, and salivary glands of infected (n = 11) and uninfected (n = 12) Am. gemma ticks, a vector of E. ruminantium in East Africa, collected from cattle in Kajiado County, Kenya, using near-full-length 16S rRNA gene amplicon sequencing on the Oxford Nanopore platform. Community composition, alpha and beta diversity, co-occurrence networks, keystone taxa, and PICRUSt2-inferred functional profiles were compared across tissue-infection status groups. We identified 226 bacterial genera dominated by Coxiella , Pseudomonas , Acinetobacter , Proteus , and Rickettsia . Infection was associated with tissue-specific shifts in community composition (PERMANOVA R [2] = 0.14, p < 0.001) and co-occurrence network structure, with midgut networks showing complete hub taxon turnover (Jaccard = 0.000, p = 0.043). Haemolymph communities converged around Luteimonas as a keystone taxon, while opportunistic Proteobacteria, including Acinetobacter and Serratia , emerged as keystones in infected midgut. Endosymbiotic Rickettsia was near-absent in infected tissues (0.3% vs 9.3% mean relative abundance in midgut), consistent with competitive exclusion. Functional inference identified FDR-significant enrichment of predicted aerobactin siderophore biosynthesis, antimicrobial efflux, and oxidative stress response gene families in infected microbiota. These findings show tissue-specific restructuring of the Am. gemma microbiome associated with E. ruminantium infection and point to candidate targets for microbiome-based interventions against heartwater.<br><br>IMPORTANCE: Heartwater, caused by the bacterium Ehrlichia ruminantium and transmitted by Amblyomma ticks, kills up to 90% of susceptible ruminants and is one of the most devastating tick-borne diseases in sub-Saharan Africa. Controlling heartwater requires understanding how the pathogen interacts with the microbial communities living inside its tick vector. In this exploratory study, we show that E. ruminantium infection is associated with tissue-specific shifts in the Amblyomma tick microbiome, including reduced abundance of beneficial symbionts, elevated representation of opportunistic bacteria among community hubs, and enrichment of iron acquisition and antimicrobial resistance functions. The midgut, the first tissue colonised during infection, showed the most marked structural reorganisation. These tissue-resolved microbiome signatures point to potential targets for novel control strategies, such as anti-microbiota vaccines or approaches that reinforce natural colonisation resistance, offering new strategies to reduce heartwater transmission and protect livestock livelihoods across Africa.}, }
@article {pmid42244638, year = {2026}, author = {Zeng, X and Meng, X and Weakley, AM and Jarrett, KE and Higginbottom, S and Lopez, EM and Cabrera, AV and Gray, IJ and DeFelice, BC and Terasaki, M and Lai, R and Brearley-Sholto, M and Zhao, A and Hall, KR and Levia, M and Arreola, J and de Aguiar Vallim, TQ and Fischbach, MA}, title = {Ecology and engineering to modify the bile acid output of a defined microbial community.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.23.727444}, pmid = {42244638}, issn = {2692-8205}, abstract = {The bile acid pool, which is synthesized collaboratively by the host and its microbiome, impacts metabolism, immunity, and disease risk. Targeted microbiome interventions could in principle reshape the bile acid pool for therapeutic benefit, but practical strategies remain elusive. In the course of screening a complex defined community for metabolic phenotypes by dropping out individual strains, we observed that several of the single-strain dropout communities had markedly increased deoxycholic and lithocholic acid levels and a larger bile acid pool. In each of these communities, a second strain- Lactobacillus plantarum- had bloomed. The bile salt hydrolase activity of L. plantarum was necessary and sufficient to expand the size of the bile acid pool. An engineered community in which the bsh gene is overexpressed in multiple Lactobacillus strains confers on mice increased levels of secondary bile acid levels and a larger pool size. By overexpressing a different pair of bile acid metabolic genes in multiple strains of Lactobacillus -7α- and 7β-hydroxysteroid dehydrogenase-we changed the composition of the bile acid pool, enlarging it and redirecting it toward ursodeoxycholic acid. Together, these results demonstrate that fine details of the microbiome's strain composition can have a substantial effect on bile acid metabolism, and that rational manipulation of the microbiome can alter the size and composition of the bile acid pool.}, }
@article {pmid42244647, year = {2026}, author = {Zeng, X and Meng, X and Weakley, AM and Higginbottom, S and Lopez, EM and Cabrera, AV and Gray, IJ and DeFelice, BC and Terasaki, M and Zhao, A and Hall, KR and Levia, M and Arreola, J and Fischbach, MA}, title = {A single-strain dropout screen reveals mechanistic links between microbial ecology and metabolism.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.23.727446}, pmid = {42244647}, issn = {2692-8205}, abstract = {The complexity of the gut microbiome has made it challenging to define the role of individual species in community-level function. Here, we constructed 56 single-strain dropout variants of a defined 118-member community and used each one to colonize a group of germ-free mice. In many cases, removing a single strain triggered a large reordering of a small group of species, which in turn altered the community's metabolic output. En bloc removal of the eight-strain acetogen compartment markedly reduced acetate production and caused intestinal H 2 accumulation and bloating; a specific subset of four acetogens was sufficient to relieve bloating and restore acetate production. Together, these data show that small disturbances in community composition can trigger a confined ecological reorganization with a large chemical phenotype, and they reveal novel strategies for engineering communities with altered metabolic output.}, }
@article {pmid42244659, year = {2026}, author = {De Silva, GLSN and Vinzelj, J and Miller, SL and Jemmett, AM and Elshahed, MS and Youssef, NH}, title = {Diversity and community structure of anaerobic gut fungi in camels.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.28.728439}, pmid = {42244659}, issn = {2692-8205}, abstract = {Anaerobic gut fungi (AGF) are key members of the herbivorous gut microbiome. While AGF communities have been well-studied in foregut and hindgut fermenters, they remain poorly characterized in pseudoruminants such as camels. Here, we present a comprehensive culture-independent diversity survey of 142 fecal samples from all three extant camel species (Camelus dromedarius , Camelus bactrianus , and Camelus ferus). The AGF community in Camelus was highly diverse, with representatives of 42 AGF genera identified. However, this diversity was unevenly distributed, with three genera (Neocallimastix , Caecomyces , and Orpinomyces) accounting for 70.7% of sequences encountered, and only 12 genera exceeding 1% relative abundance in the entire dataset. While several of the genera identified as major components of the AGF community in camels are highly ubiquitous in all herbivores, others, such as Oontomyces, Aestipascuomyces , Liebetanzomyces , and the yet uncultured genera NY09, NY03, and JV-2025d are extremely rare in ruminants and hindgut fermenters, hinting at their preference and potential co-evolution with the Camelidae . Ordination approaches identified host species and biogeography as key determinants driving AGF community structure differences between various camel species. Comparative community structure analysis between AGF community in camels versus reference foregut and hindgut fermenters identified the relative enrichment of the genera Oontomyces and Aestipascuomyces in pseudoruminants datasets. Our results demonstrate a distinct AGF community composition in Camelidae , elucidate factors impacting AGF diversity and community structure variations in Camelus, and identify key distinct taxa differentially enriched in psuedoruminants compared to ruminants and hindgut fermenters. The ecological and evolutionary drivers of such patterns are discussed.}, }
@article {pmid42244690, year = {2026}, author = {Tao, J and Gomez, D and Abu, YF and Rojas, K and Roy, S}, title = {Short-term oxycodone exposure produces delayed and persistent gut microbiome disruption in mice.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.26.727957}, pmid = {42244690}, issn = {2692-8205}, abstract = {UNLABELLED: The gut microbiome is a critical part of host homeostasis, yet its resilience following opioid exposure remains poorly understood. While opioid-induced short-term dysbiosis is well documented, the long-term recovery dynamics following oxycodone remain unclear. This study characterized the temporal dynamics of the fecal microbiota in male C57BL/6J mice following a brief 3-day oxycodone regimen (5mg/kg, BID). 16S rRNA gene sequencing was performed at baseline, day 3, 10, 17, and 70. While acute post-treatment phases (day 3 to 10) showed subtle taxonomic shifts in Clostridium_sensu_stricto_1 and Romboutsia , significant community disruption emerged later. By day 17, beta diversity significantly differed from saline controls (P =0.002). At day 70, both alpha diversity (p=0.02) and beta diversity (P=0.007) remained significantly altered, characterized by enriched Akkermansia and Marvinbryantia alongside depleted Eubacterium_xylanophilum . These findings demonstrate that even brief oxycodone exposure triggers persistent, non-recovering dysbiosis that became detectable only after treatment cessation and persisted through day 70. This suggests that the window for microbiome recovery exceeds two months in mice (equivalent to several human years), highlighting a potential long-term risk for patients prescribed short-term opioid courses.<br><br>IMPORTANCE: Short-term opioid exposure is generally assumed to cause only transient disruption of the gut microbiome. However, the duration of microbiome recovery following clinically relevant opioid treatment remains poorly defined. In this study, we show that a brief three-day course of oxycodone in mice resulted in delayed and persistent alterations in gut microbial community structure that remained detectable for at least 70 days after treatment cessation. Notably, significant divergence in microbial composition emerged weeks after exposure rather than immediately following treatment, suggesting that short-term opioid use may initiate longer-lasting remodeling of the gut microbiome than previously appreciated. These findings highlight the importance of considering extended recovery timelines when evaluating the microbiological consequences of opioid exposure.}, }
@article {pmid42244733, year = {2026}, author = {Grossman, A and Weng, J and Silverman, AD and Bor, B}, title = {Resolving Host-Episymbiont Interaction Dynamics through Continuous Cultivation.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.01.722272}, pmid = {42244733}, issn = {2692-8205}, abstract = {UNLABELLED: Patescibacteria are an elusive linage of "microbial dark matter" bacteria predicted to represent ∼25% of total bacterial diversity. Despite this abundance and ubiquity, these organisms are challenging to cultivate, resulting from their specialized episymbiotic lifestyle. All cultivated representatives to date, predominantly composed of Saccharibacteria from the oral microbiome, depend on cognate prokaryotic hosts for growth and reproduction. Studying the growth dynamics of episymbiotic bacteria and their hosts in batch cultures has suggested that many episymbionts initially reduce host populations, and that hosts eventually adapt to episymbiont stress after serial passaging. However, discontinuous batch cultures do not reflect natural interactions between these organisms due to their drastically different growth rates. An episymbiont requires several (∼2-4) serial passages alongside its host to reach the high cell densities needed to impact host growth, which complicates investigation of host inhibition and adaptation to episymbiont stress. To describe these dynamics accurately, we utilized continuous culture via small-scale Raspberry Pi powered bioreactors, called Pioreactors. Within a bioreactor, host bacteria can be cultivated at a consistent growth rate indefinitely, providing the perfect substrate for cultivation of model Saccharibacteria. Quantification of time until host crash, crash severity, time until recovery, and stable co-culture density provides mechanistic ways to describe episymbiont-host interactions. First, we used these techniques to compare episymbiont infection by three different episymbionts, revealing distinct infection patterns ranging from mild inhibition with rapid host adaptation, to rapid host collapse followed by "arms race" oscillation dynamics. Then, bioreactors were used to quantify the episymbiotic role played by a known host-binding type 4 pili (T4P-2), demonstrating that loss of long-distance host binding significantly delayed the host crash without altering general crash dynamics. These experiments reveal that episymbionts can have drastically different effects on bacterial communities and provide the tools necessary to describe strain/species differences and molecular interactions.<br><br>IMPORTANCE: Episymbiotic Patescibacteria represent one of the largest branches of life on Earth, as well as one of the least understood. Furthermore, because Patescibacteria can manipulate their hosts growth and morphology they have immense ecological potential to be shaping the communities they occupy, both environmental and microbiome-associated. Our study highlights for the first time the potential of small-scale continuous cultivation for studying episymbiotic interactions that cannot be captured in discontinuous cultures. Herein we used these techniques to interrogate inter-species variation in host inhibition potential and to determine how loss of a long-distance episymbiosis factor mechanistically alters the cycle of episymbiont infection; however, this cultivation platform will enable researchers to answer many new questions about these ubiquitous host-episymbiont interactions.}, }
@article {pmid42244821, year = {2026}, author = {Gao, X and Zou, Y and Fang, J and Wu, X and Zheng, W and Zhang, Y and Hao, W}, title = {The association between tongue features and tongue coating microbiota and gastrointestinal cancer: a systematic review and meta-analysis.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2681268}, pmid = {42244821}, issn = {2000-2297}, abstract = {BACKGROUND: Gastrointestinal (GI) cancers pose a significant health burden, highlighting the need for non-invasive biomarkers. Tongue inspection, a traditional diagnostic method in Chinese medicine, has been increasingly quantified via imaging and microbiome analysis.<br><br>OBJECTIVE: This review synthesizes evidence on tongue features and coating microbiota in GI cancer detection.<br><br>DESIGN: We systematically searched PubMed, EMBASE, Cochrane and Chinese databases until July 2025 for case-control or cohort studies comparing tongue characteristics or microbiota between GI cancer patients and healthy controls. Data were pooled using fixed- or random-effects models.<br><br>RESULTS: Sixteen studies (n = 4,994) were included. GI cancer patients showed significantly higher rates of abnormal tongue body morphology (OR = 5.33, 95% CI 3.26-8.72), abnormal tongue body color (OR = 17.85, 95% CI 7.01-45.54), abnormal tongue coating texture (OR = 5.98, 95% CI 4.02-8.91) and abnormal tongue coating color (OR = 3.24, 95% CI 2.00-5.26) versus controls. Although &#x3b1;-diversity did not differ, certain taxa (e.g. Actinobacteria, Prevotella_7) were reduced in cancer patients. Subgroup analyses by cancer type showed generally consistent directions of association for abnormal tongue manifestations in gastric, colorectal and esophageal cancers, despite significant heterogeneity.<br><br>CONCLUSION: Abnormal tongue features and specific microbial shifts are associated with GI cancers, suggesting potential non-invasive tools for early detection. However, due to heterogeneity and methodological limitations, further large-scale prospective studies are needed for validation.}, }
@article {pmid42245041, year = {2026}, author = {Hu, S and Cheng, H and Gillenwater, L and Manpearl, K and Mandava, A and Wang, Y and Pividori, M and Stranger, B and Krishnan, A and Greene, CS and Gao, Y}, title = {Beyond Identifier Matching: An Empirical Characterization of Failure Modes in Biomedical Knowledge Graph Integration.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.26.26354182}, pmid = {42245041}, abstract = {OBJECTIVE: Biomedical knowledge graphs (KGs) such as PrimeKG, Hetionet, UMLS, and PharmGKB are increasingly used as the substrate for downstream machine-learning, retrieval-augmented generation, drug-repurposing, and electronic health record (EHR) augmentation pipelines. The dominant assumption in published work is that integrating two or more such KGs is a tractable engineering step solved by identifier (ID) matching. This paper interrogates that assumption empirically. We quantify how much concept overlap survives realistic alignment, and we characterize the new failure modes introduced by the methods that practitioners reach for when ID matching is insufficient.<br><br>MATERIALS AND METHODS: We compared four widely used biomedical KGs (PrimeKG, Hetionet v1.0, the full UMLS Metathesaurus, and PharmGKB) across eleven node types using a tiered alignment pipeline: (1) direct ID matching for nodes sharing a primary vocabulary; (2) cross-ontology bridging using standard mappings (e.g., MONDO&#x2194;DOID, HPO&#x2194;UMLS, HPO&#x2194;UMLS&#x2194;MeSH for side effects, NCBI Gene&#x2194;HGNC&#x2194;UMLS, UBERON&#x2194;FMA/SNOMEDCT_US/NCI/MeSH for anatomy); (3) ClinicalBERT cosine-similarity grouping at threshold &#x2265; 0.98 for over-segmented disease nodes, with a deterministic suffix-stripping canonicalizer; (4) exact name matching for ontology-poor types (anatomy, REACTOME pathways); and (5) embedding-based fuzzy matching with UMLS lookup (SapBERT and ClinicalBERT) for free-text microbiome concepts. We applied the pipeline to a 698-concept gut-microbiome benchmark spanning taxa, pathways, and disease labels, validated grouping decisions against the curated SSSOM mappings released by the MONDO project, and audited the ClinicalBERT consolidation against five clinical-genetics case studies drawn from the literature.<br><br>RESULTS: Per-type pairwise coverage was strikingly asymmetric. Genes/proteins and the three Gene Ontology categories aligned cleanly across PrimeKG and Hetionet (mutual coverage 94-99%), but disease overlap was sparse: only 0.7% of PrimeKG individual disease nodes mapped to Hetionet, rising to 2.0% after MONDO grouping (versus 78.7% and 18.4% from the Hetionet side). PrimeKG-to-UMLS coverage spanned 100% (effect/phenotype via HPO) down to 20.8% (REACTOME pathways), with drugs at 73.7% and anatomy at 58.8%. PrimeKG-to-PharmGKB drug coverage required up to two bridging hops (DrugBank &#x2192; UMLS &#x2192; RxNorm/ATC/MeSH). Bigger was not uniformly more complete: on a 698-concept microbiome drug benchmark, Hetionet missed 0 concepts while PrimeKG missed 16. ClinicalBERT-based grouping consolidated 22,205 raw MONDO disease nodes into 17,080 groups but introduced three reproducible failure modes documented in case studies: (i) peer over-merging: for example, all 22 osteogenesis imperfecta subtypes collapsed into a single node despite distinct severity classes; (ii) parent-child collapse: e.g. acute myeloid leukemia merged with myeloid leukemia, erasing the acute/chronic distinction that drives clinical management; and (iii) lexical false positives: neurofibromatosis and schwannomatosis grouped together despite cellular-pathology differences.<br><br>DISCUSSION: Identifier matching alone is a weak baseline for biomedical KG integration. Cross-ontology bridges and embedding-based consolidation expand coverage but do so at the cost of clinically meaningful resolution, and the resulting failures are systematic rather than random. Reporting only aggregate coverage statistics obscures these losses, which propagate silently into downstream tasks.<br><br>CONCLUSION: We provide reusable per-type coverage tables, a taxonomy of three integration failure modes, and concrete recommendations for downstream studies that depend on a unified biomedical KG. We argue that future KG integration work should report per-type coverage and per-cluster confidence rather than aggregate match rates.}, }
@article {pmid42245388, year = {2026}, author = {Benjelloun, J and Hnini, M and Bouzroud, S and El Attar, I and Mghazli, N and Hami, A and Talbi, C and Aurag, J and Smouni, A and Guedira, A and Taha, K}, title = {Bioprospecting Cycas revoluta-associated bacterial endophytes for tomato (Solanum lycopersicum L.) growth promotion under salt stress.}, journal = {3 Biotech}, volume = {16}, number = {6}, pages = {253}, pmid = {42245388}, issn = {2190-572X}, abstract = {UNLABELLED: Twenty endophytic bacterial strains isolated from Cycas revoluta coralloid roots were characterized for their salt stress tolerance and phyto-beneficial properties, mainly indole-3-acetic acid production, siderophore secretion and phosphate solubilization under both optimal and stressful conditions. Their genetic diversity was assessed through 16 S rRNA gene sequencing. Results demonstrated a significant diversity of genera, including Agrobacterium, Pseudomonas, Pantoea, Bacillus, Peribacillus, Ochrobactrum, and Stenotrophomonas. Salt tolerance assays and PGP screening revealed the high tolerance threshold and PGP potential of two of isolated bacteria (Pantoea sp. LMR-C62 and Bacillus sp. LMR-C11). Tomato (Solanum lycopersicum L. cv Campbell 33) seeds bio-priming with these strains significantly improved germination rate (up to 75.3% at 150 mM NaCl) and decreased the mean germination time compared to non-inoculated seeds. In greenhouse trials, plantlet inoculation with these two strains led to significant improvements in root length (up to +55%), shoot dry weight (+72%), leaf area (+33%), and relative water content (+92%) under salt stress conditions. Indeed, tomato inoculation improved root development, leaf area, and plant height. At the physiological level, the results indicated positive effects of the inoculation on chlorophyll and anthocyanin contents. These findings demonstrate that Cycas revoluta-associated bacterial endophytes, particularly Panteoa sp. LMR-C62 and Bacillus sp. LMR-C11, hold robust potential as biofertilizer candidates for enhancing tomato growth and resilience under saline conditions. To our knowledge, this is the first report prospecting the unique coralloid root microbiome of Cycas revoluta for agricultural purposes, revealing novel halotolerant endophytes with notable biofertilizer potential.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material at 10.1007/s13205-026-04861-5.}, }
@article {pmid42245391, year = {2026}, author = {Kumari, J and Das, S and Ranjan, S and Singh, S}, title = {From intake to impact: dietary modulation of the gut-brain axis across health and neurological disease.}, journal = {3 Biotech}, volume = {16}, number = {6}, pages = {247}, pmid = {42245391}, issn = {2190-572X}, abstract = {The gut-brain axis (GBA) is an intricate, bidirectional communication network linking the gastrointestinal microbiota to the central nervous system. Mounting evidence underscores its critical role in the pathogenesis of neurological and neurodegenerative disorders. Diet serves as a primary modulator of this axis, possessing the capacity to profoundly reshape microbial diversity, metabolic output, and host-microbiota interactions. This review highlights the modulatory effects of distinct dietary patterns-specifically the Western, Mediterranean, and Ketogenic diets-on GBA signaling and overall neurological health. We comprehensively analyzed how these diets alter gut microbiota composition, influence the production of neuroactive microbial metabolites, and regulate neuroimmune signaling pathways. Furthermore, the mechanistic correlations between diet-driven microbiota alterations and the pathophysiology of neurodegenerative diseases were explored. By evaluating preclinical data on the neuroprotective potential of specific dietary components, this review underscores the therapeutic promise of microbiome-targeted dietary interventions while critically addressing the translational challenges for clinical application.}, }
@article {pmid42245491, year = {2026}, author = {León, ED and Francino, MP}, title = {Correction: Roles of secretory immunoglobulin A in host-microbiota interactions in the gut ecosystem.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1868593}, doi = {10.3389/fmicb.2026.1868593}, pmid = {42245491}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2022.880484.].}, }
@article {pmid42245495, year = {2026}, author = {Kuźniar, A and Das, AP and Goraj, W}, title = {Editorial: Unveiling microbiome interactions and functions in soil hotspots.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1820854}, doi = {10.3389/fmicb.2026.1820854}, pmid = {42245495}, issn = {1664-302X}, }
@article {pmid42245499, year = {2026}, author = {Wang, X and Wang, S and Chang, Z and Zhao, M and Zhang, X and Fayzullo, N and Bunyod, E and Li, S and Wang, J}, title = {A transformer based deep learning framework for accurate single nucleotide variant correction in heterogeneous samples.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1838029}, pmid = {42245499}, issn = {1664-302X}, abstract = {Profiling host genetic variations in heterogeneous host-microbiome mixtures is crucial for understanding cross-species interactions and microenvironmental dynamics. However, the variable host DNA fraction (purity) in bulk sequencing data severely compromises the performance of standard variant callers, leading to significant systematic biases in quantifying single nucleotide variants (SNVs). To address this, we developed a Transformer-based computational framework designed to model sequence context and technical artifacts in low-purity samples. The architecture employs a group-encoding mechanism to process multidimensional features-including variant allele frequency (VAF) distributions, base-level purity estimates, sequencing depth, and local genomic context (such as repeat regions and chromatin accessibility). By capturing long-range dependencies among these diverse signals, the model effectively neutralizes purity-induced biases to accurately recover the true host SNV count. We evaluated the framework using simulated sequencing data across a broad purity gradient (0.2-1.0). Our approach significantly reduced quantification errors, achieving high concordance between the corrected and actual ground-truth SNV counts. Benchmarking the corrected counts against the raw outputs of conventional callers (Mutect, Freebayes, LoFreq, and Platypus) demonstrated substantial performance gains, particularly in ultra-low purity conditions (0.2-0.3) where traditional statistical priors typically fail to provide reliable quantifications. Feature ablation and residual analyses further validated the independence of the multidimensional inputs and the unbiased, zero-centered nature of the count corrections. This deep learning pipeline provides a robust solution for the accurate quantification of host SNVs in complex biological mixtures, facilitating reliable downstream genetic analyses in highly heterogeneous microenvironments.}, }
@article {pmid42245500, year = {2026}, author = {Dinh-Hung, N and Mohammed, H and Linh, NV and Tran, NT}, title = {Editorial: Probiotics in aquaculture: enhancing health and sustainability.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1864753}, pmid = {42245500}, issn = {1664-302X}, }
@article {pmid42245502, year = {2026}, author = {Abdulsamad, MA and Bardaa, S and Elleuch, M and Mathlouthi, NEH and Ben Ali, M}, title = {Metagenomic characterization of infected diabetic foot ulcers in North Africa: microbial diversity, virulome, and resistome profiling.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1825173}, pmid = {42245502}, issn = {1664-302X}, abstract = {This study provides the first shotgun metagenomic characterization of infected diabetic foot ulcers (DFUs) from North Africa. We analyzed two independent datasets with distinct roles: 25 non-infected US DFUs (PRJNA506988) served as an ecological reference cohort to characterize depth-stratified microbial community patterns and pre-infection ARG ecology; 15 infected Libyan DFUs constituted the primary characterization cohort. Metagenomic sequencing, taxonomic classification, resistome and virulome profiling, and metagenome-assembled genome (MAG) reconstruction were performed. In the US reference cohort, depth-dependent community shifts were documented: Fusobacteriota predominated in deeper ulcers, while Staphylococcaceae and Pseudomonadaceae were enriched in superficial wounds. Eighty ARGs were detected across depth groups, including mecA and the mexAB-oprM efflux system, in clinically non-infected wounds. In the Libyan cohort, four major opportunistic pathogens were identified: Pseudomonas aeruginosa, Staphylococcus aureus, Acinetobacter baumannii, and Corynebacterium striatum. From sample M13, a high-quality P. aeruginosa MAG (99.68% completeness, 0.89% contamination) was reconstructed, classified as ST664 and carrying 220 virulence factors, 60 antibiotic resistance genes (all confirmed by RGI v6.0.2), and 213 mobile genetic elements. These findings represent the first genomic evidence of ST664 in a North African DFU and underscore the need for metagenomics-guided antimicrobial stewardship in chronic wound management.}, }
@article {pmid42245509, year = {2026}, author = {Wang, Z and Li, L and Dong, Y and Zhang, Y}, title = {The microbiota-tryptophan-brain axis in neurodegenerative diseases: pathogenic mechanisms, disease-specific roles, and translational therapeutics.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1820111}, pmid = {42245509}, issn = {1664-302X}, abstract = {The pathogenesis of neurodegenerative diseases (NDDs) such as Alzheimer's disease (AD) and Parkinson's disease (PD) is very complex. Recent studies have shown that gut microbiota and their metabolites play a key role in the progression of these diseases. Tryptophan (Trp) is an essential amino acid, which mainly produces a variety of biologically active compounds in the intestine through the metabolism of indole pathway, Kynurenine pathway (KP) and serotonin pathway, including indole derivatives, Kynurenine (KYN) and serotonin (5-HT). These metabolites affect the central nervous system (CNS) through the Microbiota-gut-brain axis (MGBA) and affect CNS in a variety of mechanisms, including immune regulation, neuroprotection and maintenance of intestinal barrier function. They are involved in key pathological processes such as neuroinflammation, oxidative stress and pathological protein aggregation. This paper systematically reviews the mechanism of the role of Trp metabolites derived from gut microbiota in NDDs, and explores their specific roles in AD, PD, Amyotrophic Lateral Sclerosis (ALS) and Huntington's disease (HD), and summarizes the potential therapeutic value of the current pathway strategy. These strategies include nutritional intervention, targeted microbiome therapy [such as probiotic and fecal microbiota transplantation (FMT)], and metabolite-derived drugs. Future research must clarify its dynamic mechanism in the human body, develop relevant biomarkers, and promote personalized prevention and treatment strategies through clinical transformation, so as to provide a new direction for early intervention and treatment of NDDs.}, }
@article {pmid42245510, year = {2026}, author = {Patel, M and Ijoma, GN and Ziarno, M}, title = {Editorial: Bifidobacteria: exploring the roles of these microbiome guardians and their effects on human health.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1861676}, doi = {10.3389/fmicb.2026.1861676}, pmid = {42245510}, issn = {1664-302X}, }
@article {pmid42245514, year = {2026}, author = {Shen, X and Yu, FXD and Xie, S and Hsu, CD and Domingos, JA and Gibson-Kueh, S}, title = {Temporal microbiome dynamics and fish health-associated dysbiosis in freshwater aquarium systems: a case study from River Wonders Singapore.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1739391}, pmid = {42245514}, issn = {1664-302X}, abstract = {INTRODUCTION: Aquarium systems are engineered yet biologically dynamic ecosystems where microbial communities underpin nutrient cycling, organic matter decomposition and water quality regulation. These processes directly affect aquatic animal health.<br><br>METHODS: This study conducted a two-month time series analysis of waterborne microbiomes across six freshwater exhibits at River Wonders, Singapore, using 16S rRNA gene sequencing. Exhibits were categorized as "Healthy" (LM, MJ, EE) or "Stressed" (P, MJR, RG) based on fish health, and as indoor or semi-indoor/outdoor by system design.<br><br>RESULTS AND DISCUSSION: Temporal fluctuations in microbial composition and diversity were evident over time, with distinct profiles between indoor and semi-indoor/outdoor. Potential opportunistic or pathogenic genera, including Edwardsiella, Flavobacterium, Aeromonas, Pseudomonas and Mycobacterium, were consistently among the 30 most abundant taxa. The most severe dysbiosis occurred in exhibit P, characterized by a transient Pseudomonas bloom (51.4%), loss of nitrifiers (Nitrosomonas, Nitrospira) and concurrent fish health issues. MJR and RG harbored persistent polymicrobial risks, while "Healthy" exhibits maintained relatively more balanced microbial communities with lower pathogen loads. Routine husbandry interventions (e.g., partial water changes, substrate cleaning) coincided with improved microbial evenness and reductions in opportunistic taxa. These findings highlight diagnostic potential of microbiome profiling to detect early dysbiosis and support evidence-based husbandry in managed aquatic systems.}, }
@article {pmid42245662, year = {2026}, author = {Cabanero-Navalon, MD and Carda-Diéguez, M and Mira, A and Moral Moral, P and Diaz Luna, MM and Balastegui-Martín, H and Salavert Lletí, M and Garcia-Bustos, V}, title = {Multiniche mycobiome profiling identifies distinctive fungal dysbiosis in common variable immunodeficiency.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1804724}, pmid = {42245662}, issn = {1664-3224}, abstract = {BACKGROUND: Common variable immunodeficiency (CVID) is associated with bacterial dysbiosis, particularly in patients with immune dysregulation, but the contribution of the fungal microbiome (mycobiome) remains poorly understood.<br><br>METHODS: We conducted a cross-sectional, multi-compartment study in 41 adults with CVID (24 with immune dysregulation, dCVID; 17 with infectious-only manifestations, iCVID) and 15 matched healthy controls. Saliva, sputum and stool samples were analyzed using ITS1 amplicon sequencing with amplicon sequence variant-based taxonomic assignment, followed by &#x3b1;/&#x3b2;-diversity analyses, multivariate modeling, differential abundance testing and machine learning approaches for biomarker identification.<br><br>RESULTS: Across all three niches, mycobiome composition differed significantly between CVID and controls, whereas dCVID and iCVID did not separate. Fungal richness and evenness were reduced in CVID, most prominently in respiratory and oral samples. ANCOM-BC revealed a reproducible "Candida-skewed" configuration in both phenotypes, with marked enrichment of Candida albicans in sputum, stool and saliva, accompanied by increased abundance of other opportunistic yeasts such as Nakaseomyces glabratus. In contrast, environmental or putatively commensal taxa were consistently depleted. Random forest models based on fungal profiles accurately discriminated CVID from controls, with AUC up to 0.96 (95% CI 0.91-0.99) in saliva and 0.94 (95% CI 0.88-0.99) in stool, whereas classification of dCVID versus iCVID was modest.<br><br>CONCLUSION: Together, these findings provide the first integrated view of mycobiome alterations across multiple ecological niches in CVID, highlighting consistent enrichment of opportunistic yeasts over commensals. The expansion of C. albicans supports a potential pathobiont role, and the strong discriminatory performance of fungal signatures underscores their promise as non-invasive biomarkers in this immunodeficiency.}, }
@article {pmid42245783, year = {2026}, author = {Edielu, A and Lo, CW and Mawa, PA and Webb, EL and Elliott, AM and Mugerwa, JK and Oduru, G and Nassuuna, J and Ayebazibwe, GK and Struebig, M and Friedman, JF and Bustinduy, AL and Holland, MJ}, title = {Schistosoma mansoni infection is associated with changes in gut microbiota in preschool age children in Albertine Region, Uganda.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-9768290/v1}, pmid = {42245783}, issn = {2693-5015}, abstract = {Current understanding of gut microbiota alterations during helminthiasis is largely derived from experimental models, often focusing on a narrow range of metrics. This study investigates the structural and functional shifts in the gut microbiome associated with Schistosoma mansoni infection in a paediatric cohort. We conducted a cross-sectional study of preschool-aged children (12-47 months) comparing S. mansoni -infected individuals (56) to uninfected controls (57). Microbial DNA was extracted from stool samples and sequenced via the Illumina MiSeq v3 platform targeting the V4-16S rRNA region. Diversity was assessed through alpha (Chao1, Simpson, Shannon) and beta (UniFrac and Bray-Curtis distance) metrics. Functional potential was predicted using PICRUSt2 mapped against the KEGG database. The infected group (median age 36 months) exhibited significantly higher alpha diversity and species richness compared to uninfected peers (median age 26 months). Beta diversity analysis confirmed distinct microbial clustering between the two groups (p-value = 0.001). Notably, S. mansoni infection was characterized by the proliferation of pro-inflammatory taxa and a concomitant depletion of short-chain fatty acid (SCFA) producers. Functional modeling indicated a significant downregulation of metabolic pathways involved in energy metabolism and SCFA biosynthesis. S. mansoni infection is associated with profound structural and functional dysbiosis in preschool-aged children. The depletion of SCFA producers and altered metabolic pathways suggest that infection may impair host nutritional status and influence the parasite's lifecycle, necessitating further longitudinal investigation.}, }
@article {pmid42245806, year = {2026}, author = {Cunningham, ME and Williams, MT and Spaine, KM and Marcinkowska, A and Matveyev, AV and Hur, BJ and Natterer, HO and Chatterjee, RB and Oldfield, CJ and Edupuganti, L and Zhu, B and Jefferson, KK and Iii, JFS and Olex, AL and Serrano, MG and Buck, GA}, title = {Differential Host Gene Expression Associated with Non-Lactobacillus-dominant Vaginal Microbiomes During Pregnancy.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-9268667/v1}, pmid = {42245806}, issn = {2693-5015}, abstract = {Background The vaginal microbiome significantly influences gynecological and obstetric health, yet the interrelationship between host vaginal gene expression and the microbiota during pregnancy is understudied-particularly in racioethnically diverse cohorts. Here, we leveraged metatranscriptomic data from 123 participants from the Multi-Omic Microbiome Study-Pregnancy Initiative (MOMS-PI) cohort to perform a novel integrated analysis of human host gene expression and vaginal microbiota composition during pregnancy. We hypothesized that host gene expression at the vaginal-mucosal interface would exhibit distinct transcriptional profiles when colonized by bacteria commonly present in bacterial vaginosis (BV), termed BV-associated vagitypes, compared to Lactobacillus -dominated microbiomes. Such distinct host response would provide evidence linking vaginal inflammation to microbiome composition during pregnancy in a majority Black cohort. By profiling host expression with different BV-associated vagitypes, these host-microbiome signatures could inform clinically actionable biomarkers for microbiome-focused interventions during pregnancy in historically underrepresented populations. Results Host transcriptomic profiles differed significantly between BV-associated and Lactobacillus -dominated vagitypes, with this association remaining significant when analyses were restricted to Black participants. We identified 13 consistently differentially expressed genes in women with BV-associated vagitypes-vaginal microbiomes comprised of high relative abundance of either Gardnerella spp., Candidatus Lachnocurva vaginae, or a mixture of multiple anaerobic taxa-compared to women with Lactobacillus crispatus vagitypes. These differentially expressed genes are involved in host immune response (DKK1, H2BC21, ILRUN, S100A9), oxidative stress response and inflammasome activation (CSTB), transcription modulation (CLK1, PAX9), vesicle trafficking (EXPH5), ubiquitination (FBXO32), membrane integrity (PIEZO1), and ion transport (S100A16, SCNN1A, SLCO4A1). Conclusion BV-associated vagitypes are correlated with distinct host immunomodulatory gene expression profiles during pregnancy, independent of self-reported racioethnicity. We demonstrated novel molecular insights into microbiome-host interaction during pregnancy within the context of adverse cervicovaginal health.}, }
@article {pmid42245824, year = {2026}, author = {de Azevedo-Lopes, A and Traulsen, A}, title = {Multilevel selection in multitype populations.}, journal = {PNAS nexus}, volume = {5}, number = {6}, pages = {pgag180}, pmid = {42245824}, issn = {2752-6542}, abstract = {Multilevel selection has important implications for understanding the origin, ecology, and evolution of host-associated microbiomes. Selection on the host-level can have a substantial impact on the evolution of microbial lineages, favoring microbes that are beneficial to the host. However, previous research has focused on the evolution of interactions among only two types. We alter this perspective by examining the role of multilevel selection in shaping the interaction dynamics of a population with many microbial types-a case of particular relevance for microbiomes. We ask how multilevel selection influences the selection of interactions among various microbial types, whether it promotes microbial diversity within the population, and whether it increases the likelihood of microbial lineages evolving beneficial interactions with their host and other microbes. To address these questions, we simulate a multitype population structured into groups, where individuals interact within groups through an evolutionary game that determines their fitness. We classify pairwise interactions by their dynamical outcomes: dominance, coexistence, or bistability. We find that multilevel selection reshapes interactions dynamics in complex ways, depending on the details of the population structure. We show the impact of the interaction patterns emerging in such a system.}, }
@article {pmid42246001, year = {2026}, author = {Chen, S and Liu, J and Ni, H and Zhu, F and Liu, H and Lin, R}, title = {Gut microbiota and the kidney-gut-skin axis in chronic kidney disease-associated pruritus: mechanisms and therapeutic implications.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1811786}, pmid = {42246001}, issn = {2235-2988}, mesh = {Humans ; *Pruritus/therapy/etiology/microbiology ; *Renal Insufficiency, Chronic/complications/microbiology/therapy ; Animals ; *Gastrointestinal Microbiome/physiology ; *Skin/microbiology/pathology ; *Kidney/microbiology ; Dysbiosis ; Probiotics/therapeutic use ; }, abstract = {Chronic kidney disease-associated pruritus (CKD-aP) is a highly prevalent and debilitating symptom in patients with chronic kidney disease (CKD) and end-stage kidney disease (ESKD), severely impairing quality of life, sleep quality, mental health, and clinical outcomes. Its pathogenesis is multifactorial and remains incompletely understood, involving chronic inflammation, immune imbalance, abnormal neuro-opioid pathways, mineral metabolism disorders and skin barrier damage. The kidney-gut-skin axis has attracted increasing attention as a novel theoretical framework to elucidate the roles of gut microbiota dysbiosis, gut-derived uremic toxins, intestinal barrier impairment and systemic inflammation in the development of CKD-aP. This review summarizes the traditional pathogenic mechanisms of CKD-aP, reviews recent advances linking gut microbial alterations to pruritus-related pathways, and systematically evaluates gut-targeted and metabolism-targeted interventions, including probiotics, prebiotics, synbiotics, AST-120, fecal microbiota transplantation, phytochemicals, Uremia Clearance Granules, and vitamin D-related strategies. Current evidence is mostly associative and is mainly derived from general CKD/ESKD populations, animal models, and in vitro studies; specific clinical validation in CKD-aP cohorts remains limited. Accordingly, gut microbiome-related mechanisms and interventions remain hypothetical and adjunctive, without established causal relationships or validated standard therapies for CKD-aP. Future studies are required to identify CKD-aP-specific pathological alterations, adopt longitudinal design and multi-omics analysis, conduct mechanistic verification, and perform randomized controlled trials with pruritus as a predefined primary endpoint.}, }
@article {pmid42246005, year = {2026}, author = {Orcel, E and Sentausa, E and Hage, H and Louis, K and Taha, M and Bellais, S and Villain, A and Beloeil, L and Sijmons, S and Devos, N and Saliou, A}, title = {UMI-guided single locus sequence typing method for phylotyping Cutibacterium acnes from skin samples.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1807759}, pmid = {42246005}, issn = {2235-2988}, mesh = {Humans ; *Skin/microbiology ; Skin Microbiome ; DNA, Bacterial/genetics ; Phylogeny ; Sequence Analysis, DNA ; *Molecular Typing/methods ; *Propionibacteriaceae/genetics/classification/isolation &amp; purification ; *Bacterial Typing Techniques/methods ; }, abstract = {INTRODUCTION: Cutibacterium acnes is a dominant member of the human skin microbiota and displays substantial strain-level diversity with relevance for skin health and disease. However, accurate characterization of C. acnes lineages directly from skin samples remains challenging due to low biomass, host DNA contamination, and limitations of short-read sequencing.<br><br>METHODS: Here, we present SLST-Seq, a culture-independent approach based on single-locus sequence typing (SLST), enabling strain-level profiling of C. acnes from low-input skin-strip samples. SLST-Seq adapts the LUMI-Seq&#xae; synthetic long-read sequencing technology to the C. acnes SLST marker, combining unique molecular identifier barcoding with de novo assembly to reconstruct full-length SLST sequences with high accuracy.<br><br>RESULT: Method performance was validated using single-isolate controls, defined genomic DNA mixtures, spike-in dilution series, and run-specific controls, demonstrating high specificity, quantitative accuracy across a wide range of target-to-background DNA ratios, and strong run-to-run reproducibility. Applied to skin-strip samples from healthy volunteers, SLST-Seq generated robust SLST profiles and revealed marked inter-individual variability, with donor-specific community structures largely conserved between face and back skin sites.<br><br>DISCUSSION: Overall, SLST-Seq provides a sensitive and scalable framework for in situ analysis of C. acnes population structure and supports high-resolution studies of skin microbiome composition from challenging clinical samples.}, }
@article {pmid42246191, year = {2026}, author = {Das, D and Dixit, R and Pandey, M}, title = {The Biliary Multi-Omics Landscape: Integrating Microbiome and Metabolomics in Gallbladder Carcinogenesis.}, journal = {Journal of gastroenterology and hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jgh.70462}, pmid = {42246191}, issn = {1440-1746}, abstract = {BACKGROUND: Gallbladder cancer (GBC) is a highly aggressive malignancy with a dismal prognosis, frequently diagnosed at advanced stages. While cholelithiasis is a primary risk factor, the role of the biliary microbiome and its metabolic products in driving carcinogenesis is increasingly recognized. This review synthesizes multi-omics data to elucidate the interplay between microbial dysbiosis and metabolomic shifts in GBC.<br><br>METHODS: A systematic literature search was conducted on PubMed (up to January 2026) focusing on biliary bacteria, the gut-bile axis, and multi-omics markers. A narrative synthesis integrated findings from metagenomic, metaproteomic, and metabolomic studies involving human cohorts and experimental models.<br><br>RESULTS: GBC is characterized by profound biliary dysbiosis, specifically the enrichment of Enterobacteriaceae, Streptococcus, and Helicobacter species. This taxonomic shift triggers a pro-carcinogenic metabolomic flux, where microbial 7&#x3b1;-dehydroxylation converts primary bile acids into secondary bile acids, such as deoxycholic acid (DCA), which induce DNA damage and promote tumor growth. Metaproteomic signatures identify bacterial proteins (e.g., QDR3, ompA) that facilitate biofilm formation and oxidative stress evasion. Furthermore, emerging paradigms like cross-species horizontal gene transfer (HGT) suggest that microbial genetic material can directly modulate host oncogenic pathways.<br><br>CONCLUSION: The GBC multi-omics landscape reveals a complex gut-bile axis where microbial and chemical factors converge. These integrated signatures offer potential as noninvasive biomarkers for early diagnosis and precision therapy.}, }
@article {pmid42246268, year = {2026}, author = {Yun, S and Choi, KS and Min, H and Jo, YK and Jang, S}, title = {Development strategies for engineered live biotherapeutic products for metabolic diseases.}, journal = {Critical reviews in biotechnology}, volume = {}, number = {}, pages = {1-21}, doi = {10.1080/07388551.2026.2653692}, pmid = {42246268}, issn = {1549-7801}, abstract = {Metabolic diseases, such as obesity and diabetes, have risen due to lifestyle changes. Traditional treatments, including dietary modifications and pharmacological interventions, are limited by low compliance and adverse effects, highlighting the need for alternative therapeutic approaches that offer improved patient compliance and long-term effectiveness. Engineered live biotherapeutic products (eLBPs) have emerged as a promising strategy that combines bacterial chassis with synthetic genetic circuits for precise and targeted disease treatment. Unlike conventional therapeutics, eLBPs can colonize the intestinal tract and enable localized and condition-responsive therapeutic activity while offering improved safety profiles through defined mechanisms of action. This review highlights key strategies for eLBP development, particularly chassis selection and genetic circuit design. Applications in metabolic diseases, including inherited disorders such as phenylketonuria (PKU), demonstrate how engineered gene circuits can modulate specific metabolic pathways. However, several challenges remain, including genetic stability, interindividual variability, biological safety, and production scalability. In addition, further research on host-microbiota interactions is required to improve therapeutic predictability and efficacy, supporting the development of safe and effective personalized eLBP-based therapies for metabolic diseases.}, }
@article {pmid42246374, year = {2026}, author = {Pauwels, A and Devolder, L and Falony, G and D'haeseleer, M and Nagels, G and Van Remoortel, A and Derrien, M and D'hooghe, M and Raes, J}, title = {Deconfounded, quantitative microbiome profiling identifies robust multiple sclerosis markers and clinical covariate associations.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2681876}, doi = {10.1080/19490976.2026.2681876}, pmid = {42246374}, issn = {1949-0984}, abstract = {Despite a wealth of gut microbiota studies in multiple sclerosis (MS), consistent results are lacking. Here, we study confounder effects and use of quantitative microbiome profiling (QMP) in 228 MS patients (103 untreated) and 2860 population controls (Flemish Gut Flora Project (FGFP)). Total bacterial load was lower in relapsing remitting (RR)MS, while strong fecal moisture effects, indicative of longer transit times, in MS vs. FGFP, were driven by primary progressive (PP)MS. Applying cell count and moisture in deconfounded QMP, we identified 21 differentially abundant genera in MS, with a.o. Lachnobacterium, Blautia enriched, and Clostridium, Bacteroides depleted. Deconfounded QMP across 10 published studies (1065 patients, 874 controls) did not confirm commonly detected markers (Akkermansia, Roseburia), yet lowered Bacteroides, and higher Blautia and Methanobrevibacter emerged as robust MS biomarkers. Lowered butyrate producers (Butyricicoccus, Butyricimonas) merit further investigation. Enterotype stratification linked the low cell count Bacteroides 2 enterotype to low-efficacy DMTs, and the Prevotella enterotype to lower disease severity. Serum glial fibrillary acidic protein (GFAP), a disease progression biomarker, was identified as a covariate of gut microbial variation and inversely correlated with Faecalibacterium and Roseburia abundance in PPMS. Overall, our study provides robust disease markers and emphasizes the importance of QMP and confounder control.}, }
@article {pmid42247160, year = {2026}, author = {Palani Kumar, MK and Iyer, KS and Shahi, SK and Raygoza Garay, JA and Mangalam, A and Dayal, S}, title = {Age and sex dependent shift in murine gut microbiome reveals pathological links to host cardiovascular and metabolic pathways.}, journal = {GeroScience}, volume = {}, number = {}, pages = {}, pmid = {42247160}, issn = {2509-2723}, support = {HL168630/HL/NHLBI NIH HHS/United States ; HL007344/HL/NHLBI NIH HHS/United States ; BX007087//U.S. Department of Veterans Affairs/ ; AI162778//National Institute of Allergy and Infectious Diseases/ ; 18IPA4180014//American Heart Association/ ; P30 ES005605/ES/NIEHS NIH HHS/United States ; 1I01CX002212//Iowa City Veterans Affairs Medical Center/ ; }, abstract = {The gut microbiome undergoes dynamic, sex-dependent changes across the lifespan. However, comprehensive studies examining the combined effects of age and sex are limited. This study investigated both compositional and functional alterations in the gut microbiome of young (4 months, n = 14) and aged (20 months, n = 20) C57BL/6 J mice of both sexes using 16S rRNA gene (V3-V5) sequencing. Microbial community structure and predicted functional profiles were analyzed via QIIME2 and PICRUSt2, with pathway annotation based on MetaCyc. Compared to aged mice, young mice exhibited higher alpha diversity, with the highest increase observed in young females. This sex-specific difference was lost in aged mice. Aging was also associated with an increased Firmicutes-to-Bacteroidetes ratio, and distinct shifts in key taxa, including increased Lactobacillus and Roseburia and reduced Bacteroides and Lachnospiraceae. Functional prediction revealed substantial age-related metabolic shifts, especially in females showing alteration in 45 pathways including upregulation of branched-chain amino acid (BCAA) metabolism, uric acid metabolism, and lipopolysaccharide biosynthesis. To directly link alterations in microbial BCAA metabolism with host metabolic outcomes, fecal abundance of the bacterial BCAA aminotransferase gene (ilvE) was quantified and found to be significantly increased in aged mice. Concurrently, aged mice exhibited higher plasma levels of BCAA, insulin, and random glucose, indicating age-associated metabolic dysregulation. Fecal ilvE abundance associated positively with plasma BCAA levels, and negatively with blood glucose in aged mice, suggesting a link between microbial BCAA metabolism and host glucose homeostasis. Our findings demonstrate that gut microbiome composition and function are influenced by both age and sex. We also showed that these alterations in microbial BCAA metabolism are associated with host metabolic parameters during aging. Our findings underscore the importance of incorporating both age and sex as biological variables in microbiome research and may inform development of age- and sex-specific microbiome-targeted interventions.}, }
@article {pmid42247343, year = {2026}, author = {Somboonna, N and Rujirawan, P and Promvaranon, T and Wongtada, C and Triwatcharikorn, J and Chottawornsak, N and Kantikosum, K and Wongsaroj, L and Parinyanitikul, N and Chongpison, Y and Chiewchengchol, D and Rerknimitr, P}, title = {Skin Barrier Dysfunction, Antimicrobial Peptide Alterations, and Microbiome Changes in Solid Cancer Patients Treated with Epidermal Growth Factor Receptor Inhibitors.}, journal = {Dermatology (Basel, Switzerland)}, volume = {}, number = {}, pages = {1-14}, doi = {10.1159/000551797}, pmid = {42247343}, issn = {1421-9832}, abstract = {INTRODUCTION: Epidermal growth factor receptor inhibitors (EGFRIs) are targeted therapies for solid cancers. Their use is associated with cutaneous adverse events (cAEs). This study aimed to investigate cAEs and changes in skin biophysics reflecting the skin barrier function, alterations in antimicrobial peptides (AMPs), and the skin microbiome in patients undergoing treatment with EGFRIs.<br><br>METHODS: A 2-year prospective cohort study was conducted involving patients receiving EGFRIs for solid cancers. cAEs and skin biophysical properties, including transepidermal water loss (TEWL), skin pH, elasticity, sebum, and pigmentation, were measured at baseline and follow-up visits up to 48 weeks. AMPs were assessed using a tape-stripping technique from the cheeks at months 0, 1, and 6, with protein assays and ELISA to determine the levels of human beta-defensin (hBD)-3 and ribonuclease (RNase)-7. Skin microbiome analysis was performed through 16S rRNA sequencing of cheek swabs collected at months 0, 1, and 6.<br><br>RESULTS: Eighty-four patients were enrolled. The cumulative incidence of cAEs was 94.05%. Skin biophysical properties showed significantly increased TEWL and pH, decreased pigmentation, and no significant changes in elasticity and sebum. AMP analysis from 15 patients revealed significant reduction of RNase-7 levels after 6 months into EGFRIs, while hBD-3 level change was insignificant. A microbiome study from 18 patients showed statistically increased Corynebacterium kroppenstedtii at months 1 and 6, while Cutibacterium acnes, Corynebacterium aurimucosum, Staphylococcus epidermidis, and Staphylococcus aureus were not significantly different among groups.<br><br>CONCLUSION: Treatment with EGFRIs compromises skin barrier function and AMP production, leading to skin microbiota changes.}, }
@article {pmid42247989, year = {2026}, author = {Tang, Y and Qi, F and Yu, Y and Fu, Y and Zhu, P}, title = {Knowledge mapping of cholestatic liver disease and TGR5 research: A bibliometric study of trends and frontiers.}, journal = {Computational biology and chemistry}, volume = {124}, number = {Pt 1}, pages = {109158}, doi = {10.1016/j.compbiolchem.2026.109158}, pmid = {42247989}, issn = {1476-928X}, abstract = {OBJECTIVE: This study aims to provide a comprehensive bibliometric analysis of global research trends surrounding TGR5 in cholestatic liver diseases from 2006 to 2025, with the objective of elucidating publication outputs, geographic and institutional contributions, collaborative networks, journal co-citation analysis and reference co-citation mapping, key research themes, and emerging frontiers.<br><br>METHODS: Bibliographic data were retrieved from the Web of Science Core Collection (WoSCC) and supplemented by validation against Scopus and PubMed to mitigate database selection bias.Analyses were performed using CiteSpace (version 6.2.R2), VOSviewer (version 1.6.20), and the bibliometrix R package. Performance analysis was employed to evaluate productivity and impact across countries, institutions, and authors. Advanced science mapping techniques, including Thematic Map analysis, network topology metrics, and citation burst detection, were conducted to provide deeper computational and systems-level biological insights.<br><br>RESULTS: A total of 418 publications were included. Annual publications showed a steady upward trend, with the United States leading in productivity (n&#x202f;=&#x202f;138), total citations (n&#x202f;=&#x202f;14,638), and H-index (59), followed by China with high output but relatively lower citation impact. European countries, notably Italy and Germany, demonstrated strong collaborative networks and influence relative to output volume. Keyword and thematic analyses revealed a shift from molecular mechanisms to clinical applications and, more recently, to gut microbiota and metabolic interactions. Major research clusters encompassed bile acid receptors, gut-liver axis mechanisms, and metabolic disorders. Quantitative network analysis revealed a modularity of 0.8238 and mean silhouette of 0.96, indicating well-defined cluster structures. Although prominent research groups were identified, international collaboration remained limited.<br><br>CONCLUSION: The study illustrates the dynamic and evolving nature of TGR5 research, marked by a transition from basic science to translational and systems-level approaches. As the first comprehensive bibliometric and systems-level mapping analysis of TGR5 research in cholestatic liver diseases, this study uniquely integrates computational network analysis with microbiome-host interaction frameworks.While research productivity continues to grow, future efforts would benefit from enhanced international collaboration, microbiome engineering, systems medicine, biomarker discovery, and AI-integrated hepatology research. These findings provide valuable insights for researchers and policymakers aiming to navigate and advance this promising field.}, }
@article {pmid42248042, year = {2026}, author = {Wang, L and Gong, X and Rao, S and Huang, L and Cheng, H and Cheng, S and Luo, J and Li, Q and Wei, Y and Xu, H}, title = {Biological effects of selenium on Hypnum plumaeforme and the underlying mechanisms mediated by physiology and microbiome.}, journal = {Ecotoxicology and environmental safety}, volume = {322}, number = {}, pages = {120341}, doi = {10.1016/j.ecoenv.2026.120341}, pmid = {42248042}, issn = {1090-2414}, abstract = {Bryophytes provide vital ecosystem services, yet the biological effects of selenium (Se) on them remain largely unknown. This study simulated ecological scenarios with different selenite exposure levels to investigate the response patterns of growth, physiology, and symbiotic bacterial communities in Hypnum plumaeforme. Overall, its inorganic, organic, and total Se content increased with increasing selenite exposure levels. At 2 mg/L, H. plumaeforme accumulated more biomass, carotenoids and selenomethionine (SeMet), but less lipid and phosphorus (P). Enhanced methylselenocysteine (MeSeCys) biosynthesis facilitated its Se detoxification. At 4 mg/L, H. plumaeforme had more photosynthetic pigments, carbohydrates and protein, but fewer chloroplasts and less P. H2O2 accumulation did not result in elevated malondialdehyde (MDA) content and growth inhibition, which was attributed to the activation of superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPX), as well as increased SeMet biosynthesis for Se detoxification. The enrichment of Variovorax and TM7a might support its starch accumulation and Se tolerance. At 8 mg/L, H. plumaeforme had more photosynthetic pigments and protein, but fewer chloroplasts and less P. Excessive SeMet synthesis induced Se toxicity. Although SOD, CAT and GPX were activated, H2O2 and MDA accumulation occurred in this bryophyte, resulting in reduced biomass and impaired nitrogen (N) uptake. The enrichment of bacterial taxa, including Alphaproteobacteria, might facilitate its antioxidant defense. This study identifies the growth-promoting, neutral, and inhibitory effects of Se on H. plumaeforme, and illustrates the underlying physiological and microbial regulatory mechanisms. These findings provide important theoretical support for bryophyte conservation and Se ecological risk assessment.}, }
@article {pmid42248044, year = {2026}, author = {Wang, X and Yin, S and Zheng, Y and Yu, X and Li, Y and Zhang, B and Liu, J and Zhang, Y and You, X}, title = {Hydrochar decreased the enantioselective bioaccumulation of prothioconazole-desthio in the tobacco through rhizosphere soil metabolic regulation.}, journal = {Ecotoxicology and environmental safety}, volume = {322}, number = {}, pages = {120333}, doi = {10.1016/j.ecoenv.2026.120333}, pmid = {42248044}, issn = {1090-2414}, abstract = {Pollution of soil environments by pesticides is a serious global issue. Char amendments (pyrochar and hydrochar) have been widely used to remediate contaminated soils. However, the rhizosphere soil metabolic mechanisms underlying the hydrochar remediated prothioconazole pollution in the soil-plant ecosystem are poorly understood. Therefore, cattle manure derived hydrochar (CHC) and pyrochar (CPC), and reed straw derived hydrochar (RHC) and pyrochar (RPC) were prepared to investigate their effect on mitigating plant enantioselective bioaccumulation of prothioconazole and metabolites using the 30-day tobacco bioassay, and to clarify the remediation mechanisms underlying hydrochar-remediated prothioconazole-polluted soil-tobacco ecosystem via rhizosphere soil microbiome and metabolite analysis. Char amendments had little effect on prothioconazole bioaccumulation in tobacco tissues, whereas primarily decreased bioaccumulation of prothioconazole-desthio in tobacco roots, following inhibition order of S-enantiomer (63.8-73.4%) > R-enantiomer (67.3-75.6%). Pyrochar efficiently inhibited transfer of prothioconazole-desthio from soils to tobacco roots than hydrochar, with the order of RPC (67.5-71.1%) ≈ CPC (62.7-68.6%) > CHC (48.1-56.4%) ≈ RHC (34.0-47.5%). Hydrochar efficiently weakened the prothioconazole abiotic degradation in the soils could account for decreased bioaccumulation of prothioconazole-desthio in the tobacco roots. The promoted prothioconazole microbially hydroxylated and recruited prothioconazole-degrading bacteria due to enhanced secretion of root exudates (e.g., phenolic acids) were the rhizosphere metabolic mechanisms on prothioconazole enantioselective degradation in the hydrochar-amended soils. These findings provide the basis for developing char-based remediation measures to mitigate prothioconazole pollution.}, }
@article {pmid42248217, year = {2026}, author = {Steininger, HM and McCauley, KE and Braga, GE and Morin, A and Lee, KE and Visness, CM and Fadrosh, DW and Dapas, M and O'Connor, GT and Bacharier, LB and Rivera-Spoljaric, K and Kattan, M and Lemanske, RF and Zoratti, EM and Martinez, FD and Gold, DR and Hartert, TV and Johnson, CC and Miller, RL and Seroogy, CM and Wood, RA and Togias, A and Jackson, DJ and Gern, JE and Ober, C and Lynch, SV and , }, title = {Upper Airway Microbiome Interacts with GSDMB and ORMDL3 Asthma Risk SNPs to Influence Early-Life Wheeze Risk.}, journal = {The Journal of allergy and clinical immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jaci.2026.05.021}, pmid = {42248217}, issn = {1097-6825}, abstract = {BACKGROUND: Single-nucleotide polymorphisms (SNPs) in the chromosome 17q12-q21 region and, independently, early-life nasal microbiota dominated by Moraxella, Streptococcus, or Haemophilus increase risk of chronic wheeze and asthma development.<br><br>OBJECTIVE: Determine if 17q12-q21 risk SNPs and nasal microbiota interact to modulate childhood wheeze risk.<br><br>METHODS: Nasal wash samples from 12-month-old infants in two birth cohorts, Childhood Origins of Asthma (COAST; n = 180) and Urban Environment and Childhood Asthma (URECA; n = 139), underwent 16S rRNA V4 sequencing. Nasal microbiota dominated by Moraxella, Streptococcus or Haemophilus (MSH) or Corynebacterium, Dolosigranulum, Staphylococcus or Bacillus (CDSB) were assessed. Paired blood was genotyped for nine 17q12-q21 risk SNPs. Logistic regression tested interactions between 17q12-q21 SNPs and MSH or CDSB on wheeze risk in the first three years of life. A549 lung epithelial cells, CRISPR-edited to encode the rs7216389 risk genotype (rs7216389[TT]) were compared to the heterozygous (rs7216389[CT]) line using bulk RNA sequencing.<br><br>RESULTS: SNPs, particularly those in the Orsomucoid-like sphingolipid biosynthesis regulator 3 (rs8076131; OR = 1.72, CI = 1.09-2.71, Pint = 0.031) and Gasdermin B (rs2305480, OR = 1.72, CI = 1.09-2.71, Pint = 0.042 and rs7216389, OR = 1.73, CI = 1.09-2.70, Pint = 0.047) genes, interact with MSH microbiota to increase early-life wheeze risk (false discovery rate [FDR] Pint = 0.016 for all), while interactions with CDSB reduce risk. A549 airway epithelial cells homozygous for rs7216389[TT] exhibited decreased expression of genes involved in antimicrobial responses and neutrophil recruitment and evidence increased microbial adherence compared with the heterozygous cell line.<br><br>CONCLUSION: Airway microbiota interact with SNPs at the 17q12-q21 locus in genes involved in sphingolipid metabolism and intracellular antimicrobial responses, to modulate wheeze risk.<br><br>CLINICAL IMPLICATION: Interventions aimed at decreasing pathogenic bacterial colonization of the airways may reduce wheeze burden in genetically susceptible children.<br><br>CAPSULE SUMMARY: Upper airway microbiota interact with asthma-risk genetic variants to influence early-life wheeze risk.}, }
@article {pmid42248250, year = {2026}, author = {Ortega-Reyes, D and Asami, S and Suda, W and Ohno, H}, title = {Host genetics, diet, and the gut microbiome: Addressing methodological and reproducibility challenges in human studies.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {101646}, doi = {10.1016/j.tjnut.2026.101646}, pmid = {42248250}, issn = {1541-6100}, abstract = {The interplay between host genetics, diet, and the gut microbiome is a key focus in human health research. However, progress has been slowed by substantial methodological differences and limited reproducibility across studies. This narrative review examines major sources of variability throughout the research process, with a focus on design, measurement, and analysis. It highlights how factors such as cohort structure, confounder control, dietary assessment, sample collection and preservation, DNA extraction, sequencing methods, and statistical approaches can significantly influence microbiome taxonomic assignments and abundances, and hinder the replication of host-microbiome-diet associations. We discuss how these issues complicate the interpretation of microbiome heritability estimates, genome-wide association signals, and reported gene-diet-microbiome links, which often have small effects and depend heavily on context. We then review ongoing efforts to improve reproducibility and harmonization, including consensus reporting standards, protocol harmonization, and validation techniques such as standardized workflows, mock communities, controls, and absolute quantification methods. Finally, we outline key priorities to enhance cross-study comparability and meta-analyses, including thorough confounder assessment, transparent reporting, and diverse, longitudinal study designs to advance the application of precision nutrition and microbiome-based public health strategies.}, }
@article {pmid42248727, year = {2026}, author = {Hudson, J and Taylor, N and Coffey, MJ and Pushpakumara, BLDU and Prentice, B and Jaffe, A and Visser, S and Sivam, S and Day, AS and Oliver, M and Ranganathan, S and Selvadurai, H and Wainwright, C and Ooi, CY and van Dorst, J}, title = {Is the gut a reservoir of non-tuberculous mycobacteria in people with cystic fibrosis?.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jcf.2026.06.001}, pmid = {42248727}, issn = {1873-5010}, abstract = {Non-tuberculous mycobacteria (NTM) represent a significant disease burden in the cystic fibrosis (CF) population. Whilst the acquisition of NTM to the respiratory tract is predominantly attributed to environmental exposures, the contribution of the gut-lung axis to NTM pulmonary disease remains poorly understood. In this study, we retrospectively examined 1285 stool microbiomes from 121 children and 52 adults with CF, and 135 healthy control (HC) children, in order to assess the prevalence, abundance and clinical significance of NTM in the gut. We detected various species of low clinical concern in the stool of 2% of people with CF and 1% of HC sampled, with longitudinal sampling revealing their occurrence to be sporadic and transient. Of the participants studied, only 11 had a history of prior clinical NTM respiratory colonisation or infection, but there was limited evidence to support ongoing persistence in the intestinal tract. This study suggests that the gut is not a meaningful reservoir for pulmonary NTM infections and it is unlikely to serve as a transmission route within the CF population.}, }
@article {pmid42248728, year = {2026}, author = {van Dorst, J and Taylor, N and Pushpakumara, BLDU and Tan, ZT and Buchanan, DD and Haber, PS and Nash, E and Visser, S and Volovets, A and Sivam, S and Ooi, CY}, title = {Genotoxic pks + E. coli is strongly associated with ileocolonic neoplasia in adults with Cystic Fibrosis.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jcf.2026.05.016}, pmid = {42248728}, issn = {1873-5010}, abstract = {BACKGROUND: Polyketide synthase island-positive (pks+) Escherichia coli is a genotoxic gut bacterium linked to colorectal cancer (CRC) tumorigenesis via the genotoxin colibactin. In adults with Cystic Fibrosis (CF), there is an increased incidence and earlier development of CRC but the biological mechanisms underlying this increased risk remain incompletely understood. We aimed to determine the prevalence of pks+ E. coli in adults with CF.<br><br>METHODS: Stool samples and DNA were analyzed from the SCREENCF study cohort. Metagenomic libraries were sequenced on the NovaSeq X Plus platform, using Illumina protocols. Detection of the pks island was assessed with polymerase chain reaction (PCR) targeting the clbB gene.<br><br>RESULTS: Of the 49 CF participants; pks+ E. coli was detected in 1/35 (3%) of the no pathology (NORMAL) group, 5/12 (42%) in the adenomatous polyps (AP) group, and 2/2 (100%) in the ileocolonic cancer (ICC) group. Individuals with any ileocolonic neoplasia were 34 times more likely to harbor pks+ E. coli than those with NORMAL colonoscopy findings (OR = 34.0, 95% CI 5.00-691, p = 0.002). The presence of pks+ E. coli correlated with higher overall E. coli burden (p = 0.0009), but not with fecal inflammation, other genotoxic bacterial species or overall bacterial composition.<br><br>CONCLUSION: pks+ E. coli is infrequently detected among adults with CF, but its presence is associated with ileocolonic neoplasia, indicating a potential role in pathogenesis. If validated in larger cohorts, pks+ E. coli could provide a clinically meaningful biomarker for early detection, risk stratification and a potential target for precision intervention.}, }
@article {pmid42248767, year = {2026}, author = {Grant, JM and Tu, C and Roberts, KE and Souza-Fonseca-Guimaraes, F}, title = {Pseudomyxoma peritonei and the microbiome: Emerging observations and unanswered questions.}, journal = {Trends in cancer}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.trecan.2026.05.004}, pmid = {42248767}, issn = {2405-8025}, abstract = {Pseudomyxoma peritonei is a rare, heterogeneous appendiceal cancer characterized by mucus-secreting tumor cells. Evidence suggests a microbial association, though its significance remains unclear. This forum article synthesizes links among microbial communities, mucin biology, and tumor behavior, highlighting key research challenges and how spatial multiomics may clarify disease mechanisms and therapeutic opportunities.}, }
@article {pmid42248895, year = {2026}, author = {Ma, J and Li, Q and Xia, G and Zhang, J and Usman, S and Guo, X}, title = {Lactiplantibacillus plantarum-inoculated silage improves milk fat in dairy goats by reprogramming rumen microbiota to promote pyruvate metabolism.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01031-6}, pmid = {42248895}, issn = {2055-5008}, support = {2022YFD130100202//National Key Research and Development Program of China/ ; }, abstract = {Silage inoculated with homofermentative lactic acid bacteria exhibits superior nutritional quality and improves ruminant production performance. However, the mechanisms by which the inoculated silage modulates microbial and metabolic alterations along the rumen-mammary gland axis remain unclear. Here, Lactiplantibacillus plantarum BX62 inoculation enhanced silage quality and flavonoid content through reshaping the microbiome, which promotes carbohydrate-active enzyme secretion. Feeding the silage to dairy goats modulated ruminal microbiota through changes in silage flavonoid, fiber, and crude protein contents. Notably, increased flavonoid intake enriched ruminal flavonoid-degrading bacteria, leading to enhanced flavonoid transformation, fiber degradation, and pyruvate-centered carbohydrate metabolism, promoting acetate production. The increased ruminal acetate and upregulated expression of mammary lipogenic genes ultimately improved milk fat synthesis. Our findings reveal how L. plantarum links silage quality to rumen function and mammary gland metabolism, offering a mechanistic basis for improving lactation performance of dairy goats via modulating silage fermentation.}, }
@article {pmid42248917, year = {2026}, author = {Yan, W and Huang, C and Li, D and Feng, J and Feng, G and Ma, H and Jansa, J and Klironomos, J and Zhuang, M and Zhang, F and Zhang, L}, title = {The precisely regulated keystone taxa facilitate microbial mineralization of soil organic phosphorus via niche partitioning.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01036-1}, pmid = {42248917}, issn = {2055-5008}, support = {32130094//the National Natural Science Foundation of China/ ; 2022YFD1901304 and 2024YFE0105000//the National Key Research and Development Program of China/ ; MOE, #00975101//the Disciplinary Breakthrough Project of Ministry of Education/ ; PC2024B02003//Pinduoduo-China Agricultural University Research Fund/ ; }, abstract = {Rhizosphere keystone taxa critically drive microbial community stability and soil biogeochemical cycles. However, the manipulation of such taxa remains a challenge. This study simulated plant-mediated modulation of keystone taxa via simplified synthetic root exudates to track their compositional shifts. The combination of luteolin, myristic acid, and glucose enhanced rhizosphere phosphatase activity, significantly enriched Domibacillus indicus D99, and converted it into a keystone taxon. This precise regulation was driven by transcriptional upregulation of C metabolism and an unusual fatty acid assimilation pathway. Additionally, metabolites produced by D. indicus D99 (such as bergapten and lactate) were preferentially utilized by phosphate-mineralizing bacteria, Bacillus sp. C67 and Domibacillus sp. C94. These partner bacteria exhibited less substrate overlap and pronounced resource partitioning, forming an efficient synergistic relationship with D. indicus D99 that amplified rhizosphere phosphatase activity and plant growth. This study highlights opportunities to utilize the ecological roles of keystone taxa in manipulating the microbiome.}, }
@article {pmid42249248, year = {2026}, author = {Dave, AM and Chatrizeh, M and Wolf, MS and Morowitz, MJ and Simon, DW}, title = {The Role of Microbiome-Associated Metabolites and Their Clinical Implications in Traumatic Brain Injury: A Scoping Review.}, journal = {Neurocritical care}, volume = {}, number = {}, pages = {}, pmid = {42249248}, issn = {1556-0961}, support = {5T32HD040686//Foundation for the National Institutes of Health/ ; NINDS R21 NS115173/NS/NINDS NIH HHS/United States ; NINDS R01 NS127372/NS/NINDS NIH HHS/United States ; }, abstract = {Traumatic brain injury (TBI) is a major public health challenge, with heterogeneous mechanisms and limited targeted therapies. Despite advances in neurocritical care, interventions to meaningfully alter long-term outcomes have been elusive, and treatment remains largely supportive. Parallel to this, increasing evidence from both preclinical models and human studies implicates the gut microbiome as a dynamic modulator of neurologic injury and recovery through the microbiome-gut-brain axis, a bidirectional network linking the central nervous system, gastrointestinal tract, and intestinal microbiota. TBI and neurointensive care including mechanical ventilation, sedation, dietary modification, and antibiotics contribute to the development of dysbiosis and altered production of microbial metabolites. These bioactive molecules, such as short-chain fatty acids, tryptophan metabolites, bile acids, and polyamines, play critical roles in regulating blood-barrier integrity, immune activation, neurotransmission, and energy metabolism. In TBI, emerging preclinical and clinical data suggest that altered levels of these metabolites may influence secondary injury cascades and shape recovery. In this review, we synthesize current TBI-specific preclinical and clinical data on microbiome alterations and microbiome-associated metabolite signaling following TBI, and we place these findings in the broader context of microbiome-gut-brain research. Understanding these pathways could inform future strategies to optimize treatment, including targeted microbiome modulation, dietary interventions, or metabolite supplementation. We identify key knowledge gaps and outline priorities for translational research needed to determine whether monitoring and therapeutic manipulation of the microbiome-gut-brain axis can enhance patients' recovery trajectory.}, }
@article {pmid42249250, year = {2026}, author = {Xie, J and Yang, Y and Chen, W and Wang, L and Weng, S and Lyu, Q and Cao, G}, title = {Synergistic Intervention for Obesity: Integrating Central Appetite Regulation and Peripheral Energy Expenditure.}, journal = {Current obesity reports}, volume = {15}, number = {1}, pages = {}, pmid = {42249250}, issn = {2162-4968}, mesh = {Humans ; *Energy Metabolism/drug effects/physiology ; *Obesity/therapy/physiopathology/metabolism ; *Appetite Regulation/physiology/drug effects ; *Anti-Obesity Agents/therapeutic use/pharmacology ; Animals ; Weight Loss ; Energy Intake ; }, abstract = {PURPOSE OF REVIEW: Obesity stems from a chronic imbalance between energy intake and expenditure. Current therapeutic strategies primarily focus on reducing caloric intake, yet their long-term efficacy is often limited by compensatory metabolic adaptations that lead to weight regain. This review outlines the neural mechanisms through which the central nervous system regulates appetite and the peripheral metabolic pathways that drive adipose thermogenesis. Furthermore, it examines how integrated approaches-spanning from approved to preclinical and clinical-stage investigational agents (e.g., dual- or multi-target agonists), microbiome-targeted interventions (e.g., probiotics), and exercise therapy-can synergistically overcome the limitations of single-pathway strategies. Ultimately, this review provides a theoretical foundation for designing next-generation, personalized, multimodal obesity management regimens.<br><br>RECENT FINDINGS: Traditional weight-loss drugs primarily act by centrally suppressing appetite, reducing food intake through modulation of neural circuits in regions such as the hypothalamus. However, studies show that relying on appetite suppression often triggers compensatory metabolic adaptation, ultimately leading to weight regain. Current anti-obesity drug development is therefore shifting toward integrated central-peripheral dual mechanisms. GLP&#x2011;1/glucagon dual-receptor agonists and triple-receptor agonists (such as retatrutide) have exhibited unprecedented weight-loss efficacy in clinical trials. These novel agents overcome the limitations of single-target appetite suppression by synergistically integrating central anorexigenic signaling with peripherally mediated increases in energy expenditure, thereby achieving more potent and durable weight reduction. The sustainability of obesity treatment relies on a dual-pronged intervention strategy: suppressing appetite to reduce energy intake while actively promoting energy expenditure, thereby overcoming the metabolic adaptation and weight rebound associated with monotherapy.}, }
@article {pmid42249284, year = {2026}, author = {Wang, L and Li, Y and Zhang, W and Zhao, Y and Lu, Y and Song, J and Guan, W}, title = {Melatonin-mediated dual regulation of physiological-biochemical traits and rhizosphere microbial communities alleviates drought stress in Bougainvillea.}, journal = {BMC plant biology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12870-026-09179-1}, pmid = {42249284}, issn = {1471-2229}, support = {202507AB040003//the Central Guidance for Local Science and Technology Development Fund Project/ ; 202302AE090018//the Key Technologies Research for the Germplasm of Important Woody Flowers in Yunnan Province/ ; }, abstract = {BACKGROUND: Drought conditions limit the distribution of Bougainvillea varieties, reduce their ornamental value, and increase maintenance costs. Although the rhizospheric melatonin-mediated mechanisms of plant drought resistance have been extensively documented. its role in the drought stress response of Bougainvillea, especially the regulatory effect on rhizosphere microorganisms, remains unclear. Using Bougainvillea glabra 'Cypheri' as plant material, this study employed a pot-based natural drought experiment combined with physiological indicator measurement, rhizosphere microbiome high-throughput sequencing, microbial network analysis, PICRUSt2 functional prediction, and redundancy analysis (RDA) to systematically investigate the regulatory mechanisms of melatonin on aboveground-belowground synergistic drought resistance.<br><br>RESULTS: Compared with the control group, drought stress significantly enhanced the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), as well as the proline (Pro) content in Bougainvillea, while increasing malondialdehyde (MDA) accumulation. Conversely, leaf relative water content (RWC) and chlorophyll (Chl) content were markedly reduced. Simultaneously, the rhizosphere microbial community balance was disrupted, bacterial network robustness diminished, and carbon metabolic pathways were suppressed. Exogenous melatonin application further significantly enhanced antioxidant enzyme activities and Pro accumulation under drought stress, reduced MDA content, and improved the physiological status of plants. Simultaneously, it promoted the enrichment of Proteobacteria, modulated the abundance balance of Ascomycota, enhanced microbial network stability, and optimized carbon, nitrogen, and energy metabolic pathways. Collectively, these results demonstrate that melatonin enhances drought tolerance in Bougainvillea by regulating the structure and network stability of rhizosphere microbial communities, synergistically improving aboveground drought resistance physiology, and mediating aboveground-belowground synergistic interactions.<br><br>CONCLUSION: This study provides a theoretical foundation for the application of melatonin in drought-resistant cultivation practices for Bougainvillea species.}, }
@article {pmid42249293, year = {2026}, author = {Tang, F and Zhao, C and Cao, Y and Liu, C and Mi, G and Cao, J and Li, Y and Wang, C}, title = {Unraveling microbial signatures in the comorbidity of autoimmune diseases and depression.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05223-0}, pmid = {42249293}, issn = {1471-2180}, support = {tsqn202408369//Taishan Scholars Program of Shandong Province-Young Taishan Scholars/ ; 202328057//Science and Technology Plan Project of Jinan/ ; 82304247//National Natural Science Foundation of China/ ; ZR2022QB152//Natural Science Foundation of Shandong Province/ ; 2021ZD0201808//National Key Research and Development Program of China/ ; 21320082164070//Young Scholars Program of Shandong University/ ; }, abstract = {BACKGROUND: Depression is a common comorbidity in autoimmune diseases (ADs), including inflammatory bowel disease (IBD), a well-characterized AD with prominent gut involvement and strong host-microbiome interactions. Yet, its underlying microbial associations remain insufficiently understood. This study aimed to explore the gut microbial composition and function in patients with ADs comorbid depression, including a subgroup with IBD comorbid depression, and to identify potential microbial and metabolic signatures associated with this comorbidity.<br><br>METHODS: We analyzed two curated cohorts from the American Gut Project: an AD cohort (n&#x2009;=&#x2009;344; AD with depression: n&#x2009;=&#x2009;115, AD without depression: n&#x2009;=&#x2009;120, healthy controls: n&#x2009;=&#x2009;109), and an IBD subgroup (n&#x2009;=&#x2009;75; IBD with depression: n&#x2009;=&#x2009;25, IBD without depression: n&#x2009;=&#x2009;30, healthy controls: n&#x2009;=&#x2009;20). Gut microbial profiles were evaluated using 16S rRNA gene sequencing (V4 region). Microbial diversity was assessed via &#x3b1;- and &#x3b2;-diversity indices. Differential abundance analysis was conducted using Linear Discriminative Analysis Effect Size (LEfSe) and Linear Discriminant Analysis (LDA) methods. Functional predictions were performed based on Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology inference. Microbial co-occurrence networks were also constructed to explore taxonomic interaction patterns.<br><br>RESULTS: In the AD cohort, &#x3b2;-diversity was significantly reduced in patients with comorbid depression compared to those without, whereas &#x3b1;-diversity did not show statistically significant differences. A total of 40 microbial taxa were significantly different between patients with AD comorbid depression and AD without depression. In the IBD subgroup, 12 taxa were differentially abundant between patients with and without depression. Functional pathway predictions suggested disruptions in carbohydrate metabolism, energy metabolism, and glycan biosynthesis in patients with AD and comorbid depression compared to those without depression. Microbial network analysis revealed distinct co-occurrence structures in patients with comorbid depression.<br><br>CONCLUSIONS: This exploratory study suggests that individuals with ADs or IBD and comorbid depression exhibit distinct gut microbiome compositions and functional potentials compared to non-depressed counterparts. These associations may offer insights into gut-brain interactions in autoimmunity and mental health. However, due to the cross-sectional design, mechanistic and clinical inferences remain speculative and require validation in future studies.}, }
@article {pmid42249511, year = {2026}, author = {Stahl, S and Widmaier, H and Sakk, V and Nalapareddy, K and Kissmann, AK and Rosenau, F and Mulaw, MA and Haslam, DB and Geiger, H}, title = {Aging of the adaptive immune system affects the gut microbiome and systemic levels of vitamin B6.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42249511}, issn = {2049-2618}, support = {GRK 2254 HEIST//Deutsche Forschungsgemeinschaft/ ; }, abstract = {BACKGROUND: Age-associated dysregulation of the gut microbiota is a hallmark of aging and has been linked to multiple age-related diseases, yet upstream host factors driving these changes remain incompletely defined. Extensive bidirectional crosstalk between gut microbiota and mucosal immunity has been described. Aging is accompanied by a progressive decline in immune function, collectively termed aging-associated immune remodeling (AAIR). AAIR encompasses widespread compositional and functional changes that impair an effective response to pathogens, vaccines, and tissue damage. We examined whether AAIR is an upstream host factor influencing the composition of the microbiome upon aging.<br><br>RESULTS: Hallmarks of AAIR were also present in the ileal lamina propria, including reduced na&#xef;ve CD4[+] and CD8[+] T cell populations and expansion of memory and regulatory T cell subsets. To test whether mucosal AAIR reflects intrinsic aging of the hematopoietic system, we used an HSC transplantation model where young RAG1[-/-] recipients develop an adaptive immune system derived exclusively from either young or aged donor HSC in an otherwise young host environment. Recipients of aged HSCs recapitulated key features of mucosal AAIR, particularly loss of na&#xef;ve T cells, demonstrating that AAIR in the ileal LP is driven at least in part by aged HSCs. Shotgun metagenomic sequencing of fecal samples revealed that ileal AAIR is associated with alterations in gut microbiota. In detail, there was a reduced abundance of taxa associated with the vitamin B6 (VB6) biosynthesis and salvage pathways. Accordingly, VB6 levels in serum were reduced in mice with aged immune systems.<br><br>CONCLUSION: Our findings link AAIR to reduced microbial VB6 pathway abundance and lower systemic VB6 availability, suggesting that immune aging shapes the functional output of the microbiome in ways that diminish its VB6 biosynthetic capacity. This postulates an immune-microbiome-VB6 association that warrants further investigations for therapeutic strategies to increase VB6 levels upon aging. Video Abstract.}, }
@article {pmid42249581, year = {2026}, author = {Xi, Y and Liping, Z and Yating, X and Yang, X and Jian, C and Caiyun, C and Shuwen, L and Zian, Z and Xiaojian, Y and Shuwen, H and Wei, W}, title = {Genomic Map of Escherichia coli and Single Nucleotide Polymorphism Markers in Colorectal Cancer.}, journal = {Microbial biotechnology}, volume = {19}, number = {6}, pages = {e70397}, pmid = {42249581}, issn = {1751-7915}, support = {2023GZ86//Public Welfare Technology Application Research Program of Huzhou/ ; 2025KY328//Medical and Health Research Project of Zhejiang Province/ ; }, abstract = {Gut microbial single nucleotide polymorphisms (SNPs) offer stable, specific genetic markers for disease diagnosis. Escherichia coli (E. coli), a dominant gut bacterium, is associated with colorectal cancer (CRC), but limited enteric reference genomes hinder SNP annotation in intestinal strains. Metagenomic sequencing profiled gut microbiota in 200 CRC patients and 200 healthy controls. The E. coli strain WDP was fully sequenced via PacBio single-molecule technology for genome assembly and functional annotation. Wilcoxon tests identified differentially abundant microbes, while Lasso regression models integrated microbial features (bacteria, viruses, virus-host pairs) and E. coli SNPs to predict CRC risk. E. coli abundance did not differ between groups, but genomic analysis revealed 7460 CRC-associated SNPs. The SNP-based model achieved superior accuracy (92.86% training, 93.33% testing, 84.00% validation) and AUC (0.986, 0.983, 0.913), outperforming models based on microbial abundances (e.g., Staphylococcus capitis, Zindervirus) or virus-host interactions. PacBio-generated E. coli genomic maps enable precise SNP annotation, establishing E. coli SNPs as highly accurate biomarkers for CRC risk prediction. This approach leverages microbial genetic stability to advance non-invasive early detection, offering a novel target for precision microbiome-based diagnostics.}, }
@article {pmid42249636, year = {2026}, author = {Zhang, B and Yue, H and Skalse, A and Sangfuang, N and Shorthouse, D and Gaisford, S and Basit, AW}, title = {High-throughput identification of bacterial β-glucuronidase inhibitors using machine learning.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2681789}, doi = {10.1080/19490976.2026.2681789}, pmid = {42249636}, issn = {1949-0984}, abstract = {The human gut microbiome plays a vital role in regulating host physiological functions and influencing the pharmacokinetics of interventions, particularly drug metabolism, which in turn affects pharmacodynamics. Gut microbial β-glucuronidase (GUS) is a key bacterial enzyme that modulates drug therapeutic outcome and gastrointestinal toxicity through deconjugating glucuronidated drug metabolites. Despite this, systematic high-throughput prediction of GUS inhibitors remains limited by sparse experimental data and the translational shortcomings of known compounds. Here, machine learning is applied as a powerful tool to identify potential GUS inhibitors from more than 10,000 FDA-approved drugs, food additives, and excipients. In this study, both unsupervised and supervised machine learning models were trained on literature-derived data describing the inhibitory potency of 122 compounds against Escherichia coli GUS (EcGUS). These models were compared with a newly developed SMILES-based 1D feature-embedded, self-attention classification model (IC-tf) designed for high-throughput screening. To improve interpretability, a dual-level analysis that combines SHAP attribution of handcrafted descriptors with branch-level transformer attention was applied to the IC-tf model. All models demonstrated strong predictive performance, with ROC-AUC values of 85.9%-89.3% under 3-fold cross-validation, with the IC-tf model showing the highest predictive power. In vitro validation with an external set of 20 compounds confirmed strong predictive accuracy for the Random Forest and IC-tf models. This work establishes a scalable computational framework for high-throughput discovery of gut microbial GUS inhibitors, facilitating efficient screening of co-administered drugs and excipients with the translational potential to improve drug bioavailability and reduce gastrointestinal toxicity.}, }
@article {pmid42249801, year = {2026}, author = {Bivens, E and Atiq, O and Evans, T and Bimali, M and Brown, G and Crane, J and Darwish, N and Faulkner, JL and Govindarajan, R and Johnson, A and Kurilung, A and Lazarenko, O and Lu, YW and Marsh, K and Moreno, M and Nookaew, I and Robeson, M and Sunde, J and Ussery, D and Vural, E and Wilman, M and Nakagawa, M}, title = {A randomized double-blind placebo-controlled phase I/II clinical trial of a human papillomavirus therapeutic vaccine, PepCan, for reducing head and neck squamous cell carcinoma recurrence.}, journal = {Oncotarget}, volume = {17}, number = {1}, pages = {291-305}, doi = {10.18632/oncotarget.28892}, pmid = {42249801}, issn = {1949-2553}, abstract = {UNLABELLED: Copyright: &amp;copy; 2026 Bivens et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.<br><br>OBJECTIVES: The main goals were to assess safety and efficacy (i.e., recurrence reduction).<br><br>RESULTS: Seventeen patients were enrolled. The most common adverse events were grades 1 and 2 injection site reactions, and they occurred more frequently in the PepCan group (p < 0.0001). Two patients had allergic reactions (grade 2 and grade 3), at the 6th vaccination, which were considered to be a dose-limiting toxicity. No serious adverse events were reported. In the intention-to-treat analyses, 45% (5/11) had non-recurrence in the PepCan group while 80% (4/5) had non-recurrence in the placebo group (p = not significant). Those who received PepCan and experienced non-recurrence showed a trend of having higher new peripheral T cell immune responses to human papillomavirus type 16 E6 (p = 0.05). Pre-vaccination T helper type 1 cells were higher in the PepCan non-recurrence group compared to the PepCan recurrence group (p = 0.01).<br><br>METHODS: PepCan consists of four human papillomavirus type16 E6 peptides and a Candida skin testing reagent. Patients with head and neck squamous cell carcinoma who had no evidence of disease after standard of care treatments were randomized at 3:1 to PepCan versus placebo (saline). Seven intradermal injections were given followed with two observational visits. Safety was assessed using CTCAE version 5, and efficacy was assessed based on not having recurrence within 2 years. In addition, immune responses and oral and gut microbiome were assessed.<br><br>CONCLUSIONS: PepCan was well tolerated. PepCan does not seem to be effective in reducing recurrence; however, the results are inconclusive given the small patient numbers.}, }
@article {pmid42249994, year = {2026}, author = {Faridi, U and Mir, R and Algehainy, NA and Alharbi, ZM and Tayeb, FJ and Barnawi, J and Jalal, MM and Altayar, MA and Moawadh, M and Mustafa, SK and Mir, MM and Alfaifi, J and Almazni, IA}, title = {Understanding the mechanisms underlying obesity induced tumorigenesis: therapeutic perspectives to manage dysregulated lipid metabolism.}, journal = {Discover oncology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12672-026-05200-z}, pmid = {42249994}, issn = {2730-6011}, abstract = {Obesity has emerged as one of the most significant global public health challenges of the twenty-first century and is now firmly established as a major risk factor for multiple cancer types. Hypertrophic adipose tissue generates chronic low-grade inflammation, adipose hypoxia, and fibrosis, which leads to activation of IL-6/STAT3, NF-κB, and PI3K/Akt/mTOR signaling. Hyperinsulinemia and insulin resistance increase oncogenic pathways, while dysregulated adipokines by elevated leptin and reduced adiponectin enhance proliferation, angiogenesis, epithelial mesenchymal transition, and immune evasion. Obesity further remodels the tumor microenvironment by promoting extracellular matrix deposition, angiogenesis, immunosuppressive cell expansion, and metabolic competition that impairs antitumor immunity. Emerging evidence also implicates obesity-driven epigenetic reprogramming, altered microbiome composition, and metabolic heterogeneity as key determinants of tumor aggressiveness and treatment response. Conventional oncologic therapies rarely account for host metabolic status, which may contribute to variable therapeutic efficacy in obese patients. This review integrates mechanistic and translational evidence to define actionable vulnerabilities within obesity-induced tumorigenic pathways. We evaluate targeted metabolic interventions, cytokine blockade, adipokine modulation, immune checkpoint optimization, microbiome-directed strategies, and precision stratification frameworks. The present review outlines a multidimensional therapeutic roadmap to improve prevention, treatment response, and long-term outcomes in obesity-associated malignancies.}, }
@article {pmid42250036, year = {2026}, author = {Prajapati, KK and Pandey, R and Pandey, V and Upadhyay, KM and Singh, S and Pandey, VS and Pandey, VN}, title = {Unveiling the Nutraceutical Potential of Yam Dioscorea alata L.: A Comprehensive Review.}, journal = {Plant foods for human nutrition (Dordrecht, Netherlands)}, volume = {81}, number = {2}, pages = {}, pmid = {42250036}, issn = {1573-9104}, abstract = {Dioscorea alata L. (water yam and purple yam) is a traditionally important food and medicinal plant widely used in Asia and the Pacific Islands. It has long been utilized in traditional medicine for treating weakness, inflammation, menstrual disorders, wound healing, and gastrointestinal ailments. The dual role as a dietary and therapeutic resource highlights its ethnopharmacological importance and supports the need for scientific validation. This review evaluates existing knowledge on the nutraceutical potential of D. alata. Recent studies report diverse biological activities, including antioxidant, anti-inflammatory, antidiabetic, anticancer, antihypertensive, cardioprotective, and gut microbiome-modulatory effects. These activities are largely attributed to bioactive compounds such as saponins and anthocyanins. The species shows considerable promise as a functional food and natural therapeutic resource. Moreover, its cultivation and utilization may contribute to food security and public health (SDG 2 and 3). Further, phytochemical and clinical studies are required to fully establish its nutraceutical value.}, }
@article {pmid42250066, year = {2026}, author = {Fu, Y and Jiang, H and Peng, D and Bai, Z and Wang, S and Liu, H and Zhang, W and Shang, W}, title = {Fecal Microbiome and Serum Metabolome Profiles of the Ovarian Failure Mouse Model.}, journal = {Applied biochemistry and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {42250066}, issn = {1559-0291}, support = {KFKT-2024-KY-019//the Key Project Program of the 2024 Scientific Research Fund, Chinese Association of Rehabilitation Medicine/ ; }, abstract = {Ovarian dysfunction is closely associated with reproductive aging and systemic metabolic disturbances; however, the underlying microbial and metabolic mechanisms remain unclear. In this study, we analyzed fecal microbiome and serum metabolome profiles in young (7-week-old) and aged (12-month-old) female C57BL/6J mice using shotgun metagenomic sequencing and untargeted ultra-high-performance liquid chromatography-tandem mass spectrometry. Microbial and metabolic data were processed using QIIME2, HUMAnN, and MetaboAnalyst 5.0. Differential taxa and metabolites were identified using DESeq2 and linear discriminant analysis effect size (LEfSe), and their associations were evaluated using Spearman's correlation analysis. Our results showed that aged mice exhibited significant alterations in gut microbiota composition, including a decreased abundance of Firmicutes and an increased abundance of Bacteroidetes, along with enrichment of the genera Alistipes and Akkermansia. Serum metabolomic profiling identified 246 differential metabolites, primarily involved in amino acid and energy metabolism pathways. Integrated analysis revealed that tryptophan metabolism represents a key pathway linking microbial dysbiosis with systemic metabolic alterations. Notably, enriched microbial taxa, including Akkermansia muciniphila and species within the genus Alistipes, were strongly correlated with tryptophan-related metabolites. These findings indicate that ovarian failure is associated with coordinated alterations in the gut microbiome and serum metabolome, converging on tryptophan metabolism. This study provides new insights into host-microbiome-metabolite interactions in ovarian failure and highlights potential microbial and metabolic targets for therapeutic intervention.}, }
@article {pmid42250132, year = {2026}, author = {Dweh, TJ and Taye, M and Deka, D and Samanta, SK and Talukdar, NC}, title = {Fusobacterium nucleatum in oral squamous cell carcinoma: molecular mechanisms, tumor microenvironment and translational implications.}, journal = {Archives of microbiology}, volume = {208}, number = {8}, pages = {}, pmid = {42250132}, issn = {1432-072X}, abstract = {Fusobacterium nucleatum has increasingly emerged as a microorganism of major interest in microbial dysbiosis-associated carcinogenesis, particularly in oral squamous cell carcinoma (OSCC), where chronic inflammatory remodeling, immune dysfunction, and epithelial plasticity contribute to aggressive tumor behavior and poor clinical outcomes. Recent experimental findings suggests that F. nucleatum may participate in multiple biologic processes linked to OSCC progression, including activation of inflammatory signaling pathways, disruption of epithelial integrity, metabolic adaptation, immune checkpoint-associated suppression, and resistance-related phenotypes. In this review, we critically evaluate current evidence regarding the molecular and cellular interactions of F. nucleatum within the OSCC tumor microenvironment, with particular emphasis on FadA- and Fap2-associated signaling, β-catenin-, NF-κB-, and STAT3-mediated pathways, epithelial-mesenchymal transition (EMT), stromal remodeling, and immune exhaustion signatures. We additionally examine the growing application of spatial transcriptomics, single-cell sequencing, and integrated multi-omics approaches for host-microbe characterization in OSCC. Importantly, current findings remain heterogeneous and context-dependent, varying according to tumor site, HPV status, microbial burden, host immune composition, and methodological variability across studies. Although microbiome-informed biomarkers and therapeutic strategies are increasingly being explored, most remain at early experimental stages and require robust OSCC-specific mechanistic and clinical validation before translational implementation.}, }
@article {pmid42250135, year = {2026}, author = {Das, K and Jaiswal, P and Priya, H and Sangwan, S and Paul, S and Prasanna, R and Grover, M}, title = {Microbial innovations for climate-resilient agriculture: mechanisms, applications, and emerging technologies.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {7}, pages = {}, pmid = {42250135}, issn = {1573-0972}, abstract = {Agriculture is increasingly challenged by climate change-driven stresses, including rising temperatures, erratic rainfall, soil degradation, with increased frequency of pests and disease outbreaks. This disrupts crop productivity and threatens global food security, underscoring the urgent need for sustainable, adaptive strategies, which are environment-friendly. Microorganisms, integral to soil health, nutrient cycling, and plant stress physiology, offer promising nature-based solutions for climate resilient agriculture. Yet their potential remains underutilized due to technical, ecological, and socio-economic barriers that hinder widespread adoption. This review addresses these research gaps and practical challenges, while outlining future perspectives for scaling up microbe-based technologies through integration with omics and AI tools. The major points addressed in this review are (1) Major advances in microbial applications that directly support crop resilience and ecosystem sustainability. It examines recent progress made towards enhancing the effectiveness of biofertilizers (including mycorrhizal fungi), biopesticides and developing novel products, detailing how these innovations enhance nutrient acquisition, regulate phytohormonal balance, improve water-use efficiency, mitigate abiotic stresses such as drought, salinity, heat and pH, and minimize losses incurred due to pathogen and pests; (2) Mechanistic insights into microbial mediation of nutrient cycling, soil aggregation, and stress alleviation in terms of plant-microbe or soil-plant microbiome networking; (3) The role of emerging biotechnological tools, including metagenomics, microbiome engineering, and synthetic biology, that enable the design of more effective and context-specific microbial interventions that can be integrated with artificial intelligence (AI) and machine learning (ML) tools for precise application (4) Emphasis on both the benefits and constraints of microbial inoculants is documented as well as novel strategies for their effective use as sustainable solutions for climate ready agriculture. Ultimately, microbial innovations are positioned as pivotal in building climate-resilient agroecosystems capable of sustaining productivity and reducing environmental footprints.}, }
@article {pmid42250251, year = {2026}, author = {Mirzai, M and Eslami, M and Azizi, AH and Lotfi, P and Alavi Khoshhall, SA and Mirzaei, A and Habibi, MA}, title = {Interplay Between the Ketogenic Diet and the Gut Microbiome in Glioblastoma: A Comprehensive Review of Mechanisms and Clinical Implications.}, journal = {Nutrition and cancer}, volume = {}, number = {}, pages = {1-25}, doi = {10.1080/01635581.2026.2684070}, pmid = {42250251}, issn = {1532-7914}, abstract = {Glioblastoma (GBM) is an aggressive glioma associated with poor prognosis and a median survival of under one year. Standard therapies-surgery, radiotherapy, and temozolomide-impose substantial financial burdens and reduce quality of life, driving interest in less invasive adjunctive approaches. The ketogenic diet (KD) has shown promise by targeting tumor metabolic vulnerabilities, as GBM cells rely heavily on glucose and exhibit limited capacity for ketone metabolism. Although KD is well-validated in epilepsy and diabetic ketoacidosis, its application in GBM yields inconsistent results due to small trials, low adherence, and variability in study designs. Emerging evidence suggests that interindividual differences in gut microbiota (GM) composition may significantly contribute to this inconsistency. GM modulates host metabolism, influences KD efficacy, and exhibits bidirectional interactions with tumor progression. Notably, glioma patients display distinct GM profiles that may alter therapeutic responses. This comprehensive review synthesizes current literature on the interplay between KD and GM in GBM, highlighting mechanisms by which GM variability affects metabolic outcomes. Understanding these interactions is essential to reconcile discrepant findings and optimize patient selection for KD-based interventions, ultimately advancing personalized metabolic strategies in neuro-oncology.}, }
@article {pmid42250371, year = {2026}, author = {Maerten, P and Wolthuis, A and D'Hoore, A and Bislenghi, G and De Hertogh, G and Sagaert, X and Dresen, R and Broeckhoven, V and Rasschaert, G and Tejpar, S and Van Herpe, F and Van Cutsem, E and Dekervel, J and Haustermans, K}, title = {Multi-omic biomarkers of neoadjuvant treatment response in rectal cancer: A narrative review.}, journal = {European journal of surgical oncology : the journal of the European Society of Surgical Oncology and the British Association of Surgical Oncology}, volume = {52}, number = {8}, pages = {111910}, doi = {10.1016/j.ejso.2026.111910}, pmid = {42250371}, issn = {1532-2157}, abstract = {BACKGROUND: Neoadjuvant treatment response in rectal cancer is highly heterogeneous, complicating patient selection for organ-preservation strategies. Robust biomarkers capable of accurately predicting treatment response are needed to improve personalized treatment decisions.<br><br>METHODS: We conducted a narrative review of studies published since 2015 evaluating predictors of response to neoadjuvant therapy in rectal cancer. A comprehensive PubMed/MEDLINE search identified evidence across six domains: (1) genomic and molecular biomarkers, (2) imaging-based biomarkers, (3) histopathological and digital pathology biomarkers, (4) liquid biopsy biomarkers (cfDNA and ctDNA), (5) patient-derived tumor models and (6) microbiome-associated biomarkers.<br><br>RESULTS: Treatment response in rectal cancer reflects a complex interplay between tumor-intrinsic, immune microenvironment and stromal features. Immune-enriched tumors, characterized by high intratumoral CD8[+] T-cell infiltration, CMS1/iCMS3 subtype and high Immunoscore, consistently demonstrate higher rates of pathological and clinical complete response. Conversely, KRAS, TP53, BRAF and SMAD4 mutations, fibroblast activation, TGF&#x3b2; signaling, inflammatory cancer-associated fibroblasts and epithelial-mesenchymal transition programs are associated with treatment resistance. Artificial intelligence applied to MRI, endoscopy and digital pathology enables accurate response prediction, particularly when incorporating longitudinal features. Emerging technologies including ctDNA monitoring, patient-derived tumor models and microbiome profiling provide additional insight into treatment sensitivity and show promise for predicting treatment response.<br><br>CONCLUSIONS: Neoadjuvant treatment response in rectal cancer is dependent on genomic alterations, immune activation and stromal interactions. AI-driven biomarkers hold promise for personalized treatment and organ-preservation. Prospective, multicenter validation is essential to enable further clinical implementation.}, }
@article {pmid42250690, year = {2026}, author = {Chao, Z and Zhang, Q and Pang, L and Sheng, Y and Zhang, J and Feng, T and Yu, L and Shi, W and Xu, Z and Huang, J and Chen, J}, title = {Copper-based nanoparticles trigger fitness decline in parasitoid wasps via gut microbiota-induced fatty acid dysregulation.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128501}, doi = {10.1016/j.envpol.2026.128501}, pmid = {42250690}, issn = {1873-6424}, abstract = {The application of copper-based nanoparticles (Cu-based NPs, e.g., CuO-NPs and Cu-NPs) as nanopesticides represents a promising avenue for sustainable agriculture. However, their potential ecotoxicological effects on beneficial arthropods, particularly parasitoid wasps which are crucial for biological pest control, remain poorly understood. Here, we investigated the chronic toxicity of CuO-NPs and Cu-NPs to the endoparasitoid wasp Asobara japonica and elucidated the underlying mechanisms. We found that dietary exposure induced concentration-dependent lethality, primarily driven by released copper ions rather than the particles themselves. Sublethal exposure severely impaired wasp fitness, with reduced host-searching locomotion thereby mediating a decline in parasitism efficiency. Mechanistically, integrated transcriptomic and metabolomic analyses revealed a coordinated downregulation of some key genes in fatty acid homeostasis pathways and a consequent decline in free fatty acid levels. This disruption in energy mobilization likely compromised the energy supply necessary for sustained activity, thereby explaining the observed locomotion behavioral deficits. Furthermore, Cu-based NPs exposure selectively altered the rare gut microbiota, and shifts in specific bacterial genera correlated with the suppression of host fatty acid metabolism genes. Our results demonstrate that Cu-based NPs impair parasitoid wasp fitness through the disruption of gut microbiome homeostasis and energy metabolism, highlighting the need to consider these impacts in nanomaterial risk assessment for sustainable agriculture.}, }
@article {pmid42250808, year = {2026}, author = {Sabina, R and Kharmawphlang, IM and Charan, K and Hussain, N}, title = {Per- and polyfluoroalkyl substances stress in soil ecosystems: decoding microbial dysbiosis mechanisms and advanced remediation strategies.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135036}, doi = {10.1016/j.biortech.2026.135036}, pmid = {42250808}, issn = {1873-2976}, abstract = {Per- and polyfluoroalkyl substances (PFAS), the so-called "forever chemicals," are emerging contaminants that severely disrupt soil ecosystems by rewiring microbial networks that sustain biogeochemical processes. This review deciphers the mechanisms underlying PFAS-induced microbial dysbiosis, revealing how these contaminants reconfigure community architecture, metabolic functions, and enzyme-mediated processes critical for biogeochemical cycling. It further integrates multi-omics approaches, spanning genomics to metabolomics, to elucidate molecular signatures and adaptive responses that govern microbial resilience and vulnerability across trophic hierarchies. Furthermore, the review examines PFAS biotransformation pathways, emphasising oxidoreductase-mediated mechanisms, kinetic bottlenecks, and catalytic constraints within complex soil matrices. By bridging microbial ecology with advanced material science, the review introduces a transformative paradigm of hybrid catalytic systems, including nanozyme-enabled transformations, engineered enzymes, and photocatalytic assemblies for targeted PFAS degradation. Thus, by linking microbial dysfunction with engineered catalytic innovation, the review offers a systems-level blueprint for sustainable and efficient strategies to restore PFAS-contaminated soils. Notably, this review highlights the urgent need for integrated multidisciplinary approaches to mitigate PFAS-induced ecological risks and advance sustainable soil restoration technologies.}, }
@article {pmid42250809, year = {2026}, author = {Xia, X and Babar, S and Wang, J and Yan, B and Jiang, C}, title = {Nitric acid-modified biochar ameliorates saline-alkali soil and promotes cotton growth by regulating microbiomes and metabolites.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135087}, doi = {10.1016/j.biortech.2026.135087}, pmid = {42250809}, issn = {1873-2976}, abstract = {Biochar is extensively utilized for saline-alkali soil remediation; however, the effects of feedstock origin on its performance remain unclear. Moreover, there is a growing need to develop modified biochar with improved efficiency in saline-alkali soil. Therefore, cotton straw biochars derived from saline-alkali soil (SBC) and non-saline-alkali (NBC), along with their nitric acid-modified forms (HSBC and HNBC), were prepared and assessed via a cotton pot experiment. The results showed that the pH and total soluble salts (TSS) of SBC were significantly higher than those of NBC by 0.33 units and 306.80%, respectively. Nitric acid modification significantly reduced the pH value, salt and alkaline mineral content of biochar, and enriched acidic oxygen-containing functional groups. Meanwhile, SBC treatment increased the contents of Na[+], HCO3[-] and CO3[2-] in soil and showed no promoting effect on cotton growth. In contrast, the acid-modified biochar treatment reduced soil pH by 0.25-0.32 units, decreased TSS by 9.81%-12.11%, and significantly increased cotton dry biomass by 3.63-3.88 times. In addition, acid-modified biochar increased the complexity of the soil microbial network and promoted the enrichment of acid-producing microorganisms as well as stress-resistant microbial groups, such as Actinobacteria and Nocardioides. Simultaneously, it significantly induced the production of metabolites that enhance plant tolerance to saline-alkali stress, such as flavonoids and betalamic acid. In summary, acid-modified biochar enhances its beneficial effects on soil improvement and cotton growth through the coordinated regulation of rhizosphere acid-producing microorganisms and stress-responsive metabolites. This work highlights the scientific significance of biochar modification for advancing sustainable agriculture in saline-alkali regions.}, }
@article {pmid42250830, year = {2026}, author = {Chen, L and Yuan, S and Wang, R and Chen, L and Zhang, B and Zhang, Z and Zhao, Y and Feng, W and Zheng, X and Li, K and Zhou, N}, title = {Revealing the enhancing mechanism and material basis of bile-processed Coptidis Rhizoma in anti-anxiety from perspective of cross organ regulation.}, journal = {Journal of ethnopharmacology}, volume = {}, number = {}, pages = {121969}, doi = {10.1016/j.jep.2026.121969}, pmid = {42250830}, issn = {1872-7573}, abstract = {Coptidis Rhizoma (CR) is a typical cold-attribute herb with potential anti-anxiety properties. Bile is of cold nature and can also interfere with the central nervous system. Bile-processed CR (BCR) exhibits synergistically enhanced anti-anxiety performance. However, the underlying mechanism and material basis for this synergism are not clear.<br><br>AIM OF THE STUDY: To decipher the enhanced anti-anxiety mechanism and material basis of BCR from the perspective of cross-organ regulation.<br><br>METHODS: A rat model of anxiety with sthenic heat syndrome was established to systematically evaluate the enhanced anti-anxiety efficacy of BCR in terms of anxiety behaviour, liver metabolism, and histopathology. Subsequently, the gut microbiome sequencing and untargeted metabolomics of the brain, liver, and serum were performed to explore the mechanism of BCR and CR in regulating the gut-liver-brain axis. In vivo and in vitro molecular biology experiments were performed to further clarify the mechanisms underlying the differential efficacy of BCR and CR. Finally, supramolecular self-assembly simulation and tissue distribution in target organs were carried out to predict the material basis for the enhanced efficacy of BCR.<br><br>RESULTS: BCR performed better than CR in improving the anxiety behaviour and liver metabolism and in alleviating cerebral injury in the rat model of anxiety. The results of gut microbiome and metabolomic analyses indicated that BCR was superior to CR in reshaping the gut microbiota composition and correcting the metabolic disorders in the brain, liver, and serum. Mechanistically, multiomic analysis revealed that BCR and CR (especially BCR) could block the TLR4/NF-&#x3ba;B pathway in the colon, attenuate hepatic inflammation, improve the integrity of the intestinal mucosa and blood-brain barrier, and inhibit the NLRP3/Caspase-1/IL-1&#x3b2; pathway in the brain, thereby blocking the transmission of inflammation along the gut-liver-brain axis and exerting anti-anxiety effects. BCR and CR (particularly BCR) could suppress the overactivation of ammonia-induced MAPK/NF-&#x3ba;B/iNOS pathway and overexpression of glutamine synthetase in the brain, consequently maintaining the normal morphology and glutamate uptake function (GLAST and GLT-1 activities) of astrocytes, alleviating neuronal apoptosis caused by glutamate excitotoxicity (GluN2B), and ultimately blocking the transmission of neurotoxicity along the gut-liver-brain axis to relieve anxiety. The alkaloid-bile acid supramolecules assembled during the decoction of BCR enabled more alkaloids and bile acids to be distributed in the brain and liver, providing material support for the enhanced effect of BCR.<br><br>CONCLUSIONS: BCR was superior to CR in blocking the transmission of inflammation and neurotoxic substances along the gut-liver-brain axis and, hence, exerted stronger efficacy in alleviating neuroinflammation and improving neuronal survival in the rat model of anxiety. The alkaloid-bile acid supramolecules may provide the material foundation. This study fully considers the characteristic of traditional Chinese medicine being able to exert therapeutic effects through multiple pathways, providing novel avenues for research on the processing mechanism.}, }
@article {pmid42251030, year = {2026}, author = {Yang, J and Qin, K and Wang, Q and Guo, W and Yang, X}, title = {Gut commensal Parabacteroides goldsteinii-derived CDCA mediates FXR signalling to improve mucosal barrier function.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01035-2}, pmid = {42251030}, issn = {2055-5008}, support = {32502961//National Natural Science Foundation of China/ ; 32272916//National Natural Science Foundation of China/ ; 2023YFD1301400//National Key Research and Development Program of China/ ; }, abstract = {The gut microbiome plays a crucial role in maintaining barrier integrity. However, it remains urgently needed to mining the gut microbiota that contribute to intestinal mucus barrier and to understand their biological mechanisms. In this study, the Lueyang black-boned chicken (LBC, a Chinese native breed) exhibited higher abundances of Bacteroidetes and Parabacteroides and stronger intestinal barrier function than Arbor Acres (AA, a commercial breed) broilers. Microbiota transplantation from LBC to AA broilers improved the intestinal barrier function. Bacteroides expanded the exclusive metabolic niche of Parabacteroides goldsteinii by producing small metabolites, thereby increasing P. goldsteinii abundance within the gut. P. goldsteinii was identified as the main contributor to the enhanced intestinal mucosal barrier. P. goldsteinii bio-transformed the taurochenodeoxycholic acid into chenodeoxycholic acid, promoting mucin production via farnesoid X receptor activation. Collectively, these findings highlight that the gut microbiota of LBC creates an exclusive metabolic niche for P. goldsteinii through cross-feeding, and reveal the critical role of P. goldsteinii-mediated bile acid biotransformation in enhancing intestinal mucosal barrier function.}, }
@article {pmid42251226, year = {2026}, author = {Kim, E and Jang, ES and Nam, Y and Hwang, HJ and Lee, YJ and Kim, TG and Hong, C and Lee, SR}, title = {The human microbiome as a source of novel bioactive natural products: structures, bioactivities, and biosynthetic insights.}, journal = {Journal of natural medicines}, volume = {}, number = {}, pages = {}, pmid = {42251226}, issn = {1861-0293}, support = {2025-glocal-02-004-511-002//Ministry of Education and Busan Metropolitan City/ ; RS-2025-23525419//National Research Foundation of Korea/ ; RS-2024-00403999//Korea Basic Science Institute/ ; WISET-2025-392//Ministry of Science and ICT, South Korea/ ; }, abstract = {The human microbiome, comprising trillions of microorganisms in distinct anatomical locations such as the gut, oral cavity, skin, and vagina, has emerged as a source of bioactive natural products with diverse scaffolds. Through co-evolution with the host, the human microbiome produces small molecules tailored to physicochemical environments that contribute to immune regulation, epithelial barrier maintenance, pathogen defense, and neurochemical signaling. Recent advances in metagenomics, single-cell genomics, synthetic biology, and integrated omics approaches have enabled rapid discovery and structural elucidation of biosynthetic gene clusters (BGCs) and metabolites. Cultivation-driven and genome mining strategies combined with omics analyses have improved the efficiency of discovering microbiome-derived drug leads. These metabolites mediate competitive and cooperative interactions within microbial ecosystems and hold high promise for therapeutic applications such as immunomodulators, anti-infectives, and neuroactive agents. This review outlines the structural features, biosynthetic pathways, and bioactivities of key metabolites across major microbial niches, together with strategies for their discovery, highlighting their potential in advancing drug development and human health.}, }
@article {pmid42251237, year = {2026}, author = {Zheng, W and He, XR and Zheng, JW and Zhu, ZY and Ye, DY and Jia, XY and Xu, QC and Jiang, MZ}, title = {Effects of Helicobacter pylori infection on gastric mucosal microbiota.}, journal = {World journal of pediatrics : WJP}, volume = {}, number = {}, pages = {}, pmid = {42251237}, issn = {1867-0687}, support = {2023YFC2706504//Key Technologies Research and Development Program/ ; 2023YFC2706500//Key Technologies Research and Development Program/ ; }, abstract = {BACKGROUND: Helicobacter pylori (H. pylori) is a Gram-negative obligate pathogen that colonizes the human gastric environment. Its identification fundamentally altered the historical perception of the stomach as sterile, marking a pivotal shift in gastric microbial research. For 30 years, the dynamic interplay between this bacterium and the gastric lining has been a key research focus.<br><br>DATA SOURCES: The development of next-generation sequencing and advanced bioinformatics has provided powerful, culture-independent tools for probing the intricate diversity of the gastric microbiome. Current investigations extensively cover microbe-microbe interactions within the stomach, the relationship between the resident microbiota and H. pylori, and the dialogue between the microbiome and the host.<br><br>RESULTS: This article reviews current evidence detailing how H. pylori infection reshapes the microbial community on the human gastric mucosa.<br><br>CONCLUSION: Future research employing integrated multi-omics strategies is essential to unravel the long-term consequences of H. pylori on the mucosal ecosystem and host physiology.}, }
@article {pmid42251252, year = {2026}, author = {Lockwood, S and Ranaivoson, HC and Randriambolamanantsoa, TH and Razanajatovo, N and Raharinosy, V and Ahyong, V and Héraud, JM and Dussart, P and Lacoste, V and Brook, CE}, title = {Identifying viral infections through metagenomic Next Generation Sequencing of undiagnosed respiratory fevers in Madagascar (2014-2019).}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13715-7}, pmid = {42251252}, issn = {1471-2334}, support = {P200A210054//U.S. Department of Education/ ; GCE/ID OPP1211841//Bill and Melinda Gates Foundation/ ; }, abstract = {BACKGROUND: Respiratory illness contributes to substantial global morbidity and mortality. In Madagascar, an island nation off the southeastern coast of the African continent, hospital-based public health surveillance for respiratory pathogens screens for common respiratory viruses. However, many cases remain undiagnosed.<br><br>METHODS: We conducted metagenomic Next Generation Sequencing (mNGS) to identify the pathogen profile of 102 undiagnosed febrile patients who presented to public hospitals with respiratory symptoms and screened negative on a 14-virus multiplex RT-qPCR. We analyzed the diversity of the respiratory microbiome of each patient from mNGS data and identified viral infections potentially linked to undiagnosed fever. We assembled whole genome consensus sequences of viruses with sufficient read depth and coverage, characterized each phylogenetically, and identified any discrepancies with the primers used in the multiplex RT-qPCR panel. Finally, we compared all whole genome sequences against publicly available global databases in a phylogenetic analysis.<br><br>RESULTS: We identified evidence of infection by a wide range of known human viruses in approximately two thirds (64.7%) of study participants from nine different families of viruses and generated 30 complete or nearly complete consensus sequences of known respiratory viruses including orthopneumoviruses, metapneumoviruses, rhinoviruses, coronaviruses, parainfluenza virus, and bocaparvovirus. mNGS-attributed evidence of infection was predominantly due to orthopneumovirus (also called respiratory syncytial virus [RSV]; n&#x2009;=&#x2009;24; n&#x2009;=&#x2009;8 previously diagnosed) and rhinovirus (n&#x2009;=&#x2009;18) detections, despite previous negative RT-qPCR results for the majority of these cases. Finally, phylogenetic analysis identified two distinct phylogenetic clusters of RSV subtype A, suggesting local transmission following distinct international introductions for this virus.<br><br>CONCLUSION: mNGS provides a sensitive pan-pathogenic tool for virus detection. We demonstrate the diversity of viruses associated with undiagnosed respiratory fevers in Madagascar, emphasize the importance and relevance of the existing respiratory surveillance in the country, and highlight the interconnectedness of regional respiratory infection dynamics with global networks of respiratory pathogen transmission.}, }
@article {pmid42251273, year = {2026}, author = {Li, L and Xu, M and Liu, M and Mao, J and Xiong, P and Li, R and Chen, J and Wu, X}, title = {Metatranscriptomic analysis of upper and lower respiratory tract microbiomes in patients with tuberculosis and community-acquired pneumonia.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13614-x}, pmid = {42251273}, issn = {1471-2334}, support = {31970174//National Natural Science Foundation of China/ ; 2023YFC260550//National Key Research and Development Program of China/ ; }, abstract = {BACKGROUND: Although changes in the lung microbiome have been observed in many respiratory diseases, the lung microbiome of patients with tuberculosis (TB) remains largely undefined. The aim of this study was to determine and compare the composition of upper and lower respiratory microbial communities, changes in host gene expression, and functional pathway activation in patients with TB and community-acquired pneumonia using a Metatranscriptomic approach.<br><br>METHODS: From November 2020 to November 2021, 42 bronchoalveolar lavage fluid samples, 10 oropharyngeal swabs, and 10 nasopharyngeal swabs were collected from patients hospitalized with TB or community-acquired pneumonia for RNA-sequencing, within 72&#xa0;h of admission. Data from 28 healthy controls were downloaded from the National Center for Biotechnology Information database.<br><br>RESULTS: The most common microorganisms in the samples from patients with TB were Prevotella, Escherichia, Mycobacterium, and Verrucoccus. Notable differences in microorganism diversity were observed between the TB and community-acquired pneumonia groups as well as between the upper and lower respiratory tracts compared to that in healthy controls. Altered microbial interactions were also observed. Rothia and Mycobacterium were identified as marker microorganisms in the TB group, which exhibited increased expression of SNAP25, MGAM2, CNTN4, MMP12, and GPR174, in parallel to IL36A, RHCG, and CYP2B6 downregulation relative to the community-acquired pneumonia group. The pathways enriched for differential genes were similar among all patient groups, particularly involving neuroactive ligand receptor interaction and Ca[2+] signaling. Patients with TB differed from those with community-acquired pneumonia, particularly with regard to the cytokine-cytokine receptor interaction pathway. The most commonly detected antibiotic resistance genes conferred resistance against &#x3b2;-lactams and macrolides. Antibiotic resistance genes were more abundant in oropharyngeal than in nasopharyngeal samples.<br><br>CONCLUSIONS: The composition of microbial communities and host expression landscapes differs between TB and community-acquired pneumonia as well as between different respiratory tract sites. These changes in lung microbiota may impact lung disease development and prognosis.}, }
@article {pmid42251288, year = {2026}, author = {Ramirez, SC and Lewis, ZJ and Hale, VL and Coffey, EL}, title = {Impact of sample processing method and volume on 16 S rRNA profiling of the urobiome.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05274-3}, pmid = {42251288}, issn = {1471-2180}, support = {T35OD011118/NH/NIH HHS/United States ; 1K08ES034821-01A1/NH/NIH HHS/United States ; K12TR004373/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: The urinary microbiome (urobiome) plays important roles in both human and animal urogenital tract health. Characterization of these microbial communities presents several technical challenges, largely due to the low microbial biomass of urine. Whereas other low biomass liquid systems, such as aquatic samples, frequently employ small-pore vacuum filtration for microbial DNA concentration, urobiome studies have traditionally relied on centrifugation and pelleting of smaller volumes. Therefore, this study compared the effects of processing method (vacuum filtration versus pelleting) and sample volume on bacterial DNA yield, contaminant burden, and microbial diversity in canine urine.<br><br>RESULTS: A total of 50 urine aliquots were obtained across samples. Urine from 15 healthy dogs was pooled into five unique batches and divided into duplicate aliquots at volumes of 1, 3, 10, 30, and 50 mL. One aliquot was pelleted and one filtered (0.2&#xa0;&#x3bc;m pore filter) prior to DNA extraction of the pellet or filter, respectively, and 16&#xa0;S rRNA gene (V4) sequencing. Three aliquots&#x2009;&#x2265;&#x2009;30 mL could not be filtered due to clogging. Sequence depth, DNA recovery, contaminant abundance, and microbial diversity were similar across urine volumes. Filtered samples contained a higher proportion of reads classified as contaminants (&#x1d443; = 0.002). Although beta diversity differed between methods (Bray-Curtis PERMANOVA, P&#x2009;=&#x2009;0.007), the effect size was small (R[2]&#x2009;=&#x2009;0.03) relative to the influence of urine batch (&#x1d443; = 0.001, R[2]&#x2009;=&#x2009;0.65).<br><br>CONCLUSIONS: These findings indicate that interindividual variation predominates over methodological effects. Higher urine volumes (&#x2265;&#x2009;30 mL) were associated with technical challenges in filtered samples, whereas moderate urine volumes (1-10 mL) appear sufficient for urobiome characterization. Similar microbial recovery, increased contaminant signal, and occasional clogging with filtration suggests that pelleting remains an appropriate approach for urobiome characterization.}, }
@article {pmid42251420, year = {2026}, author = {Helmbrecht, H and Ardalan, M and Kelly, L and Robinson, S and Fleiss, B and Doherty, DG and Gressens, P and Mallard, C and Molloy, EJ and Jantzie, LL}, title = {The role of persistent inflammation in failed recovery after perinatal brain injury: is resolution the cure?.}, journal = {Journal of neuroinflammation}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12974-026-03900-5}, pmid = {42251420}, issn = {1742-2094}, abstract = {Perinatal brain injury (PBI) is a major predictor of neurological disability. Commonly associated with prematurity, infection, stroke, hypoxia-ischemia, hemorrhage, and/or toxin exposure, PBI triggers acute and persistent systemic inflammation. There are many stages of vulnerability to PBI during development including pregnancy, birth - term and preterm, and neonatal age. The vulnerable stages can compound inflammation through injury to the placental-fetal-brain axis, adaptive and innate immune system development, neural-immune communication, and central nervous system maturation. Neonates exhibit unique inflammatory signatures and lasting neural-immune responses to various etiologies. Chronic immune dysregulation and priming to a secondary, later-in-life immune challenge defines different forms of PBI while shaping the neonatal and adult immune response with long-term changes. Immunomodulated changes impact regulatory, helper and innate T cells, neutrophils, natural killer cells and immune responsiveness. The major routes of persistent and compounding inflammation in PBI are perinatal neural-immune interactions, cytokine influx, and glial crosstalk. Most treatments are not administered long enough or in the optimal time window to combat sustained inflammation in tertiary and quaternary phases of PBI pathophysiology and are ineffective in reducing neonatal mortality and morbidity and promoting functional recovery. Indeed, persistent systemic and central inflammation is a likely explanation for failed recovery of PBI after the resolution of acute insults. We propose attenuating persistent inflammation and normalizing systemic immune reactivity as key to reducing the functional impact of PBI throughout the lifespan through various avenues including therapeutic treatment, gut microbiome modulation, and novel immunomodulation from preclinical research.}, }
@article {pmid42251450, year = {2026}, author = {Tan, L and Liu, X and Ma, Y and Yang, J and Zhang, Q and Zhang, J and Bai, B and Ma, H and Meng, R and Degen, A and Palevich, N and Shi, P and Hao, L}, title = {The price of survival: comparative adaptation to high altitudes between yaks and cattle.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00584-3}, pmid = {42251450}, issn = {2524-4671}, support = {2024-ZJ-905//Qinghai Provincial Natural Science Fund for Distinguished Young Scholars/ ; 2025KTST04//Qinghai University Research Ability Enhancement Project/ ; 2022YFD1302103//the National Key R&amp;D Sub-project/ ; 2025, L.Z.H.//Qinghai University Graduate Supervisor Innovation Team/ ; 2019QZKK0606//Special Topics of the Second Comprehensive Scientific Expedition of the Qinghai-Tibet Plateau/ ; QHKLYC-GDCXCY-2024-071, L.Z.H.//Leading talent of "Kunlun Talents High-level Innovation and Entrepreneurial Talents" in Qinghai Province/ ; }, abstract = {The yak (Bos grunniens) serves as an exceptional model for studying high-altitude adaptation mechanisms due to its evolutionary success in the hypoxic environment of the Qinghai-Tibet Plateau. Previous research has largely focused on genetic and physiological traits of yaks; however, the interactions between rumen microbiota and host physiology under hypoxic conditions are poorly understood. As the largest digestive organ in ruminants, the rumen and its microbiota play a central role in digestion and host nutrition. In this study, a comparative analysis of digestive metabolism and rumen microbiota was carried out in yaks and cattle (Bos taurus) under two distinct atmospheric oxygen scenarios: baseline (2,200 m) and hypoxic (3,800 m). Our findings reveal that yaks have developed unique microbial strategies to cope with energy deficits in hypoxic stress. These strategies include a shift in rumen microbiota toward amino acid degradation, providing more available energy substrates for host utilization, and enhanced long-chain fatty acid biosynthesis, enabling more efficient energy storage and utilization. This improves energy acquisition in yaks despite their reduced nutritional intake. However, this metabolic adaptation comes at a physiological cost - reduced microbial crude protein (MCP) synthesis, leading to elevated ruminal NH3-N levels, and increased fatty acid metabolism and urea cycle activity contributing to hepatic stress. Our results showed that under high-altitude conditions, yak MCP synthesis decreased by 47.3%; and ruminal NH3-N and serum ALT (a hepatic stress marker) increased by 147.2 and 19.7%, respectively. This study presents evidence of potential metabolic trade-offs in high-altitude adaptation, indicating that yaks may optimize microbially mediated energy production at the cost of liver health. These insights deepen our understanding of host-microbiome coevolution mechanisms in extreme environments and highlight biological costs associated with adaptation to high altitudes.}, }
@article {pmid42251689, year = {2026}, author = {Tao, M and Zhang, Z and Dai, L and Zeng, Y and Zhang, X}, title = {Metagenomic insights into potential horizontal transfer of resistance/virulence genes in gut microbiota from patients with Crohn disease.}, journal = {Inflammatory bowel diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/ibd/izag090}, pmid = {42251689}, issn = {1536-4844}, support = {2025JJ50123//Hunan Provincial Natural Science Foundation of China/ ; 32101368//National Natural Science Foundation of China/ ; 1053320242393//Fundamental Research Funds for the Central Universities of Central South University/ ; }, abstract = {BACKGROUND: Unraveling the potential horizontal transfer of resistance genes/virulence genes (RGs/VGs) in gut microbiota from patients with Crohn disease (CD) is an interesting but poorly characterized issue.<br><br>METHODS: Quantitative assessment was performed to estimate the relative abundance and diversity of RGs/VGs/mobile genetic elements (MGEs). Differential analysis was applied to identify the CD-specific enriched genetic subtypes. A species-RGs/VGs/MGEs association network was constructed to explore possible co-occurrence patterns of these genetic elements across potential microbial hosts. Integrated with topological metrics and Zi-Pi computational modeling, co-occurrence network analysis was conducted to characterize potential associations among RGs, VGs, and MGEs.<br><br>RESULTS: Comparative metagenomic analyses indicated that the microbiome in group CD exhibited significantly higher relative abundance of RGs compared to that in healthy controls (HC; P&#x2009;=&#x2009;.040), with 131 specific RG/VG subtypes (eg, acrA/T6SS) exhibiting marked enrichment (P&#x2009;<&#x2009;.05). The co-occurrence network revealed intensified interconnectivity between RGs/VGs and MGEs in group CD, in which MGEs accounted for 71% of network nodes (vs 60.80% in HC), and 99.14% of the edges were positively correlated (vs 93.60% in HC). Network topology and Zi-Pi analysis further suggested reduced modularity (0.709 vs 0.979 in HC) and enhanced intergene connectivity (average degree: 12.288 vs 2.156; average weighted degree: 23.359 vs 3.688 in HC). There were no network hubs (0 vs 5 in HC) but abundant modular hubs (60 vs 25 in HC), peripheral nodes (2317 vs 1549 in HC), and connectors (61 vs 36 in HC), which may reflect conditions favorable for enhanced gene transfer potential. Cross-species transfer events were predicted across clinical-environmental-commensal boundaries, exemplified by tet(M) dissemination between Clostridioides difficile and Bacteroides sp., probably implying progressive erosion of ecological barriers.<br><br>CONCLUSIONS: Collectively, we inferred that the gut microbiome of CD patients might represent a high-risk reservoir for the horizontal transfer of pathogenic determinants, which may pose a potential threat for public health and biosecurity.}, }
@article {pmid42251779, year = {2026}, author = {Leiva-Soto, S and Rubilar, O and Fincheira, P and Fernández-Baldo, M and Fernández-Triana,  and Schoebitz, M and Larama, G and Rodriguez, R and López-Mena, E and Tortella, GR}, title = {Soil microbial functional recovery and community resilience driven by biogenic magnetite nanoparticles under carbendazim stress.}, journal = {Microbiological research}, volume = {311}, number = {}, pages = {128573}, doi = {10.1016/j.micres.2026.128573}, pmid = {42251779}, issn = {1618-0623}, abstract = {The persistence of fungicides in agricultural soils poses a major threat to soil health, as these compounds disrupt microbial communities and compromise key ecosystem functions. Carbendazim, a commonly used systemic fungicide, is known for its ability to inhibit microbial activity and nutrient cycling. This study assessed the capacity of biogenic magnetite nanoparticles to mitigate carbendazim-induced disturbance and facilitate the recovery of soil microbial function. Citrate-stabilized magnetite nanoparticles were applied to an agricultural Andisol intentionally contaminated with carbendazim (10 mg kg[-1]) under controlled microcosm conditions. Soil enzyme activities related to carbon, nitrogen, and phosphorus cycling (β-glucosidase, urease, acid phosphatase), microbial gene abundances (16S rRNA, amoA, amoB copy number), community structure, and pesticide dissipation kinetics were measured for a 30-day period. Magnetite nanoparticles significantly accelerated carbendazim dissipation, reducing their half-life by approximately 50% compared to pesticide-only treatments. Nanoparticle application partially mitigated the inhibitory effects of carbendazim on soil enzymes. It showed trends towards the recovery of bacterial and nitrifier abundances, with community composition and diversity patterns aligning more closely with those of untreated soils. Co-occurrence network and multivariate analyses of the soil bacterial community, assessed through 16S rRNA amplicon sequencing, revealed patterns indicative of a partial restoration of bacterial interaction structure, with Carb/FeNPs-EC treatments showing increased network connectivity and modularity compared to carbendazim-only soils, approaching the interaction patterns characteristic of undisturbed bacterial assemblages. These findings offer preliminary evidence that biogenic magnetite nanoparticles may reduce pesticide pressure in agricultural soils while supporting microbial functional trends indicative of recovery. The use of onion peel waste as an eco-friendly precursor further highlights the circular potential of this approach. Onion peel is a widely generated agro-industrial by-product particularly rich in polyphenolic compounds, especially quercetin and its derivatives, which act as natural reducing and stabilizing agents during nanoparticle biosynthesis, eliminating the need for toxic chemical reagents and contributing to a lower environmental footprint. This dual role as both a waste valorization strategy and a source of bioactive capping agents warrants further evaluation of this approach as a sustainable soil amendment strategy.}, }
@article {pmid42251923, year = {2026}, author = {Alum, EU and Emeruwa, AP and Obasi, DC and Okoroh, PN and Aniokete, UC and Akwari, AA and Uzor, S and Eji, MO and Amadi, EB}, title = {Gut microbiome-derived metabolites as predictors of bariatric surgery outcomes.}, journal = {Clinica chimica acta; international journal of clinical chemistry}, volume = {591}, number = {}, pages = {121153}, doi = {10.1016/j.cca.2026.121153}, pmid = {42251923}, issn = {1873-3492}, abstract = {BACKGROUND: Bariatric surgery remains the most effective treatment for severe obesity and obesity-associated metabolic disorders. However, substantial interindividual variability exists in postoperative weight loss and type 2 diabetes mellitus remission. Increasing evidence suggests that gut microbiome-derived metabolites may influence metabolic responses after bariatric surgery.<br><br>OBJECTIVE: This narrative review synthesizes current evidence regarding the predictive role of gut microbiome-derived metabolites, particularly short-chain fatty acids, bile acids, and tryptophan-derived metabolites, in bariatric surgery outcomes.<br><br>METHODS: A narrative literature review was conducted using PubMed, Web of Science, Embase, and ClinicalTrials.gov to identify studies published through May 2026. Studies examining associations between microbiome-derived metabolites and postoperative bariatric outcomes were reviewed and narratively synthesized.<br><br>RESULTS: Available evidence suggests that higher preoperative levels of beneficial microbiome-derived metabolites are associated with improved postoperative weight loss, enhanced insulin sensitivity, and greater likelihood of type 2 diabetes mellitus remission. Short-chain fatty acids appear to influence satiety and glucose metabolism, bile acids regulate metabolic signaling through farnesoid X receptor and Takeda G protein receptor 5 pathways, and tryptophan metabolites modulate inflammation and gut-brain communication. Nevertheless, findings remain inconsistent because of methodological heterogeneity, limited cohort sizes, and differences in metabolomic profiling techniques.<br><br>CONCLUSION: Gut microbiome-derived metabolites represent promising candidate biomarkers for predicting bariatric surgery outcomes. However, large-scale longitudinal studies using standardized metabolomic approaches are required before clinical implementation can be achieved.}, }
@article {pmid42251996, year = {2026}, author = {da Cruz, LL and Shlisky, J and Bellando, BJ and Chen, JR and Edwards, T and Fiecke, C and Larson-Prior, LJ and McCorkle, L and Moore, MB and Slaton, C and Sobik, S and Thakali, K and Whiteside, M and Andres, A}, title = {Longitudinal evaluation from birth to adolescence of soy-protein based infant formula compared to cow's-milk based formula and breastfeeding: A comprehensive summary of findings.}, journal = {Advances in nutrition (Bethesda, Md.)}, volume = {}, number = {}, pages = {100669}, doi = {10.1016/j.advnut.2026.100669}, pmid = {42251996}, issn = {2156-5376}, abstract = {Breastfeeding is widely recognized as the gold standard food for infants. However, many families use infant formulas, including soy-based products, which have not been studied for their long-term safety and developmental effects. The Beginnings Study and the Beginnings Follow Up Study represent one of the most comprehensive prospective cohorts designed to examine how early infant feeding is related to growth, body composition, cardiovascular, microbiome, and skeletal outcomes, neurodevelopment, and reproductive maturation through adolescence. Conducted in Arkansas, U.S., the study enrolled 600 healthy, term infants fed soy-based infant formula, cow's milk-based infant formula, or human milk during infancy (200 per group). Of these, 385 participants (73.2%) completed the 6-year visit, and 190 (31.7% of enrolled and 49.4% of 6-year visit completers) participated in the 14-year Follow Up Study. Breastfeeding was associated with slower weight gain velocity during infancy, and consistent lower body mass index, fat mass index, and waist circumference extending into adolescence, compared to formula feeding. Formula-fed infants had comparable results to breastfed infants for skeletal mineralization, most neurocognitive parameters, and reproductive organ development. However, cardiovascular autonomic measures, including heart rate and vagal tone, differed by feeding group, with some sex-specific effects. Novel contributions included analyses of the gut microbiome and metabolomics profiles in early life, which revealed distinct dietary signatures, as well as neurodevelopmental assessments using electroencephalography, which highlighted transient differences in language-related brain responses among feeding groups. Together, these results demonstrate more similarities than differences between soy-based infant formula and cow's milk-based infant formula in health outcomes and supports the lasting benefits of breastfeeding. This evidence can help guide healthcare professionals in infant feeding recommendations and highlight critical windows to prevent obesity and promote lifelong health.}, }
@article {pmid42252003, year = {2026}, author = {Júnior, AMCA and da Silva, AH and Buroxid, RP and Padovan, JR and Nunes, AT and Poleti, MD and Fukumasu, H and Gobesso, AAO}, title = {Impact of collagen supplementation on the fecal microbiome of young horses in training.}, journal = {Journal of equine veterinary science}, volume = {}, number = {}, pages = {106047}, doi = {10.1016/j.jevs.2026.106047}, pmid = {42252003}, issn = {0737-0806}, abstract = {BACKGROUND: Intense training in athletic foals may alter fecal microbiota, highlighting the need for nutritional strategies such as hydrolyzed collagen supplementation.<br><br>AIMS/OBJECTIVES: This study aimed to evaluate the effects of dietary hydrolyzed collagen on the fecal microbiome of weanlings in training.<br><br>METHODS: Twenty Mangalarga Marchador foals (206 &#xb1; 18 kg; 7 &#xb1; 1 mo age) were assigned to two groups: a supplemented group (50 g/day of hydrolyzed collagen for 180 days) and a control group. A completely randomized design with repeated measures over time was used. Foals were exercised five consecutive days per week. Fecal samples (10 g) were collected every 90 days (D0, D90 and D180) and analyzed by next-generation sequencing of the 16S rRNA gene. Alpha diversity was assessed using Chao1, Shannon, and Simpson indices, while beta diversity was evaluated by Principal Coordinate Analysis. Beta diversity differences were tested using PERMANOVA, and differential abundance at the phylum and genus levels was analyzed using the Wilcoxon rank-sum test.<br><br>RESULTS: A significant treatment effect (P < 0.05) was observed on D180 at the phylum level, with a higher abundance of Fibrobacterota in control foals. At the genus level in D180, Saccharofermentans, Lachnospiraceae UCG-009, and Fibrobacter were more abundant in the control group, whereas Intestinimonas, Lachnospiraceae UCG-010, and Phascolarctobacterium were more abundant in the supplemented group. There was no effect (P > 0.05) between groups on alpha diversity.<br><br>CONCLUSION: These results indicate that hydrolyzed collagen supplementation modulates the fecal microbiome of training young horses, reducing fibrolytic bacteria over time.}, }
@article {pmid42252139, year = {2026}, author = {Barbé, A and Boland, L and Kanaan, N and Darius, T and Buemi, A and France, Y and Ronsyn, MA and Rahal, S and Lingurski, M and Van Bambeke, F and Bindels, LB and Haufroid, V and Devresse, A and Elens, L}, title = {ElucidatiNg Immunosuppressant pharmacokinetic variabilities by investigating Gut Microbiome modulations After kidney transplantation (ENIGMA): study protocol of a prospective longitudinal trial.}, journal = {BMJ open}, volume = {16}, number = {6}, pages = {e106623}, doi = {10.1136/bmjopen-2025-106623}, pmid = {42252139}, issn = {2044-6055}, abstract = {INTRODUCTION: In kidney transplantation, immunosuppressive therapy is essential to control alloimmune reactions, prevent graft rejection and improve patient survival rates. However, commonly used drugs like tacrolimus (TAC) and mycophenolate mofetil (MMF) have a narrow therapeutic window and exhibit significant inter- and intra-individual variability in pharmacokinetics (PK) and dose-response relationships. Recent pilot studies suggest that the gut microbiome may influence this variability.<br><br>METHODS AND ANALYSIS: ElucidatiNg Immunosuppressant pharmacokinetic variabilities by investigating Gut Microbiome modulations After kidney transplantation (ENIGMA) is a prospective, low-interventional, naturalistic longitudinal trial designed to identify biomarkers of TAC and MMF PK variability by examining gut microbiome changes and modulations after kidney transplantation and their link with TAC and MMF PK. Biological samples from 50 patients will be collected at nine specific timepoints pre- and post-transplantation using a rich PK and biological sampling strategy. This approach will enable the derivation of PK parameters for the investigated drugs and the creation of a biobank for future hypothesis testing.<br><br>ETHICS AND DISSEMINATION: The ENIGMA trial has received ethical approval from the European Medicines Agency (EMA). The reference number of our project is R&amp;D/1325226 and is registered on the Clinical Trial Information System (CTIS) platform with European Union Clinical Trial number 2023-5&#x2009;08&#x2009;335-31-00. Results of the trial will be published in scientific journals and presented at different (inter)national conferences.<br><br>TRIAL REGISTRATION NUMBER: 2023-5&#x2009;08&#x2009;335-31-00 EMA.}, }
@article {pmid42252320, year = {2026}, author = {Zhou, J and Qiao, Y and Chen, H and Li, L and Su, W}, title = {Spatial scaling of metagenomic diversity reveals ecological disruption in the gut microbiome of gout patients.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-55351-w}, pmid = {42252320}, issn = {2045-2322}, support = {No: 24JRRJ001//Provincial Science and Technology Plan (Basic Research Plan-Natural Science Foundation) Project of Gansu Province in 2024/ ; }, abstract = {Gout, a painful inflammatory arthritis, is characterized by hyperuricemia and monosodium urate crystal deposition, with growing evidence linking its pathogenesis to gut microbiome dysbiosis. However, traditional diversity metrics fail to capture the complex spatial organization of microbial communities. This study addresses this gap by applying the novel metagenomic Diversity-Area Relationship (m-DAR) model to investigate scaling laws in the gout microbiome-quantifying how metagenomic diversity changes with the number of individuals sampled. Our analysis of gut microbiomes from gout patients and healthy controls revealed fundamental ecological disruptions. We found that gout microbiomes exhibited significantly altered scaling patterns: they showed greater inter-individual dissimilarity (higher z-values) at the level of rare genes (q = 0), but weaker scaling of dominant genes (q = 1-3) compared to healthy controls. Crucially, the maximal accrual diversity (MAD) was substantially lower in gout patients, indicating a severely constrained potential for total microbial gene diversity. Furthermore, profiling of metagenomic functional gene clusters (MFGCs) uncovered widespread functional perturbations, including increased diversity scaling for carbohydrate-active enzymes (CAZy) but decreased scaling in essential metabolic pathways (KEGG, KO). These results demonstrate that the gout gut microbiome is defined by a loss of ecological structure, featuring reduced homogeneity in dominant taxa, expanded rare biosphere variation, and an overall collapsed diversity capacity. This work introduces an ecological framework for characterizing dysbiosis in gout that complements traditional diversity metrics and may inform the development of microbiome-based therapeutic strategies. Further research is needed to translate these ecological patterns into clinical applications.}, }
@article {pmid42252383, year = {2026}, author = {Pichon, V and De Vrieze, M and Bellameche, F and Cristea, R and L'Haridon, F and Falquet, L and Weisskopf, L}, title = {Potato foliar infection with Phytophthora infestans drives strong, cultivar-specific shifts in rhizosphere communities.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00910-x}, pmid = {42252383}, issn = {2524-6372}, support = {207917/SNSF_/Swiss National Science Foundation/Switzerland ; }, abstract = {BACKGROUND: Potato is an important crop worldwide, yet its production is severely threatened by Phytophthora infestans, the causal agent of late blight. Alternatives to the current control strategies are needed, as these rely heavily on environmentally harmful treatments. The recruitment of beneficial microbes by plants upon stress ("cry-for-help" mechanism) may represent an opportunity to find new biocontrol agents but this has not yet been reported for potato. The aim of this study was to analyse whether foliar late blight infection induces shifts in the phyllosphere, rhizosphere and soil bacterial communities associated with two potato cultivars of differing sensitivity to late blight. Moreover, we aimed at isolating plant microbiota members to test whether bacteria putatively recruited upon infection would be particularly active in protecting the plant against late blight.<br><br>RESULTS: Controlled foliar infection triggered substantial, cultivar-specific shifts in rhizosphere communities across two successive generations. Despite the number of differentially abundant ASVs detected being ten times higher in the second generation than in the first one, the same taxonomic groups were involved in the shifts: Burkholderiales, Flavobacteriales, and Bacillales. Furthermore, the communities linked to the susceptible cultivar consistently shifted more strongly upon infection than the communities linked to the resistant cultivar. The obtained ASV sequences were used to identify 163 corresponding isolates through sequence alignment. Their inhibition potential against P. infestans sporangia and zoospores was assessed through biological assays. These revealed the biocontrol potential of genera otherwise not yet known to inhibit phytopathogenic organisms, such as Advenella, Nocardioides and Phyllobacterium strains. Although we found no correlation between the relative abundance shift of the ASVs upon infection and the activity of the corresponding strains, we observed that the overall activity of strains isolated from the resistant cultivar was higher than that of the strains isolated from the susceptible one.<br><br>CONCLUSION: Taken together, the higher activity of the strains isolated from the resistant cultivar, along with its comparatively modest microbiome shifts upon infection suggest that the investigated resistant cultivar might harbour specific microbiota enriched in strains that are able to inhibit pathogen development and possibly contribute to its higher resistance against P. infestans.}, }
@article {pmid42252406, year = {2026}, author = {Zhang, J and Wang, Y and Duan, X and Wang, R and Wang, Y and Lou, F}, title = {Comparative analysis of morphology and gut microbiome underlying trophic niche differentiation in three stomatopod species.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05258-3}, pmid = {42252406}, issn = {1471-2180}, support = {ZR2024MD076//Shandong Provincial Natural Science Foundation Committee/ ; BH202401//Observation and Research Station of Bohai Strait Eco-Corridor, MNR/ ; }, abstract = {Given that predatory strategies and trophic niche in stomatopods vary with raptorial appendage differentiation, a comparative analysis was conducted on three species (Odontodactylus japonicus, Lysiosquilla sulcirostris, and Oratosquilla oratoria) exhibiting distinct habitats and morphologies. The study measured their raptorial appendage morphology, digestive tract morphology, and gut microbiota. The results revealed significant differences in the raptorial appendages and digestive tract morphology among the three stomatopod species. O. japonicus has the significantly largest merus length, merus width, merus height and, L. sulcirostris has the significantly largest propodus length, dactylus length, hepatopancreas length and midgut length, while O. oratoria has the significantly largest hindgut length, cardiac stomach length and pyloric stomach length. Regarding digestive tract morphology, O. japonicus possessed the widest villus and tallest villus, in contrast to O. oratoria, which displayed the smallest values for these features. A total of 8,273 operational taxonomic units (OTUs) were obtained from all 16S rRNA sequences. The OTU numbers for O. oratoria, L. sulcirostris, and O. japonicus were 344, 113, and 82, respectively, with only 17 OTUs shared among all three species. The gut microbiota of O. japonicus was dominated by the phylum Pseudomonadota (88.90%), primarily comprised of the genus Cupriavidus (68.40%). In contrast, the dominant phylum in both L. sulcirostris and O. oratoria was Bacillota, with Mycoplasma being the dominant genus in each, respectively. Furthermore, O. oratoria exhibited the highest gut microbial diversity, whereas L. sulcirostris had the lowest. Functional profiling revealed that the relative abundance of gut microbiota associated with amino acid, lipid, and carbohydrate metabolism was significantly higher in O. japonicus than in both O. oratoria and L. sulcirostris. In conclusion, our findings provide further evidence for feeding habit differentiation and associated regulatory mechanisms among the three stomatopod species. The high gut microbial diversity in O. oratoria may contribute to its adaptability to the dynamic, heterogeneous habitats it occupies. Although the microbial abundance in O. japonicus is intermediate between that of O. oratoria and L. sulcirostris, its microbiota appears to be more efficient in digestive function, particularly in the metabolism of key nutrients. This study systematically elucidates the regulatory mechanisms underlying trophic niche differentiation in stomatopods from integrated morphological and physiological perspectives. Our findings provide a valuable foundation for future research on the evolution of higher taxonomic groups within Stomatopoda based on nutritional ecology.}, }
@article {pmid42252471, year = {2026}, author = {Horton, DB and Verma, C and Rege, S and Crystal, S and Gerhard, T and Iizuka, A and Iozzio, M and Koffman, D and Parlett, LE and Varga, J and Rose, CD and Strom, BL}, title = {Recent antibiotic exposure and response to treatment of juvenile idiopathic arthritis: a retrospective cohort study.}, journal = {Arthritis research &amp; therapy}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13075-026-03842-6}, pmid = {42252471}, issn = {1478-6362}, support = {R01AR074436/AR/NIAMS NIH HHS/United States ; R01HD109335//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; UL1TR003017, UM1TR004789/TR/NCATS NIH HHS/United States ; }, abstract = {BACKGROUND: Juvenile idiopathic arthritis (JIA) has been tied to microbiome disruption and antibiotic exposure. Gut microbiota may affect how adults with rheumatoid arthritis respond to methotrexate. We tested if exposure to antibiotics was associated with response to methotrexate for JIA.<br><br>METHODS: We conducted a retrospective cohort study using national US public and private insurance claims data (2001-2023). We included children ages 1-17 continuously enrolled for &#x2265;&#x2009;10 months and diagnosed with JIA who initiated methotrexate monotherapy or, for comparison, tumor necrosis factor inhibitor (TNFi) monotherapy without prior disease-modifying antirheumatic drug (DMARD) exposure. Antibiotic exposure during the 10-month baseline period was characterized by number of courses, timing, and type. The primary outcome was initiation of a second DMARD after &#x2265;&#x2009;30 days (proxy of treatment ineffectiveness). Associations between antibiotic exposure and treatment change were estimated using Cox regression, adjusting for database and baseline demographic, disease, treatment, and health utilization covariates, and represented by adjusted hazard ratios (HRs) with 95% confidence intervals (CIs). In additional analyses, we examined differences based on JIA category (juvenile spondyloarthritis vs. others), outcome specification, and follow-up starting up to 90 days after initial DMARD exposure.<br><br>RESULTS: We identified 6,135 new methotrexate users (54.4% antibiotic-exposed) and 1,554 new TNFi users (49.5% antibiotic-exposed), among whom approximately 20% experienced the primary outcome over 10 months of follow-up. No relationships were observed between pre-DMARD antibiotic exposure and DMARD changes in methotrexate users (aHR 1.01, 95% CI 0.90, 1.13) or TNFi users (aHR 1.10, 95% CI 0.86, 1.40). Number of antibiotic courses, antibiotic timing, and type of antibiotic exposure, as well as nonbacterial antimicrobial drug exposure, were also not associated with treatment changes in methotrexate or TNFi users. Findings based on JIA category, alternative outcome definitions, and delayed start of follow-up were consistent.<br><br>CONCLUSIONS: Recent antibiotic exposure is not associated with changes in DMARD treatment in children with JIA. This finding is reassuring for a population with higher risks for serious infections than other children and with high rates of antibiotic exposure.}, }
@article {pmid42243719, year = {2026}, author = {Almutrafy, AM and Aloufi, AS and Al-Andal, A and Refai, MY and Tashkandi, M and Alnahari, AA and Bagabas, SS and AlDowsari, FMF and Abuauf, HW and Alshehrei, FM and Alshareef, SA and Abulfaraj, AA and Hassan, RN and Jalal, RS}, title = {Comprehensive in silico analysis of eggNOG-annotated orthologous genes infers functional dynamics and energy metabolism in the microbiome of Abutilon fruticosum.}, journal = {BMC plant biology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12870-026-09123-3}, pmid = {42243719}, issn = {1471-2229}, support = {PNURSP2026R357//Princess Nourah bint Abdulrahman University Researchers Supporting Project/ ; }, abstract = {BACKGROUND: Abutilon fruticosum is an ecologically and pharmacologically important wild Malvaceae species whose rhizospheric microbiome remains poorly resolved at the level of orthologous-group (OG) genes. Shotgun metagenomic sequencing and eggNOG/COG-based annotation were used to compare rhizosphere and bulk-soil microbiomes, quantify OG repertoires, and infer in silico functional modules.<br><br>RESULTS: Principal coordinate and Bray-Curtis analyses of COG categories revealed clear functional segregation between rhizosphere and bulk communities, with the rhizosphere enriched in high-abundance OGs linked to energy metabolism, nutrient transport, stress response, and secondary metabolism. Computational ranking identified a cohort of highly recurrent OGs, predominantly associated with Actinobacteria and Proteobacteria but also with Streptophyta, that dominate the predicted functional landscape and are markedly more abundant in silico in rhizospheric soil. Using eggNOG/COG assignments, ten interacting putative functional modules were delineated in silico, encompassing NADH-quinone oxidoreductase-centered bioenergetics, ABC-type nitrogen and sulfur acquisition, fatty-acid and propionate catabolism, sulfur scavenging and detoxification, cell-envelope and biofilm formation, multidrug efflux, DNA maintenance, environmental sensing and transcriptional regulation, specialized competition/protection, and mobile genetic elements. Conceptual, hypothesis-generating frameworks integrating selected modules posit that rhizosphere dominance could arise from the coordinated coupling of ATP/proton motive force (PMF) generation with high-affinity nutrient uptake, sulfur and carbonyl detoxification, iron-sequestering and antioxidant secondary metabolism, and stress-responsive multidrug efflux, based on our analyses.<br><br>CONCLUSIONS: These predictions suggest that specific OG cohorts act as keystone energetic, metabolic, and defense hubs in the A. fruticosum rhizosphere and provide testable hypotheses for future experimental work linking module-level functions to root colonization, stress tolerance, and plant performance. (249 words).}, }
@article {pmid42243780, year = {2026}, author = {Kim, NH and Lee, JH and Oh, J and Lee, S and Jung, ES and Suh, DH and Kang, HJ and Kim, B and Kim, HS and Kim, H and Yun, INR and Kim, EH and Kim, E and Jeong, JY and Ji, Y and Cho, SY and Lee, SW}, title = {Emphysema severity-associated gut microbiota modulates smoke-induced emphysema: evidence from fecal microbiota transplantation.}, journal = {Respiratory research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12931-026-03743-x}, pmid = {42243780}, issn = {1465-993X}, support = {2021R1A2C3008021//National Research Foundation of Korea/ ; RS-2023-NR077159//National Research Foundation of Korea/ ; RS-2022-NR067421//Bio&amp;Medical Technology Development Program of the NRF/ ; 2024ER080601//National Institute of Health research project/ ; }, abstract = {BACKGROUND: Cigarette smoking is the key risk factor for chronic obstructive pulmonary disease, but even similar levels of smoking can result in different disease severity. We hypothesize that differences in gut microbiota and metabolites contribute to differences in emphysema severity through the gut-lung axis. In this study, we compared the microbiome and metabolome among non-emphysema, non-severe emphysema and severe emphysema groups. Additionally, the impact of fecal microbiota transplantation from non-emphysema, non-severe emphysema and severe emphysema groups on emphysema were investigated.<br><br>METHODS: A total of 78 participants with a smoking history were included in this study and categorized into three groups: non-emphysema, non-severe emphysema, and severe emphysema. Gut microbiota and metabolites were analyzed, and germ-free mice underwent fecal microbiota transplantation with feces from donors representative of each group prior to smoking exposure.<br><br>RESULTS: Significant differences in gut microbiota and metabolites were observed among the groups, with lower acetic acid levels in patients with severe emphysema, and a greater abundance of Prevotellaceae and Megasphaera in patients without emphysema. Fecal microbiota transplantation from donors with severe emphysema worsened lung pathology in mice subjected to smoking exposure, whereas fecal microbiota transplantation from donors without emphysema attenuated emphysema development.<br><br>CONCLUSIONS: Gut microbiota and metabolites in participants with a smoking history differ according to the presence of emphysema and its severity, and can affect emphysema development. This suggests a role for gut microbiota in lung disease and provides a foundation for exploring gut microbiota as a potential therapeutic target for chronic obstructive pulmonary disease.}, }
@article {pmid42243811, year = {2026}, author = {Byrne, AL and Günther, G and Tadyanemhandu, C and de Almeida, CPB and Dewi, IM and Mitnick, CD and Koenig, SP and Romanowski, K and Wallis, RS}, title = {Interventions to reduce the impact of post-tuberculosis lung disease: a scoping review of the literature.}, journal = {BMC pulmonary medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12890-026-04355-3}, pmid = {42243811}, issn = {1471-2466}, abstract = {BACKGROUND: Post tuberculosis lung disease (PTLD) is an increasingly recognized contributor of long-term morbidity among the estimated 155 million survivors of Mycobacterium tuberculosis disease. While a range of interventions may influence PTLD risk, the full spectrum has not been systematically reviewed.<br><br>METHODS: We conducted a scoping review following Joanna Briggs Institute methodology to identify interventions delivered during or after TB treatment with potential to affect PTLD outcomes. Embase was searched from inception to March 31, 2025, for seven intervention categories: host-directed therapy (HDT), therapeutic drug monitoring (TDM), inhaled pharmacotherapy, antimicrobials beyond TB treatment, treatment shortening, thoracic surgery, and microbiome-altering interventions. Outcomes were grouped into disability, lung function, radiology, biomarkers, and histopathology, and categorized as showing improvement, worsening, or no effect on PTLD.<br><br>RESULTS: Of 7,965 records screened, 87 studies were included. Most were small, uncontrolled, and designed to assess microbiological cure rather than post-TB sequelae. Radiology and unstructured symptom reports were the most common outcomes, while validated disability tools and advanced lung function measures were rarely used. Corticosteroids and several HDTs showed signals of radiological or spirometric benefit, but the findings were inconsistent. Doxycycline and metformin improved cavity resolution in small trials. Inhaled bronchodilators demonstrated short-term spirometric gains in two studies and a survival benefit in one retrospective cohort. Antifungals for chronic pulmonary aspergillosis improved symptoms, radiology, and inflammatory biomarkers, whereas evidence for antibacterial or NTM-directed therapy was lacking. TDM was associated with faster culture conversion in some studies but was not linked to PTLD-specific outcomes. Microbiome studies consistently reported reduced diversity and altered composition during TB treatment, but no direct associations with PTLD.<br><br>CONCLUSION: Evidence for interventions to prevent or mitigate PTLD remains sparse, heterogeneous, and largely incidental. High-quality studies using standardized, person-centered outcomes are urgently needed to guide care for TB survivors worldwide.}, }
@article {pmid42243940, year = {2026}, author = {Li, C and Wang, C and Wu, S and Di, K and Zhu, Q and Yang, X and Wang, M and Wang, Z and Li, G and Tian, P}, title = {A coordinated toolbox strategy integrating direct pathogen suppression, host-associated responses, and microbiome remodeling for crop protection.}, journal = {Journal of nanobiotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12951-026-04644-3}, pmid = {42243940}, issn = {1477-3155}, support = {2023YFA0914700//National Key Research and Development Program of China/ ; }, abstract = {Although integrated pest management promotes the coordinated use of multiple disease-control tactics, single sprayable formulations that consolidate complementary crop-protection functions remain underdeveloped. Here, we combined semi-rational screening with supramolecular co-assembly to construct a ternary nanoassembly comprising glycyrrhizic acid (GA, a plant-derived amphiphile), magnolol (MN, a plant-derived antifungal phenolic), and Zn[2+], termed G-M@Zn NPs. Compared with free MN, G-M@Zn NPs enhanced MN photostability by 3.7-fold and increased rainfastness by 2.1-fold, indicating improved formulation persistence under simulated photolytic and wash-off stresses. The nanoformulation exhibited broad-spectrum antifungal activity in vitro against representative phytopathogenic fungi and, in a wheat-spike infection model of Fusarium graminearum, reduced the disease index from 52.5 ± 2.46 in the infected control to 22.3 ± 3.4. Under toxin-inducing conditions, G-M@Zn NPs also reduced deoxynivalenol (DON) accumulation and downregulated key TRI genes. Mechanistic assays linked the antifungal activity of G-M@Zn NPs to fungal membrane injury and mitochondria-associated oxidative stress in F. graminearum, with free MN eliciting qualitatively similar but weaker responses. G-M@Zn NP treatment was also accompanied by host defence-related physiological and metabolic responses involving redox regulation and tryptophan/indole-related pathways, together with treatment-associated shifts in the wheat spike microbiome. Preliminary biosafety assays indicated crop compatibility under the tested conditions and low acute toxicity toward earthworms. Serial-passage assays with F. graminearum showed only a modest increase in EC50 after eight passages. Overall, this ternary co-assembly provides a strategy for integrating complementary crop-protection functions within a single multifunctional nanoformulation and supports IPM-compatible control of F. graminearum infection in wheat. It may also inform the design of bioinspired nanopesticide systems that combine improved formulation persistence with direct antifungal activity and crop-associated biological responses.}, }
@article {pmid42243959, year = {2026}, author = {Su, C and Mao, Y and He, M and Van Doren, VE and Kelley, CF and Hu, YJ}, title = {TestNet: a method for inferring microbial networks with false discovery rate control for clustered and unclustered samples.}, journal = {Genome biology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13059-026-04103-0}, pmid = {42243959}, issn = {1474-760X}, support = {R01GM141074/NH/NIH HHS/United States ; R01GM141074/NH/NIH HHS/United States ; R01GM141074/NH/NIH HHS/United States ; }, abstract = {Most existing methods for inferring microbial networks generate only point estimates of Pearson's correlations without assessing their significance, and none accounts for clustering. We introduce TestNet, a novel method that delivers well-calibrated results by controlling the false discovery rate (FDR). TestNet uses a permutation-based procedure to generate valid null replicates that account for compositional effects, excess zeros in microbiome data, and clustering within samples when present. Our results demonstrate that TestNet is the only evaluated method that effectively controls the FDR while maintaining high power across a wide range of scenarios.}, }
@article {pmid42244002, year = {2026}, author = {Ansari, MH and Staubach, F and Alacatli, N and Obbard, DJ}, title = {A diverse gut virome in natural populations of Drosophila melanogaster.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00585-2}, pmid = {42244002}, issn = {2524-4671}, abstract = {BACKGROUND: Drosophila melanogaster is not only one of the most important models of antiviral immunity in invertebrates, but is also a powerful model for research of the gut microbiome. Although recent studies have continued to improve our knowledge of the fly gut microbiota, the viral component of the microbiome has remained unexplored.<br><br>RESULTS: Here we explore the viral component of the Drosophila melanogaster gut microbiome using deep metagenomic DNA sequencing. We recovered 3040 non-redundant viral contigs, most of which were bacteriophage-associated sequences, resulting in 167 viral Metagenome-Assembled Genomes. Many of these sequences showed limited similarity to reference viruses and included bacteriophages related to tailed double-strand DNA phage lineages, with putative links to major gut-associated bacteria of D. melanogaster, including Lactobacillus, Acetobacter, and Gluconobacter. Our functional annotation and discovery of auxiliary metabolic genes suggested that these bacteriophages encode putative functional potential related to microbial metabolism and genetic information processing. We also identified evidence of known fly pathogens Drosophila Kallithea nudivirus, Vesanto bidna-like virus, and Drosophila Linvill Road densovirus, some of which were common in our studied populations.<br><br>CONCLUSIONS: Our findings reveal a complex and diverse phage community in the D. melanogaster gut microbiome, paving the way to study host-phage related research in the natural microbial communities.}, }
@article {pmid42244171, year = {2026}, author = {Li, M and Sun, Y and Wang, J and Zhang, Y and Dou, T and Chen, C and Yuan, B and Cui, P and Liu, Y}, title = {A pH-Responsive Antimicrobial Peptide Coating with Efficient Antibacterial Activity and Preserved Oral Microbiota Homeostasis during Clear Aligner Treatment.}, journal = {ACS applied materials &amp; interfaces}, volume = {}, number = {}, pages = {}, doi = {10.1021/acsami.6c05016}, pmid = {42244171}, issn = {1944-8252}, abstract = {Bacterial adhesion and biofilm formation pose significant clinical challenges in clear aligner therapy, adversely affecting both oral health and aesthetics. In this study, a machine learning-driven strategy was used to develop a novel antimicrobial peptide (AMP), IW (sequence: IDFYRKTHWWNKLLAKWWAMR), which was subsequently covalently immobilized onto the surface of clear aligners to construct a pH-responsive antibacterial coating. In response to cariogenic acidic microenvironments, the coating is specifically activated to effectively inhibit the proliferation of cariogenic bacteria and subsequent biofilm formation. Moreover, IW reduces the abundance of potential pathogens while enriching health-associated bacterial genera, exerting a beneficial modulatory effect on the oral microbiome. This dual-functional strategy, integrating antibacterial activity with microbiota homeostasis preservation, offers a promising approach to combat cariogenic bacterial infection and oral dysbiosis, presenting substantial potential for clinical translation in orthodontic applications.}, }
@article {pmid42244179, year = {2026}, author = {Wang, Y and Zhu, Z and Zhang, Y and Luo, Q and Niu, T and Liu, Y and Chen, J and Yang, R and Zhu, S and Chen, H}, title = {Dynamic microbiome turnover and glycerol-3-phosphate-linked metabolic adjustments underlie resilience to desiccation in intertidal algae.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71330}, pmid = {42244179}, issn = {1469-8137}, support = {2021Z103//Major Scientific and Technological Project of Ningbo/ ; CARS -50//China Agriculture Research System of MOF and MARA/ ; 32373099//National Natural Science Foundation of China/ ; //Ningbo Yongjiang Talent Program/ ; 2021C02069 -9//Key Scientific and Technological Grant of Zhejiang for Breeding New Agricultural (Aquaculture) Varieties/ ; }, abstract = {Tolerance to extreme dehydration has emerged across the tree of life, yet current understanding relies heavily on terrestrial host traits. Marine lineages facing rapid, tide-driven hydration oscillations remain largely unexplored. We used Pyropia haitanensis as a model to determine if intertidal resilience arises from a coordinated holobiont strategy. We integrated time-resolved microbiome profiling and metagenomics. Mechanisms were validated through multi-omics of desiccation-stressed bacterial isolates, inoculation, and antibiotic-depletion experiments, and host physiological assessment. Rapid drying reshaped the microbiome through selective loss of osmosensitive taxa and occupation by stress-tolerant lineages, whereas rehydration promoted selective recolonization and network recovery. Metagenomic analysis revealed enrichment of functional potential for microbial antioxidant, osmoprotective, and extracellular polysaccharide pathways, alongside enrichment of glycerol-3-phosphate (G3P) ABC transporter modules. Host G3P secretion increased, creating a selective nutrient niche that recruited symbionts possessing specialized G3P transporters. Inoculation and microbiota-depletion experiments established a causal role for the microbiome in host resilience. Keystone isolates Sulfitobacter sp. and Alteromonas sp. utilized host-derived G3P to fuel complementary protective mechanisms, with their combination outperforming either taxon alone. These findings highlight an integrated host-microbiome partnership shaped by tidal filtering, a cross-domain strategy that buffers hydration stress and supports intertidal resilience and mariculture practices.}, }
@article {pmid42244234, year = {2026}, author = {Tanasov, A and Tiplica, GS}, title = {Pathogenesis of Male Genital Lichen Sclerosus: Autoimmunity versus the Urine/Occlusion Hypothesis - A Narrative Review.}, journal = {Clinical and experimental dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1093/ced/llag237}, pmid = {42244234}, issn = {1365-2230}, abstract = {Male genital lichen sclerosus (MGLSc) is a chronic inflammatory dermatosis with significant morbidity, yet its pathogenesis remains incompletely understood. Two main hypotheses have emerged: an autoimmune model, and the urine/occlusion hypothesis, specific to male genital anatomy. This narrative review critically analyses evidence supporting each paradigm. Epidemiological data reveal that autoimmune comorbidities occur significantly less frequently in men with MGLSc than in women with vulvar disease, with some studies reporting prevalence no higher than general population rates. Histopathologically, cytotoxic CD8+ and CD57+ T-lymphocyte infiltration suggests immune-mediated tissue injury, yet extracellular matrix protein 1 autoantibodies show no significant seroreactivity in males. Conversely, the urine/occlusion hypothesis is supported by the near-universal association of MGLSc with intact foreskin, high prevalence of post-micturition micro-incontinence, anatomical mapping demonstrating disease concentration in maximally occluded preputial regions, and case series showing disease resolution following urinary diversion and induction at urostomy sites. Microbiome studies demonstrate convergence between balanopreputial and urinary microbial communities in affected patients, while molecular evidence shows urea-induced fibroblast changes consistent with fibrogenesis. Recent transcriptomic analyses identifying distinct molecular subtypes suggest heterogeneity, with autoimmune mechanisms potentially operative in only a subset of patients. The evidence reviewed supports urine exposure and occlusion as the predominant pathogenic drivers in most MGLSc cases, with autoimmune phenomena likely representing secondary responses to tissue injury rather than primary etiological mechanisms.}, }
@article {pmid42244278, year = {2026}, author = {Yoon, YN and Kim, SH and Lim, JW and Kim, MJ and Kim, HJ and Sul, WJ and Kim, D and Jeong, W and Hwang, J and Yu, DA and Choe, YB and Lee, YW}, title = {Clinical Efficacy and Scalp Microbiome Changes Induced by AMPamide-Containing Shampoo in Patients With Seborrheic Dermatitis.}, journal = {Annals of dermatology}, volume = {38}, number = {3}, pages = {237-247}, doi = {10.5021/ad.25.234}, pmid = {42244278}, issn = {2005-3894}, support = {//Neopharm Co., Ltd./Korea ; }, abstract = {BACKGROUND: Seborrheic dermatitis (SD) is a chronic inflammatory scalp disorder associated with Malassezia dysbiosis and increased sebum production. AMPamide has been suggested to have anti-inflammatory and sebum-regulating effects, but its clinical efficacy and microbiome-modulating effects in SD remain unclear.<br><br>OBJECTIVE: To evaluate the clinical efficacy and scalp microbiome changes following 4 weeks of use of an AMPamide-containing shampoo in patients with SD.<br><br>METHODS: In this observational study, 30 patients with SD applied an AMPamide-containing shampoo for 4 consecutive weeks. Clinical outcomes, including sebum levels and overall severity scores, were assessed. Scalp bacterial and fungal communities were analyzed to evaluate &#x3b1;- and &#x3b2;-diversity and changes in Malassezia composition.<br><br>RESULTS: Treatment resulted in significant reductions in sebum levels and clinical severity scores, particularly in erythema, dandruff, and pruritus. Bacterial community composition remained largely stable, while fungal &#x3b1;-diversity increased, and &#x3b2;-diversity analysis revealed a decrease in the ratio of Malassezia restricta to Malassezia globosa.<br><br>CONCLUSION: AMPamide-containing shampoo was associated with improved clinical symptoms and a shift toward a more balanced fungal community composition in patients with SD, supporting its potential as a non-steroidal therapeutic option for SD.}, }
@article {pmid42244408, year = {2026}, author = {Loroña, NC and LaBrie, S and Thomas, CE and Yin, H and Huyghe, JR and Qu, C and Thomas, S and Nayemi, S and Ammar, H and Kahsai, O and Hsu, L and Curtis, KR and Koehne, A and Redwood, DG and Li, L and Li, CI and Peters, U and Thomas, TK and Phipps, AI and Figueiredo, JC and Hullar, M}, title = {Site- and age-dependent associations between Fusobacterium nucleatum and colorectal cancer mortality.}, journal = {Cancer}, volume = {132}, number = {12}, pages = {e70484}, doi = {10.1002/cncr.70484}, pmid = {42244408}, issn = {1097-0142}, support = {S10OD028685//Office of Research Infrastructure Programs, National Institutes of Health/ ; //GSF/ ; SR-202221337//M.J. Murdock Charitable Trust/ ; //V Foundation for Cancer Research/ ; P20CA252733/NH/NIH HHS/United States ; P30 CA015704/NH/NIH HHS/United States ; P50CA285275/NH/NIH HHS/United States ; R01CA155101/NH/NIH HHS/United States ; R01CA238087/NH/NIH HHS/United States ; R01CA248931/NH/NIH HHS/United States ; R01CA280639/NH/NIH HHS/United States ; R01CA284732/NH/NIH HHS/United States ; T32CA094880/NH/NIH HHS/United States ; U01CA290673/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: Fusobacterium nucleatum (Fn) is a bacterium typically found in the human oral cavity that has been implicated in the development and progression of colorectal cancer (CRC).<br><br>OBJECTIVE: This study examines the association between prevalence of Fn in tumor tissue and CRC-specific mortality in a heterogeneous United States population.<br><br>METHODS: The present study includes 233 participants with stage I-III CRC who died of CRC, matched to 458 participants with CRC who did not die from their disease, within the Translational Research Program in Cancer Differences across Populations. Genomic DNA was extracted from formalin-fixed paraffin-embedded tumor tissue samples. Droplet digital polymerase chain reaction was used to assess the prevalence of Fn. The authors fit logistic regression models for the association between Fn positivity and CRC-specific mortality, adjusting for age, year of diagnosis, sex, stage, tumor site, population group, and tumor macrodissection status.<br><br>RESULTS: Presence of Fn in CRC tumor tissue was associated with 79% greater odds (95% CI, 1.20-2.67) of CRC-specific mortality. This association was more pronounced in participants with rectal (odds ratio [OR], 7.73; 95% CI, 2.13-34.79) than proximal colon (OR, 1.17; 95% CI, 0.65-2.08) or distal colon tumors (OR, 1.51; 95% CI, 0.74-3.04, p value for interaction&#xa0;=&#xa0;.023), and more pronounced with respect to early-onset (age <50 years; OR, 10.30; 95% CI, 2.09-70.53) than later-onset CRC (age &#x2265;50 years; OR, 1.51; 95% CI, 0.98-2.33, p value for interaction&#xa0;= .010).<br><br>CONCLUSIONS: These findings support an association between presence of Fn in CRC tumor tissue and CRC-specific mortality, particularly for rectal tumors and early-onset CRC, in a heterogeneous population.}, }
@article {pmid42020537, year = {2026}, author = {Zarrabian, M and Sherif, SM}, title = {Taxonomic Restructuring of Rhizosphere Guilds is Driven By Agricultural Management and Scion Genotype in Apple.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, pmid = {42020537}, issn = {1432-184X}, support = {33522-38314//Biotechnology Risk Assessment Research Grants Program (BRAG)/ ; }, abstract = {UNLABELLED: Rhizosphere microbiomes are critical for agricultural health, but how they are interactively shaped by management and host genetics in perennial systems remains largely unknown. Using an apple orchard system, we show that long-term agricultural management does not alter soil biodiversity but also selects for fundamentally opposing microbial life strategies. Our findings showed that organic management selects resource-decomposition specialists, while conventional management selects abiotic stress-tolerance and xenobiotic remediators. We found that this is achieved via taxonomic restructuring of functional guilds, where the potential for essential ecosystem services is maintained across both systems but is facilitated by distinct, habitat-adapted specialists. This was most evident in fungi, where management-driven shifts in taxonomy were tightly coupled to functional capacity. Moreover, challenging the prevailing ecological theory that stress simplifies networks, we found that conventional fungal communities were paradoxically more complex, forming a rigid Stress-Clique of co-dependent survivors, while organic bacterial networks were more modular. This structural divergence provides a new mechanistic framework for rhizosphere assembly. We also showed that the host scion’s recruitment of fungi is entirely dependent on the management backdrop, while bacterial recruitment is not. These findings reveal that microbiome-optimized breeding should be conducted within the management framework of the intended production system.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00248-026-02774-7.}, }
@article {pmid42021335, year = {2026}, author = {Wang, N and Yan, T and Sun, H and Guo, W}, title = {Tryptophan metabolism in glaucomatous optic neuropathy: from metabolic dysregulation to therapeutic opportunities.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {42021335}, issn = {1479-5876}, abstract = {BACKGROUND: Glaucoma, a leading cause of irreversible blindness, involves progressive retinal ganglion cell loss. Beyond intraocular pressure, growing evidence implicates metabolic dysregulation as a key amplifying mechanism in glaucomatous damage. Among these metabolic changes, dysregulated tryptophan metabolism is increasingly recognized as a significant contributor to neurodegeneration. This review synthesizes clinical associations and preclinical mechanistic evidence linking tryptophan metabolism to glaucoma, discusses the potential underlying pathogenic mechanisms, and evaluates therapeutic strategies and research gaps.<br><br>MAIN TEXT: Current evidence suggests that dysregulated tryptophan metabolism in glaucoma shifts the balance toward neurotoxic metabolites (e.g. quinolinic acid) and reduces protective ones (e.g. kynurenic acid, indole derivatives). These changes are linked to alterations in AhR-mediated immunomodulation, NMDAR excitotoxicity, oxidative stress, intraocular pressure and vascular regulation. Therapeutic interventions span enzyme modulation, receptor targeting, microbiome optimization, lifestyle adjustments, and metabolite supplementation. Clinical parallels from neurology offer proof-of-concept for translational potential, though challenges remain in bioavailability, patient stratification, and long-term adherence.<br><br>CONCLUSIONS: Targeting tryptophan metabolism represents a promising, adjunctive strategy for neuroprotection in glaucoma. Future integration with multi-omics, biomarker development, and personalized medicine has the potential to shift glaucoma management from pressure-lowering to neuroprotection and metabolic restoration, providing a novel therapeutic framework for vision preservation.}, }
@article {pmid42021369, year = {2026}, author = {Xu, X and Qin, B and Lei, T and Liu, X and Li, X and Li, Y and Zhang, J and Chen, F and Liu, C and Zhang, L and Hou, H and Teng, T and Zhou, X}, title = {Gut microbiota alterations and signatures across subthreshold depression and major depressive disorders in adolescents.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {42021369}, issn = {1479-5876}, abstract = {BACKGROUND: Adolescent depression, including subthreshold depression (SD) and major depressive disorder (MDD), is a growing public health concern, yet objective signatures remain lacking. Accumulating evidence implicates gut microbiota alterations in depression. Our study aimed to characterize gut microbiota alterations among healthy controls (HCs), SD, and MDD, and to identify microbial signatures with potential discriminative value in adolescents.<br><br>METHODS: We profiled gut microbiota from 411 adolescents, including 117 HCs, 87 with SD, and 117 with MDD in the discovery set, along with an independent validation cohort of 45 HCs and 45 MDD patients. 16S rRNA sequencing was used to assess compositional and predicted functional differences. Random forest (RF) models and Linear discriminant analysis Effect Size (LEfSe) were applied to identify microbial signatures associated with depressive states.<br><br>RESULTS: Adolescents with MDD exhibited significantly reduced microbial diversity compared with HCs and SD, accompanied by compositional differences, with modest effect sizes observed for beta-diversity. Using LEfSe and RF modeling, twelve microbial features were identified that showed discriminative capacity across depressive states. Among these, Turicibacter (amplicon sequence variant, ASV792) and Clostridiaceae (ASV6392) emerged as the most consistently discriminative features, both showing a stepwise decrease across groups. The rsulting multi-ASV panel demonstrated reproducible classification performance, achieving area under the curve (AUC) values of 0.89 for MDD vs. HCs and 0.83 for MDD vs. SD. PICRUSt2-based functional prediction suggested differences in amino acid- and carbohydrate metabolsm-related pathways in MDD.<br><br>CONCLUSIONS: Our observational study demonstrates distinct gut microbiota profiles across different levels of depressive symptom severity in adolescents. The identified microbial features provide a research framework for future studies examining microbiome-associated patterns in adolescent depression.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-026-08138-6.}, }
@article {pmid42026592, year = {2026}, author = {Li, Y and Zhu, Y and Zhang, F and Huang, C and Wang, Z}, title = {The interaction between microbes and cytokines in cancer: unraveling the underlying effects.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {42026592}, issn = {1479-5876}, support = {Nos. 32370628,92159302, 32170592//National Natural Science Foundation of China/ ; Nos. 2022ZDZX0018, 2023NSFSC004,2024NSFSC0402//Jiangsu Provincial Agricultural Science and Technology Independent Innovation Fund/ ; No. 2023-YF09-00039-SN//National Science and Technology Planning Project/ ; No. ZYGD22009//1.3.5 project for Disciplines of Excellence, West China Hospital, Sichuan University/ ; }, abstract = {An increasing number of studies have found that microbes are involved in the development and treatment of tumors, and the impact of microbes on the tumor microenvironment has emerged as a prominent field in cancer studies. Although microbiome–immunity interactions in cancer have extensively reviewed in previous studies, the molecular integration of microbes with cytokines within the tumor microenvironment remains insufficiently resolved. This review examines how microbes influence the immunological and inflammatory regulatory systems in cancer. The activation of important signaling axes, such as IL-6/STAT3, TNF-α/NF-κB, and interferon pathways, by microbial components and metabolites (LPS, SCFA, and EPS) changes immune surveillance, encourages immune evasion, and affects the spread of metastases. Recent studies indicate that Microbiota-induced alterations in cytokine signaling increasingly influence cancer immunotherapy, suggesting that microorganisms and their metabolites may emerge as potential targets for novel anti-tumor immunotherapy. Evidences from multiple cancer types, combined with studies on specific non-malignant diseases, reveals synergistic alterations in microbial communities and cytokine networks. These interactions form a microbe-cytokine axis linking inflammation, tumor progression, and treatment response. Understanding the mechanisms underlying the interplay between microbial ecology and host cytokines may provide strategic guidance for enhancing precision cancer immunotherapy.}, }
@article {pmid42241861, year = {2026}, author = {Li, Y and Li, P and Li, H and Zhuang, L and Wang, L}, title = {Case study: Metagenomic analysis of microbial restructuring and nitrogen metabolism under probiotic and Chinese herb applications during post-antibiotic-ban shrimp farming.}, journal = {Journal of environmental management}, volume = {410}, number = {}, pages = {130128}, doi = {10.1016/j.jenvman.2026.130128}, pmid = {42241861}, issn = {1095-8630}, abstract = {China's 2020 aquaculture antibiotic ban has driven widespread use of probiotics and Chinese herbs in shrimp farming, yet their ecological effects on microbial communities remain unclear. This case study investigated three commercial Litopenaeus vannamei ponds in eastern China that exhibited contrasting nitrite accumulation and production outcomes under a post-antibiotic ban regime using probiotics and Chinese herbs. All ponds received daily Bacillus licheniformis probiotics and weekly supplements of Effective Microorganisms and a multi-herb blend, including Coptis, Elsholtzia, Sophora, Ligusticum, and Artemisia argyi. Our analysis revealed that Firmicutes-dominated communities replaced typical Proteobacteria-dominated microbiomes. Pond A, characterized by stable production, maintained low nitrite levels (a peak of 0.5 mg/L) and was dominated by Planococcus. In contrast, Ponds B and C, which exhibited elevated nitrite accumulation (peaks of 1.3 mg/L for Pond B and 1.5 mg/L for Pond C) and reduced production, were dominated by Paenisporosarcina. Metagenomic reconstruction indicated that this difference may result from aberrant nitrogen-transforming pathways. Paenisporosarcina correlated positively with nitrite accumulation, whereas Planococcus exhibited negative correlations. Virulence factor gene analysis revealed low abundance of pathogenic Vibrio spp.-associated genes. Importantly, even high-nitrite ponds exhibited minimal antibiotic resistance genes, including the absence of common aquaculture-associated ones such as those conferring resistance to sulfonamides (sul1, sul2), quinolones (qnr), and tetracyclines (tet), confirming the effectiveness of the antibiotic ban. Our case findings indicate that Paenisporosarcina dominance is linked to nitrite accumulation, highlighting a potential target for microbiome management in antibiotic-free shrimp farming.}, }
@article {pmid42241916, year = {2026}, author = {Brix, F and Demetrowitsch, T and Jensen-Kroll, J and Roeder, N and Rohmann, N and Hasler, M and Kosch, R and Waschina, S and Szymczak, S and Schreiber, S and Laudes, M and Zacharias, HU and Schwarz, K}, title = {Educational inequalities are associated with distinct metabolomic and gut microbiome patterns in adults.}, journal = {Social science &amp; medicine (1982)}, volume = {403}, number = {}, pages = {119454}, doi = {10.1016/j.socscimed.2026.119454}, pmid = {42241916}, issn = {1873-5347}, abstract = {Educational attainment is a well-established determinant of health inequalities and non-communicable diseases. While social gradients in health are consistently observed, the biological mechanisms through which educational disadvantage becomes embedded in human physiology remain insufficiently understood. We analyzed baseline data from 1773 adults in the population-based Food Chain Plus (FoCus) cohort. Phenotype, lifestyle, and nutrition were integrated with non-targeted serum and urine metabolomics and 16S rRNA gut microbiome profiles. Educational attainment was categorized as low, medium, or high. Associations were assessed using confounder-adjusted regression models, differential abundance analyses, and mixed graphical models to explore cross-domain associations relevant to population health. Educational attainment was associated with an accumulation of adverse behavioral, clinical, and dietary factors, providing social context within which the omics findings are interpreted. MGM analyses identified three mechanistic bridges linking educational attainment to cardiometabolic and inflammatory risk, including sedentary behavior, adiposity and insulin resistance, and dietary quality and plant food intake. A panel of 15 education-associated metabolites across biofluids captures these patterns, clustering around dietary quality, glycemic markers, and adiposity. Gut microbiome composition differed modestly but significantly across educational groups (PERMANOVA R[2] < 0.003, p = 0.001), whereas α-diversity metrics did not differ. Twenty-four microbial genera were differentially abundant by educational attainment, including taxa related to short-chain fatty acid production and inflammation. These findings support the concept that social disadvantage is biologically embodied through three converging pathways connecting socially patterned behavior and diet to measurable metabolic and microbial signals. The MGM framework reveals the specific network positions through which these pathways operate, providing population-level, hypothesis-generating evidence relevant for understanding and addressing persistent health inequalities.}, }
@article {pmid42242027, year = {2026}, author = {Li, J and Ji, J and Ma, X and Xu, Z and Zhou, L and Guan, Y and Ling, X and Jia, X and Xi, B and Zhao, M}, title = {Bifidobacterium longum alleviation of metabolic dysfunction-associated steatotic liver disease: A multi-omics landscape of microbiota and metabolome reconfiguration.}, journal = {Microbiological research}, volume = {310}, number = {}, pages = {128569}, doi = {10.1016/j.micres.2026.128569}, pmid = {42242027}, issn = {1618-0623}, abstract = {The gut microbiome-host metabolism axis plays a critical role in the pathogenesis of metabolic dysfunction-associated steatotic liver disease (MASLD). Although the probiotic Bifidobacterium longum (B. longum) shows promise in ameliorating metabolic disorders, its functional impact on the microbiome-metabolome interplay in MASLD remains elusive. Herein, we established a MASLD mouse model using a high-fat, high-fructose (HFHF) diet and conducted integrated multi-omics analyses, including liver transcriptomics, gut metagenomics, and serum metabolomics, following B. longum intervention. B. longum supplementation effectively attenuated systemic metabolic dysfunction, hepatic steatosis, and intestinal barrier impairment in MASLD. This amelioration was driven by a two-pronged functional reorganization: the restoration of intestinal integrity and a profound remodeling of the hepatic transcriptome, featuring the downregulation of crucial mediators within the CD14-TLR4-NF-κB signaling cascade, including Cd14 and Runx1. Such functional reorganization coincided with a reconfigured gut microbiota, characterized by an increased abundance of beneficial taxa (e.g., Parabacteroides distasonis, Muribaculum intestinale) and suppression of opportunistic pathobionts (e.g., Ruminococcus gnavus, Clostridioides difficile). Furthermore, these microbial shifts were intrinsically linked to a reconfigured serum metabolome, highlighted by the enrichment of protective tryptophan-derived metabolites (e.g., indole-3-propionic acid) and the reduction of detrimental ones (e.g., 17α-methyltestosterone, 7-HDoHE). Collectively, our results suggest that B. longum mitigates MASLD through modulation of the gut microbiota and host serum metabolome, supporting its potential as a probiotic candidate for the management of metabolic health.}, }
@article {pmid42242028, year = {2026}, author = {Mishra, J and Arora, NK}, title = {Toward predictive plant microbiomes: From assembly rules to deployment.}, journal = {Microbiological research}, volume = {310}, number = {}, pages = {128566}, doi = {10.1016/j.micres.2026.128566}, pmid = {42242028}, issn = {1618-0623}, abstract = {Plants operate as holobionts whose productivity, resilience, and ecosystem functions are inseparable from their associated microbiomes. Recent advances in multi-omics and systems ecology have revealed how plant-microbe interactions regulate nutrient cycling, immunity, stress tolerance, and biogeochemical processes. Yet, much of this knowledge remains descriptive, limiting its translation into solutions for global challenges. This Review argues for a shift from microbiome cataloguing to predictive and application-oriented plant microbiome engineering. We synthesize fundamental principles of microbiome assembly-including rhizodeposition, host developmental control, functional trait selection, and microbial network dynamics-and connect them to emerging translational strategies. We examine how plant microbiomes can be harnessed to enhance crop biofortification and bioprotection, restore degraded ecosystems, modulate carbon and nitrogen cycling for climate resilience, and support sustainable bioenergy production on marginal lands. We highlight synthetic microbial communities, microbiome-aware breeding, and trait-based microbial selection as key frameworks for establishing causality. Finally, we discuss major constraints to field deployment, including ecological instability, host specificity, unintended greenhouse-gas feedbacks, and regulatory uncertainty. By integrating mechanistic insight with ecological realism, this review positions plant microbiomes as central levers for sustainable agriculture, climate action, and the bio-based economy.}, }
@article {pmid42242076, year = {2026}, author = {Bai, H and He, LY and Qiao, LK and Gao, FZ and Liu, YS and Ying, GG}, title = {Human-associated microbial inputs and bacterial-fungal ecological coupling shape antibiotic resistance risk in environmental dust.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142602}, doi = {10.1016/j.jhazmat.2026.142602}, pmid = {42242076}, issn = {1873-3336}, abstract = {Environmental dust represents a critical exposure matrix, yet the relationships between multi-kingdom dust microbiomes and antimicrobial resistance (AMR)-associated health risks remain insufficiently characterized. We applied shotgun metagenomics to dust samples from pharmaceutical factories, a dairy farm, railway stations, and schools to comprehensively characterize bacterial, fungal, and viral communities, alongside resistome structure. Microbial community composition exhibited significant differences across all three domains among the sampled environments. Specifically, dust from railway stations displayed the strongest human-associated microbial signal and harbored the highest diversity of antibiotic resistance genes (ARGs), and MetaCompare-derived AMR risk. Functional analyses revealed shared bacterial-fungal metabolic organization, with cross-domain taxonomic and functional associations pointing to structured ecological coupling. Variation partitioning analysis showed that shared explanatory components accounted for most of the variation in MetaCompare-based human-health AMR risk, particularly the overlap among bacterial composition, humanization, and fungal functional structure. Notably, Candida and Aureobasidium emerged as divergent fungal indicators, tracking microbiome humanization and resistome risk in opposite directions. By contrast, viral auxiliary metabolic genes accounted for only 3.92% of the abundance-weighted virome, consistent with a host-linked auxiliary layer rather than a dominant independent pathway. Collectively, these findings demonstrate that AMR-related signatures in environmental dust are shaped by the interplay of human-associated microbial inputs and ecologically coupled bacterial-fungal interactions.}, }
@article {pmid42242179, year = {2026}, author = {Whiley, L and Zhu, HX and Garcia-Bennett, AE and Jaschke, PR}, title = {Bacteriophage nanoparticles: an emerging modular delivery platform.}, journal = {Current opinion in biotechnology}, volume = {100}, number = {}, pages = {103527}, doi = {10.1016/j.copbio.2026.103527}, pmid = {42242179}, issn = {1879-0429}, abstract = {Nanoparticles are now central to many drug and vaccine delivery strategies, but most require reformulation for each application. Bacteriophage‑derived nanoparticles offer a genetically encoded, structurally defined, and modular alternative. This review organizes recent advances along three tunable axes - scaffold, surface, and cargo - and highlights hybrid phage-polymer/lipid/inorganic constructs that expand stability, targeting, and loading. We survey applications from multivalent vaccines and oversized gene transfer to precision microbiome editing, and outline translational hurdles. Phage-derived products are approaching translation, with virus-like particle-based vaccines and CRISPR-enhanced antimicrobial phages in clinical trials. Finally, we preview emerging opportunities, including AI‑guided capsid and receptor‑binding protein design, cell‑free phage synthesis, and standardized 'reference' phage chassis that can be combined with traditional nanoparticles, positioning phage nanoparticles as reusable, plug-and-play nanomedicines.}, }
@article {pmid42242180, year = {2026}, author = {Jeepipalli, S and Gurusamy, P and Martins, ARL and Reddy, SSP and Sahay, B and Chan, EKL and Kesavalu, L}, title = {Polymicrobial periodontal infection selectively alters the fecal microbiome in mice: Implications for the oral-gut microbial axis.}, journal = {Archives of oral biology}, volume = {189}, number = {}, pages = {106635}, doi = {10.1016/j.archoralbio.2026.106635}, pmid = {42242180}, issn = {1879-1506}, abstract = {OBJECTIVE(S): This study aimed to evaluate the impact of polybacterial oral infection with Streptococcus gordonii, Fusobacterium nucleatum, Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia on the gut microbiota in a murine model.<br><br>DESIGN: We investigated alterations in fecal bacterial microbiome in infected mice. Fecal samples were collected after the 15th week of infection. Libraries of 16S rRNA amplicons generated from fecal DNA were sequenced using the Illumina sequencing platform.<br><br>RESULTS: Feces from infected mice showed upregulation in the classes Verrucomicrobiae, Bacteroidia, Bacilli, and downregulation of Actinomycetia, Coriobacterota, and Clostridia. The genera Lactobacillus (p-value < 0.001) were significantly upregulated, and Acutalibacter (p-value < 0.05), Limosilactobacillus (p-value < 0.05) were downregulated in the infection compared to sham-infected mice. The infection process upregulated 15 strains of bacteria most prominently Akkermansia muciniphila and Dubosiella and downregulated 19 strains. Feces from sham infection had 21 strains of bacteria that completely disappeared in the infected mice, and the feces from infected mice detected 16 strains (Bacteroides, Bifidobacterium globosum) absent in sham-infected mice. Fecal microbiome data indicate that bacterial infection disrupts gut microbiome composition (selective dysbiosis) at class, genus, and strain levels. Periodontal infection appeared to eliminate certain bacterial strains and promoted the emergence of new strains.<br><br>CONCLUSION: Using the Illumina sequencing platform, the present study found that polymicrobial periodontal infection selectively altered the gut microbiome at the class, genus, and strain levels of fecal bacteria. The genomic DNA for S. gordonii, F. nucleatum, and P. gingivalis was detected in the infected mice's feces.}, }
@article {pmid42242208, year = {2026}, author = {Mishra, AA and Palmer, SN and Zarek, CM and Coughlin, LA and Poulides, N and Dakour, J and Chiu, RS and Sabaeifard, P and Li, W and Morrill, AC and Kim, J and Gan, S and Behrendt, CL and Antczak, MI and Zhan, X and Winter, SE and Ready, JM and Hooper, LV and Koh, AY}, title = {Microbiota-derived short-chain fatty acids mediate Candida albicans gastrointestinal colonization resistance.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.05.007}, pmid = {42242208}, issn = {1934-6069}, abstract = {The gut microbiota plays critical roles in constraining Candida albicans colonization of the gastrointestinal (GI) tract, which is a key precursor to disseminated fungal infection in immunocompromised hosts. Depletion of commensal microbiota, such as by antibiotic treatment, increases C. albicans burden and promotes dissemination, yet the mechanisms of colonization resistance remain unclear. Here, we show that microbiota-derived short-chain fatty acids (SCFAs) directly inhibit C. albicans growth by inducing fungal metabolic reprogramming, impairing hexose uptake, and inducing intracellular acidification. In vivo, SCFAs enhance Candida colonization resistance only in the presence of an intact gut microbiome, which drives SCFA-induced taxonomic shifts that augment resistance. A Bacteroides thetaiotaomicron mutant unable to produce SCFAs exhibits diminished capacity to restrict C. albicans colonization, while prebiotic therapy that increases luminal SCFAs enhances C. albicans clearance. These findings define a critical microbiota-metabolite mechanism underlying Candida colonization resistance and suggest strategies to modulate GI fungal burden and prevent invasive disease.}, }
@article {pmid42242497, year = {2026}, author = {Han, J and Lisco, A and Che, Y and Anderson, MV and Laidlaw, E and Kim, CS and Hou, P and Conlan, S and Proctor, DM and Lee-Lin, S and Amirkhani, A and Holmes, CJ and Suh, GS and Brownell, I and ,  and Segre, JA and Sereti, I and Kong, HH}, title = {Expansion of pathogens and restoration of human skin microbiome in CD4 T-cell lymphopenia.}, journal = {The Journal of investigative dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jid.2026.05.019}, pmid = {42242497}, issn = {1523-1747}, abstract = {The microbiome and host immune system maintain a dynamic homeostatic equilibrium at the skin interface. Prior studies have shown that the skin microbiome is profoundly altered in immunodeficient conditions. Patients with idiopathic CD4 lymphopenia (ICL), a rare clinical syndrome with obscure cause, and people living with HIV (PLWH) are two etiologically distinct groups of individuals with CD4 T-cell lymphopenia. We conducted shotgun metagenomic sequencing, metagenome assembly, and read-based mapping to characterize the multi-kingdom taxonomic diversity of skin microbiomes in patients with ICL and PLWH who were followed longitudinally before and after antiretroviral therapy (ART) initiation. Compared with healthy individuals, the skin microbiomes of patients with ICL and ART-naïve PLWH showed greater inter-individual variation and higher relative abundances of eukaryotic viruses. Both patient groups carried pathogenic microbes, including high-oncogenic-risk human papillomaviruses (HPVs) and dermatophytes such as Trichophyton rubrum, which were rarely seen in healthy individuals. In PLWH, high-oncogenic-risk HPV types persisted after 2 months of ART but were mostly cleared after 14 months. The loss of peripheral blood CD4 T-cells was associated with shifts in the skin microbiome and a relative expansion of pathogenic microbes. Investigating microbiome dynamics during immunodeficiency and subsequent immune reconstitution provides additional insights into host-microbial interactions.}, }
@article {pmid42242549, year = {2026}, author = {Doumat, G and Haroon, S and Maalouf, NM and Jain, R}, title = {Bone Disease in Non-Cystic Fibrosis Bronchiectasis: Connections, Mechanisms, and Care Gaps.}, journal = {Chest}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chest.2026.05.034}, pmid = {42242549}, issn = {1931-3543}, abstract = {TOPIC IMPORTANCE: Non-cystic fibrosis bronchiectasis (NCFB) is a heterogeneous chronic airway disease increasingly recognized worldwide and associated with a substantial burden of extra-pulmonary manifestations. Osteoporosis has emerged as a highly prevalent yet underappreciated comorbidity. Unlike cystic fibrosis, where bone health guidelines exist, no screening or management recommendations are available for NCFB despite overlapping risk factors, including chronic inflammation, malnutrition, hypoxia, medication exposure, and physical inactivity.<br><br>REVIEW FINDINGS: Reported prevalence of osteoporosis and osteopenia in NCFB varies widely (12-70% and 15-40%, respectively), reflecting disease heterogeneity and differences in study methodology. Mechanisms include persistent systemic inflammation, hypoxemia, nutritional deficiencies, and exposure to inhaled or systemic corticosteroids, all of which disrupt bone remodeling. Emerging contributors, such as microbiome dysbiosis and reduced physical activity, may further drive skeletal fragility. Clinically, osteoporosis in NCFB is linked to greater symptom burden, increased comorbidity, poorer quality of life, higher healthcare costs, and elevated mortality. Despite these consequences, bone health is rarely discussed in bronchiectasis literature, and current comorbidity indices do not include osteoporosis as a prognostic factor.<br><br>SUMMARY: This review synthesizes current evidence on the epidemiology, mechanisms, and clinical impact of osteoporosis in NCFB, highlighting significant knowledge gaps and opportunities for early intervention. There is an urgent need for systematic screening, heightened awareness among pulmonologists and primary care clinicians, and interdisciplinary management approaches. Recognizing and addressing this overlooked comorbidity has the potential to improve outcomes and quality of life for patients with NCFB and to inform future disease-specific guidelines.}, }
@article {pmid42242743, year = {2026}, author = {Lestari, K and Sutema, IAMP and Latarissa, IR and Oon, SF and Tamsir, NM and Noor, A and Widowati, IGAR and Sartika, CR and Ciptasari, NWE}, title = {Oral probiotics and topical secretome to enhance clinical outcomes and microbiome restoration in acne vulgaris: a double-blind, randomised controlled trial protocol.}, journal = {BMJ open}, volume = {16}, number = {6}, pages = {e109586}, pmid = {42242743}, issn = {2044-6055}, abstract = {BACKGROUND: Acne vulgaris is a chronic inflammatory condition primarily caused by Cutibacterium acnes, which disrupts skin homeostasis, thereby triggering immune responses and sebum metabolism. Dysbiosis is an imbalance in the skin and gut microbiota identified as a significant factor contributing to acne progression. Standard therapy often relies on antibiotics, but the long-term use has increased antibiotic resistance, including in Indonesia. Consequently, alternative methods, such as probiotics and mesenchymal stromal cell secretomes, are gaining attention for immunomodulatory and regenerative properties. These novel therapies have shown promising results in modulating the skin and gut microbiota while reducing inflammation.<br><br>METHODS AND ANALYSIS: A phase 2 double-blind randomised controlled trial will be conducted using a parallel group design with four arms, namely: (1) standard therapy with oral probiotics and topical secretome (placebo), (2) standard therapy with oral probiotics (placebo) and topical secretome, (3) standard therapy with oral probiotics and topical secretome and (4) standard therapy with oral probiotics (placebo) and topical secretome (placebo). Sixty-four patients with mild to moderate acne vulgaris will be randomly allocated to these groups. Interventions will be administered over a period of 8 weeks, with outcomes to be measured at baseline and post-therapy. This study will be conducted at the Dermatology and Venereology Department of Bali Mandara General Hospital (RSBM). The primary outcome will be the reduction of comedones and inflammatory lesions, assessed using the Yolov8 method. Secondary outcomes will include gut and skin health parameters, such as tryptophan metabolites, collagen, pH, moisture, sebum levels and IL-6, to explore the relationship between microbiome balance, skin condition and inflammation in acne.<br><br>ETHICS AND DISSEMINATION: This study will be conducted in accordance with the ethical principles outlined in the Declaration of Helsinki and the International Conference on Harmonisation-Good Clinical Practice guidelines. Ethical approval has been granted by the Health Research Ethics Committee of Bali Mandara Regional Hospital (Approval Reference Number: 060/EA/KEPK.RSBM.DINKES/2024). All participants will provide written informed consent prior to enrolment. Data confidentiality and participant safety will be upheld throughout the trial. The results of this study will be disseminated through journals, scientific conferences and relevant academic platforms to ensure wide accessibility and to support further research and clinical application in the field of dermatology, particularly in addressing antibiotic resistance and microbiome-based acne therapies.<br><br>TRIAL REGISTRATION NUMBER: NCT06925386.}, }
@article {pmid42242952, year = {2026}, author = {Chen, J and Cai, X and Ma, Q and Hao, H and Zheng, X}, title = {GPR35 in host-microbe interaction: Mechanisms and translational prospects.}, journal = {Trends in pharmacological sciences}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tips.2026.05.007}, pmid = {42242952}, issn = {1873-3735}, abstract = {Understanding the mechanism of host-microbe interaction expands the landscape of drug discovery. Challenges, however, exist in the discovery of druggable targets from their signaling network. G protein-coupled receptors are versatile sensors at the host-microbe interface, and G protein-coupled receptor 35 (GPR35) is increasingly shown to play a role via metabolic, immune, and neural mechanisms. These advances not only enrich the pharmacology of this orphan receptor but also suggest an alternative path for microbiome-based therapeutics. We update the knowledge on GPR35-mediated host-microbe interaction in health and disease. We discuss the need to probe endogenous ligands of GPR35 with pathophysiological and human relevance, highlighting the complexities from species selectivity and signaling bias. We also propose potential strategies to translate the emerging insights into therapeutics with a balanced efficacy and safety profile.}, }
@article {pmid42243088, year = {2026}, author = {Wang, Y and Xu, M and Dong, Q and Lin, X and Zhang, Q and Shi, H and Lin, X and Liu, H and Yu, M and Shen, J}, title = {The gut-bone axis: impact of diet on gut microbiome and osteoporosis.}, journal = {Bone research}, volume = {14}, number = {1}, pages = {}, pmid = {42243088}, issn = {2095-4700}, support = {82301785//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2025J08239//Natural Science Foundation of Fujian Province (Fujian Provincial Natural Science Foundation)/ ; }, abstract = {Osteoporosis, a global health challenge characterized by reduced bone mineral density (BMD) and increased fracture risk, is closely linked to interactions between dietary patterns and gut microbiota (GM). Recent advances in GM research highlight the gut-bone axis as a pivotal focus in osteoporosis studies, revealing that variations in dietary habits and nutrient intake differentially modulate GM composition and metabolic activity, thereby influencing skeletal health. This review synthesizes current evidence on the interplay between dietary practices, GM, and bone health, aiming to identify preventive and therapeutic strategies for osteoporosis management. Collectively, these findings underscore the potential of dietary interventions targeting GM modulation as a novel therapeutic approach, advocating for personalized nutritional strategies to improve skeletal health in high-risk populations.}, }
@article {pmid42243136, year = {2026}, author = {Weidinger, S and Aoiki, V and Dhar, S and Dlova, NC and Kabashima, K and Ma, L and Flohr, C and Irvine, AD}, title = {Atopic dermatitis.}, journal = {Nature reviews. Disease primers}, volume = {12}, number = {1}, pages = {}, pmid = {42243136}, issn = {2056-676X}, abstract = {Atopic dermatitis (AD) is the most common inflammatory skin disease and carries the highest disability-adjusted life-years burden, ranking 15th among all non-fatal diseases globally. It is characterized by intensely itchy skin and is associated with multiple comorbidities, such as food allergy, asthma, allergic rhinitis and eosinophilic oesophagitis, which are mainly driven by type 2 immune responses. Other comorbidities include mental health disorders, disordered bone health, and cutaneous and extracutaneous infections. AD is also associated with other immune-mediated inflammatory diseases, including alopecia areata, vitiligo and inflammatory bowel disease. AD most often starts in the first 2 years of life but can occur at any life stage and onset at >60 years of age is increasingly common. The twenty-first century has brought greater insights into disease pathology, with an understanding of the complex interplay between the skin barrier, cutaneous and systemic immune pathways, cutaneous microbiome and neural networks. This improved mechanistic understanding has enabled rational drug design and a shift from non-specific broad immunomodulation to targeted biologic therapies and small molecules for severe disease and from topical corticosteroids to next-generation therapies for mild and moderate disease. Yet, considerable global inequity remains in access to these novel therapeutics.}, }
@article {pmid42243260, year = {2026}, author = {Carranco, AS and Romo, D and Torres, ML and Wilhelm, K and Gillingham, MAF and Sommer, S}, title = {Egg microbiome of the yellow-spotted Amazon river turtle (Podocnemis unifilis) modulates fusariosis fungal infection and hatching success.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-10404-8}, pmid = {42243260}, issn = {2399-3642}, support = {DFG SO 428/19-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, abstract = {Turtle egg fusariosis, caused by pathogens of the Fusarium solani species complex (FSSC), threatens turtle populations globally, through embryonic mortality and hatching failure. Host-associated microbiomes, including the bacteriome and mycobiome, are hypothesized to mediate disease outcomes in oviparous vertebrates, but this remains largely unexplored. Here, we characterised the inner-egg bacteriome and mycobiome of uninfected and FSSC-infected eggs at three developmental stages in the vulnerable yellow-spotted Amazon river turtle (Podocnemis unifilis). Lower mycobiome evenness was strongly associated with increased FSSC infection propensity and intensity. Regardless of infection status, higher microbial diversity positively correlated with hatching success, and hatched eggs showed more complex interkingdom interactions. We also identified bacterial and fungal genera whose relative abundance was negatively associated with FSSC infection. These findings support the hypothesis that the egg microbiome may influence infection and hatching outcomes, with implications for microbiome-informed conservation strategies for threatened turtle populations.}, }
@article {pmid42243284, year = {2026}, author = {Song, MH and Oh, EK and Kim, IH and Son, JS and Yoon, SJ and Kim, JY and Kim, MJ and Jeong, SY and Park, JW and Ku, JL}, title = {Bacteriophage-mediated restoration of epithelial integrity, DNA damage response, and transcriptomic homeostasis in colon organoids exposed to ETBF and pks + E. coli.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-56205-1}, pmid = {42243284}, issn = {2045-2322}, support = {RS-2020-NR119695//National Research Foundation of Korea/ ; 0431-20210023//iNtRON Biotechnology, Inc/ ; }, abstract = {Colorectal cancer (CRC)-associated pathobionts such as Enterotoxigenic Bacteroides fragilis (ETBF) and colibactin-producing (pks+) Escherichia coli disrupt epithelial barrier function, promote chronic inflammation, and induce genotoxic stress. To investigate how these pathogenic interactions with the host epithelium can be modulated, we employed patient-derived normal human colon organoids as an ex vivo model. Two lytic bacteriophages, Bac-FRP-3 (targeting ETBF) and Esc-COP-23 (targeting pks + E. coli), were applied to bacterial cultures, and the resulting phage-conditioned supernatants were used to challenge organoids. Exposure to ETBF and pks + E. coli induced strong pro-inflammatory transcriptional responses, DNA damage signaling, and epithelial disruption, whereas phage treatment attenuated these effects. Transcriptomic profiling revealed restoration of inflammatory and DNA damage-related gene expression, while confocal imaging confirmed recovery of epithelial junctional integrity and reduced DNA double-strand breaks. These findings highlight phage-mediated modulation of host-pathobiont interactions and provide mechanistic insight into how targeted viral predation can reshape pathogenic impacts within the human intestinal environment.}, }
@article {pmid42243302, year = {2026}, author = {Baghoveh, F and Matin, MM and Fereidoni, M and Makhdoumi, A}, title = {Heat-inactivated Bacillus spores attenuate poly I:C-induced lung inflammation and microbiome alterations through modulation of host immune responses.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-56948-x}, pmid = {42243302}, issn = {2045-2322}, support = {56692/3//Ferdowsi University of Mashhad/ ; }, abstract = {Uncontrolled cytokine responses are a major driver of acute lung injury and poor outcomes in respiratory viral infections such as COVID-19. Strategies that can safely restrain hyperinflammation while preserving host defense remain limited. Here, we show that pretreatment with heat-inactivated Bacillus spores markedly protects against the viral mimetic polyinosinic-polycytidylic acid (poly I:C)-induced pulmonary inflammation in BALB/c mice. Structural and in vivo imaging system analyses confirmed that heat treatment was successful in eliminating the viability of spores without rupturing or changing their penetration into the airway via instillation. The results indicated that in a poly I:C-induced model of acute lung injury, spore parabiotics reduced pulmonary edema, histopathological damage, and pro-inflammatory cytokine release. Moreover, parabiotic spores suppressed Ace2 and Tlr3 expression in murine macrophages, suggesting regulation of receptors implicated in downstream inflammatory signaling. Parabiotic treatment attenuated lung microbial alteration triggered by viral mimic challenge. Together, these findings identify spore-based parabiotics as a potentially safe immunomodulatory approach capable of limiting excessive inflammatory responses and supporting respiratory function in the context of viral-like lung inflammation.}, }
@article {pmid42243307, year = {2026}, author = {Zhang, Q and Jacobson, R and Nelson, M and Bergonzi, C and Sadowsky, MJ and Elias, MH}, title = {Enzymatic quorum quenching alters the phyllosphere microbiome and suppresses a bacterial-induced plant disease.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-53522-3}, pmid = {42243307}, issn = {2045-2322}, abstract = {Bacterial plant pathogens cause hundreds of millions of dollars in annual crop losses in the United States alone, further stressing an already strained global food supply. Numerous bacteria in the phyllosphere use N-acyl homoserine lactone (AHL)-mediated quorum sensing (QS) systems to coordinate behaviors and shape microbial communities. Strategies that interfere with bacterial QS systems employ enzymes to degrade or transform AHLs in a process called quorum quenching (QQ). This interference results in altered microbial community structure and function. We previously isolated and engineered SsoPox, a highly stable AHL-degrading lactonase that interferes with QS. Here, we evaluated the effects of SsoPox-mediated QS disruption on the Zea mays phyllosphere in a Goss's wilt infection model caused by Clavibacter nebraskensis. In this proof-of-concept work, we found that infection significantly altered the composition and structure of the leaf microbial community. SsoPox QQ lactonase treatment substantially reduced this shift, resulting in a leaf surface community resembling the uninfected controls. qPCR experiments revealed a small, yet significant reduction of pathogen abundance on plant leaves following enzymatic treatment. As a result, the formulated QQ lactonase spray reduced disease severity. This study demonstrates the critical role of microbial signaling in the phyllosphere and highlights the potential of QQ lactonases to control plant diseases.}, }
@article {pmid42243316, year = {2026}, author = {Wang, J and Qi, Z and Zhu, Y and Tang, D and Wang, N and Li, J}, title = {Hyperuricemia aggravates acute pancreatitis through CNR1-mediated inflammatory signaling and gut-pancreas axis dysregulation: a multi-omics and clinical study.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-54458-4}, pmid = {42243316}, issn = {2045-2322}, support = {YX202208//Talent Cultivation Project of the Third Xiangya Hospital of Central South University/ ; 82472736//National Natural Science Foundation of China/ ; }, abstract = {Hyperuricemia (HUA) is implicated in various metabolic and inflammatory diseases. Its role in the pathogenesis of acute pancreatitis (AP), particularly in gut-pancreas crosstalk and the underlying molecular mechanisms, remains poorly understood. This study integrates clinical epidemiology (UK Biobank cohort and the Third Xiangya Hospital cohort), (L-arginine-induced AP mouse models), and multi-omics analyses (RNA sequencing, fecal metabolomics, and gut microbiome profiling) to elucidate the role and mechanistic pathways of uric acid in the onset and severity of AP. Key molecular targets and regulatory relationships identified were further validated via in vitro cellular experiments using pancreatic acinar cells and bone marrow-derived macrophages. In the UK Biobank cohort, over a median follow-up period of 13.69 years, participants in the highest uric acid quartile exhibited a significantly increased risk of developing AP compared to the lowest quartile (hazard ratio [HR], 1.25; 95% confidence interval [CI], 1.10-1.43). In the Third Xiangya Hospital cohort, AP patients with elevated serum uric acid levels exhibited more severe symptoms. The combination of uric acid and calcium demonstrated superior predictive capability for AP severity (AUC 0.9504). In the preclinical models, HUA aggravated AP progression, as demonstrated by increased pancreatic histopathological damage, elevated serum amylase levels, multi-organ dysfunction, and higher mortality. Mechanistically, HUA exacerbated AP in mice via cannabinoid receptor 1 (CNR1)-mediated retrograde endocannabinoid signaling, which enhanced macrophage-derived IL-1β and IL-6 production. Metabolomics revealed that the gut-derived flavonoid maesopsin exerted a protective anti-inflammatory effect in the context of HUA-augmented AP. Additionally, Limosilactobacillus genus, particularly Limosilactobacillus reuteri D, was enriched in the HUA + AP group and strongly associated with maesopsin levels. Uric acid exacerbates AP progression via CNR1 driven inflammatory signaling and modulates gut microbiota composition and metabolism. Serum uric acid, especially when combined with calcium, may be integrated into routine clinical assessment for AP risk stratification and severity prediction, while CNR1 and gut microbiota-related targets provided potential directions for the developing adjunctive therapies for HUA-associated AP.}, }
@article {pmid42243405, year = {2026}, author = {Su, H and Xu, T and Hu, W and Wang, H and Pei, Z and Lu, W}, title = {A multi-strain biofilm consortium enhances gut microbiota resilience and restores post-antibiotic homeostasis.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {6}, pages = {}, pmid = {42243405}, issn = {1573-0972}, support = {32172216//National Natural Science Foundation of China/ ; JUSRP202504013//Fundamental Research Funds for the Central Universities/ ; }, abstract = {Antibiotics can significantly disrupt gut microbiota homeostasis, reducing microbial diversity and causing dysbiosis associated with health issues. Gut biofilms play a critical role in resilience and stress tolerance of the intestinal ecosystem. Mucosal microbial communities also help restore the gut microbiota after interventions like probiotics, antibiotics, or fecal transplants. Previously, we developed a core bacterial consortium with strong in vitro biofilm-forming and stress-resilient properties, but its colonization ability and in vivo function remained unclear. In this study, we first validated the in vivo biofilm formation of the microbial consortium using a germ-free (GF) mouse model, then introduced single-, dual-, and multi-strain combinations with varying biofilm-forming abilities into specific-pathogen-free mice to assess their potential for recovering antibiotic-disrupted gut microbiota. Our findings indicate that the robust, in vitro-selected consortium continued to form substantial biofilms in GF mouse intestines. 16 S rRNA sequencing showed that, compared to single- or dual-strain treatments, administering the core consortium significantly increased microbial richness and diversity. The gut microbiota of consortium-treated mice more closely resembled healthy controls, suggesting the core consortium has superior potential to restore healthy gut microbiota. Overall, our research demonstrates the core consortium markedly improves gut microbiota resilience to antibiotic-induced disruptions in mice, accelerates restoration of health-associated taxa, and reestablishes gut homeostasis. This approach could transform probiotic interventions from passive supplementation to active ecological engineering, providing a theoretical and experimental basis for next generation of engineered probiotics and microbiome restoration therapies.}, }
@article {pmid42243668, year = {2026}, author = {Yuan, J and Wang, J and Wang, H and He, Z and Chen, Z and Hu, Y and Zhou, X and Yan, S and Wei, L and He, M and Jiang, Y and Su, R and Yu, H and Wang, S and Tan, W and Ding, W and Feng, L and Wang, Z}, title = {Phenotypic, genomic, and functional characterization of Corynebacterium sp. nov. isolated by droplet-based cultivation from vaginal swabs of a preeclampsia patient.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05255-6}, pmid = {42243668}, issn = {1471-2180}, support = {82502046//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Members of the genus Corynebacterium are widely distributed across human mucosal surfaces and are increasingly recognized as important components of the female reproductive tract microbiota. However, their diversity is underestimated due to limitations of conventional cultivation approaches.<br><br>RESULTS: In this study, a novel bacterial strain, designated TJG_1[T], was isolated from vaginal swab samples of a pregnant woman with preeclampsia (PE) using droplet-based microfluidic single-cell cultivation. Strain TJG_1[T] was characterized as a Gram-positive, non-spore-forming, non-motile short rod. Phylogenetic analysis based on the 16&#xa0;S rRNA gene sequence placed the strain within the genus Corynebacterium, with the highest sequence similarity to Corynebacterium coyleae (97.39%). Whole-genome sequencing revealed a genome size of 2,481,283&#xa0;bp with a G&#x2009;+&#x2009;C content of 61.52&#xa0;mol%. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain TJG_1[T] and its closest relatives were below the accepted species thresholds, supporting its classification as a novel species. Functional genome annotation identified genes associated with metabolism, transport systems, putative antimicrobial resistance, and predicted host interaction-related traits. In vitro assays showed that neither bacterial metabolites nor live cells significantly affected trophoblast cell viability or oxidative stress-related gene expression under the tested conditions. Although alterations in cell migration behavior were observed following exposure to live bacteria, these changes were not accompanied by significant differences in migration-related gene expression.<br><br>CONCLUSIONS: Strain TJG_1[T] represents a novel species within the genus Corynebacterium. This study highlights the utility of droplet-based cultivation for recovering previously underrepresented vaginal bacteria and expands current knowledge of Corynebacterium diversity in the female reproductive tract.}, }
@article {pmid42243682, year = {2026}, author = {Chen, Y and Kuang, M and Li, Q and Chen, Z and Zhou, H}, title = {Lower respiratory microbiota as modulators of tumor immunity in lung adenocarcinoma.}, journal = {BMC immunology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12865-026-00852-6}, pmid = {42243682}, issn = {1471-2172}, abstract = {BACKGROUND: Lung adenocarcinoma is common type of cancer with high morbidity and mortality. Emerging evidence suggests that microbial colonization in the lower respiratory airways may modulate immune activation and response to immunotherapy. However, the immunologic relevance of microbiome diversity in lung cancer remains unclear.<br><br>METHODS: We analyzed bronchoalveolar lavage fluid (BALF), serum cytokines, immune cell subsets, and checkpoint molecule expression from 350 patients with lung adenocarcinoma. Microbiome diversity was quantified by phylum- and genus-level richness derived from binary detection of specific bacterial groups. Associations between microbial diversity, immune parameters, and clinical prognosis were evaluated using correlation and comparative statistical analyses.<br><br>RESULTS: Among 350 samples, there was no major compositional difference between patients who died and those who recovered. Microbial diversity showed no significant associations with systemic cytokines, including IL-6, IL-1&#x3b2;, TNF-&#x3b1;, IL-10, and IFN-&#x3b3;. Genus richness showed positive correlation with PD-1 expression, while phylum richness correlated inversely with PD-L1. Specific taxa demonstrated distinct immune associations: TM7 correlated with increased regulatory T cells, Actinobacteria and Veillonella correlated with lower IL-1&#x3b2;, while Neisseria correlated with CTLA-4 expression.<br><br>CONCLUSION: Lower airway microbiota in lung adenocarcinoma display moderate diversity and meaningful immunologic associations, particularly with PD-1/PD-L1 pathways, Tregs, and IL-1&#x3b2; regulation. Although diversity alone is not prognostic, specific microbial taxa may shape immune landscapes relevant to immunotherapy response and represent potential targets for future microbiome-based interventions.<br><br>CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid41974789, year = {2026}, author = {Jia, Z and Zhu, LF and Wang, L and Zhang, J and Liu, S and Tian, F and Yi, Y and Wang, J and Tang, J and Gong, J}, title = {Phosphorus application, nutrient absorption, and endophytic root bacterial communities in maize grown in phosphorus-deficient rocky arid soils, China.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41974789}, issn = {2045-2322}, support = {Qiankehechengguo[2022] zhongdian 010//Major Scientific and Technological Special Project of Guizhou Province/ ; Qianjiaoji [2023] No.004//Science and Technology Research Project of Guizhou Provincial Department of Education/ ; QKHZC[2021]YB459//Science and Technology Support Project of Guizhou Province/ ; }, abstract = {Phosphorus deficiency is one of the major constraints for crop growth in Karst rocky desertification regions. Different phosphorus treatments have become important strategies for enhancing agricultural productivity; however, the effects of phosphorus fertilization on nutrient allocation and root endophytic microbiome at different growth stages under field conditions remain inadequately explored. Therefore, this study implemented four phosphorus application treatments in a field-based maize cultivation system: P0 (0 kg ha[-1]), P1 (75 kg ha[-1]), P2 (150 kg ha[-1]), and P3 (225 kg ha[-1]). Nutrient distribution and root endophytic microbial community dynamics were analyzed at the jointing and milk-ripening stages. The results demonstrated that: (1) With increasing phosphorus application, the total nitrogen (TN) and total phosphorus (TP) in roots and leaves at the jointing, silking, and milk-ripening stages exhibited a pattern of “low phosphorus treatment enhancing TP content, while high phosphorus treatment suppressing TP uptake.” Total potassium (TK) content showed a decreasing trend, with the highest nutrient uptake observed at the phosphorus application rate of 150 kg ha[-1]. (2) Analysis of the root bacterial community revealed a decline in bacterial diversity with increasing phosphorus levels, but the abundance of Proteobacteria and Actinobacteria were significantly enhanced. (3) Correlation analysis indicated that low phosphorus treatment (P0) induced microbial community restructuring, high phosphorus treatment (P3) promoted the proliferation of functional taxa such as Pseudomonadaceae, while medium phosphorus treatment (P2) showed the most significant correlation between microbial community structure and phosphorus availability. This study provides valuable scientific insights for optimizing phosphorus fertilization in maize production in karst regions.}, }
@article {pmid42236792, year = {2026}, author = {Wortmann, E and Groll, T and Strigli, A and Peuker, K and Volet, C and Arps, L and Bernier-Latmani, R and Zeissig, S and Steiger, K and Middelhoff, M and Clavel, T}, title = {Modulation of intestinal bile acids influences colonic mucosal responses.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42236792}, issn = {2045-2322}, abstract = {BACKGROUND: Elevated levels of secondary bile acids produced by the gut microbiome, in particular deoxycholic acid (DCA), influence epithelial cell proliferation and accelerate the development of colorectal cancer (CRC) under adverse dietary conditions, such as long-term, high fat intake. However, their effects on the intestinal epithelium have not been studied in detail.<br><br>AIM: To determine gut epithelial responses to bile acid modulation in vivo and in situ.<br><br>METHODS: We performed targeted colonization of gnotobiotic mice followed by single-cell RNA sequencing (scRNA-Seq) of colonic epithelial cells combined with immunostaining of human biopsies from: (i) an observational patient cohort with hyperproliferative polyps or cancer; (ii) an interventional study with bile acid-scavenging drugs.<br><br>RESULTS: Colonization of mice with a defined bacterial community including the 7&#x3b1;-dehydroxylating species Extibacter muris resulted in DCA production. ScRNA-Seq of colonic epithelial cells revealed increased cell density of bile acid-sensitive enterocytes but fewer stem cells, goblet cells, and transit amplifying cells in mice exposed to DCA. This was associated with increased expression of pyruvate dehydrogenase kinase (Pdk4) and decreased expression of mucin (Muc2). PDK expression was also increased in human hyperplastic polyps and adenomas, whilst MUC2 expression was reduced in adenomas and carcinomas compared to normal mucosa. In addition, treatment of ileostomy patients with chologenic diarrhea using bile acid sequestrants was associated with enhanced epithelial proliferation in colorectal biopsies.<br><br>CONCLUSION: This study provides insight into intestinal epithelial cell responses to bile acids and their potential clinical relevance.}, }
@article {pmid42236864, year = {2026}, author = {Attri, K and Sharda, D and Tanwar, I and Gautam, P and Choudhury, D}, title = {Curcumin-stabilized silver nanoparticles target the Helicobacter pylori-tumor interface in gastric cancer.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-54162-3}, pmid = {42236864}, issn = {2045-2322}, abstract = {Gastric cancer remains a major global health burden, ranking among the leading causes of cancer-related mortality worldwide. Chronic infection with Helicobacter pylori is a well-established etiological factor, promoting sustained gastric inflammation, epithelial transformation, and tumor progression through modulation of the gastric microenvironment. Therapeutic strategies that simultaneously target microbial virulence and tumor cell survival remain limited. In this study, we developed curcumin-stabilized silver nanoparticles (AgNPs) as a dual-functional nanoformulation designed to modulate the tumor-associated microbiome while exerting direct anti-cancer effects. The nanoparticles were chemically synthesized with a controlled diameter of 15 ± 2 nm, enabling enhanced surface reactivity and biological interaction. Antimicrobial evaluation revealed potent activity against H. pylori, with an IC50 of 3.86 µg/mL. Furthermore, AgNPs significantly inhibited urease activity-a critical virulence determinant for gastric colonization-achieving 80.46 ± 1.15% inhibition at 160 µg/mL. Broad-spectrum antibacterial efficacy was also observed against other tested strains, indicating potential for reshaping the tumor microbiome. Cytotoxicity assessment in AGS human gastric adenocarcinoma cells demonstrated substantial anti-proliferative activity, with 73.99 ± 2.13% reduction in cell viability. The integration of curcumin, a bioactive polyphenol with established anti-inflammatory and anti-neoplastic properties, with silver nanoparticles provides a synergistic platform targeting both microbial and tumor components of gastric carcinogenesis. Collectively, these findings highlight AgNPs as a promising microbiome-directed nanotherapeutic strategy for gastric cancer management, warranting further mechanistic and translational investigation.}, }
@article {pmid42236946, year = {2026}, author = {Song, D and Duncan-Lowey, B and Khetrapal, V and Hamchand, R and Deng, T and Brown, H and Wu, A and Martin, AL and Bauer, KM and Zhao, Y and Nguyen, MT and Sonnert, ND and Leopold, SR and Wu, Q and Crawford, JM and Palm, NW}, title = {Commensal-derived acetylcholine enhances mucosal immune education.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {42236946}, issn = {1476-4687}, abstract = {The microbiota produces thousands of potentially bioactive small molecules[1-3]. High-throughput bioactivity screens of in vitro commensal cultures have exposed microbiota metabolites that shape host physiology by activating diverse G-protein-coupled receptors (GPCRs)[4-7]. However, owing to technical limitations, the GPCRome-wide bioactivities of in vivo metabolomes, which result from complex diet-microorganism-host interactions, remain unclear. Here we used a multiplexed GPCR screening technology to assess GPCRome-wide bioactivities of 100 commensal strains grown in vivo in monoassociated germ-free mice or in vitro in bacterial culture medium. In vivo and in vitro commensal metabolomes exhibited distinct GPCR activation patterns due to (1) host-mediated metabolite degradation; (2) in vivo microbial metabolic reprogramming; and (3) biotransformation of dietary substrates. Notably, we found that multiple commensal strains produced acetylcholine (ACh) in vivo through the conversion of dietary choline, including select Bifidobacterium strains that dominate the microbiome in early life and a probiotic Pediococcus strain. Mechanistically, we identified and characterized the bacterial enzymes that mediate this biotransformation in Bifidobacterium breve and Pediococcus pentosaceus, and generated an isogenic mutant B. breve strain lacking ACh production. Mice colonized with ACh-producing B. breve exhibited enhanced intestinal immunoglobulin A (IgA) production, altered microbiota composition and increased resistance to enteric infection. These findings underscore the profound impacts of the in vivo environment on microbiota metabolism and reveal a diet-microbiome-host axis that strengthens mucosal immune defences and reinforces host-microbiota mutualism.}, }
@article {pmid42236978, year = {2026}, author = {Le Bras, A}, title = {Microbiome clues to extreme longevity.}, journal = {Lab animal}, volume = {55}, number = {6}, pages = {197}, doi = {10.1038/s41684-026-01759-w}, pmid = {42236978}, issn = {1548-4475}, }
@article {pmid42237056, year = {2026}, author = {Xing, Y and He, W and Chen, W and Gao, C and Zhang, M and Wu, Y and Qu, C and Dai, K and Huang, Q and Cai, P}, title = {Cadmium Stress Favours Biofilm Cooperation and Polysaccharide-Enriched Matrix Remodelling in Bacterial Consortia.}, journal = {Environmental microbiology}, volume = {28}, number = {6}, pages = {e70347}, doi = {10.1111/1462-2920.70347}, pmid = {42237056}, issn = {1462-2920}, support = {42225706//National Natural Science Foundation of China/ ; 42407174//National Natural Science Foundation of China/ ; 460324005//Natural Science Foundation of Hubei Province of China/ ; BX20230139//China National Postdoctoral Program for Innovative Talents/ ; 202405AF140079//Science and Technology Talents and Platform Program (Workstation for Academicians and Experts)/ ; 2023AFA009//Innovative Research Group Project of Hubei Provincial Natural Science Foundation/ ; }, abstract = {Environmental stressors trigger complex adaptations in microbial communities, yet the associations between social network dynamics and metabolic strategies remain poorly understood, limiting our ability to design robust synthetic microbiomes. Here, we show that Cd stress was associated with structural simplification of soil bacterial co-occurrence networks, characterized by a 48.5% reduction in connectivity. In vitro assays further revealed a 93% increase in cooperative interactions within biofilms under Cd exposure. This shift in biofilm-associated cooperation coincided with altered physiological patterns, including a 45.9% increase in EPS synthesis and a 13.7% decrease in community CO2 emissions. Crucially, our analysis suggests that the intensity of cooperative interactions was associated with specific extracellular matrix allocation patterns. High-intensity cooperation was linked to a higher proportion of polysaccharide-rich matrices, which improved the stability and efficiency of Cd sequestration in vitro. Leveraging these interaction-informed patterns, we assembled a synthetic core consortium that modulated the rhizosphere microbiome in a proof-of-concept hydroponic system and reduced Cd accumulation in rice leaves by 52.9%. These findings support a conceptual framework in which biofilms may act as sites of social integration and altered extracellular matrix production, offering an interaction-informed basis for assembling stress-resilient microbiomes.}, }
@article {pmid42237178, year = {2026}, author = {Zhang, Q and Khan, I and Lei, E and Chen, H and Tang, X and Ding, L and Hong, M}, title = {The gut-brain-gonad axis mediates salinity adaptation in an invasive turtle: causal evidence from microbiota transplantation and metabolite supplementation.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00583-4}, pmid = {42237178}, issn = {2524-4671}, abstract = {BACKGROUND: Preliminary studies have shown that salinity stress can impair the differentiation of spermatogonial stem cells (SSC) in red-eared slider (Trachemys scripta elegans) through the gut-brain-gonad axis, thereby affecting their reproductive ability. However, a direct causal link between salinity-induced gut microbiota alterations and reproductive suppression remains unclear. To test the hypothesis that gut microbiota and their metabolites mediate salinity adaptation by modulating the gut-brain-gonad axis, we conducted fecal microbiota transplantation (FMT) and metabolite supplementation experiments.<br><br>RESULTS: Results showed that the FMT group successfully recapitulated the donor's gut microbial profile and exhibited significant changes in intestinal metabolites. Both FMT and GABA supplementation mimicked the reproductive inhibitory phenotype observed under direct salinity stress: altered brain neurotransmitter levels (increased dopamine, decreased serotonin), downregulated expression of reproductive genes (e.g. GnRH1, FSH&#x3b2;), and impaired SSC self-renewal and differentiation in testes, as evidenced by reduced marker gene expression (e.g. PLZF, Stra8) and disrupted testicular histology.<br><br>CONCLUSION: Our findings demonstrate that salinity stress reshapes the gut microbiota and metabolome. This leads to increased inhibitory signaling, notably via GABA, along the gut-brain-gonad axis. Ultimately, this signaling cascade suppresses reproductive function. This study provides novel mechanistic insights into the environmental adaptation strategies of an invasive species and highlights the potential of targeting the microbiome-metabolite axis for developing innovative, environmentally friendly biocontrol approaches against this invasive species.}, }
@article {pmid42237220, year = {2026}, author = {Von, KY and Ab Majid, AH}, title = {16S rRNA gene amplicon data of midgut microbial diversity in German cockroach, Blattella germanica.}, journal = {BMC genomic data}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12863-026-01449-z}, pmid = {42237220}, issn = {2730-6844}, abstract = {OBJECTIVES: Blattella germanica, commonly known as German cockroach, is a globally prevalent household pest. The gut microbiota of B. germanica is influenced by multiple factors, yet their interactive effects remain poorly understood compared with other insect taxa. Midgut-specific microbial communities also remain understudied relative to whole gut or hindgut microbiota. In this study, 16S rRNA gene sequencing datasets were generated from midgut samples collected across varying life stages (adult and nymph), sexes (male and female), environmental origins (laboratory-reared and field-collected), and physiological states (fed and starved).<br><br>DATA DESCRIPTION: Genomic DNA was extracted using the HiYield Genomic DNA isolation kit and amplified targeting the V3-V4 hypervariable regions of the 16S rRNA gene using primer pair 338&#xa0;F/806R. Raw sequences reads were subsequently analyzed using QIIME2 pipeline following quality control and host decontamination. Taxonomic classification consistently identified the bacterial families Lactobacillaceae, Desulfovibrionaceae, Lachnospiraceae, Dysgonomonadaceae, Christensenellaceae, and Rikenellaceae across all treatment groups. Diversity indices (Shannon, Simpson, and Chao1) showed similar trends across samples, indicating stable patterns of microbial diversity and richness. These datasets support the exploration of specific midgut-associated taxa as potential targets for biological control strategies against B. germanica.}, }
@article {pmid42237362, year = {2026}, author = {Liu, S and Wang, S and Zhang, J and Tao, C and Ravanbakhsh, M and Xu, X and Wen, K and Xiang, D and Sheng, O and Shen, Z and Li, C and Li, R and Shen, Q and Kowalchuk, GA}, title = {Host-guided microbiome-metabolite interactions enable cross-kingdom SynComs for disease suppression.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02430-9}, pmid = {42237362}, issn = {2049-2618}, support = {KJYQ2025053//Fundamental Research Funds for the Central Universities/ ; KTTQ2025018//Fundamental Research Funds for the Central Universities/ ; 42477316//National Natural Science Foundation of China/ ; 2024YFD1401105//National key research and development program of China/ ; 322MS092//Hainan Provincial Natural Science Foundation of China/ ; NAUSY-CG-ZD-01//Achievement Transformation Fund project of Hainan Research Institute of Nanjing Agricultural University/ ; }, abstract = {BACKGROUND: The plant microbiome plays a crucial role in enhancing disease resistance, yet microbiome-based plant protection strategies remain limited by an incomplete understanding of how host selection, microbial interactions, and rhizosphere chemistry jointly shape pathogen suppression.<br><br>RESULTS: Here, we adopt a "learning from nature" approach to design synthetic microbial communities (SynComs) that recapitulate naturally evolved disease-suppressive interactions, using banana Fusarium wilt as a model system. High-throughput profiling revealed that both bacterial and fungal communities contribute to varietal resistance. Resistance-associated microbial taxa were identified and isolated to assemble bacterial, fungal, and cross-kingdom SynComs representative of resistant versus susceptible hosts. SynComs derived from resistant varieties suppressed pathogen growth more effectively than those from susceptible hosts, with cross-kingdom SynComs exhibiting the strongest effects. Cross-kingdom SynCom inoculation significantly reduced disease severity and restructured both the composition and functional potential of the rhizosphere microbiome. Integrative transcriptomic and metabolomic analyses revealed coordinated host metabolic reprogramming, characterized by increased accumulation of diverse metabolites, including alkaloids, amino acids, and flavonoids. Notably, supplementation with resistance-associated rhizosphere metabolites, such as stearic acid and shikimic acid, further enhanced disease suppression.<br><br>CONCLUSIONS: Together, our findings establish a mechanistic framework in which host-guided microbiome assembly and metabolite-mediated interactions jointly enable effective cross-kingdom SynComs for disease suppression, providing ecological principles for microbiome-based plant protection strategies. Video Abstract.}, }
@article {pmid42237386, year = {2026}, author = {Chen, X and Feng, P and Zhang, J and Wu, J and Xie, Z and Huang, J and Yang, X and He, F and Chen, R}, title = {Multi-omics biomarkers in endometrial receptivity: from mechanisms to clinical translation.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-08257-0}, pmid = {42237386}, issn = {1479-5876}, abstract = {BACKGROUND: Endometrial receptivity (ER) serves as a critical determinant for successful embryo implantation, yet its molecular complexity and limited clinical assessment methods pose significant challenges. Despite advancements in assisted reproductive technology (ART), recurrent implantation failure (RIF) linked to ER abnormalities persists, creating a need for precise, non-invasive diagnostics.<br><br>MAIN BODY: This review outlines ER research, from the biology of the window of implantation (WOI) to the roles of immune components and the microbiome in shaping the receptive microenvironment. Multi-omics integration reveals regulatory networks across transcriptomic, epigenomic, proteomic, and metabolomic levels, with uterine fluid biomarkers emerging as promising non-invasive candidates. The analysis further covers how chronic endometritis (CE), adenomyosis, and polycystic ovary syndrome (PCOS) impair ER: through mechanisms including inflammatory imbalance, microbial dysbiosis, abnormal extracellular matrix remodeling, and hormonal dysregulation. Commercial ER tests face limitations, including insufficient evidence and inconsistent results, which undermine their clinical reliability.<br><br>CONCLUSIONS: A significant translational gap remains between biomarker discovery and clinical application. Current challenges involve technical standardization and data integration, and poor model generalizability. Future progress requires combining multi-omics with artificial intelligence (AI) to establish standardized clinical pathways, advancing ER assessment into precision medicine, and improving global infertility management.}, }
@article {pmid42237409, year = {2026}, author = {Guo, D and Chen, Y and Wu, Y and Cheng, J and Lin, Y and Lai, W and Ma, W and Yang, H and Han, L and Ma, L and Jia, H and Liu, X}, title = {Multi-omics characterization of the skin microbiota reveals the anti-aging roles of Stenotrophomonas maltophilia.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02433-6}, pmid = {42237409}, issn = {2049-2618}, support = {WDZC20220819134430002//Shenzhen Science and Technology Program/ ; QD2021005N//Scientific Research Start-up Funds/ ; }, abstract = {BACKGROUND: Shifts in the skin microbiome have shown a close link to chronological age. However, the contribution of the skin microbiome in skin-aging phenotypes remains unclear.<br><br>RESULTS: To explore this, we performed phenotypic, metabolomic, metagenomic, and functional analyses on a cohort with divergent skin-aging phenotypes. Genome-scale metabolic models (GEMs) integrated with metabolomic analysis revealed that Stenotrophomonas maltophilia, enriched in the younger group (categorized by AI-predicted age and skin elasticity), utilizes the glutathione cycle to maintain redox homeostasis. Cellular experiments showed its metabolites enhanced GSH synthesis and alleviated oxidative-stress-induced phenotypic skin-aging by upregulating key genes in fibroblasts, including GCLM, PGD, SOD2, and NQO1. In addition, GEMs highlighted its potential in maintaining youthful skin phenotypes through the regulation of host metabolic pathways involving betaine, lysolecithin, and porphyrin. In parallel, Acinetobacter guillouiae was found to influence host melanin metabolism by degrading dopamine (DA) and 3-methoxytyramine (3-MT), offering potential therapeutic strategies for mitigating pigmentation.<br><br>CONCLUSIONS: Our findings highlight the dynamic interplay between skin microbiota and the host in phenotypic skin-aging, offering new insights for designing interventions to maintain youthful skin. Video Abstract.}, }
@article {pmid42237424, year = {2026}, author = {Yang, L and Chen, J}, title = {mPower: a real data-based power analysis tool for microbiome study design.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02427-4}, pmid = {42237424}, issn = {2049-2618}, support = {R01 GM144351/GM/NIGMS NIH HHS/United States ; }, abstract = {Power analysis is a critical step in designing a microbiome study. Existing power calculation tools for microbiome studies mainly rely on parametric models of the sequencing counts, which underestimate the complexity of microbiome data and could produce overly optimistic power estimates. In this work, we present a new simulation-based power analysis tool, mPower, for microbiome study design. The tool uses a real data-based semi-parametric simulation framework to generate realistic microbiome data, upon which the power assessment is performed. Coupled with a select differential analysis tool, our power tool supports different study designs, including cross-sectional, case-control, and matched-pair studies, with or without confounders. It allows power analysis for both community-level and taxon-level testing. By using microbiome reference datasets from different environments, the users could perform power calculation based on the environment of interest. The mPower is primarily designed for 16S amplicon sequencing data, and it also incorporates a parametric simulation framework that enables power analysis for shotgun metagenomic data. We showcase the application of mPower with several real-world examples. The web interface of mPower is available at https://microbiomestat.shinyapps.io/mPower/. Video Abstract.}, }
@article {pmid42237550, year = {2026}, author = {Boubaker, F and Sallem, O and Dridi, I and Chabbou, A}, title = {Clockwork symbiosis: The vital interplay of microbiota and human chronobiology.}, journal = {Chronobiology international}, volume = {}, number = {}, pages = {1-9}, doi = {10.1080/07420528.2026.2682478}, pmid = {42237550}, issn = {1525-6073}, abstract = {The human microbiota and host circadian system engage in a bidirectional dialogue with consequences for metabolism, immunity, and barrier physiology. This narrative review examines the microbiota-chronobiology interface across the gut and selected extra-intestinal niches and uses the term "clockwork symbiosis" as an organizing framework for this crosstalk. A structured, non-exhaustive search of PubMed, Scopus, Web of Science, Cochrane Library, and Embase was conducted for studies published between 2000 and 2024, with priority given to human evidence and mechanistic studies with clear translational relevance. The strongest evidence concerns the gut microbiota, for which both human and preclinical studies support diurnal variation in microbial composition, metabolite production, and host metabolic signaling. By contrast, evidence for vaginal, oral, skin, and respiratory microbiota remains comparatively limited and is best treated as emerging and largely hypothesis-generating. Across the literature, circadian disruption is associated with altered microbial rhythmicity and adverse metabolic or inflammatory phenotypes, but causality is often difficult to isolate from co-occurring changes in diet, sleep, stress, light exposure, medication use, and host disease state. Microbiota-derived metabolites, particularly short-chain fatty acids and bile-acid derivatives, provide plausible mechanistic links to peripheral clocks, although evidence for direct clinical manipulation remains preliminary. Overall, preserving host-microbiota temporal alignment appears biologically important, but clinical applications such as chrononutrition, timed biotics, and chronotherapy still require rigorous time-standardized human studies.}, }
@article {pmid42237575, year = {2026}, author = {Tilves, C and Xiao, S and Tanaka, T and Differding, MK and Spira, AP and Ferrucci, L and Mueller, NT}, title = {Longitudinal associations of the gut microbiome with arterial stiffness in US adults: findings from the Baltimore Longitudinal Study of Aging.}, journal = {American journal of epidemiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/aje/kwag119}, pmid = {42237575}, issn = {1476-6256}, abstract = {The gut microbiome affects arterial stiffness in experimental murine models; however, evidence in human longitudinal studies is lacking. In this study, we investigated longitudinal between-person (average) and within-person (change) associations of microbiome features with arterial stiffness. We assessed the fecal microbiome using whole genome metagenomic sequencing, and arterial stiffness using carotid-femoral pulse wave velocity (cfPWV). Our analytic sample consisted of 349 adults from the Baltimore Longitudinal Study of Aging, who contributed 915 visits between 2013-2019. Using linear mixed models, we found higher microbiome evenness and butyrate-producing bacteria were associated with lower cfPWV on average (between-person), but changes in diversity were not associated with changes in cfPWV (within-person). Several potentially pathogenic bacteria were positively associated with cfPWV, both between- and within-person. Butyrate-production pathways were inversely associated with cfPWV between-person and borderline within-person. Trimethylamine-production genes were positively associated with cfPWV between-person and borderline within-person. In addition, changes in other functional pathways including peptidoglycan biosynthesis and L-arginine biosynthesis were associated with changes in cfPWV. In conclusion, cfPWV was associated with both between-person and within-person differences in gut microbiome features, with strength and consistency depending on the feature. These results can inform which microbiome features to target in interventions to improve arterial stiffness.}, }
@article {pmid42237634, year = {2026}, author = {Wang, N and Liu, X and Yan, Z and He, H and Wang, P and Ali, A and Wang, Z and Dong, H and Guo, J and Zhang, Y}, title = {Beauveria bassiana B094 as a dual-action biocontrol agent: Combining direct pathogenicity and endophytic colonization against Spodoptera exigua in sweet corn.}, journal = {Insect science}, volume = {}, number = {}, pages = {}, doi = {10.1111/1744-7917.70306}, pmid = {42237634}, issn = {1744-7917}, support = {2024YFD1400300//National Key Research and Development Program of China/ ; CARS-02-26//China Agriculture Research System/ ; //The Science and Technology Innovation Project, the Chinese Academy of Agricultural Sciences/ ; }, abstract = {This study investigates the endophytic biocontrol potential of Beauveria bassiana strain B094 against Spodoptera exigua in sweet corn through laboratory, greenhouse and field assessments. Laboratory virulence screening identified B094 as pathogenic to S. exigua, inducing 99.8% mortality and exceeding 75% infection in 1st- and 3rd-instar larvae at 1 × 10[8] spores/mL. The LC50 for 3rd-instar larvae was 4.8 × 10[5] spores/mL. B094 established endophytic colonization in sweet corn varieties Zhetian 19 and Zaotiannuo 211 via seed inoculation. Colonization peaked at 7 d after emergence (DAE), with leaves exhibiting markedly higher frequency and density (91.1%, 1367 ± 95 CFU/g) than stems (40%, 353 ± 12 CFU/g) and roots (37.8%, 93 ± 9 CFU/g), then progressively declined to 24.3% in leaves and below 17.3% in stems and roots by 28 DAE. Feeding bioassay demonstrated that leaves from colonized plants at 14-21 DAE significantly increased larval mortality and disrupted development. Greenhouse and field trials confirmed efficacy, with inoculated plants exhibiting less foliar damage than controls and similar colonization patterns and biocontrol effects across varieties. Rhizosphere microbiome analysis revealed community shifts after B094 colonization. Bacterial genera often associated with plant growth promotion or biocontrol (e.g., Bacillus, Gemmatimonas), increased by 22.5% and 81.6%, whereas fungal genera commonly reported as plant pathogens (e.g., Gibberella and Fusarium), decreased by 87.7% and 78.1%, respectively. Our findings establish B. bassiana B094 as a dual-action biocontrol agent against S. exigua, combining direct pathogenicity with endophytic effects, supporting seed-treatment as an environmentally friendly strategy for sustainable pest management in sweet corn systems.}, }
@article {pmid42237711, year = {2026}, author = {Oriquat, G and Al-Hasnaawei, S and Mousa, HM and Malathi H,  and Singla, S and Sahoo, S and Arora, V and Chauhan, AS and Nourizadeh, M}, title = {Gut Microbiome-Sleep Crosstalk: Mechanistic Pathways, Dysbiosis Signatures, and Microbiome-Based Interventions.}, journal = {Brain and behavior}, volume = {16}, number = {6}, pages = {e71525}, doi = {10.1002/brb3.71525}, pmid = {42237711}, issn = {2162-3279}, abstract = {BACKGROUND: This review examines the bidirectional relationship between sleep regulation and the gut microbiome within the gut-brain axis, with particular attention to mechanistic pathways, disorder-associated dysbiosis patterns, and microbiome-targeted interventions in insomnia, obstructive sleep apnea, circadian disruption, and sleep loss-related states.<br><br>METHODS: We critically synthesized evidence from both human and preclinical studies, focusing on microbial metabolites, neuroimmune and neuroendocrine signaling, circadian regulation, and intervention-based approaches. Rather than only summarizing individual studies, we aimed to distinguish associative human findings from mechanistic evidence derived mainly from animal models.<br><br>RESULTS: Current evidence supports a bidirectional link between sleep and the gut microbiome. Microbiota-derived metabolites, particularly short-chain fatty acids, tryptophan-related metabolites, and gamma-aminobutyric acid, appear to influence sleep homeostasis through effects on intestinal barrier integrity, inflammatory tone, stress-axis regulation, and central signaling pathways. Across sleep disorders, recurrent microbial patterns include reduced abundance of potentially beneficial taxa such as Bifidobacterium and Faecalibacterium and enrichment of pro-inflammatory or stress-associated taxa, although these signatures are not yet fully consistent across cohorts or disorders. In humans, most data remain observational and support association rather than causation, whereas stronger mechanistic support comes from experimental models of sleep deprivation, intermittent hypoxia, and microbiota transfer. Early intervention studies suggest that selected probiotics, prebiotics, dietary modulation, and related microbiome-directed strategies may improve sleep-related outcomes, but the magnitude and reproducibility of these effects remain uncertain.<br><br>CONCLUSION: The gut microbiome represents a promising mechanistic and therapeutic target in sleep medicine, but clinical translation is still constrained by heterogeneity in microbiome profiling, sleep phenotyping, intervention design, and strain-specific effects. Future work should prioritize longitudinal human studies, standardized outcome measures, and mechanistically informed trials capable of identifying clinically actionable and biologically credible microbiome signatures.}, }
@article {pmid42237734, year = {2026}, author = {Kim, TH and Kim, SM and Kim, MH}, title = {Unveiling the Molecular Repertoire of Akkermansia muciniphila: From Mechanistic Insights to Precision Biotherapeutics.}, journal = {Journal of microbiology and biotechnology}, volume = {36}, number = {}, pages = {e2604017}, doi = {10.4014/jmb.2604.04017}, pmid = {42237734}, issn = {1738-8872}, abstract = {The gut microbiota has been established as a cornerstone of host physiological homeostasis. Among its diverse members, Akkermansia muciniphila has gained significant prominence as a premier next-generation probiotic candidate, demonstrating broad efficacy in alleviating metabolic disorders, inflammatory bowel disease, and neurodegenerative conditions. While early research primarily focused on clinical correlations and population abundance, recent scientific paradigms have shifted toward elucidating the underlying molecular mechanisms and specific host-microbe interactions. This review provides a comprehensive synthesis of recent breakthroughs in identifying A. muciniphila-derived bioactive effectors, including structural components, secreted enzymes, and signaling peptides. We examine how these molecular postbiotics orchestrate host health by reinforcing intestinal barrier integrity, modulating systemic immune responses, and reprogramming the tumor microenvironment. By integrating these multifaceted modes of action into a unified framework, we evaluate the therapeutic potential of both live bacteria and cell-free derivatives. Furthermore, we address the critical challenges regarding strain-specific efficacy and ecological impacts, providing a strategic roadmap for the clinical translation of A. muciniphila into the next frontier of precision microbiome medicine.}, }
@article {pmid42237904, year = {2026}, author = {Lei, H and Du, S and Li, C and Yung, L and Wang, P and Leung, LY and Graham, CA and Yen, HL and Li, Y and Lucaci, AG and Mason, CE and Lee, PKH}, title = {Sustained Chlorination of Hospital Surfaces Restructures the Microbiome and Virome and Diversifies Resistance Genes.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c01505}, pmid = {42237904}, issn = {1520-5851}, abstract = {Routine disinfection can reduce microbial burden on hospital surfaces in the short term, but its long-term impacts on surface microbiomes and antimicrobial resistance dynamics remain unclear. We conducted a year-long metagenomic study of 197 in situ hospital surface samples subjected to sustained chlorination to investigate changes in microbiomes, resistomes, and phage-host interactions. Microbial α-diversity increased during the early months, with a decline in dominant Enterobacteriaceae and enrichment of taxa including Propionibacteriaceae and Micrococcaceae, indicating niche replacement. Over time, both diversity and previously suppressed taxa approached baseline levels, suggesting adaptation to sustained disinfection, with evidence of functional shifts. Viral communities exhibited similar temporal dynamics, with composition and relative abundance distinctly shifting. Concurrently, the resistome underwent substantial, largely irreversible restructuring, with decreased total relative abundance and increased diversity of antibiotic resistance genes (ARGs). Chlorination also reduced ARG mobility and pathogenic potential, indicated by weakened co-occurrence with mobile genetic elements and virulence factor genes and lower predicted resistome risks. Phage and host relative abundances remained strongly correlated, although a shift toward lytic viral lifestyles occurred, potentially limiting phage-mediated ARG dissemination. These findings highlight disinfection as both a microbial control measure and ecological pressure, underscoring the need for ecologically informed strategies to manage clinical antimicrobial resistance.}, }
@article {pmid42237944, year = {2026}, author = {}, title = {Correction to: Quantitative genetics of microbiome-mediated traits.}, journal = {Evolution; international journal of organic evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/evolut/qpag092}, pmid = {42237944}, issn = {1558-5646}, }
@article {pmid42237982, year = {2026}, author = {Utreja, S and Andreani, GA and Mahmood, S and Patel, MS and Buck, MJ and Rideout, TC}, title = {Dietary pulse prebiotic fibre intake in a rat obese pregnancy model alters maternal caecal microbiome and protects against steatosis in newly weaned offspring.}, journal = {Journal of nutritional science}, volume = {15}, number = {}, pages = {e37}, pmid = {42237982}, issn = {2048-6790}, abstract = {We assessed if supplementation of an obese-inducing diet with yellow pea fibre throughout pre-pregnancy (PP), gestation, and lactation could influence maternal gut microbiome composition and improve metabolic health and liver steatosis in newly weaned rat male and female offspring. Forty female Sprague-Dawley rats were fed a low (CON) or high (HC) calorie diet for a 6-week PP period. At the end of PP, HC animals were randomly assigned to either remain on the HC diet or the HC diet with yellow pea fibre (HC + FBR) for an additional 4-weeks prior to mating and throughout gestation and lactation. At the end of lactation, caecal microbiome profile was evaluated in mothers with shotgun metagenomic sequencing, and newly weaned male and female pups were assessed for serum biochemistry and hepatic fat outcomes. Maternal obesity reduced the beta-diversity of the maternal microbiome and lowered total caecal short-chain fatty acid (SCFA) concentration. HC + FBR consumption increased caecal SCFA concentration and differentially altered the maternal caecal microbiome profile of several species that have been linked with hepatic steatosis including Bifidobacterium pseudolongum, Porphyromonas gingivalis, and several Provetella species. Newly weaned offspring from HC mothers exhibited hepatic steatosis; however, male and female pups from HC + FBR mothers demonstrated normalised liver lipid concentrations (cholesterol and triglyceride) and an increase in caecal acetate and propionate concentrations. Findings suggest that maternal obesity enhances the risk of liver steatosis in offspring and that maternal dietary fibre supplementation may have a protective influence that is partly mediated through changes in the caecal microbiome profile and activity.}, }
@article {pmid42238109, year = {2025}, author = {Sirko, J and Bor, B and He, X}, title = {Microbial dark matter and the future of dentistry.}, journal = {JADA foundational science}, volume = {4}, number = {}, pages = {100043}, pmid = {42238109}, issn = {2772-414X}, }
@article {pmid42238119, year = {2025}, author = {Mark Welch, JL and Borisy, GG}, title = {Dental plaque: Who is in the neighborhood and why it matters.}, journal = {JADA foundational science}, volume = {4}, number = {}, pages = {100051}, pmid = {42238119}, issn = {2772-414X}, }
@article {pmid42238322, year = {2026}, author = {Hao, Y and Chu, D and Li, H and Zheng, L and Liu, Y and Xi, Q and Liu, S}, title = {Functionalized polysaccharides for infection-resistant and regenerative therapies in gynecology.}, journal = {International journal of pharmaceutics: X}, volume = {11}, number = {}, pages = {100568}, pmid = {42238322}, issn = {2590-1567}, abstract = {Gynecological infections and implant-related complications, such as bacterial vaginosis (BV), pelvic inflammatory disease (PID), and endometritis, are exacerbated by biofilm-forming pathogens such as G. vaginalis, E. coli, and S. aureus, posing significant clinical challenges worldwide. These biofilms, resistant to antibiotics, contribute to chronic infections and device failures in gynecological implants. Rising antibiotic resistance underscores the need for innovative biomaterials. Chitosan, hyaluronic acid (HA) and alginate are three representative natural polysaccharides, showing broad application potential in antibacterial materials and tissue engineering due to their excellent biocompatibility, biodegradability and modifiable structures. In their natural forms, they exhibit a certain degree of anti-biofilm activity by inhibiting bacterial adhesion and disrupting bacterial membranes. Functional modification significantly enhances their antibacterial performance such as AMPs grafting, cross-linking, quaternization, and nanocomposites. This review explores the antibacterial mechanisms of natural polysaccharides in the vaginal microbiome and endometrial tissue, highlighting advances in functionalization with antimicrobial peptides, nanoparticles, and chemical modifications to enhance antibacterial efficacy. The toxicological effects of natural polysaccharide materials on gynecological tissues generally show the characteristics of mainly protective and restorative effects, rather than causing damage. Natural polysaccharides and their applications offer promising potential for infection-resistant, regenerative therapies in gynecology, promising safer and more effective interventions.}, }
@article {pmid42238443, year = {2026}, author = {Bode, MR and Lydecker, AD and Robinson, GL and Roghmann, MC and Kalan, LR}, title = {Long-Term Daily Chlorhexidine Foot Cleansing Reduces Staphylococcal Burden on the Feet of People with Prior Diabetic Foot Complications.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.14.26352248}, pmid = {42238443}, abstract = {BACKGROUND: Individuals with diabetes remain at high risk for diabetic foot ulcers (DFUs) even after ulcer healing. Dysbiosis of the skin microbiome has been associated with ulcer formation. Topical chlorhexidine gluconate (CHG) is a broad-spectrum antiseptic commonly used to reduce microbial burden. In a prior randomized clinical trial comparing daily CHG foot treatment with soap-and-water treatment, no statistically significant reduction in new DFUs was observed, prompting evaluation of whether CHG produced durable changes in the skin microbiota.<br><br>OBJECTIVE: To compare changes in foot skin microbiota (including bacterial bioburden, diversity, and community composition) associated with daily CHG versus soap-and-water use over one year in people with diabetes and prior foot complications.<br><br>METHODS: In a single-center, double-blind, placebo-controlled randomized trial, 87 participants were randomized to daily CHG wipes or soap-and-water wipes for 12 months. Foot swabs were collected at baseline, 3 and 12 months, and 4 weeks post-treatment. Bacterial bioburden was quantified. Microbiota composition was assessed using 16S rRNA and ITS amplicon sequencing.<br><br>KEY RESULTS: CHG treatment significantly reduced bacterial bioburden, increased microbial diversity, and altered community composition, including sustained reductions in Staphylococcus abundance. Several microbiota changes persisted more than 4 weeks after treatment cessation. Soap&#x2370;and&#x2370;water treatment showed similar but smaller and largely nonsignificant trends.<br><br>CONCLUSIONS: Daily CHG use durably modifies foot skin microbiota in high-risk individuals with diabetes. However, this alone may be insufficient to prevent new foot complications, highlighting the need for additional interventions. These findings have implications for long-term CHG use in populations at risk for staphylococcal infections.<br><br>KEY POINTS: Long-term daily chlorhexidine foot cleansing in adults with diabetes reduces Staphylococcus abundance and overall bacterial burden more effectively than soap-and-water, with microbiota effects persisting for up to one month after treatment cessation, demonstrating durable pathogen suppression.}, }
@article {pmid42238447, year = {2026}, author = {Chen, J and Li, A and Wu, W and Xu, W and Zhao, T and Starkweather, AR and Rodriguez, L and Chen, MH and Cong, XS}, title = {Gut microbiota signatures differentiate trajectory-defined response phenotypes and predict self-management outcomes in irritable bowel syndrome.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.18.26353470}, pmid = {42238447}, abstract = {BACKGROUND: Heterogeneity in symptom presentation and treatment response in irritable bowel syndrome (IBS) remains poorly understood. The gut microbiota may contribute to this variability, but its role in shaping symptom trajectories and responses to self-management interventions is unclear.<br><br>OBJECTIVE: To identify symptom trajectory phenotypes and determine whether gut microbiota composition and function distinguish these phenotypes and predict multidimensional responses to pain self-management interventions in young adults with IBS.<br><br>DESIGN: Ancillary data analysis from a randomized control trial (NCT03332537).<br><br>METHODS: Participants with longitudinal data (n = 62) were analyzed using longitudinal k-means clustering (KML) based on trajectories of measures in IBS quality of life (QOL), Brief Pain Inventory (BPI), and psychoneurological outcomes (anxiety, applied cognition, depression, fatigue, global health, positive affect, and sleep disturbance) over 12 weeks. Baseline differences between clusters were assessed with Wilcoxon rank-sum tests, and longitudinal changes were evaluated with linear mixed models. Gut microbiota composition and predicted functional pathways were compared between phenotypes. Bayesian Additive Regression Trees (BART) models were used to identify baseline microbial taxa and pathways predictive of longitudinal changes in QOL, BPI pain interference, and severity.<br><br>RESULTS: Two distinct trajectory-defined response phenotypes were identified: a Constrained Response Phenotype (Phenotype A, n = 35) and an Adaptive Multidomain Response Phenotype (Phenotype B, n = 27). At baseline, Phenotype B showed lower pain severity and interference, but higher levels of anxiety, depression, and fatigue compared to Phenotype A. Over 12 weeks, both phenotypes showed improvements in pain outcomes (all p < 0.05), but only Phenotype B demonstrated broad improvements across psychoneurological domains and QOL (all p < 0.05). Phenotype A exhibited more limited improvements and worsening in several psychoneurological domains. Gut microbiota functional pathways differed between phenotypes, including pathways related to xenobiotic degradation, amino acid metabolism, bile secretion, and immune-related processes (all raw p < 0.05), although these did not remain significant after multiple testing correction. Machine learning models identified distinct, phenotype-specific microbial predictors of intervention response. In Phenotype A, genera such as Alistipes and Sutterella were consistently identified across models, whereas in Phenotype B, predictors included Phascolarctobacterium , Collinsella , and Parabacteroides . Functional pathways also differed between phenotypes, suggesting distinct microbiome-linked mechanisms underlying symptom trajectories and responses to pain interventions.<br><br>CONCLUSIONS: Young adults with IBS exhibit distinct multidimensional response phenotypes that are associated with differential clinical and microbiome profiles. Baseline gut microbiota composition and functional capacity demonstrate phenotype-specific predictive signatures of treatment response, supporting a microbiome-informed framework for stratifying patients and advancing personalized self-management strategies in IBS.<br><br>WHAT IS KNOWN: &#x25a1; Substantial heterogeneity exists in irritable bowel syndrome symptoms and treatment response, with variability across pain, psychological distress, and quality of life domains.&#x25a1; Gut microbiota composition and function are linked to IBS pathophysiology, including associations with pain sensitivity, inflammation, and brain-gut signaling.&#x25a1; Self-management interventions (e.g., mindfulness, behavioral strategies) can improve IBS symptoms, but responses are inconsistent and difficult to predict.<br><br>WHAT IS NEW HERE: &#x25a1; Distinct longitudinal symptom trajectory phenotypes were identified, separating individuals with pain-predominant and limited psychoneurological improvement from those with lower pain and greater multidomain psychoneurological improvement.&#x25a1; Gut microbiota composition and functional profiles varied between trajectory-defined clusters, indicating a biological foundation for differences in symptom patterns.&#x25a1; Machine learning models showed that gut microbiota features predict pain severity, interference, quality of life, and their longitudinal changes, supporting microbiome-based stratification for self-management outcomes.}, }
@article {pmid42238882, year = {2026}, author = {Skow, C and Ott, LC and Wannemuehler, MJ and Mellata, M}, title = {A defined microbiota mouse model for Salmonella Paratyphi A oral infection.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1824783}, pmid = {42238882}, issn = {1664-302X}, abstract = {INTRODUCTION: Salmonella Paratyphi A (SPtA) is an emerging pathogen that primarily infects humans and causes enteric fever, yet it has not received sufficient research attention. To facilitate further investigation, an appropriate animal model is necessary for testing SPtA infection.<br><br>METHODS: In this study, we utilized gnotobiotic mice harboring the altered Schaedler flora (ASF) from either C3H/HeN or 129S6/SvEv genetic backgrounds. These mice, subjected to various inflammatory conditions, were orally challenged with SPtA. The colonization and persistence of the pathogen were assessed in both intestinal and extraintestinal tissues, while also examining changes in gut microbiota, the expression of tight junction proteins, cytokines, and histopathological changes.<br><br>RESULTS: Our findings revealed that both the inflammatory state and the sex of the ASF mice significantly affected the colonization of SPtA. Notably, infection of the 129S6/SvEv IL10[-/-] mice with SPtA replicated key features observed in humans. This included the extraintestinal dissemination of SPtA, the inhibition of pro-inflammatory cytokines, and progressively worsening pathological changes over time following infection in IL10[-/-] ASF mice.<br><br>CONCLUSION: The results of this study suggest that ASF mice represent a suitable low-cost model for investigating the pathogenesis of SPtA infection. The presence of ASF creates an open niche for SPtA colonization, allowing for the retention of a defined microbiome. This enables researchers to study perturbations in the microbiome without the limitations inherent to an antibiotic-treated model alternative. Furthermore, the chronic inflammatory conditions associated with IL10[-/-] phenotype enable SPtA extraintestinal invasion and disease progress in the murine host, facilitating a functional model of SPtA pathogenesis.}, }
@article {pmid42238894, year = {2026}, author = {Gilardini, F and Sabatucci, A and Cifani, C and Segura-Garcia, C and Pucci, M and Rania, M and D'Addario, C}, title = {Dysregulation of neurodevelopmental regulatory networks in Anorexia Nervosa: an integrated multi-layered omics analysis.}, journal = {Frontiers in cell and developmental biology}, volume = {14}, number = {}, pages = {1761785}, pmid = {42238894}, issn = {2296-634X}, abstract = {Anorexia nervosa (AN) is a severe metabo-psychiatric disorder with the highest mortality rate among psychiatric conditions. Its characteristic onset during adolescence suggests that disrupted neurodevelopmental processes during critical periods may contribute to disease pathophysiology. In this exploratory study, we conducted an integrated multi-layered omics analysis to identify molecular alterations affecting neurodevelopmental pathways in individuals with AN. We employed three complementary approaches: DNA methylation sequencing via Reduced Representation Bisulfite Sequencing (RRBS), microRNA (miRNA) expression profiling using panel-based qPCR, and microbiome characterization through 16S rRNA sequencing in a sample of 38 patients with AN and 40 healthy controls. Analyses focused on molecular mechanisms involved in neurodevelopmental processes. RRBS analysis identified methylation differences in neurodevelopmentally relevant genes, particularly CACNA1C (voltage-gated calcium channel) and ZNHIT2 (transcription factor). miRNA profiling revealed extensive dysregulation, with 74 miRNAs showing altered levels in the AN pools. Network analysis highlighted that miR-135 family targets KCNN3 (SK3 channel involved in neuronal excitability), while miR-374b regulates IGFBP3 (IGF-1 signaling modulator). Microbiome analysis revealed that 42% of the AN group exhibited dramatic oral dysbiosis characterized by Proteobacteria dominance. Our findings demonstrate coordinated multi-level dysregulation of mechanisms governing neural circuit maturation during adolescence, supporting a neurodevelopmental framework for understanding AN. The convergence of molecular alterations on ion channels and growth factor signaling suggests systems-level perturbations in developmental regulatory mechanisms. The identified miRNAs represent potential biomarkers and therapeutic targets, while microbiome heterogeneity suggests distinct clinical subgroups. While exploratory in nature, this work provides novel insights into AN molecular architecture and generates testable hypotheses for future mechanistic studies incorporating individual-level data essential to validate these candidates and establish robust clinical correlations.}, }
@article {pmid42238975, year = {2023}, author = {Ayyadurai, VAS and Deonikar, P and Stashenko, P}, title = {Molecular systems architecture of host-microbiome interactions in periodontitis.}, journal = {JADA foundational science}, volume = {2}, number = {}, pages = {100026}, pmid = {42238975}, issn = {2772-414X}, abstract = {OBJECTIVES: To develop a systems-level understanding of host-microbial interactions that lead to the pathogenesis of periodontitis. Such an understanding may identify therapeutic targets for developing efficacious treatments for periodontitis.<br><br>SEARCH STRATEGY: Three databases are searched for relevant peer-reviewed articles published from January 1980 through April&#xa0;2022.<br><br>CITATION SOURCES: The citation sources include PubMed, MEDLINE, and Google Scholar.<br><br>STUDY SELECTION CRITERIA: The systems biology tool CytoSolve (CytoSolve) was used to perform the systematic review and to support the curation and development of the molecular systems architecture of periodontitis pathogenesis. Full-length articles that contained Medical Subject Headings key words relevant to periodontitis pathogenesis were selected for a comprehensive review.<br><br>DATA ELEMENTS INCLUDED: The molecular interactions across the 8 cell types-gingival epithelial, fibroblast, periodontal ligament, endothelial, keratinocyte, microbial, bone, and immune-of the periodontal microenvironment that leads to the pathogenesis of periodontitis are identified. These interactions are organized into 14 molecular systems involved in periodontitis.<br><br>OVERALL CONCLUSIONS: A molecular systems architecture is developed to provide a visual framework for comprehending the complexity of molecular interactions across the 8 cell types involved in periodontitis pathogenesis. The resulting architecture may be used for target identification and discovery of single and multicombination therapeutics to treat periodontitis more effectively.}, }
@article {pmid42239041, year = {2026}, author = {Phandanouvong-Lozano, V and Pastore, L and Miller, G and Lin, KY and Wolf, AR}, title = {A bidirectional nanAKE locus enables sialic acid catabolism in gut microbiome member Hungatella hathewayi.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.18.725967}, pmid = {42239041}, issn = {2692-8205}, abstract = {UNLABELLED: Sialic acids are abundant components of host- and diet-derived glycans in the human gut and serve as important nutrients that shape microbial fitness and interspecies competition. Excess free sialic acids are also linked to inflammation and pathogen susceptibility. While well-studied gut bacteria such as E. coli and Bacteroides spp. catabolize sialic acids via the NanAKE or NanLE-RokA pathways, the metabolic capacity of many microbiome members remains undefined. To identify sialic acid catabolizing bacteria, we cultured fecal samples from healthy human donors. The gut anaerobe Hungatella hathewayi was selected under sialic acid-supplemented conditions. H. hathewayi is a poorly characterized gram-positive Lachnospiraceae associated with long-lived individuals and purine metabolism. Here we establish that H. hathewayi grows robustly on sialic acids as a sole carbon source using a pathway homologous to the canonical NanAKE system of E. coli , despite the species' phylogenetic distance. We functionally validated these orthologs through growth assays and heterologous complementation in E. coli knockout strains. Comparative analyses further showed that key catalytic residues in H. hathewayi NanA are conserved despite overall sequence divergence from E. coli . Additionally, we find that colocalized sialic acid transporters and regulatory proteins are not orthologous to E. coli proteins and instead are related to proteins from other gut anaerobes. Together, these findings expand our understanding of sialic acid utilization within the human gut microbiome. We identify H. hathewayi as an overlooked but capable sialic acid degrader that can contribute to modulation of gut sialic acid levels and related inflammation.<br><br>IMPORTANCE: Sialic acids play an important role in mammalian and microbial signalling. Excess free sialic acids increase susceptibility to gut pathogens and induce inflammation. Gut bacteria can both generate and consume free sialic acids, and these pathways are conserved across diverse bacteria. E. coli and B. fragilis consume sialic acids as a carbon source, decreasing free sialic acid levels. We identify H. hathewayi as another bacteria capable of sialic acid consumption and define the enzymes responsible. H. hathewayi is a prevalent member of the human gut microbiome, but it is not genetically tractable, limiting enzymatic characterization. H. hathewayi is enriched in the gut microbiomes of long-lived individuals and expected to be an important contributor to purine degradation to limit gout risk. Defining sialic acid catabolism in non-model species is essential to understanding the evolution and conservation of this pathway as well as how nutrient competition shapes gut microbiome composition.}, }
@article {pmid42239051, year = {2026}, author = {Lalgudi, C and Kotaka, M and Yaffe, E and Lopez, JA and Yu, FB and Ng, K and Sonnenburg, JL and Good, BH and Huang, KC and Shi, H}, title = {Path-dependent recovery of the gut microbiome after antibiotics emerges from coupled ecological and evolutionary dynamics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.22.727306}, pmid = {42239051}, issn = {2692-8205}, abstract = {Recovery of the gut microbiome after antibiotic exposure is often incomplete and variable, and the processes underlying this variation remain unclear. We performed longitudinal shotgun metagenomic sequencing of 2876 daily fecal samples from replicated humanized and conventional mouse cohorts exposed to controlled antibiotic perturbations. Metagenomic profiling recapitulated ecological trajectories previously observed by 16S sequencing, while revealing extensive strain-level dynamics, including reproducible sweeps of standing variants and de novo mutations in antibiotic target sites and regulatory loci. We also identified genetic changes whose effects depended on community composition, competitive release, and perturbation history. Cross-housing experiments revealed bidirectional strain transfer, with antibiotic-induced niche clearance enabling replacement of resident strains. In parallel, phage dynamics were heterogeneous and clustered by cage. Together, these findings show that post-antibiotic microbiome recovery is a path-dependent process shaped by selection, transmission, and phage activity, producing divergent outcomes even among closely matched communities exposed to the same perturbations.}, }
@article {pmid42239183, year = {2026}, author = {Cirolia, G and Gustafson, JT and Aswani, A and Wolf, A}, title = {Performance of IBD machine learning classifiers varies across microbiome training data independent of geographic diversity.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.21.727052}, pmid = {42239183}, issn = {2692-8205}, abstract = {Microbiome-based machine learning classifiers show increasing promise for disease identification across gastrointestinal, metabolic, and immune-mediated conditions. Inflammatory bowel disease (IBD), a chronic immune-mediated disorder associated with disruption of the gut microbiome, has been a particularly successful application area. However, while many predictive models achieve high performance within individual datasets, their ability to generalize across independent populations and geographic contexts remains unclear. Here, we tested whether model class and training dataset composition influence model generalizability across geographically diverse evaluation studies. We compiled seven publicly available shotgun metagenomic studies spanning five geographic regions, comprising 697 individuals with IBD or healthy controls. We trained 246,986 model configurations across seven model classes and five distinct training dataset combinations and evaluated top-performing models on independent studies from the USA, Ireland, Germany, Israel and China. Extreme gradient boosting and random forest models showed the highest and most consistent performance across training datasets, a ranking that was maintained on independent evaluation studies. However, models trained on geographically diverse datasets did not outperform those trained on USA-only datasets. Instead, model performance was strongly dependent on the evaluation study itself, with consistent differences in achievable accuracy across studies. Despite most models achieving similar AUC scores, there was limited overlap in the key microbial species identified. Furthermore, even for the small set of disease predictive microbes shared between models, the direction of enrichment between IBD or healthy subjects often varied in opposing directions across study populations. These findings suggest that study-specific factors constrain generalization and may help explain the lack of consistent microbiome-based biomarkers for IBD.}, }
@article {pmid42239190, year = {2026}, author = {Pietropaolo, J and El Khoury, S and Guo, L and McGee, M and Shapira, M}, title = {Attraction to secreted isoamyl alcohol as a signal for beneficial commensals.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.22.727293}, pmid = {42239190}, issn = {2692-8205}, abstract = {C. elegans, a bacterivore living in microbially-complex environments, harbors a characteristic community of gut bacteria that contribute to its health and fitness. What determines which environmental bacteria end up as commensals is largely unknown in C. elegans , as in other animals. Previous work found that gut Pantoea isolates supported rapid worm development and infection resistance, while environmental congenerics were inferior. Notably, worms were preferentially attracted to the more beneficial gut isolates. Using bioactivity-guided fractionation and gas chromatography-mass spectrometry analysis, we identified bacterially derived isoamyl alcohol (IAA) as a secreted volatile attractant underlying this preference. Screening of worm mutants implicated AWC sensory neuron-associated genes in preferential attraction to beneficial Pantoea and established a causal link between IAA sensing and colonization by beneficial strains. While IAA sensing was important for initial colonization, gut-associated Pantoea strains ultimately outcompeted environmental congenerics over time, indicating that microbiome assembly is shaped by two complementary processes: host behavioral preference for high-IAA producers and bacterial competitive fitness within the gut. While IAA is a product of leucine metabolism and may function as a nutritional cue, we found that it could also directly enhance host infection resistance, suggesting an additional role in modulating host physiology. Finally, knockout analysis identified a bacterial branched-chain amino acid aminotransferase homolog as important for IAA production. Together, these findings identify bacterial volatile sensing as an important and underexplored mechanism shaping microbiome composition and its contributions to host fitness.}, }
@article {pmid42239356, year = {2026}, author = {Madamanchi, K and Gurrala, S and Watson, J and Melkani, GC}, title = {Microbiome Integrity Protects Against Glial-Mediated Tau and Amyloid Pathology Through Circadian and Autophagy Homeostasis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.20.726549}, pmid = {42239356}, issn = {2692-8205}, abstract = {Alzheimer disease referred as AD is characterized not only by tau and amyloid beta aggregation but also by systemic disruptions in circadian rhythms, metabolism, and gut-brain communication that exacerbate neuroinflammation and neurodegeneration. While glial cells play central roles in inflammatory signaling and proteostasis, the contribution of the gut microbiome to glia-driven AD pathology remains poorly understood. Here, we used Drosophila models with glial-specific expression of human tau and amyloid-associated transgenes to investigate how microbiome integrity influences disease progression. AD models exhibited significant shifts in gut microbial composition, particularly in Lactobacillus and Acetobacter species, suggesting an adaptive microbial response to pathological stress. Strikingly, microbiome depletion (axenic condition) markedly worsened behavioral and physiological outcomes, including disrupted sleep-circadian rhythms, impaired memory, and reduced locomotor function. These deficits were accompanied by amplified neuroinflammatory signaling, increased apoptotic gene expression, lipid dysregulation, and altered synaptic markers. Moreover, microbiome loss induced energy stress marked by elevated phospho-AMPK, yet failed to restore proteostasis, as evidenced by accumulation of ubiquitinated proteins and the autophagy adaptor Ref2p, indicating impaired autophagic flux. This dysfunction correlated with increased tau, phospho-tau, and Abeta42 accumulation. Together, our findings demonstrate that microbiome depletion exacerbates glial-mediated inflammation, disrupts circadian and metabolic homeostasis, impairs proteostasis, and accelerates cognitive and motor decline. This work highlights a previously underappreciated role of the gut microbiome in restraining glial dysfunction and mitigating AD like pathology, positioning microbial homeostasis as a critical modulator of neurodegenerative disease progression.}, }
@article {pmid42239363, year = {2026}, author = {Yakar, N and Hasturk, H and Rivas, CA and Zimmerman, P and Guney, Z and Yilmaz, BT and Uzun, Y and Trackman, P and Kantarci, A}, title = {Estrogen Deprivation and Periodontitis Interact Across Multiple Tissues.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.15.725533}, pmid = {42239363}, issn = {2692-8205}, abstract = {UNLABELLED: The study investigated the interaction between estrogen deprivation and periodontitis, systemically, in the bone marrow, and locally in periodontal tissues using a mouse model.<br><br>METHODS: We used the ligature-induced periodontitis (LIP) model concurrently with ovariectomy-induced estrogen deprivation. Bone marrow was assessed for myeloid cell proportion by flow cytometry. The femur metaphysis was examined histologically and by micro-CT. Cytokine responses of CD11b [+] myeloid cells to lipopolysaccharide stimulation were investigated ex vivo across ovary-intact (Sham), ovariectomized (OVX), and estrogen-replaced (OVX+E2) mice with or without periodontitis. Estrogen-related alterations in periodontitis, including microbiome composition and transcriptomic changes in the gingiva and dentoalveolar complex, were investigated by 16S rRNA sequencing and bulk RNA sequencing, respectively.<br><br>RESULTS: Ovariectomy increased osteoblast-like and adipocyte-like cell numbers in femoral marrow, whereas LIP reduced both populations (p = 0.020 and p = 0.029, respectively). LIP increased the bone marrow CD45 [+] hematopoietic fraction in Sham mice. LPS-stimulated bone marrow CD11b [+] cells from OVX mice showed lower Tnf&#x3b1;, Ccl2 , and Il10 expression than Sham mice (p = 0.003, p = 0.005, and p = 0.001, respectively). OVX exacerbated LIP-associated alveolar bone loss, reducing BV/TV (p = 0.003) and increasing osteoclast numbers (p = 0.012). Neither OVX nor E2 replacement significantly altered ligature-associated microbial composition in 16S rRNA sequencing. Bulk RNA sequencing demonstrated estrogen-responsive transcriptomic changes in both the gingiva and dentoalveolar complex, including OVX-associated gene-expression changes that returned toward Sham levels in OVX+E2 mice. These included genes related to stromal regulation (Acan, Igfbp3, Erbb3) and immunity (Gp2, Spib, B2m).<br><br>CONCLUSION: Periodontitis and estrogen deprivation exert combined effects on the bone marrow niche. Estrogen deprivation modulates immune- and healing-related gene expression in the gingiva and remaining dentoalveolar tissues during periodontitis.}, }
@article {pmid42239394, year = {2026}, author = {Almotah, K and Tran, U and Gilbert, H and Schweickart, RA and Fisher, RC and Bisikalo, Y and Ali, M and Buhaya, M and Cheng, M and Cruise, M and Chi, Z and Sarvestani, SK and Huang, EH and Wessely, O}, title = {Inflammatory Stromal Aging in Ulcerative Colitis and Colitis-Associated Cancer.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.18.725891}, pmid = {42239394}, issn = {2692-8205}, abstract = {Ulcerative colitis is a chronic inflammatory bowel disease that can progress from dysplasia to cancer. Inflammatory responses are critical drivers in this process, typically triggered by epithelial lesions and the ensuing infiltration of microbiota into the interstitial layer. Here, we focus on the pro-inflammatory state of the interstitial fibroblasts, which promotes immune infiltration and augments disease progression. The study aims to provide a mechanistic link how fibroblasts of the colitis-associated microenvironment integrate inflammatory signals, microbial infiltration and cellular memory. To this end, we investigated a large number of primary colon fibroblasts obtained from normal, colitis and colon cancer samples using a range of in vitro approaches and an in vivo co-inoculation cancer model. mRNA sequencing analysis identified that the disease-associated fibroblasts are exhibit a cellular inflammatory status, which involves the injury-induced senescence pathway. Using CXCL8, a potent chemokine upregulated in colitis and cancer colon fibroblasts, as a paradigm, this inflammatory status is triggered by the activation of the NFκB signaling via immune-derived cytokines (TNFα, IL-1β), bacterial signals (LPS) and the microbiome itself using mycoplasma as a paradigm. Finally, iPSC reprogramming studies indicate that fibroblasts from ulcerative colitis retain an epigenetic memory that sustains elevated CXCL8 expression. Together, our findings demonstrate that the senescence associated secretory phenotype of colon fibroblasts is a robust indicator for inflammation-driven colon tumorigenesis.}, }
@article {pmid42239425, year = {2026}, author = {Hasegawa, Y and Swain, O and Rajpal, U and France, M and Ncube, L and Mogno, I and Zierden, H and Ravel, J and Elovitz, MA}, title = {Exposure to Antibiotics Modifies the Immune Profiles of Bacterial Extracellular Vesicles from Common Vaginal Anaerobes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.21.726874}, pmid = {42239425}, issn = {2692-8205}, abstract = {BACKGROUND: The female lower reproductive tract harbors a complex microbiome that plays a critical role in reproductive health. A vaginal microbiome dominated by Lactobacillus crispatus (LC; Community State Type (CST) I) supports vaginal health, whereas a microbiome enriched with anaerobic species, such as Gardnerella vaginalis (GV) and Mobiluncus mulieris (MM) (CST IV) is linked to bacterial vaginosis (BV) and adverse outcomes, including sexually transmitted infections, infertility, and preterm birth. Although antibiotics such as metronidazole and clindamycin are commonly prescribed to treat BV, recurrence rates remain high, and the impact of these treatments on bacterial extracellular vesicles (bEVs), critical mediators of host-microbe interactions, is poorly understood.<br><br>RESULT: We investigated how antibiotic treatment at a dose below minimum inhibitory concentration alters the production and immunomodulatory function of bEVs derived from GV, MM, and LC. Using nanoparticle tracking analysis, cytokine profiling, and TLR pathway analyses, we found that antibiotic treatment significantly enhanced the inflammatory properties of bEVs in a species- and antibiotic-specific manner. Notably, bEVs from antibiotic-exposed GV and MM cultures induced elevated cytokine responses in epithelial and immune cells, primarily through TLR2 activation for GV bEVs, and through both TLR2 and TLR5 activation for MM bEVs. While LC bEVs are typically non-inflammatory, exposure to metronidazole, even at a lower dose than what is used clinically, rendered them immunostimulatory, suggesting a potential unintended proinflammatory consequence of treatment on beneficial microbes. We also detected bEVs in human vaginal swabs, including vaginolysin-positive bEVs, even in CST I microbiomes, indicating that low-abundance microbes, including pathogens, remain transcriptionally active.<br><br>CONCLUSIONS: These findings suggest that antibiotics not only reduce microbial load but also reshape bacterial communication via bEVs, potentially contributing to inflammation, epithelial barrier disruption, persistent dysbiosis, and recurrent infections. This work underscores the need for precision antimicrobial strategies that eliminate pathogens while preserving beneficial bacteria and their functional bEVs. Future therapies may benefit from considering the ecosystem-wide effects of antibiotics on the vaginal microbiome and its bEV-mediated signaling network.}, }
@article {pmid42239480, year = {2026}, author = {Qian, J and Ghadermazi, P and Maret, S and Kemp, JF and Frank, D and Melanson, EL and Hendricks, AE and Krebs, N and Tang, M and Olm, MR}, title = {IgA Targeting in the Infant Gut Is Modulated by Diet and Increasingly Directed Towards Persistent Species.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.19.726352}, pmid = {42239480}, issn = {2692-8205}, abstract = {BACKGROUND: IgA is the dominant antibody in the human gut and a key regulator of host-microbe interactions. Infants begin to produce IgA at around 6 months old and receive large quantities of IgA via human milk, but technical limitations have prevented species-level characterization of IgA binding in early life. This has left basic knowledge gaps about which species are targeted by IgA in infancy, and how modifiable lifestyle factors like breastfeeding and complementary feeding impact IgA targeting.<br><br>RESULTS: Here we adapt Metagenomic Immunoglobulin Sequencing (MIg-Seq) for low-biomass infant fecal samples and apply this optimized protocol to 32 longitudinal samples from 16 infants enrolled in the MINT trial, a four-arm randomized controlled trial comparing meat-based, dairy-based, plant-based, and reference complementary feeding patterns, with fecal sampling at 6 and 12 months (pre and post intervention). Infant IgA targeting mirrors adults at the phylum level, with both age groups showing significantly higher IgA targeting of Pseudomonadota and lower targeting of Bacteroidota relative to other phyla. During the substantial microbiome compositional shifts noted between 6 and 12 months, IgA targeting is significantly more stable than the microbiome itself. Among persistent colonizers, IgA targeting strengthens significantly from 6 to 12 months, with the most pronounced effect observed for Bifidobacterium , a finding robust across all dietary arms and feeding modes. The feeding arm to which infants were enrolled was not significantly associated with IgA binding, but several nutrient-specific associations were discovered. Animal-derived nutrients, particularly cholesterol, are strongly positively correlated with IgA targeting of Bifidobacterium longum , while plant-derived carotenoids are positively associated with IgA targeting of Flavonifractor plautii and Ruminococcus gnavus .<br><br>CONCLUSIONS: This study introduces an experimental and computational framework for species-level IgA profiling in the infant gut. The progressive strengthening of IgA targeting of Bifidobacterium and other beneficial persistent colonizers suggests a role for IgA in reinforcing beneficial microbes during infancy. The nutrient-specific dietary effects on IgA targeting reveal the immunological consequences of the complementary feeding period, and highlight a contrast between animal-versus plant-based diets. Together, these findings point to early nutritional interventions and IgA-based therapeutics as promising tools for promoting healthy immune-microbiome development.}, }
@article {pmid42239487, year = {2026}, author = {Aldekhail, W and Al-Beltagi, M and Indrio, F and Al-Nemri, AM and Tomerak, A and Al Sawai, A and Al-Refaee, F and Al-Ghanem, G and Rozi, IH and Alallah, J and Khan, JM and Abouhazima, K and Al-Mannaei, K and El-Atawi, K and Sleiman, R and Miqdady, M}, title = {Infant gut microbiota following cesarean section in the Middle East: a multidisciplinary expert consensus based on a targeted narrative review.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1809889}, pmid = {42239487}, issn = {2296-2360}, abstract = {BACKGROUND: Early-life dysbiosis associated with Cesarean section (C-section) delivery is increasingly recognized as a modifiable risk factor influencing short- and long-term health outcomes. This multidisciplinary expert consensus summarizes the clinical implications of C-section on infant gut microbiota. It proposes evidence-based strategies to mitigate these effects, with a focus on the critical window of the first 1,000 days of life.<br><br>METHODS: A multidisciplinary panel of 16 pediatricians, neonatologists, pediatric gastroenterologists, and nutrition experts conducted a targeted narrative review of the literature to inform a structured expert consensus process and participated in an online structured consensus process. Seventeen consensus statements were developed and validated through discussion, expert voting, and commentary, supported by a targeted review of current scientific evidence.<br><br>RESULTS: The expert panel reached consensus on the impact of C-section delivery on early microbiota composition and its clinical relevance, emphasizing that the rising prevalence of C-sections worldwide demands urgent attention. Experts unanimously emphasized the importance of exclusive breastfeeding as the primary strategy to support healthy microbiota development in infants born by cesarean section. When exclusive breastfeeding is not possible, evidence-based nutritional approaches, including selected prebiotics and probiotic strains with documented clinical efficacy, are recognized as promising alternatives for supporting microbial balance. Notably, the panel underscored that not all probiotics are equally effective and recommended shifting toward evidence-based strains shown to help restore gut dysbiosis in this population. Also, experts advocated for continuing microbiota-targeted support throughout the first 1,000 days of life, viewing this developmental window as a critical continuum rather than a limited early-life phase, while acknowledging the need for more long-term data. Additionally, education for healthcare professionals and parents about the long-term implications of C-section delivery was emphasized as a key enabler of the broader adoption of eubiosis-targeted strategies.<br><br>CONCLUSIONS: Optimizing microbial colonization in infants born by cesarean section requires a multifaceted approach that prioritizes breastfeeding, supports judicious use of evidence-based nutritional interventions when needed, and emphasizes education and continuity of care across early life. By aligning clinical practice with emerging microbiome science, early-life interventions may reduce dysbiosis-associated risks and improve long-term health outcomes.}, }
@article {pmid42239536, year = {2026}, author = {Singh, P and Saravanan, A and Seitz, J and Alkarzon, N and Medugu, N}, title = {A one health perspective on the intestinal microbiome's role in COVID-19 outcomes and recovery.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1763844}, pmid = {42239536}, issn = {2235-2988}, abstract = {Emerging infectious diseases, particularly zoonotic ones, remain major global health concerns. The Coronavirus Disease 2019 (COVID-19) pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), highlights the interconnectedness of human, animal, and environmental health within the One Health framework. The intestinal microbiome plays a central role in host immunity and systemic homeostasis, and its disruption has been linked to altered disease severity and recovery patterns in COVID-19. Evidence suggests that SARS-CoV-2 infection induces intestinal dysbiosis, modifies immune signaling, and affects the microbiota-gut-brain axis (MGBA), contributing to neuropsychiatric and metabolic complications. This review synthesizes current findings on the intestinal microbiome's role in COVID-19 pathophysiology and recovery, explores emerging therapeutic strategies including probiotics, prebiotics, and fecal microbiota transplantation, and emphasizes the importance of integrating microbiome research into pandemic preparedness through a One Health approach.}, }
@article {pmid42239539, year = {2026}, author = {Jiang, X and Chen, B and Wang, Q and Liu, Y and Li, N and Zhang, L}, title = {Structural variation analysis suggests strain-level maternal-infant microbial transmission in early life.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1765801}, pmid = {42239539}, issn = {2235-2988}, abstract = {INTRODUCTION: Structural variations (SVs)-large, functionally consequential genomic alterations-serve as high-resolution markers for strain-level differentiation in the human microbiome, yet their relevance to vertical transmission of the maternal microbiota and early-life colonization remains unclear.<br><br>METHODS: Using metagenomic data from a 98-pair longitudinal mother-infant cohort and a 25-pair multi-niche cohort, we profiled microbial taxa, functions, and SVs, characterized variable SVs (vSVs), deletion SVs (dSVs), and transmitted SVs (tSVs), and evaluated the potential influence of delivery mode, feeding regimen, and maternal ecological niches.<br><br>RESULTS: We identified 5,578 SVs across 51 reference strains, with infants showing increasing SV diversity during the first year of life, and observed significantly greater SV similarity within mother-infant pairs than unrelated pairs. Abundance-based analysis identified 90 microbial species shared between mothers and infants. However, when incorporating SV-based tracking, only 14 strains showed patterns consistent with sustained maternal contribution across time points. Furthermore, exploratory subgroup analyses suggested that both delivery mode and feeding regimen may influence the vertical transmission patterns of maternal microbial strains and transmitted SVs. Functionally, tSVs were enriched in pathways linked to carbohydrate, amino acid, and lipid metabolism, as well as transport and environmental adaptation modules such as T4SS. Multi-niche analysis further suggested that the maternal gut showed the strongest inferred signal of SV-supported strain sharing with both the infant gut and oral microbiota.<br><br>DISCUSSION: Together, these findings suggest that microbial SVs can serve as complementary markers for investigating maternal contribution and vertical transmission-related strain-level patterns in early-life microbiome development, providing new insights into microbial inheritance and early-life health trajectories.}, }
@article {pmid42239553, year = {2026}, author = {Alharbi, ZM}, title = {Integrative Approaches to Gut Microbiota: Biomarkers, Dysbiosis, and Therapeutic Potential.}, journal = {Saudi medical journal}, volume = {47}, number = {5}, pages = {787-800}, pmid = {42239553}, issn = {1658-3175}, mesh = {*Gastrointestinal Microbiome/physiology ; Biomarkers/metabolism ; Autoimmune Diseases/etiology/microbiology ; Humans ; *Dysbiosis/complications/microbiology/therapy ; Brain-Gut Axis/physiology ; Immune System/physiology ; }, abstract = {The human gut contains bacteria, viruses, and archaea that influence health depending on age, diet, and location. An individual harbours about 150 bacterial species. An imbalance of these microorganisms, known as dysbiosis, can negatively impact health. Commensal bacteria maintain microbial homeostasis by building short chain fatty acids. The 2-way communication channel that connects the gut and the brain is referred to as the gut-brain axis. Dysbiosis of the gut leads to some autoimmune diseases. A decline of beneficial bacteria causes the progression of rheumatoid arthritis. Gut dysbiosis increases intestinal permeability, allowing toxins and cytokines to enter the bloodstream and damage neurons. Through interactions with the immune system, the gut microbiota plays a complex role in both health and disease, including contributing to the development of type 1 diabetes. This review stresses the need to integrate measures to identify microbial biomarkers and also metabolic and genetic interplay between the microbiome and health.}, }
@article {pmid42239568, year = {2026}, author = {El-Mokaddem, OK and Elmasry, GF and Mahmoud, WR and Abdel Ghany, LMA}, title = {Bridging the gap in Alzheimer's therapy: strategic design and SAR evolution of coumarin-based hybrids as potent MTDLs.}, journal = {RSC advances}, volume = {16}, number = {32}, pages = {29631-29660}, pmid = {42239568}, issn = {2046-2069}, abstract = {Due to their multitargeting potential, coumarin-based hybrid molecules represent a new and valuable drug development strategy for the treatment of Alzheimer's disease (AD). This review summarizes recent advances in the design, synthesis, and evaluation of coumarin hybrids as multi-target-directed ligands (MTDLs) for AD. This review covers various coumarin hybrid classes, including those incorporating triazole, thiazole, quinoline, chalcone, and other pharmacophores, highlighting their diverse mechanisms of action, such as acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) inhibition, amyloid-beta (Aβ) aggregation prevention, BACE-1 inhibition, MAO-B modulation, antioxidant activity, and metal ion chelation. Structure-activity relationship (SAR) studies have identified key structural features for optimal activity, including linker length, substitution patterns, and physicochemical properties influencing CNS penetration. Molecular docking and dynamics simulations reveal information about drug-target interactions and demonstrate the ability to engage multiple targets. Coumarin hybrids are already showing ecological in vivo efficacy in animal models, and also the desired safety window and metabolic stability make them potential clinical candidates. Future research directions include incorporating emerging therapeutic targets, advanced computational design, and a focus on the microbiome-gut-brain axis to develop more effective and disease-modifying AD therapeutics.}, }
@article {pmid42239715, year = {2026}, author = {Yang, H and Zhang, N}, title = {Effects of omega-3 PUFA-enriched egg consumption on metabolic parameters in elderly adults with metabolic syndrome: study protocol for a randomized controlled trial.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1831128}, pmid = {42239715}, issn = {2296-861X}, abstract = {BACKGROUND: Metabolic syndrome (MetS) affects approximately one-third of community-dwelling older adults (≥65 years) and is characterized by concurrent dysregulation of glucose and lipid metabolism alongside chronic low-grade inflammation. Poor long-term adherence to conventional omega-3 supplementation has prompted interest in sustainable, food-based delivery systems. Omega-3 polyunsaturated fatty acid (PUFA)-enriched eggs-produced through dietary modification of hen feed to enhance eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) content-represent a palatable and easily incorporated dietary vehicle for sustained intervention.<br><br>METHODS: This is a three-arm, parallel-group randomized controlled trial that will enroll 180 community-dwelling adults aged &#x2265; 65 years with MetS. Participants will be randomly allocated (1:1:1) to receive either omega-3 PUFA-enriched eggs, regular eggs, or no egg intervention (usual diet) for 12 weeks. Those assigned to the egg intervention groups will consume one boiled egg daily, five days per week. The control group will maintain their habitual dietary patterns without additional egg consumption. Biological samples (blood, urine, and stool) will be collected at baseline and weeks 4, 8, and 12. Plasma concentrations of omega-3 fatty acids, lipid metabolism indicators,inflammation and oxidative stress markers will be measured. Exploratory outcomes include comprehensive multi-omics profiling, encompassing metabolomics and gut microbiome will be tested.<br><br>RESULTS: The primary outcome will be the longitudinal changes in fasting triglycerides (TG) measured at Weeks 0, 4, 8, and 12, with comparisons between the omega-3 PUFA-enriched eggs group and the regular eggs control group. Secondary outcomes will include glucose levels, insulin concentrations, lipid profiles, as well as biomarkers of inflammation and oxidative stress. Integrative multi-omics analyses will be conducted to explore the pathways linking omega-3 PUFA-enriched eggs consumption to alterations in metabolomic features and gut microbiota.<br><br>CONCLUSIONS: This trial will aim to assess the efficacy, feasibility, and mechanisms of omega-3 PUFA-enriched eggs in elderly adults with MetS, so as to provide insights and evidence to support scalable community-based dietary interventions.<br><br>TRIAL REGISTRATION: The protocol has been registered on the website of Chinese Clinical Trial Registry. The Identifier code is ChiCTR2600120125. The Registry date is 10 March, 2026. Registry name is "Interventional Effect of &#x3c9;-3 Polyunsaturated Fatty Acid-Fortified Eggs on Elderly Patients with Metabolic Syndrome." Registration URL is [https://www.chictr.org.cn/bin/userProject].}, }
@article {pmid42240192, year = {2026}, author = {Wang, T and Fan, N and Cao, X and Wang, Z}, title = {Entire Journey of Foliar Applied Nanomaterials with Different Surfactants Modification on Tomato Leaves and Subsequent Modulation of Stress Resistance.}, journal = {ACS nano}, volume = {}, number = {}, pages = {}, doi = {10.1021/acsnano.6c06235}, pmid = {42240192}, issn = {1936-086X}, abstract = {Foliar application of nanomaterials (NMs) offers great potential for sustainable crop disease management. However, how the presence of surfactants alters the behavior of NMs on leaf surfaces and their subsequent modulation of disease resistance remains unclear. Here, surfactants were incorporated into NMs suspensions to enhance foliar adhesion and deposition, thereby suppressing early blight (Alternaria solani) in tomato. Nonionic surfactants (Tween-80 and Silwet L-77) significantly improved the foliar deposition and translocation of La10Si6O27 nanorods (NRs). The treatment combining La10Si6O27 NRs with Silwet L-77 (NRs + L77) achieved the highest efficacy, reducing disease severity by 70%, which is 19.99% higher than La10Si6O27 NRs alone treatment. Mechanistically, (1) NRs + L77 activated the antioxidant defense system, increasing superoxide dismutase and peroxidase activities by 21.22% and 140.10%, respectively, while decreasing malondialdehyde content by 28.72%; (2) NRs + L77 optimized the phyllosphere microbiome, enriching beneficial genera such as Bacillus, Pantoea, and Klebsiella and restoring microbial network complexity; and (3) NRs + L77 upregulated defense-related gene expression, activated phenylpropanoid and flavonoid metabolic pathways, and induced systemic acquired resistance. In addition, NRs + L77 exhibited favorable biosafety toward nontarget organisms. This study demonstrates the potential of surfactant-modified NMs in improving disease control efficiency and contributing to sustainable crop protection.}, }
@article {pmid42240277, year = {2026}, author = {Liu, W and Wang, X and Zhang, Y and Liu, J and Li, M and Zhou, Q and Wang, L and Liu, S and Chen, W and Chu, ES and Lau, HC and Song, Q and Zhou, X and Gou, H and Zhang, JX and Tian, GB and Wang, L and Li, X and Peng, S and Wong, CC and Kuang, M and Xu, L and Yu, J}, title = {Gut pathobionts translocate into liver and reshape intrahepatic microbiome to facilitate hepatocellular carcinoma.}, journal = {Cancer discovery}, volume = {}, number = {}, pages = {}, doi = {10.1158/2159-8290.CD-25-1355}, pmid = {42240277}, issn = {2159-8290}, abstract = {The role of intrahepatic microbiome in hepatocellular carcinoma (HCC) remains elusive. Here, we profiled matched gut and intrahepatic microbiomes from HCC patients and healthy subjects. Compared to healthy subjects, we observed increased gut-liver microbiome similarity and a gut pathobionts-centred network in HCC, implying microbial transfer via gut-liver axis. Consistently, HCC stool transplantation to germ-free mice impaired gut barrier function and increased bacterial load in liver. Multi-site analysis of intrahepatic microbiome and host transcriptome revealed that gut pathobionts in tumor regions positively correlate with host cytokine expression and oncogenic pathways. Administration of HCC-enriched Bacteroides fragilis disrupted gut barrier in mice and led to live bacteria translocation to liver. Bacteroides fragilis exacerbated liver damage and promoted HCC development in mice. Mechanistically, Bacteroides fragilis surface protein Enolase interacts with and activates Vimentin on hepatocytes, triggering oncogenic cascades. Our findings provide insight into how gut pathobionts translocate to liver to promote hepatocarcinogenesis.}, }
@article {pmid42240365, year = {2026}, author = {Chen, B and Su, Z and Sun, Y and Shao, Z and Yu, X and Jiang, X and Xue, X and Yu, L and Wang, L and Zhao, W and Feng, Y and Ning, K and Zhang, M and Cao, A and Zhang, L}, title = {Gut microbial culturomics identifies autism-associated Shigella and reveals species-level remodeling during fecal microbiota transplantation.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0079726}, doi = {10.1128/spectrum.00797-26}, pmid = {42240365}, issn = {2165-0497}, abstract = {Autism spectrum disorder (ASD) has been repeatedly linked to gut microbiota alterations, yet mechanistic insight remains limited by the scarcity of ASD-specific cultured isolates. Here, we performed large-scale gut microbial culturomics on fecal samples from 41 children with ASD and 12 typically developing (TD) controls, generating 1,724 isolates across six phyla. Longitudinal culturomics profiling was further conducted in 17 ASD children undergoing a 9-week fecal microbiota transplantation (FMT) intervention. All isolates underwent 16S rRNA sequencing and non-redundant clustering to assess species-level diversity, ASD-TD differences, and microbial dynamics associated with clinical response. ASD children harbored a distinct culturable microbiota enriched for Shigella flexneri and Shigella boydii, whereas TD children were enriched in beneficial taxa, such as Bifidobacterium catenulatum subsp. and other health-associated species. Notably, 20 species isolated from ASD children and 20 from TD children were absent from major existing gut microbiota biobanks, thereby expanding the cultivable repertoire. Among FMT participants, clinical responders exhibited increased alpha diversity, progressive enrichment of TD-associated beneficial taxa, such as Bacteroides fragilis, Anaerostipes hadrus, Parabacteroides merdae, and Turicibacter sanguinis, and a marked reduction of ASD-associated Shigella flexneri and Shigella boydii, whereas non-responders showed minimal shifts. Acquisition of TD-enriched strains at week 9 was strongly correlated with clinical improvement, suggesting that species-level ecosystem remodeling may contribute to FMT efficacy. This work establishes one of the first ASD-focused gut microbial culturomics resources, identifies Shigella as a potential ASD-associated taxon, and provides foundational evidence and testable mechanistic hypotheses for future microbiome-based interventions in ASD.IMPORTANCEMost autism spectrum disorder (ASD) microbiome studies rely on sequencing, which identifies associations but lacks live strains needed for mechanistic tests. We cultured 1,724 isolates from ASD and typically developing (TD) children, providing an ASD-focused, strain-level resource. ASD samples showed a significantly higher prevalence of Shigella flexneri. Longitudinal profiling during fecal microbiota transplantation (FMT) showed that clinical responders gained TD-enriched taxa and lost Shigella spp., and these shifts correlated with symptom improvement. This resource enables functional assays and gnotobiotic studies with ASD-relevant strains and provides a foundation for rational microbiome-based interventions.}, }
@article {pmid42240375, year = {2026}, author = {Wirth, VR and Xie, SYL and Russell, MM and Bu, S and Sugino, KY and Keller, SF and Zhang, L and Alaimo, K and Beavers, AW and Comstock, SS}, title = {Antimicrobial resistance genes and mobile genetic elements in compost amendments, soil, and the human gastrointestinal bacterial communities of gardeners during a single gardening season.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0088225}, doi = {10.1128/msphere.00882-25}, pmid = {42240375}, issn = {2379-5042}, abstract = {UNLABELLED: The purpose of this study was to assess the antimicrobial resistance gene (ARG) and mobile genetic element (MGE) gene presence and abundance in soil, dairy manure and plant mixed compost (DMP), plant-based compost (P), and gardeners who used DMP across three time points. Soil (n = 1), DMP (n = 1), P (n = 1), and participant (n = 11) stool samples were collected at three time points during the 2019 gardening season in the Lansing, MI, area. DNA was extracted from each sample and stored at -20°C until use. Quantitative real-time PCR was used to detect ARGs and MGEs in each sample. Alpha diversity was assessed using richness, Shannon, and inverse Simpson indices. Shapiro-Wilk tests were used to assess normality. Beta diversity was assessed using Sorensen and Bray-Curtis dissimilarity indices. We detected a diverse composition of ARGs and MGEs in soil, compost, and human stool samples. DMP and soil exhibited greater ARG richness than P compost. In human stool, ARG and MGE profiles showed inter-participant variability but remained largely consistent within individuals across the gardening season. Alpha and beta diversity metrics revealed no significant shifts in the overall human gut resistome diversity across the gardening season. However, MGE gene composition differed significantly between DMP compost and human stool samples. Although ARG and MGE were detected in the soil and compost samples, there was no change in the ARG and MGE composition of gardeners' gut resistomes over the gardening season. These findings suggest that short-term exposure to AMR-rich compost or soil may not substantially alter gut resistome structure in healthy adult populations.<br><br>IMPORTANCE: Antimicrobial resistance is a growing public health concern, and compost and soil can contain genes that help bacteria resist antibiotics or share resistance with other bacteria. Many gardeners use manure-based compost, but it is unclear whether short-term exposure affects antimicrobial resistance in bacteria residing within the human gut. In this study, we detected antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) in soil, two types of compost, and stool from gardeners across the 2019 gardening season near Lansing, MI. We found that manure-based compost and soil contained more ARGs than plant-based compost, but gardeners' gut resistomes remained stable over time. These results suggest that short-term compost exposure through gardening may not substantially alter the gut resistome.}, }
@article {pmid42240627, year = {2026}, author = {Corsello, A and Romano, A and Romano, C}, title = {Proton pump inhibitors in children: indications and safety.}, journal = {Expert review of gastroenterology &amp; hepatology}, volume = {}, number = {}, pages = {1-13}, doi = {10.1080/17474124.2026.2683678}, pmid = {42240627}, issn = {1747-4132}, abstract = {INTRODUCTION: Proton pump inhibitors (PPIs) are among the most frequently prescribed medications in pediatric practice. While highly effective in acid-mediated disorders, concerns regarding overuse, inappropriate indications, and potential adverse effects have emerged, particularly in infants and children with nonspecific symptoms.<br><br>AREAS COVERED: This review summarizes the current evidence on the indications, efficacy, and safety of PPIs in the pediatric population. A literature search was performed in PubMed/MEDLINE and Embase, supplemented by landmark earlier studies and current clinical practice guidelines. We discuss guideline recommendations and examine the role of PPIs across different clinical scenarios including gastroesophageal reflux disease, esophagitis, eosinophilic esophagitis and special populations. Particular attention is given to emerging data on adverse outcomes, including infections, microbiome alterations, and long-term safety concerns. Strategies for appropriate prescribing, deprescribing, and individualized patient management are also addressed.<br><br>EXPERT OPINION: PPIs remain overprescribed in pediatrics, often for indications lacking clear benefit. Future efforts should prioritize diagnostic precision, short-term therapeutic trials and systematic deprescribing strategies. A shift toward stewardship-based prescribing, combined with improved clinician education and use of objective diagnostic tools, is essential to optimize outcomes and minimize unnecessary exposure.}, }
@article {pmid42240700, year = {2026}, author = {Ghorab, MA and Khalil, MS and El-Sayyad, GS and Nada, HG and Elfadil, D and El-Sherif, DM and Gaballah, MS and Elgarahy, AM and Abouelnasr, HS and Saleh, DM and Liu, M and Chen, S}, title = {Microbial degradation of organophosphorus pesticides: mechanisms, environmental impacts, and future perspectives.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {6}, pages = {}, pmid = {42240700}, issn = {1573-0972}, support = {2024A04J6583//Guangzhou Basic and Applied Basic Research Project, China/ ; }, abstract = {The pervasive global dispersion of organophosphorus pesticides (OPs) as a primary insecticidal agent for enhanced agricultural productivity presents an enduring ecological and human health exigency. Unfettered field-scale applications result in the ubiquitous contamination of diverse ecosystems, precipitating deleterious effects extending from the disruption of soil microbiome homeostasis and attendant biogeochemical cycles to significant morbidity in non-target biota and human populations. The pronounced hazards associated with specific OPs, including methamidophos, methyl parathion, and parathion, categorized as highly hazardous by the World Health Organization (WHO) and consequently restricted in numerous countries - underscore the imperative for effective remediation strategies. This review critically examines the natural attenuation of OPs, accentuating the burgeoning field of bioremediation and biodegradation as environmentally sustainable and efficacious approaches for decontaminating affected niches. We provide a comprehensive synthesis of the current understanding of the remarkable metabolic versatility exhibited by a phylogenetically diverse consortium of fungal and bacterial genera, exemplified by genera such as Pseudomonas, Bacillus, Acinetobacter, and Aspergillus, capable of catabolizing a broad repertoire of OP compounds in both soil and aqueous matrices. Furthermore, this analysis elucidates the central role of specific microbial organophosphorus hydrolase genes (oph, opd, mph, hocA, and opaA) in the evolutionary adaptation of novel metabolic pathways and the expression of cognate hydrolase enzymes that catalyze the crucial initial steps in OP degradation. This focused synthesis highlights recent advances in deciphering the intricate molecular mechanisms governing microbial OP biodegradation and critically evaluates the potential of these biological systems as robust and scalable bioremediation interventions for the effective restoration of OP-contaminated water and soil environments.}, }
@article {pmid42240810, year = {2026}, author = {Vitiello, A and Zovi, A}, title = {Early-onset colorectal cancer: epidemiology, risk factors, and implications for clinical practice.}, journal = {Clinical &amp; translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico}, volume = {}, number = {}, pages = {}, pmid = {42240810}, issn = {1699-3055}, abstract = {The incidence of colorectal cancer (CRC) in individuals under 50 years of age has increased steadily over the past two decades in several high-income countries, contrasting with declining rates in older populations following the implementation of screening programmes. This epidemiological shift represents an emerging challenge for clinical practice and public health systems. This clinical review aims to summarise current epidemiological evidence, risk factors, and biological characteristics of early-onset colorectal cancer, and to examine its implications for screening strategies and health policy. Although hereditary cancer syndromes account for a minority of cases, most earlyonset CRCs occur in individuals without a recognised genetic predisposition. Identified risk factors include obesity, unhealthy dietary patterns, physical inactivity, microbiome alterations, and early-life environmental exposures. Diagnostic delays are common, as symptoms such as rectal bleeding or changes in bowel habits are frequently attributed to benign conditions in younger adults, leading to presentation at more advanced stages. Growing epidemiological data and modelling studies support lowering the age of average-risk screening initiation to 45 years, a strategy already adopted in several countries. However, implementation requires careful consideration of healthcare capacity, cost-effectiveness, and equitable access. Early-onset colorectal cancer represents a significant and evolving public health concern. Enhanced clinical vigilance in symptomatic young adults, together with evidence-based adjustments to screening policies, will be essential to mitigate the increasing burden of disease in this population.}, }
@article {pmid42241172, year = {2026}, author = {Chen, Q and Xu, Z and Zheng, T and Pang, H and He, Z}, title = {Association between lipid metabolism and lung adenocarcinoma: Evidence from Mendelian randomization and tissue microbiome analysis.}, journal = {Journal of cancer research and therapeutics}, volume = {22}, number = {2}, pages = {403-414}, pmid = {42241172}, issn = {1998-4138}, abstract = {BACKGROUND: Tissue-resident microbiota play an important role in lung cancer development. This study aimed to characterize the microbiota profile associated with fatty acid metabolism and related genes and examine its effect on treatment outcomes in lung cancer.<br><br>METHODS: Genome-wide association data on saturated fatty acid ratio, total cholesterol, and linoleic acid ratio were analyzed with lung adenocarcinoma as the outcome. Mendelian randomization (MR) and multivariable MR using significant single nucleotide polymorphisms assessed causal effects with sensitivity analyses. TCGA and GEO microbial data were explored via GSEA, STRING, and CIBERSORT, and Bacillus velezensis was validated in tumor tissue by quantitative polymerase chain reaction.<br><br>RESULTS: MR identified saturated fatty acids and total cholesterol as risk factors for lung adenocarcinoma (LUAD), while linoleic acid was protective. Microbial profiling showed distinct tumor versus adjacent tissue communities, with Bacillus velezensis enriched in LUAD. Its abundance was negatively associated with the cholesterol-response pathway (GOBP_CELLULAR_RESPONSE_TO_CHOLESTEROL). Twelve cholesterol-related genes were differentially expressed, and a derived risk model predicted poor prognosis. Among them, GPLD1 exhibited tumor-suppressor characteristics, with lower tumor expression linked to worse survival. GPLD1 is detectable in plasma (~2.8 mg/L) and reduced in lung cancer patients, supporting its potential as a noninvasive biomarker.<br><br>CONCLUSION: Our findings suggest a causal link between the components of a high-fat diet and LUAD by identifying key genes and microbial communities. Moreover, GPLD1 represents a promising biomarker for the early diagnosis and prognosis of this patient population.}, }
@article {pmid42241374, year = {2026}, author = {Scionti, K and Schoissengeier, V and Vaclavkova, I and Fleiss, H and Cuparencu, C and Olsen, A and Jilani, H and Lucassen, DA and de Zoete, E and Feskens, E and Boshuizen, HC and Vingerhoeds, MH and Ummels, M and Haider, S and Winzer, E and Wakolbinger, M and Crevenna, R and Jordakieva, G and Hasenöhrl, T and Wolzt, M and Wallner, M and Riederer, M and Ressler, M and Fuchs-Neuhold, B and Höfler, C and Aufschnaiter, AL and Wrzesińska, MA and Binder-Olibrowska, KW and Ptaszyński, P and Rakoczy, J and Dros, C and Lammers-van der Holst, H and Kramer, A and Maier, B and Matullat, I and Papantoniou, K and Wagner, KH}, title = {Investigating the risk of obesity in European night shift workers: a study protocol for cross-sectional and mechanistic studies in the SHIFT2HEALTH Project.}, journal = {Obesity facts}, volume = {}, number = {}, pages = {1-25}, doi = {10.1159/000552231}, pmid = {42241374}, issn = {1662-4033}, abstract = {Introduction Approximately one in five workers in Europe is engaged in shift work. Studies reveal that night shift work leads to an increased risk of overweight, obesity and related diseases. Yet, the biological and behavioural mechanisms underlying these associations are not fully understood. The cross-sectional and mechanistic studies within the European SHIFT2HEALTH project aim to investigate biological, behavioural and psychosocial key risk factors responsible for the association between night work and obesity across five European countries. Methods A multi-centric cross-sectional study is designed to unravel obesogenic risk factors, eating habits and sleep patterns in night shift workers and day workers from the health- and various industrial sectors. Recruitment takes place in Austria, Denmark, Germany, Poland, and the Netherlands, aiming at 500 night shift workers and 500 day workers. Anthropometric measurements, sensory perception and food preference tests are performed, alongside extensive questionnaires. In addition, biological samples (blood, hair, urine, faeces) are collected for biomarker measurements of inflammation, oxidative stress, glycaemic and lipaemic parameters, for microbiome and metabolomics analyses and chronotype assessment. In a nested mechanistic study, night shift workers (N=200) recruited in Austria and in the Netherlands, additionally collect urine samples from all voids over 24 hours during a day shift and a night shift, as well as dried blood spots and tongue swabs at four time points and undergo continuous sleep, activity and light exposure monitoring through actigraphy. The association between night shift work and its metrics with levels of pre-obesity biomarkers will be evaluated in crude and multivariable-adjusted regression models, adjusting for potential confounders. Stratified analyses by age, gender, sector and chronotype will be conducted. Conclusion In the cross-sectional and mechanistic studies of the SHIFT2HEALTH project, biological, behavioural and psychosocial factors of night shift workers will be compared with those of day workers across sectors. The outcomes of these studies will serve as a basis for future intervention studies and, together, will contribute to the development of strategies to prevent and reduce overweight and obesity with the aim to improve the health and wellbeing of night shift workers. Trial registration: clinicaltrials.gov, ID: NCT06288568.}, }
@article {pmid42241759, year = {2026}, author = {Tabish, RW and Lin, Y and Rochell, SJ and Pacheco, WJ and Bailey, MA and Dozier, WA and Robinson, K and Hauck, R}, title = {Cecal metagenome and mucosal transcriptome of broilers after an enteric challenge and fed diets with different fiber types and concentrations[1].}, journal = {Poultry science}, volume = {105}, number = {9}, pages = {107151}, doi = {10.1016/j.psj.2026.107151}, pmid = {42241759}, issn = {1525-3171}, abstract = {This study evaluated the effects of dietary fiber supplementation on broiler gut health during a subclinical enteric challenge. Birds were assigned to either an unchallenged control or a challenged control, followed by six dietary treatments applied to challenged birds. These treatments included 3% oat hulls (OH), 3% soy hulls (SH), and four combinations of 1.5% OH or SH with 1.5% wheat middlings (WM) or sugar beet pulp (SBP). A randomized complete block design was used with 2,160 day-old YP × Ross 708 male broiler chicks allocated to eight treatments, each with nine replicate floor pens and 30 birds per pen. Birds were inoculated with Eimeria followed by Clostridium perfringens, and cecal samples were collected at 21 days of age for shotgun metagenomic and transcriptomic analyses. The enteric challenge significantly reduced microbial diversity, depleted butyrate-producing bacteria, and enriched pathways associated with bacterial growth and virulence while triggering inflammatory signaling and suppressing proliferative pathways in the host. Supplementation with dietary fiber modulated these responses through distinct yet complementary mechanisms. The group receiving OH with WM enriched butyrate-producing bacteria, including Faecalibacterium prausnitzii, reduced C. perfringens abundance, and downregulated inflammatory pathways. Birds fed OH with SBP showed increased populations of lactic acid producing bacteria and Bifidobacterium animalis while suppressing TNFα, NF-κB and IFNγ signaling. Diets containing SH combinations enhanced metabolic pathways related to pyruvate fermentation and stachyose degradation, primarily driven by Lactobacillus species. Despite having distinct microbial compositions, all fiber treatments restored epithelial proliferation pathways in the host transcriptome, indicating convergent potentially beneficial effects on intestinal health. Integration of bacteriome and transcriptome data revealed coordinated relationships between specific bacterial species, including Stutzerimonas stutzeri, Bacteroides caecae, and Eubacteriaceae bacterium ES3, and host genes involved in immune function and energy metabolism. These findings provide a mechanistic framework for developing targeted nutritional strategies using specific fiber combinations to enhance gut resilience in antibiotic-free broiler production systems.}, }
@article {pmid42241765, year = {2026}, author = {Xiong, X and Sun, H and Hu, Z and Tian, Y and Zeng, T and Lu, L and Shi, F and Li, Y}, title = {Influence of age on eggshell quality in ducks: An analysis based on calcium metabolism, gut microbiota, and uterine transcriptome.}, journal = {Poultry science}, volume = {105}, number = {9}, pages = {107182}, doi = {10.1016/j.psj.2026.107182}, pmid = {42241765}, issn = {1525-3171}, abstract = {Our current project aims to elucidate the impact of advancing date on eggshell quality in Shanma ducks and its underlying mechanisms. A total of 60 healthy Shanma ducks from the youth group (160 days old) and the elderly group (560 days old) were selected to evaluate eggshell physicochemical properties, serum calcium and phosphorus metabolism, gut microbiota, and uterine tissue transcriptomic expressions. Results demonstrated that the elderly group exhibited significantly reduced eggshell thickness and strength, with ultrastructural analysis revealing uneven calcium deposition and a thinner effective layer compared to the youth group. Elderly ducks showed decreased serum levels of 25-hydroxyvitamin D3, alongside elevated parathyroid hormone and bone remodeling markers (TRAP-5b, BAP), suggesting disrupted calcium metabolism. Histological observation identified duodenal villus atrophy, humeral matrix erosion, and uterine interstitial edema in elderly ducks. Gut microbiome analysis indicated reduced microbial diversity and simplified community structure in elderly ducks, with Helicobacter and Lactobacillus becoming dominant genera, and significant downregulation of mineral absorption-related functional pathways. Uterine transcriptomics identified 607 differentially expressed genes, significantly enriched in pathways such as calcium signaling and steroid hormone biosynthesis. Correlation network analysis further revealed that eggshell strength was closely associated with bone resorption markers, Helicobacter abundance, and the expression of multiple calcium metabolism-related genes (e.g., KCNS2, GABRA1, FOXF1, ATP1B1). Notably, the positive correlation between eggshell strength and SMAD9 observed in the youth group was absent in the elderly group. In conclusion, the age-related decline in eggshell quality results from the combined effects of calcium metabolism imbalance, enhanced bone remodeling, gut microbial dysbiosis, and uterine functional disruption, providing multi-omics insights into the decline of avian reproductive performance with age.}, }
@article {pmid42010688, year = {2026}, author = {Yadav, RK and Zhang, Y and Lv, Y and Liu, S and Yang, J and Wang, Y and Gang, X}, title = {Mechanisms of weight recurrence after bariatric surgery.}, journal = {Nutrition &amp; metabolism}, volume = {23}, number = {1}, pages = {}, pmid = {42010688}, issn = {1743-7075}, support = {YDZJ202402042CXJD, YDZJ202401410ZYTS, 82272993, 2022-CXM-06, 81972372//Science and Technology Department, and National Natural Science Fund, Jilin Province, China/ ; }, abstract = {UNLABELLED: Obesity is a major health concern in today’s growing population, significantly raising the risk of disease and death. Bariatric surgery is the most effective treatment for obesity and its related conditions. However, weight recurrence remains a common issue post-surgery. This study aims to understand the mechanisms of Weight recurrence after Bariatric surgery, other than anatomic surgery failure. Weight recurrence may result from various factors, including genetic predisposition, psychological and behavioral influences, neuroendocrine changes, alterations in the gut microbiome, bile acid signaling, and post-surgery hypoglycemia. Prevention and management strategies include lifestyle modifications, mental health support, pharmacotherapy, and, in some cases, revision surgery. This study explores the controversial hormonal changes involved in weight recurrence, as well as the roles of gut microbiota, bile acid signaling, and genetic factors. Additionally, the study highlights several preventable factors that are crucial for maintaining long-term weight loss and minimizing weight recurrence after bariatric surgery. By gaining insight into these hormonal changes and other contributing factors, we can implement effective preventive measures and medical treatments to enhance long-term weight loss success and improve patients’ quality of life. Nonetheless, further research is needed to fully understand the contributions of bile acid signaling and gut microbiota in the process.<br><br>GRAPHICAL ABSTRACT: [Image: see text]}, }
@article {pmid42228350, year = {2026}, author = {Wang, M and AlQahtani, A and Liu, L and Ran, L and Liu, C and Liang, Y and Yu, J and Wu, Y and Guan, Q}, title = {Microalgae Oil Improves Hepatic Lipid Metabolism in A High-Fat Diet-Induced Mouse Model.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {231}, pages = {}, doi = {10.3791/71168}, pmid = {42228350}, issn = {1940-087X}, mesh = {Animals ; Mice ; Diet, High-Fat/adverse effects ; *Liver/metabolism/drug effects ; *Lipid Metabolism/drug effects ; *Microalgae/chemistry ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; Docosahexaenoic Acids/pharmacology/administration &amp; dosage ; }, abstract = {Metabolically, dysfunctional steatotic liver disease is a prevalent metabolic disorder associated with gut microbiota dysbiosis and hepatic lipid imbalance. In this study, a high-fat diet-induced mouse model was established to evaluate the effects of supplementation with DHA-rich microalgae oil. Mice (n = 4 per group) were fed a high-fat diet for 8 weeks and received daily oral administration of microalgae oil, probiotics, or the combination of DHA-rich microalgae oil and probiotics. Metabolic parameters, gut microbiota composition (16S rRNA sequencing), microbial functional pathways, and hepatic metabolomic profiles were assessed. The results showed that DHA-rich microalgae oil improved lipid homeostasis, as indicated by reduced serum LDL-c and hepatic triglyceride levels and increased high-density lipoprotein (HDL-c), and was associated with alleviation of liver injury and oxidative stress. Microbiome analysis revealed selective changes in gut microbial composition, including enrichment of Lactobacillus and Bifidobacterium and reduction of high-fat diet-associated taxa such as Clostridium and Ruminococcus. Functional profiling indicated alterations in microbial metabolic pathways, including the L-methionine salvage cycle and phenylethylamine degradation. Integrated microbiome-metabolome analysis further identified associations between microbial taxa and hepatic metabolites involved in fatty acid metabolism, bile acid turnover, and amino acid pathways. These findings indicate that DHA-rich microalgae oil supplementation is associated with improvements in hepatic lipid metabolism and gut microbiota composition in this model, without implying a direct causal mechanism.}, }
@article {pmid42228448, year = {2026}, author = {Brandt, E and Koivisto, A and Pereira, P and Mustanoja, E and Auvinen, P and Saari, T and Rusanen, M and Leinonen, V and Scheperjans, F and Kärkkäinen, V}, title = {Early Gut Microbiome Alterations in Mild Cognitive Impairment Reflect Changes in Alzheimer Disease.}, journal = {Alzheimer disease and associated disorders}, volume = {}, number = {}, pages = {}, doi = {10.1097/WAD.0000000000000732}, pmid = {42228448}, issn = {1546-4156}, abstract = {INTRODUCTION: Alterations in the gut-brain axis have been increasingly linked to neurodegenerative diseases, including Alzheimer disease (AD). It remains unclear whether these microbiome changes are already present during early cognitive decline. We examined whether gut microbiome alterations characteristic of AD are detectable in mild cognitive impairment (MCI) and whether these changes follow a similar pattern across the cognitive continuum.<br><br>METHODS: This case-control study included 78 participants: 37 cognitively healthy controls, 20 individuals with MCI, and 21 individuals with prodromal or mild AD. Cognitive performance was assessed using the CERAD neuropsychological battery, and disease severity was assessed using the Clinical Dementia Rating. Dietary data were collected, and fecal samples were analyzed using 16S rRNA gene amplicon sequencing.<br><br>RESULTS: We identified 16 bacterial genera associated with cognitive status. Genera such as Lacticaseibacillus, Raoultella, and Buttiauxella were reduced in AD, with similar decreases already evident in MCI. In contrast, Anaerovorax and an unclassified Comamonadaceae genus were increased in AD. Several alterations showed a consistent trend from normal cognition through MCI to AD.<br><br>DISCUSSION: Gut microbiome alterations characteristic of AD appear already present in early cognitive decline and follow a similar pattern in MCI. These findings support the potential of microbiome profiles as early, noninvasive biomarkers of AD.}, }
@article {pmid42228521, year = {2026}, author = {Csorba, AB and Fora, CG and Balog, A}, title = {Diversity analyses of corn leaf aphid Rhopalosiphum maidis (Hemiptera: Aphididae) endosymbiotic microbiome and soil microbiome-preliminary results.}, journal = {Journal of insect science (Online)}, volume = {26}, number = {3}, pages = {}, pmid = {42228521}, issn = {1536-2442}, support = {PN-III-P4-PCE-2021-0543//UEFISCDI Romania/ ; //Faculty of Engineering and Applied Technologies/ ; //University of Life Sciences/ ; //Timi&#x219;oara/ ; }, mesh = {Animals ; *Aphids/microbiology ; *Microbiota ; *Symbiosis ; *Soil Microbiology ; Zea mays ; Europe ; Bacteria/classification/genetics ; }, abstract = {The corn leaf aphid, Rhopalosiphum maidis Fitch (Hemiptera: Aphididae), microbial symbiont and 9 soil-type microbial diversities were genetically analyzed along a gradient of maize management systems that includes 3 different crop control strategies from 3 climatic regions. The central point of interest was to assess whether any similarity could be detected between the corn leaf aphid's rapid distribution increase throughout mainland Europe and variation in its endosymbiont microbiome diversity. According to the results, it was detected that the bacterial community differs between regions. The obligate symbiont Buchnera aphidicola dominated across all climate regions, while facultative symbionts such as Serratia symbiotica and Wolbachia varied in relative abundance under different temperature conditions. Fewer effects of soil types were detected. Our study comprises analyses about a pest aphid and its associated symbiont community in relation to ambient temperature conditions, and as such, we believe it may well help in the development of new control strategies.}, }
@article {pmid42228562, year = {2026}, author = {Werner, L and Nissenbaum-Toren, T and Fibelman, M and Leibovitzh, H and Cohen, NA and Brenner, M and Lobel, L and Maharshak, N}, title = {Antibiotic disruption of the gut microbiome triggers IBD-like proteolytic activity.}, journal = {Cell reports}, volume = {45}, number = {6}, pages = {117478}, doi = {10.1016/j.celrep.2026.117478}, pmid = {42228562}, issn = {2211-1247}, abstract = {Antibiotics (Abx) are essential in medicine but can disrupt gut microbiota, potentially contributing to inflammatory bowel diseases (IBDs). This study employed fecal metagenomics and metaproteomics to evaluate the effects of Abx in patients with pouchitis, ulcerative colitis (UC), and non-IBD controls. Each group displayed distinct microbiome profiles, with metaproteomes more affected by Abx than metagenomes. Proteomic analysis revealed increased pancreatic protease activity and fecal proteolytic activity in all groups, except in patients without IBD before Abx, consistent with impaired epithelial barrier integrity. Abx also decreased bacterial protease inhibitors, which may control proteolysis and help maintain gut balance. These findings emphasize the importance of understanding Abx-induced proteolytic shifts in IBD and highlight metaproteomics as a valuable tool for studying host-microbiome interactions. Future research should explore the molecular mechanisms that regulate bacterial protease inhibitor levels and their effects on intestinal health.}, }
@article {pmid42228606, year = {2026}, author = {Waghmode, S and Viswanathan, R and Koligudde, V and Umare, P and Lavania, M}, title = {Microbial shifts in early life: the pediatric gut microbiome and its role in health and disease.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2681763}, pmid = {42228606}, issn = {1949-0984}, abstract = {This review explores the pivotal role of the pediatric gut microbiome in shaping early-life development and influencing susceptibility to disease, emphasizing its impact on immune, metabolic, and neurodevelopmental processes. The neonatal period represents a critical window for host-microbiome interactions, beginning at birth when intestinal barrier function is still developing and immune responses remain immature. During this formative stage, rapid microbial colonization and ecological succession are influenced by delivery mode, infant feeding practices, antibiotic exposure, and environmental factors. Beyond bacterial populations, the early-life gut virome composed of bacteriophages and eukaryotic viruses evolves dynamically and contributes to microbial community structure, gene exchange, and immune system maturation. Microbially derived signals and metabolites support the development of mucosal integrity, immune programming, and host microbe equilibrium, with long-term implications for systemic immune function. Breastfeeding fosters the establishment of microbial communities and metabolic profiles associated with immune tolerance, whereas formula feeding and early-life antibiotic use may disrupt normal microbiome development. Alterations in early microbial trajectories have been associated with heightened risk of pediatric conditions, including allergic diseases, obesity, inflammatory bowel disease, and neurodevelopmental disorders. The review further evaluates emerging microbiome-directed strategies, such as probiotics, prebiotics, and fecal microbiota transplantation, considering both their therapeutic promise and current challenges. Collectively, current evidence underscores the early-life gut microbiome as a central determinant of host development and a compelling target for disease prevention strategies.}, }
@article {pmid42228693, year = {2026}, author = {Marquez Rosales, S and Amitabh, P and Olmstead, EM and Avey, EPR and Wall, ES and Ortiz de Ora, L and Wiles, TJ and Parthasarathy, R}, title = {Imaging the impact of rotifer consumption on bacterial behaviors in the zebrafish gut.}, journal = {PloS one}, volume = {21}, number = {6}, pages = {e0349516}, pmid = {42228693}, issn = {1932-6203}, mesh = {Animals ; *Zebrafish/microbiology ; *Vibrio/physiology ; Larva/microbiology ; *Rotifera/microbiology/physiology ; *Gastrointestinal Microbiome/physiology ; *Enterobacter/physiology ; *Intestines/microbiology ; Microscopy, Fluorescence ; }, abstract = {The gut microbiota influence many aspects of their host's health and physiology including the digestion of food, and food intake in turn influences the composition of the gut microbiome. However, the ways in which food can alter the behavior of intestinal bacteria remain largely unknown, due in large part to the difficulty of assessing behavior in situ. Larval zebrafish provide a model for addressing this gap because of their optical transparency and their ability to be prepared germ-free and then associated with specific microbial species. Using light sheet fluorescence microscopy to visualize bacteria inside the intestines of live zebrafish larvae, we examine the properties of two commensal strains with markedly different physical characteristics. One is a zebrafish-commensal Enterobacter species that forms large aggregates in unfed larvae, and the other is a pathobiont Vibrio species, capable of damaging intestinal tissue, that is motile and planktonic. We use recently developed ultraviolet irradiation methods to dramatically lower the microbial content in rotifers, a common live food for larval fish, thereby enabling the assessment of feeding effects independent of the introduction of new microbes. Following host consumption of rotifers, Enterobacter clusters disintegrate into motile individuals. Vibrio remains planktonic in fed larvae but decreases the activity of its Type VI Secretion System, as revealed by a fluorescent fusion protein comprising one of the secretion apparatus proteins and green fluorescent protein, leading to a strong decrease in damage to host tissue. Our results reveal that feeding can have major impacts on bacterial behavior that should be considered in models of normal gut microbiome dynamics as well as pathogenesis.}, }
@article {pmid42228750, year = {2026}, author = {Qiu, C and Wang, H and Liu, R}, title = {Associations between body composition and gut microbiota in female college students with and without dance training.}, journal = {PloS one}, volume = {21}, number = {6}, pages = {e0350639}, pmid = {42228750}, issn = {1932-6203}, mesh = {Humans ; Female ; *Body Composition/physiology ; Students ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Dancing ; Young Adult ; Universities ; Feces/microbiology ; Adiposity ; Electric Impedance ; Adult ; }, abstract = {Physical activity has been associated with gut microbiota variation and body composition phenotypes, but evidence in female dance students remains limited. This study compared body composition profiles and gut microbiota characteristics between female university students majoring in dance and those from non-dance majors. Seventy students were included (n = 35 per group). Body composition was assessed using bioelectrical impedance analysis (InBody 970), and fecal samples were analyzed by 16S rRNA gene sequencing. Dance students exhibited significantly lower adiposity related parameters and central fat accumulation indices, including PBF, BFM, FMI, VFA, VFL, WC, WHR, WHtR, ABSI, and conicity index (P < 0.001), while showing higher SMM/WT, TBW/WT, and lower limb lean mass distribution (P < 0.001). No significant differences were observed in FFM, SMM, or SMI (P > 0.05). Gut microbiota composition differed between groups, with differential taxa observed across multiple taxonomic levels. Notably, Faecalibacterium and Lachnospiraceae_ND3007_group showed negative correlations with adiposity related indices and positive correlations with muscle and hydration related parameters, whereas Peptoniphilus, Ezakiella, and Fenollaria were positively correlated with adiposity related indices. In addition, Fusobacterium and Escherichia Shigella were positively associated with central adiposity measures. These findings indicate that female dance students exhibit distinct body composition profiles, while microbiome-related differences and associations appear modest and exploratory, warranting further validation in larger and well-controlled studies.}, }
@article {pmid42228922, year = {2026}, author = {Poveda, J and Silva, D and Sousa, B and Romão, IR and Carmo Gomes, JD and Soares, C and Fidalgo, F and Duarte, I and Vilchez, JI}, title = {Endophytic seed microorganisms in legumes: Natural bioinoculants for sustainable agriculture.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/erag261}, pmid = {42228922}, issn = {1460-2431}, abstract = {As global food demand rises against the backdrop of environmental and health concerns from intensive agrochemical use, there is an urgent need for sustainable crop-management strategies. In this perspective, seed-borne endophytic microbes, including bacteria and fungi, in legumes offer a naturally inherited bioinoculant system. This review integrates 35 Scopus and Web of Science studies to examine the occurrence, transmission dynamics, and functional diversity of endophytes within seeds of key legume species. Seed endophytes contribute to plant development and productivity through multiple mechanisms: atmospheric nitrogen fixation; solubilization of phosphorus and potassium; synthesis of siderophores and indole-3-acetic acid; and modulation of rhizosphere microbial communities, collectively enhancing germination rate, biomass accumulation, and yield. Under abiotic stress conditions, such as drought, nutrient deficiency, or contaminant exposure (metals and pesticides), such beneficial microbes promote root architecture remodeling, exopolysaccharide secretion, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, thereby improving stress resilience. In biotic contexts, certain bacterial endophytes may contribute to biocontrol through antibiotic production, while fungal inoculants have been reported to synthesize alkaloids that can deter herbivores. By elucidating the multifaceted roles of legume seed endophytes, this review underscores their potential as a turnkey, eco-friendly bioinoculants, paving the way for greener agricultural practices without compromising crop performance.}, }
@article {pmid42229136, year = {2026}, author = {Delgado, N and Fernández, KG and Zambrano-Alegría, C and Espinosa, ZYD and Ramos-Cabrera, E}, title = {Physiological and microbial alterations induced by pesticides in agricultural systems: A bioassay- and 16S rRNA-based approach.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142560}, doi = {10.1016/j.jhazmat.2026.142560}, pmid = {42229136}, issn = {1873-3336}, abstract = {The extensive use of pesticides in agricultural production systems has increased interest in understanding their potential impacts on soil environmental dynamics. This study evaluates the effects of pesticide application on Lactuca sativa L. and soil microbiota. An initial field survey identified the main active ingredients commercial pesticides, followed by bioassays assessing germination and early development of Lactuca sativa, as well as soil microbial structure through physiological assessments and metagenomic analyses based on 16S rRNA gene sequencing, during a three-week soil experiment. Thirty active ingredients were identified in 92 agricultural products. Chlorpyrifos was identified as one of the most commercialized insecticides, where insecticides represented 69% of marketed phytosanitary products, mainly organophosphates (18%) and pyrethroids (21%), despite its hazardous classification and ban in several countries. Germination assays showed a hormetic response at low dose (2200 mg/L), reaching 70% germination compared with 51% in the control, while the germination index decreased to 75% at the recommended dose (4400 mg/L). Statistical analyses revealed inhibition of hypocotyl elongation (p = 0.001) and cotyledon development (p = 0.029). Soil microbiome analysis showed that high chlorpyrifos concentrations reduced microbial richness and diversity, while beta diversity analyses explained 99% of the variance among treatments. Proteobacteria, Burkholderiales, and Sphingomonadales increased under pesticide exposure, indicating microbial adaptation and biodegradation potential. Functional prediction using PICRUSt2 revealed enrichment of genes K03381, K00446, K01048, and K01560 associated with potential organophosphate degradation pathways. These findings demonstrate that chlorpyrifos induces ecological and seedling alterations even at agronomically recommended concentrations. highlighting the need to strengthen sustainable pesticide management and environmental monitoring strategies.}, }
@article {pmid42229147, year = {2026}, author = {Zhao, M and Zhou, J and Yang, W and Li, R and Wang, J and Peng, Y and He, Y and Zhou, H and Ye, Q}, title = {Differential Associations of Human Herpesviruses With Oral Bacteria and Periodontitis Severity: A Cross-Sectional Analysis.}, journal = {International dental journal}, volume = {76}, number = {4}, pages = {109650}, doi = {10.1016/j.identj.2026.109650}, pmid = {42229147}, issn = {1875-595X}, abstract = {INTRODUCTION AND AIMS: The polymicrobial synergy and dysbiosis model is increasingly recognized as a key pathogenic factor in periodontitis. Human herpesviruses (HHVs), including EBV, HCMV, and HSV-1, have been linked to periodontitis development. However, current research lacks sufficient evidence to clarify the correlation between HHVs, periodontitis progression, and periodontal microbiota. This study aimed to investigate the association between HHVs in gingival crevicular fluid (GCF) and periodontitis severity, as well as the correlation patterns between viruses and periodontal microbiota.<br><br>METHODS: A total of 339 subjects (64 healthy controls, 275 periodontitis patients) were stratified according to the 2018 periodontitis classification criteria. Viral loads were quantified by quantitative real-time PCR (qPCR), and microbial communities were analysed via high-throughput 16S rRNA sequencing.<br><br>RESULTS: HCMV and EBV loads were significantly positively correlated with clinical parameters including probing depth (PD), clinical attachment loss (CAL), and bleeding on probing (BOP) (all P < .001), and their infection status was closely associated with periodontitis staging. HSV-1 showed no significant association with any periodontal indicators (P > .05). In the EBV/HCMV coinfection group, 92.9% of patients were classified as stage II-IV periodontitis, suggesting potential combined viral associations with disease severity. Microbiome analysis revealed significantly higher microbial diversity in the HCMV-H compared to the HCMV-L. HCMV load was positively correlated with known pathogens such as Porphyromonas gingivalis and Tannerella forsythia, as well as novel associated bacteria (eg, Schwartzia succinivorans, Peptostreptococcus stomatis). Functional prediction showed significant enrichment of microbial metabolic pathways in HCMV-H patients, including Helicobacter pylori infection and isoquinoline alkaloid biosynthesis.<br><br>CONCLUSION: HCMV is strongly associated with periodontitis severity and bacterial dysbiosis, while EBV acts as an independent risk factor correlated with periodontitis severity. In contrast, HSV-1 shows no significant association with periodontitis severity. This study provides new evidence for the polymicrobial pathogenesis of periodontitis and highlights virus-bacteria associations as potential therapeutic targets, although further longitudinal studies are needed to establish causality.}, }
@article {pmid42229215, year = {2026}, author = {Alharthy, OM and Alshegaihi, RM and Fayad, E and Binjawhar, DN and Alshaharni, MO and Alqurashi, M and Alhelaify, SS and Peijnenburg, W}, title = {Oxalic acid enhances wheat (Triticum aestivum L.) resilience to combined abiotic stresses through integrated physiological and rhizospheric microbial modulation.}, journal = {Plant physiology and biochemistry : PPB}, volume = {236}, number = {}, pages = {111432}, doi = {10.1016/j.plaphy.2026.111432}, pmid = {42229215}, issn = {1873-2690}, abstract = {Soil contamination and abiotic stress have become serious global problem due to rapid development of social economy. Oxalic acid (OA), an important organic acid and fertilizer component, has been found effective in enhancing plant tolerance against various abiotic stresses. For this purpose, we have designed the current experiment to explore the contribution of OA in mediating growth and eco-physiology by alleviating abiotic stresses, in wheat (Triticum aestivum L.). Seedlings of T. aestivum were subjected to the different abiotic stresses including drought, salinity, heat, and cold stress, and were supplemented with exogenous OA at 5 mM. Results from the present study revealed that the abiotic stresses induced a substantial decrease in shoot length, root length, number of leaves, leaf area, shoot fresh weight, root fresh weight, shoot dry weight, root dry weight, chlorophyll-a, chlorophyll-b, total chlorophyll, carotenoid content, net photosynthesis, stomatal conductance, transpiration rate, soluble sugar, reducing sugar, non-reducing sugar contents, calcium (Ca[2+]), magnesium (Mg[2+]), iron (Fe[2+]), and phosphorus (P) contents, microbial diversity, richness, and evenness in T. aestivum plants. In contrast, abiotic stresses in the soil significantly (P < 0.05) increased phenolic content, malondialdehyde (MDA), hydrogen peroxide (H2O2), health risk indices, bioaccumulation factors. Although, the activities of enzymatic antioxidants such as superoxide dismutase, peroxidase, catalase, ascorbate peroxidase in the T. aestivum plants and non-enzymatic such as phenolic, flavonoid, ascorbic acid, and anthocyanin contents were increased with the exposure of abiotic stresses. The application of OA significantly improved photosynthetic efficiency, microbial diversity, richness, and evenness, while reducing health risk indices, bioaccumulation factors, MDA, and H2O2 contents under stress conditions. Proteomic and transcriptomic profiling further supported the regulatory role of OA in modulating stress-responsive signaling pathways and enhancing stress tolerance in T. aestivum plants. Increased antioxidant enzyme activities in OA-treated plants appeared to play a crucial role in scavenging stress-induced reactive oxygen species. Research findings, therefore, suggested that OA application can ameliorate abiotic stresses toxicity in T. aestivum seedlings and resulted in improved plant growth and composition under abiotic stresses.}, }
@article {pmid42229603, year = {2026}, author = {Wang, J and Cao, S and Li, X and Zhou, Z and Du, R}, title = {Extracellular polymeric substances Govern granule size differentiation and microbial assembly in denitratation-Anammox systems.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135040}, doi = {10.1016/j.biortech.2026.135040}, pmid = {42229603}, issn = {1873-2976}, abstract = {The Complete Ammonium and Nitrate Removal via Denitratation-Anammox over Nitrite (CANDAN) is a promising low-carbon strategy for sustainable nitrogen removal; however, the mechanistic linkage between extracellular polymeric substances (EPS), aggregation behavior, granule size differentiation, and microbial assembly remains unclear. Here, size-fractionated granules from a CANDAN reactor were systematically investigated to establish a multi-scale framework linking EPS structural properties to aggregation-driven granule organization and microbiome assembly. Medium-sized granules (0.5-1.0 mm) exhibited the highest aggregation capacity (74.5%) and fastest aggregation kinetics, indicating a cohesive and dynamically stable matrix. This aggregation advantage was closely associated with optimized functional performance, including high specific anammox activity (8.76 ± 1.36mg N g[-1] VSS h[-1]), the highest nitrate reduction and nitrite production rates, and a high nitrite transformation ratio (90.1%), reflecting efficient pathway coupling in CANDAN systems. EPS analyses revealed that aggregation and stability were governed primarily by structural organization rather than bulk EPS content. Medium-sized granules were characterized by a lower protein-to-polysaccharide ratio, enriched hydrophobic functional groups, and β-sheet-dominated protein conformations, which collectively enhanced intercellular cohesion and stabilized the EPS matrix. This structurally optimized aggregation regime further shaped microbial assembly, promoting the enrichment and coordination of Candidatus Brocadia and Thauera. Overall, this study identifies aggregation capacity as a key mechanistic driver linking EPS structural properties to granule size differentiation and microbial assembly, highlighting granule size as a mesoscale regulator bridging physicochemical structure and ecological function.}, }
@article {pmid42229782, year = {2026}, author = {Nieboer, M and Rosenow, C and Koch, J and Barlow, J and Sanchez-Sotelo, J and O'Driscoll, S and Morrey, M}, title = {Morrey Award 2025: Cell Count and Differential of Aspirated Fluid in the Diagnosis of Periprosthetic Joint Infection of Total Elbow Arthroplasty.}, journal = {Journal of shoulder and elbow surgery}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jse.2026.05.018}, pmid = {42229782}, issn = {1532-6500}, abstract = {BACKGROUND: Periprosthetic joint infection (PJI) is a common method of failure following total elbow arthroplasty (TEA). Diagnosis is often guided by synovial fluid leukocyte counts and neutrophil percentages. While cutoff values have been defined for hip and knee arthroplasty PJI, the elbow has a different microbiome and a higher rate of PJI. Currently, there are no data to guide determination of PJI following TEA. The purpose of this study was to identify cutoff values of synovial fluid leukocyte counts, neutrophil percentage, erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) to aid in detection of periprosthetic total elbow infection.<br><br>METHODS: We identified 135 TEA undergoing revision surgery that had preoperative aspiration of the synovial fluid at a single institution. Receiver operating characteristic (ROC) curves were utilized to determine the optimal cutoff points for synovial fluid leukocyte count, the neutrophil differential, the ESR and the CRP. Sensitivity, specificity, negative predictive value and positive predictive value were determined. Patients were determined to be infected when they had a positive intraoperative culture or gross purulence at the time of reoperation.<br><br>RESULTS: 35 elbows were found to be infected and 100 were determined to be aseptic. The infected elbow group had a higher mean fluid leukocyte count (8100 vs. 687 cells/&#x3bc;L, p <0.01), higher neutrophil differential (63% vs. 18%, p<0.01), higher ESR (32 vs. 15mm/1h, p<0.01) and higher CRP (15 vs. 5mg/L, p<0.01) than the aseptic cohort. Based on the ROC curves the optimal cutoff values were a leukocyte count of 1300 cells/&#x3bc;L (sensitivity 88%, specificity 75%), neutrophil differential of 70% (sensitivity 71%, specificity 92%), ESR >13 (sensitivity 76%, specificity 67%) and CRP >7 (sensitivity 73%, specificity 83%). When both the leukocyte count and neutrophil differential were below the cutoff values, the negative predictive value was 96%. When both the neutrophil differential and ESR were above the cutoff values the positive predictive value was 95%.<br><br>DISCUSSION: This study identifies optimal synovial fluid and inflammatory marker cutoff values to help clinicians determine the presence of a TEA PJI prior to revision surgery. The optimal cutoff values were a leukocyte count >1300 cells/&#x3bc;L, neutrophil differential >70%, ESR >13 and CRP >7.}, }
@article {pmid42229820, year = {2026}, author = {Lee, DH and Kim, DY and Joung, HC and Kim, H and Jeon, Y and Lee, S and Shin, CH and Lee, YS and Bang, JY and Lee, EJ and Cha, SY and Bae, SH and Lee, HW}, title = {Probiotic-driven gut-liver redox crosstalk modulates hepatic Nrf2 signaling pathway and attenuates metabolic dysfunction-associated steatohepatitis.}, journal = {Free radical biology &amp; medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.freeradbiomed.2026.05.338}, pmid = {42229820}, issn = {1873-4596}, abstract = {Metabolic dysfunction-associated steatohepatitis (MASH) is a chronic liver disease characterized by persistent inflammation, oxidative stress, and progressive fibrosis. There is currently no effective pharmacological therapy for MASH. We investigated whether two defined probiotic bacteria strains, Lactobacillus delbrueckii subsp. lactis (L. lactis) CKDB001 and Lactiplantibacillus plantarum (L. plantarum) Q180, attenuate MASH pathology in association with modulation of gut-liver redox signaling. Using diet-induced preventive and therapeutic mouse models of MASH, we show that oral administration of these strains significantly improves hepatic steatosis, robustly attenuates fibrosis, and reduces inflammatory and oxidative stress markers. Probiotic treatment was associated with increased intestinal glutathione availability, and was accompanied by activation of hepatic nuclear factor erythroid 2-related factor 2 (Nrf2) signaling and upregulation of canonical antioxidant enzymes, consistent with improved hepatic redox homeostasis and reduced hepatocellular injury. Microbiome profiling revealed successful intestinal persistence of the administered strains and enrichment of other bacterial taxa associated with gut barrier integrity and metabolic resilience, including Akkermansia muciniphila, Parabacteroides goldsteinii, and Mediterraneibacter butyricigenes. Functional prediction analysis further suggested enhancement of microbial glutathione metabolism pathways, supporting a potential role for microbiota-driven redox modulation in host protection. Therapeutic efficacy was maintained after disease establishment and under conditions recapitulating features of a lean MASH-like phenotype, highlighting obesity-independent mechanisms of action. Collectively, our findings support a probiotic-driven association between intestinal glutathione dynamics and hepatic Nrf2 activation within the gut-liver axis, providing a mechanistically informed and translationally relevant framework for MASH intervention.}, }
@article {pmid42229856, year = {2026}, author = {Rittmann, M and Wu, G and Zhao, L and Green, TJ and Hanselman, EC and Green, R and Lam, YY and Miller, JW}, title = {Associations Between Biomarkers of Vitamin B12 Status and Gut Microbial Guilds in a Cohort of Australian Adults.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {101622}, doi = {10.1016/j.tjnut.2026.101622}, pmid = {42229856}, issn = {1541-6100}, abstract = {BACKGROUND: Vitamin B12 is an essential nutrient required for hematological and neurological function. Human gut microbes either synthesize B12 or utilize B12 consumed by hosts. Consequently, variation in gut microbiota may influence B12 status in humans.<br><br>OBJECTIVE: The goal was to assess associations between gut microbiota and serum B12 and a functional biomarker of B12 status, methylmalonic acid (MMA).<br><br>METHODS: In 90 adults (44 males/46 females; 20-75y) living in Sydney, Australia, 16S rRNA gene V3-V4 amplicon sequencing was used to profile gut microbiota at the amplicon sequence variant (ASV) level. B12 was measured by automated chemiluminescence and MMA by HPLC-tandem-mass spectrometry. Associations between tertiles of B12 and MMA and microbial alpha and beta diversity and overall microbiota composition were assessed. Microbial guilds were identified via co-abundance analysis on ASVs. Multivariate linear regression and random forest regression were used to assess the associations between guilds and the B12 biomarkers, controlling for age, sex, body mass index, and fiber intake.<br><br>RESULTS: Mean serum B12 and MMA were 389&#xb1;177 pmol/L and 210&#xb1;80 nmol/L, respectively. Gut microbial diversity and richness was significantly associated with B12 tertiles (Shannon index: p=0.010; Faith's phylogenetic diversity: p=0.048; ASV number: p=0.022). No associations were observed between B12 tertiles and beta diversity or between MMA tertiles and alpha or beta diversity. Thirty guilds were identified, with 2 guilds and age included in the final model predictive of B12 (p=0.03), and 3 different guilds and no covariates included in the final model predictive of MMA (p=0.003).<br><br>CONCLUSIONS: These results indicate that different guilds are predictive of serum B12 versus serum MMA. This suggests that some of the variance in serum MMA in adults is not specific to B12 status, which has ramifications for interpreting MMA as a marker of B12 status.}, }
@article {pmid42229880, year = {2026}, author = {Zhang, L and Sun, W and Wang, X and Zhang, Z and Chen, H}, title = {Therapeutic-Dose Enrofloxacin Immersion Induces Intestinal Immunostimulation and Microbiota Dysbiosis in Juvenile Black Seabream Acanthopagrus schlegelii.}, journal = {Journal of applied toxicology : JAT}, volume = {}, number = {}, pages = {}, doi = {10.1002/jat.70260}, pmid = {42229880}, issn = {1099-1263}, support = {2024YFD2401803//National Key Research and Development Program of China/ ; 326MS0356//Hainan Provincial Natural Science Foundation of China/ ; 426MS0365//Hainan Provincial Natural Science Foundation of China/ ; 2024RC12//Central Public-interest Scientific Institution Basal Research Fund&#xff0c;South China Sea Fisheries Research Institute&#xff0c;CAFS/ ; 2023TD06//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; }, abstract = {Enrofloxacin (ENR) is a commonly identified veterinary pharmaceutical in global aquaculture products, and short-term therapeutic applications of ENR at recommended doses may exert adverse effects on farmed fish. The present investigation evaluated the toxicological impacts of ENR on intestinal detoxification capacity, immune response, and microbial community dynamics of commercially significant Acanthopagrus schlegelii. Short-term treatment of ENR at the clinically recommended dose (5 mg/L) showed little modulation on expression levels of key detoxification enzymes, while 10 mg/L ENR (over-therapeutic concentration) induced significantly elevated Phase I/II biotransformation enzymes in treated fish. Interestingly, 5 mg/L ENR (decontaminated for 72 h) triggered immunostimulation effects via significantly promoting inflammatory cytokines and lysozyme gene expression. In addition, persistent suppression of the diversity and richness of gut microbial communities was observed following immersion in 5 and 10 mg/L ENR. ENR exposure triggered restructuring of intestinal microbial composition of black seabream, characterized by a reduction in beneficial microbiota and an expansion of opportunistic and antibiotic-resistant bacteria, which may contribute to the observed immune perturbation and long-term health risks. In summary, our findings raise concerns about the safe use of ENR in aquaculture, suggesting that current practices may pose long-term health risks to marine farmed fish.}, }
@article {pmid42230118, year = {2026}, author = {Zhong, ZW and Lu, YQ and Duan, Y and Ma, J and Liu, N}, title = {Fusobacterium nucleatum in cancer: from bystander to driver.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-338000}, pmid = {42230118}, issn = {1468-3288}, abstract = {The human microbiota comprises a diverse and extensive community of microorganisms that participate in intricate interactions with the host, several of which are increasingly acknowledged as key modulators of health and disease. Among these, Fusobacterium nucleatum (Fn), an oral commensal bacterium, has emerged as a significant oncobacterium implicated in tumour progression. The Fn genus comprises distinct subspecies, clades and strains, exhibiting marked phylogenetic and physiological heterogeneity. Consequently, pinpointing the true functional modulators within this complex community and elucidating their mechanisms in various physio-pathological states remains a critical yet challenging endeavour. Moreover, the complete mechanism underlying Fn's function across different spatial locations and physiological states remains to be fully elucidated. This review details the genetic and phenotypic heterogeneity among Fn subspecies, which underlies their differential characteristics and niche adaptation. We further delineate key effectors of Fn, such as adhesins, metabolites and exoproteins, which collectively facilitate host cell invasion, immune evasion and chemoresistance induction. We explore the translational potential of Fn, underscoring its utility as a diagnostic biomarker and a promising target for novel therapeutic strategies.}, }
@article {pmid42230119, year = {2026}, author = {Alexander, JL and Mullish, BH and Thomas, L and Weersma, RK and Sokol, H and Roberts, LA and Edwards, LA and Emmanuel, A and Gerasimidis, K and Hall, LJ and Iqbal, TH and Kinross, JM and McIlroy, J and Monaghan, TM and Sergaki, C and Shawcross, DL and Stewart, CJ and Lamb, CA and Williams, HRT and Hansen, R and Hold, G}, title = {Recent advances in our understanding of the gut microbiome: an analysis from the Gut Microbiota for Health Expert Panel of the British Society of Gastroenterology.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2026-338252}, pmid = {42230119}, issn = {1468-3288}, abstract = {At around 10 years ago, at the time of the first publication by the Gut Microbiota for Health Expert Panel of the British Society of Gastroenterology, recognition of the gut microbiome's importance in health and disease was transitioning from fringe interest towards major global pursuit. A decade on, we appraise the considerable progress made in the field, while acknowledging ongoing challenges. Earlier human work characterising the 16S rRNA gene amplicon signature of particular conditions in small cohorts has been superseded by larger, multicentre studies with extensive metadata. Studies increasingly employ shotgun metagenomics and other 'omic' techniques-coupled with refined bioinformatic tools and disease models-to better characterise perturbation in gut microbiome functionality. The arrival of 'gold standard' pipelines for microbiome analysis and increased mechanistic validation of signals are key developments towards more clinically-translatable outcomes. Novel clinical areas where the gut microbiome has relevance have emerged, including early life and the efficacy of certain treatments (including immune checkpoint inhibitors and vaccination). Enthusiasm for 'microbiome diagnostics and treatments' has grown, but barriers to widespread adoption remain. Faecal microbiota transplant (FMT) is established for treating recurrent Clostridioides difficile infection, with donor-derived 'next generation' FMT products licensed for this condition in certain countries. Beyond FMT, other microbial therapeutic techniques-including nutritional, bacteriophage and probiotic therapies-show promise, but have not fulfilled their high expectations yet. Gut microbiome research is now well-established and shows significant translational potential; the future focus will be translational work to drive its utility in clinical diagnostics, prognostics and therapeutics.}, }
@article {pmid42230163, year = {2026}, author = {Chang, X and MacIsaac, HJ and Chorus, I and Bullerjahn, GS and Kurmayer, R and Ahn, CY and Kong, X and Wilhelm, SW and Wood, SA and Tang, X and Paerl, HW and Hilt, S and Jeppesen, E and Hamilton, DP and Nakano, SI and Visser, P and Huisman, J and Wang, H and Song, L and Mckay, RM and Qin, B and Sitoki, L and Xu, R}, title = {Scanning the horizon for harmful cyanobacterial blooms.}, journal = {Trends in ecology &amp; evolution}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tree.2026.04.012}, pmid = {42230163}, issn = {1872-8383}, abstract = {Harmful cyanobacterial blooms are increasing worldwide, threatening freshwater ecosystems, animal health, and human well-being. To guide research needed for effective prediction, prevention, and management, we identify four priorities: understanding eco-evolutionary and phylogeographic drivers that promote toxigenic cyanobacterial genotypes; resolving molecular and environmental controls on cellular cyanotoxin biosynthesis; integrating microbiome science with multiomics and epidemiology to assess associated health risks beyond cyanotoxins; and quantifying ecosystem-scale bottom-up and top-down controls in understudied settings, particularly tropical and benthic habitats. New research tools for addressing these priorities enable elucidating the mechanistic basis for anticipating cyanobacterial blooms and provide the understanding needed for their control in a rapidly changing world.}, }
@article {pmid42230169, year = {2026}, author = {Octoman, A and Arrieta, MC}, title = {Early-life gut fungi as modulators of metabolic development.}, journal = {Trends in endocrinology and metabolism: TEM}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tem.2026.05.003}, pmid = {42230169}, issn = {1879-3061}, abstract = {Early life is a critical window during which microbes shape immune maturation, nutrient handling, and long-term metabolic health. Although fungi represent a minor proportion of the gut microbiome, emerging evidence suggests they exert a disproportionate influence. In this review, we synthesize current gut mycobiome knowledge during pregnancy and infancy, including ecological assembly, maternal and environmental sources, and links to early metabolic phenotypes. Recent studies on human cohorts and gnotobiotic mice demonstrate that specific fungal species can causally alter adiposity, adipose immune architecture, and bacterial function. We also highlight major knowledge gaps, including questions around true colonization, fungal activity, strain-level transmission, and the molecular basis of fungal-bacterial-host interactions. These findings position the early-life mycobiome as a promising frontier for discovery in metabolic development.}, }
@article {pmid42230260, year = {2026}, author = {Cabezas-Cruz, A and Piloto-Sardiñas, E and Obregón, D}, title = {Host-vector microbiome similarity predicts immune-mediated disturbance and vector competence.}, journal = {Trends in parasitology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pt.2026.05.010}, pmid = {42230260}, issn = {1471-5007}, abstract = {Vector-borne disease transmission is highly heterogeneous, yet existing models emphasize climate, host density, and pathogen load. We propose that host-vector microbiome similarity represents a previously unrecognized ecological axis in transmission biology. During blood feeding, vectors ingest host-derived immune effectors shaped by the host microbiota. When immune targeting depends on shared microbial features, microbiome similarity predicts the magnitude of immune-mediated disturbance within the vector gut, altering colonization resistance and influencing pathogen establishment. These effects are context-dependent and may enhance or suppress transmission. This framework generates testable predictions linking microbiome similarity, immune-mediated disturbance, and vector competence across systems. Incorporating microbiome similarity into transmission models may help explain heterogeneity and improve ecological understanding and intervention strategies.}, }
@article {pmid42230654, year = {2026}, author = {Li, J and Liang, X and Liu, P and Zhu, W and Jin, W and Mao, S and Xie, F}, title = {Rumen-derived Pichia membranifaciens modulates the rumen microbiome and metabolome and mitigates methane emissions in dairy cows.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01029-0}, pmid = {42230654}, issn = {2055-5008}, abstract = {Methane emissions from ruminants represent a significant environmental challenge and dietary energy loss. While yeasts are potential rumen modulators, specific methane-mitigating species remain poorly characterized. Here, we screened 73 rumen-derived strains in vitro, identifying Pichia membranifaciens M12 as the most effective candidate, reducing methane output by 17.1%. Subsequently, a randomized block trial with 36 dairy cows compared a control group with P. membranifaciens M12 supplementation at 2.5 and 5 × 10[11] CFU/cow/day. Methane yield per unit of dry matter intake significantly decreased in the high-dose group (18.7%, P = 0.003), without compromising lactation performance and animal health. Multi-omics analyses revealed that M12 suppressed hydrogenotrophic methanogens (e.g., Methanobrevibacter) and hydrogen-producing bacteria (e.g., Ruminococcus and Fibrobacter), while enriching specific eukaryotic taxa like Orpinomyces and Entodinium. Metabolomic profiling indicated a significant dose-dependent accumulation of metabolites. Metagenomic function analysis demonstrated the decreased abundance of key methanogenesis genes (e.g., mcrABCDG) and increased abundance of hydrogenase (hyaABC), lactate-forming (ghrB), and propionate-forming (mcmA1 and lcdB), suggesting a redirection of reducing equivalents from methanogenesis toward propionate synthesis, alongside enhanced butyrate production. These findings demonstrate that P. membranifaciens M12 mitigates methane emissions via coordinated ecological and metabolic modulation, highlighting its potential as a sustainable strategy for low-carbon ruminant production.}, }
@article {pmid42230678, year = {2026}, author = {David, H and Balu, P and Vasudevan, S and Narayanan, VHB and Solomon, AP and Ramyadevi, D}, title = {Thermoresponsive carbohydrate polymer mucoadhesive gel for synergistic delivery of acarbose and fluconazole against Candida biofilms.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-52764-5}, pmid = {42230678}, issn = {2045-2322}, abstract = {The emerging threat of drug-resistant Candida albicans, especially in recurrent vulvovaginal candidiasis (VVC) biofilms, has revealed weaknesses in existing monotherapeutic antifungal treatments. In this study, we investigated the antifungal activity of a new dual-drug in situ mucoadhesive gel system containing acarbose (AC), a pseudo-oligosaccharide sugar and FDA-approved α-glucosidase inhibitor, together with fluconazole (FLC). Although AC showed mild antifungal activity by itself, when combined with FLC, it dramatically potentiated fungicidal activity, disrupted biofilms, blocked morphogenetic switching, and arrested post-treatment hyphal regrowth. In checkerboard assays and time-kill kinetics, AC-FLC combination was highly synergistic against Candida spp., including clinical isolates, with > 2-log10 decrease in CFU/mL. The thermosensitive gel (PCH16), formulated using poloxamer 407 along with the carbohydrate-based polymers chitosan and HPMC, exhibited sustained drug release, favorable rheological properties, and strong mucoadhesion suitable for vaginal delivery. Notably, the formulation retained Lactobacillus species viability, suggesting microbiome compatibility. These results affirm the promise of repurposing acarbose as a novel, non-traditional antifungal adjuvant that, in co-administration with FLC in vaginal gel, represents an encouraging, localized, and microbiota-conserving therapy for treating recurrent and resistant VVC.}, }
@article {pmid42230679, year = {2026}, author = {Giorgini, G and Leblanc, N and Muller, C and Dumais, E and Labbé-Blondeau, MN and Thibodeau, A and Flamand, N and Di Marzo, V and Silvestri, C}, title = {Seal and fish oils partially counteract inflammation and modulate endocannabinoidome lipid and oxylipin alterations in DSS-induced colitis.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-54447-7}, pmid = {42230679}, issn = {2045-2322}, support = {IT19175//Mitacs/ ; }, abstract = {Colitis is associated with endocannabinoidome (eCBome) and gut microbiome alterations, both of which are influenced by the diet, and thus may be modulated through nutritional components as potential therapeutic targets for colitis. We assessed the effects of n-3 polyunsaturated fatty acid (PUFA)-rich fish (FO) and seal (SO) oils in the dextran sodium sulphate (DSS) colitis mouse model. Mice were assessed for effects on inflammation, intestinal permeability, anxiety-like behaviour, gut microbiota composition and colon, blood and brain eCBome mediator levels. While neither FO or SO counteracted DSS-induced loss of weight, SO mitigated the increase in intestinal permeability and was more efficacious at reducing inflammation markers (Il1b, Il6, Tnfa and Arg1) than FO. DSS-induced changes in the bacterial community were not altered by FO or SO, which however mitigated alterations in the abundance of the Family XII UCG01 genera. DSS altered several eCBome and oxylipin bioactive lipid levels in a tissue-specific manner. FO and/or SO counteracted some of these changes, especially by increasing the levels of those lipids derived from n-3 PUFAs, many of which have anti-inflammatory activities. Interestingly, the novel eicosapentaenoic acid-derived eCBome mediator 2-eicosapentaenoyl glycerol was a top defining lipid of both FO and SO groups in all tissues. These data point to FO and, particularly SO, as potentially beneficial treatments of colitis through alterations in the eCBome, which is dysregulated in colitis.}, }
@article {pmid42230754, year = {2026}, author = {Bethlehem, L and Bartu, L and Marke, G and Mar, P and Feldman, S and Eggers, J and Ruprecht, C and Britton, GJ and Aggarwala, V and Bongers, G and Li, Z and Yang, N and Hohmann, EL and Mogno, I and Faith, JJ and Grinspan, A}, title = {15-strain live biotherapeutic product or same donor fecal microbiota transplant for recurrent Clostridioides difficile infection: a randomized phase 1b trial.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, pmid = {42230754}, issn = {1546-170X}, abstract = {Fecal microbiota transplant (FMT) is an effective therapy for recurrent Clostridioides difficile infection (rCDI) but has undefined composition and poor scalability. In vitro manufactured live biotherapeutic products (LBPs) enable both scalability and defined strain composition but with higher manufacturing complexity, resulting in few LBP clinical trials. Here we show how an accessible platform to produce human-grade LBPs could accelerate LBP development. We provide regulatory documentation and manufacturing protocols to facilitate translating microbiome advances to human trials. With this platform, we conducted the first direct comparison of the same bacterial strains from donor-sourced FMT compared to an in vitro manufactured 15-strain LBP drug product, MTC01, for the treatment of rCDI. In a phase 1b randomized controlled trial, 18 of 20 screened patients met eligibility and were randomized equally to one of four arms: low-dose FMT (n = 4), high-dose FMT (n = 5), low-dose MTC01 (n = 4) or high-dose MTC01 (n = 5), with a 5:1 female:male ratio. The primary outcome of safety was met with 10 adverse events across eight patients, evenly spread across MTC01 (five events) and FMT (five events) recipients and no treatment-related adverse events across all four groups. For secondary outcomes of efficacy and engraftment, rCDI was prevented 8 weeks after dosing in seven out of nine LBP patients, similar to eight out of nine FMT patients. Strain engraftment was high and durable for both FMT and MTC01 with a dose effect for the LBP. ClinicalTrials.gov: NCT05911997 .}, }
@article {pmid42230943, year = {2026}, author = {González-Llera, L and Santos-Durán, GN and Vences, A and Buján, N and Balado, M and Barreiro-Iglesias, A}, title = {Spontaneous axon regeneration is preserved despite gut microbiota disruption after spinal cord injury in larval lampreys.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-56243-9}, pmid = {42230943}, issn = {2045-2322}, support = {PID2023-147266NB-I00//Agencia Estatal de Investigaci&#xf3;n/ ; }, abstract = {Spinal cord injuries (SCIs) often result in permanent disabilities in humans. One major reason for the lack of recovery is the inability of adult mammalian descending neurons to regenerate their axons after injury. In contrast, several fish species, such as the sea lamprey, exhibit spontaneous axon regeneration and successful functional recovery following a complete SCI. Recent studies have shown that a SCI in rodents and humans induces gut microbiome dysbiosis, which can impair recovery. Therefore, our goal was to examine how the microbiome changes after SCI in a regenerating animal model (the larval sea lamprey) and whether these changes influence the spontaneous regeneration of descending neuropeptidergic (cholecystokinergic) axons. Our data show that a complete SCI triggers an initial shift (5 weeks post-injury) in gut microbial communities in larval lampreys, characterized by an expansion of Legionellaceae family members. However, a treatment with broad-spectrum antibiotic gentamicin during the first 5 weeks post-injury, which profoundly altered the gut microbiome (eliminating Legionellaceae and promoting Bradyrhizobiaceae expansion), did not affect the spontaneous regeneration of descending cholecystokinergic axons at 10 weeks post-injury. This finding indicates that broad gentamicin-induced disruption of the gut microbiota does not detectably impair spontaneous regeneration of descending cholecystokinergic axons in larval lampreys.}, }
@article {pmid42230971, year = {2026}, author = {Lin, TY and Hung, SC and Abe, T}, title = {An oral tyrosine challenge test for functional phenotyping of microbiota-derived phenyl sulfate production.}, journal = {npj metabolic health and disease}, volume = {4}, number = {1}, pages = {}, pmid = {42230971}, issn = {2948-2828}, support = {112-2314-B-303-009 -MY3, 114-2314-B-303-004//National Science and Technology Council, Taiwan/ ; 113-2314-B-303-012, 114-2314-B-303-017-MY3//National Science and Technology Council, Taiwan/ ; TCRD-TPE-114-01//Taipei Tzu Chi Hospital, Taiwan/ ; TCRD-TPE-114-02, TCMF-CP 111-02//Taipei Tzu Chi Hospital, Taiwan/ ; }, abstract = {Phenyl sulfate (PS), a gut microbiota-derived metabolite implicated in the pathogenesis of diabetic kidney disease, is generated through microbial conversion of dietary tyrosine to phenol, followed by hepatic sulfation via SULT1A1. We developed an oral tyrosine challenge test (OTyCT) to phenotype individual PS-producing capacity. Forty-eight healthy adults underwent a standardized tyrosine load with serial plasma PS levels measured over 48 h using LC-MS. OTyCT revealed substantial interindividual variability of PS production independent of baseline PS levels, highlighting marked heterogeneity in host-microbiome metabolic interactions. Sixteen participants in the highest tertile of the incremental area under the curve of PS were defined as high-PS producers. High PS producers exhibited distinct gut microbial signatures despite comparable abundances of known phenol-biosynthetic genes and host SULT1A1 genotypes. These findings suggest that susceptibility to PS-related complications may vary according to gut microbial profiles, supporting OTyCT as a practical tool for metabolic phenotyping and microbiome-informed precision nutrition. Clinical Trial registry name and registration number: Identification of P-Cresyl Sulfate Producer Phenotype by Oral Tyrosine Challenge Test: Interactions Among Diet, Gut Microbiota, and Host Genome, NCT04204174.}, }
@article {pmid42231021, year = {2026}, author = {Lagomarsino, VN and Robinson, A and Mitchell, PE and Jiang, M and Hutchinson, LE and Sekela, JJ and Caron, P and Gehris, MK and Navas, KI and Duarte-Silva, M and Netherland, M and Hasan, NA and Guillemette, C and Redinbo, MR and Rao, M}, title = {Microbial reactivation of host androgens directs enteric neuronal regulation of gut motility.}, journal = {Nature neuroscience}, volume = {}, number = {}, pages = {}, pmid = {42231021}, issn = {1546-1726}, support = {R01DK130836//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; R01DK135707//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; R03DK125636//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; R01GM135218//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R35GM152079//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, abstract = {The coordinated transit of intestinal contents is crucial for digestion and host defense, and is regulated by cross-talk between neural circuits, the muscular gut wall and luminal factors. Here we show that androgen signaling to Nos1[+] enteric neurons and Scn10a[+] spinal afferent neurons is required for normal intestinal transit in mice and is microbiome dependent. Microbial depletion with antibiotics abolished androgen receptor expression in enteric neurons, diminished serum testosterone and caused dysmotility. Androgens were necessary for antibiotics to affect transit and partly sufficient to rescue dysmotility. Nos1 neurons upregulate androgen receptor upon puberty in parallel with shifts in fecal bacterial beta-glucuronidase (GUS) enzymes that can deconjugate steroid glucuronides in mice and humans. Intracolonic administration of a GUS enzyme found to metabolize androgen glucuronides was sufficient to restore neuronal androgen signaling in microbe-depleted mice. Thus, gut microbial reactivation of host-excreted androgens via GUS enzymes represents a dynamic microbe-host interaction that is essential for peripheral nervous system function in homeostasis.}, }
@article {pmid42231156, year = {2026}, author = {Yang, Q and Liang, Y and Liu, J and Jia, R and Li, J and Yan, Z}, title = {Fecal microbiota transplantation from Hezuo pigs alleviates intestinal inflammatory injury in Clostridium perfringens type C-infected piglets via modulation gut microbiota and intestinal barrier.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05169-3}, pmid = {42231156}, issn = {1471-2180}, support = {23JRRA1422//Natural Science Foundation of Gansu Province/ ; 32460845//National Natural Science Foundation of China/ ; GSARS10//Pig Industry in Gansu Agriculture Research System/ ; 2023-QN-135//Lanzhou Youth Science and Technology Talent Innovation Project/ ; }, abstract = {Clostridium perfringens type C (CpC)-induced piglet diarrhea is a major challenge in the swine industry. This study aimed to investigate the protective effects of fecal microbiota transplantation (FMT) from Hezuo pigs against intestinal injury in Duroc×Landrace×Yorkshire (DLY) suckling piglets infected with CpC. Piglets were divided into two groups, including CpC-challenged control group and FMT-treatment group, which received fecal suspension from Hezuo pigs prior to infection. Morphological, immunological, microbiomic, and metabolomic analyses were conducted after post-infection. The results demonstrated that FMT significantly alleviated jejunal damage, leading to a significant increase in jejunal villus height and a significant decrease in crypt depth (P < 0.01). The intervention elevated the number of goblet cells (P < 0.05) and upregulated the expression of tight junction protein genes Occludin, ZO-1, Claudin-1 and the anti-inflammatory cytokine IL-10, while significantly reducing the levels of pro-inflammatory cytokines TNF-α and IL-6 (P < 0.05). FMT enriched beneficial genera such as Akkermansia, Rothia, Peptococcus, and Proteocatella, and increased the levels of the sphingolipid metabolite ceramide (d18:1/18:0). Correlation analysis further indicated that these microbiota alterations were positively associated with intestinal barrier repair and anti-inflammatory activity, and were strongly correlated with ceramide (d18:1/18:0) levels. In conclusion, FMT mitigates CpC-induced intestinal injury by modulating the gut microbiota and metabolome, thereby enhancing intestinal barrier integrity and regulating inflammatory responses. This study provides theoretical support and practical insights for the application of FMT as a promising microbiome-based strategy to control CpC-associated intestinal diseases in piglets.}, }
@article {pmid42231158, year = {2026}, author = {Kuang, Z and Zhan, Q and Tu, J and Li, A and Guo, W and Zheng, R and Jiang, H and Xu, B}, title = {Microbiome and metabolome patterns centered on cancer cachexia link skeletal muscle and adipose tissue depletion to clinical outcomes in locally advanced rectal cancer.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05171-9}, pmid = {42231158}, issn = {1471-2180}, abstract = {BACKGROUND: Cancer cachexia is a multifactorial syndrome characterized by involuntary weight loss and tissue wasting; it was associated with adverse survival outcomes in patients with locally advanced rectal cancer (LARC). However, its biological basis and links to the gut microbiome, circulating metabolites, and body composition in LARC remain unclear.<br><br>METHODS: We conducted a retrospective cohort study of 198 LARC patients, including 30 with cachexia. Gut microbial profiles were characterized using 16S rRNA sequencing with predictive functional inference. Serum metabolites were analyzed via orthogonal partial least squares-discriminant analysis (OPLS-DA) and validated by ROC analysis. Associations among microbial taxa, metabolites, body composition, and clinical indices were assessed using correlation analyses. Survival outcomes were evaluated by Kaplan-Meier curves and multivariate Cox regression models, with subgroup and sensitivity analyses performed to validate the robustness of findings.<br><br>RESULTS: Cachectic patients exhibited marked reductions in BMI, circulating triglycerides and cholesterol, as well as visceral and subcutaneous adipose tissue (VAT and SAT) and skeletal muscle area (SMA) (all P&#x2009;<&#x2009;0.05). Microbial &#x3b1;- and &#x3b2;-diversity were comparable between groups, yet cachexia was associated with selective enrichment of Peptostreptococcaceae, Erysipelotrichaceae, Veillonella, and Fusobacterium, alongside depletion of Faecalibacterium, Roseburia, and Prevotella. Notably, UBA1819 (Ruminococcaceae) was enriched in cachectic patients and inversely correlated with Faecalibacterium, hemoglobin, and albumin, suggesting intra-family functional divergence. Specific cachexia-enriched taxa, including Veillonella and Erysipelotrichaceae, were inversely associated with SMA and VAT, whereas butyrate-producing genera showed positive correlations with muscle preservation. Functional predictions highlighted enrichment of N-acetylneuraminate degradation in cachexia versus TCA cycle pathways in non-cachectic patients. High abundance of Peptostreptococcaceae and Erysipelotrichaceae was associated with poorer overall survival. Metabolomic profiling identified lithocholic acid, cortisone, 3,5,9-trihydroxyergost-7-en-6-one, and 5,6-DHET as cachexia-associated metabolites (AUC 0.65-0.78), which formed cross-domain correlations with microbial taxa and host tissue measures.<br><br>CONCLUSION: Our findings reveal a coordinated linkage between the gut microbiome, metabolome, and host body composition in LARC cachexia. Specifically, selective microbial remodeling and metabolite perturbations are closely coupled with skeletal muscle and adipose tissue depletion and adverse survival. These results provide a conceptual foundation for future mechanistic and translational studies exploring the host-microbiome-metabolic interactions in cancer cachexia.}, }
@article {pmid42231385, year = {2026}, author = {Hu, J and Fan, D and Xiao, C and Kang, C and Shi, J and Li, Y and Liu, J and Shen, L and Lin, N}, title = {Curcumin supplementation during high-altitude exposure modulates body composition and its relationship with gut microbiota: a randomized controlled trial.}, journal = {Nutrition journal}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12937-026-01343-5}, pmid = {42231385}, issn = {1475-2891}, support = {2022NSFSC1422//Natural Science Foundation of Sichuan Province/ ; KJS2525//Open Research Project of the Provincial Key Laboratory of Prevention and Translational Medicine for Major Chronic Diseases at Soochow University/ ; }, abstract = {BACKGROUND: Body composition is crucial for athletic performance and linked to the gut microbiota. Curcumin shows potential to promote muscle regeneration and modulate fat metabolism, but evidence from high-altitude populations remains scarce. This study aimed to evaluate the effects of curcumin on body composition at high altitudes, and explore potential role of gut microbiota.<br><br>METHODS: A total of 102 male Han participants was randomized to curcumin (812&#xa0;mg/d) or placebo groups for 1-week pre-acclimatization and 6-week high-altitude acclimatization. Body composition was assessed via bioelectrical impedance analysis and gut microbiota was analyzed through metagenomic sequencing.<br><br>RESULTS: After high-altitude acclimatization, curcumin significantly reduced the percent body fat (PBF, P&#x2009;=&#x2009;0.030). Soft lean mass (SLM), skeletal muscle mass (SMM) and fat free mass (FFM) were increased in both groups, but the curcumin group exhibited greater increases although without significant difference. Curcumin supplementation significantly attenuated the upper-limbs FFM and arm muscle circumference reduction (P&#x2009;<&#x2009;0.05). The relative abundance of Eubacterium sp. CAG:180 was significantly negative with SLM and SMM (P&#x2009;<&#x2009;0.05). Curcumin significantly increased the abundance of Bifidobacterium pseudocatenulatum, Eubacterium sp. CAG:274 and Eubacterium eligens (P&#x2009;<&#x2009;0.01). Higher abundance of Eubacterium sp. CAG:274, Roseburia inulinivorans, and Bifidobacterium pseudocatenulatum were observed in high-skeletal muscle index participants. Lachnospira pectinoschiza, Clostridium leptum, and Eubacterium sp. CAG:274 were more abundant in low-PBF participants.<br><br>CONCLUSIONS: Curcumin supplementation might increase muscle mass gain and reduce PBF during high-altitude acclimatization that may correlate with changes in gut microbiota composition, and their causal association remains to be further verified.<br><br>TRIAL REGISTRATION: Chinese Clinical Trail Registry, ChiCTR220005965. Registered on May 5, 2022.}, }
@article {pmid42231413, year = {2026}, author = {Chuang, YC and Collman, RG and Ruan, SY and Chien, YC and Huang, YS and Hsu, CC and Wang, JT and Zou, HB and Chang, SC}, title = {Gut microbiome features associated with vancomycin-resistant Enterococcus acquisition in intensive care unit patients.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12941-026-00871-6}, pmid = {42231413}, issn = {1476-0711}, support = {110-2918-I-002-001//National Science and Technology Council/ ; 110-S4901//National Taiwan University Hospital/ ; }, abstract = {BACKGROUND: Vancomycin-resistant Enterococcus (VRE) infection poses a significant healthcare burden in intensive care units (ICUs), and is preceded by gut colonization. The gut microbiome may influence susceptibility to VRE, but its role in ICU patients remains incompletely defined.<br><br>METHODS: We conducted a prospective study of patients admitted to a medical ICU from 2019 to 2021. Stool samples were collected for bacterial 16&#xa0;S rRNA gene sequencing, anal swabs were screened for VRE by culture, and bile acids were measured in initial stool samples.<br><br>RESULTS: We enrolled 108 patients. Thirty-four patients were VRE&#x2009;+&#x2009;on initial screen and remained so (VRE+/+) while 74 were initially negative, of whom 23 acquired VRE (VRE-/+) and 51 remained negative (VRE-/-). There was no difference in alpha-diversity initially between VRE-/- and VRE-/+ groups, whereas VRE+/+ patients had significantly lower alpha-diversity (P&#x2009;<&#x2009;0.001). VRE-/+ patients had a significantly more rapid decrease in alpha-diversity than VRE-/- patients (P&#x2009;=&#x2009;0.04). Beta-diversity of initial stool differed among groups (P&#x2009;=&#x2009;0.001), driven mainly by VRE+/+ patients. A lower Bacteroides/Enterococcus ratio (P&#x2009;=&#x2009;0.049) and low Clostridium scindens abundance (P&#x2009;=&#x2009;0.031) were associated with VRE acquisition. Initial stool from VRE-/- patients had a higher combined concentration of deoxycholic acid and lithocholic acid than that of VRE-/+ patients (P&#x2009;=&#x2009;0.034).<br><br>CONCLUSIONS: VRE acquisition in the ICU was associated with an initial gut microbiome characterized by lower Bacteroides/Enterococcus ratios, lower C. scindens abundance, and lower deoxycholic and lithocholic acid concentrations. Our findings are consistent with a possible role of these microbiome features in colonization resistance, as suggested by in vitro and animal models. However, given the single-center design, these associations should be considered hypothesis-generating and require validation before clinical application.}, }
@article {pmid42231422, year = {2026}, author = {Maruyama, H and Sato, K and Sakai, K and Yasui, H and Okada, R and Xinheng, L and Umeda, K and Rahman, S and Nguyen, VS and Hibi, H}, title = {Near infrared photo-bacterialflora modulation technology realized controlling periodontitis: modulation of disease-associated dysbiosis in oral microbiota using near infrared photo-antibacterial targeting therapy (NIR-PAT[2]).}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {42231422}, issn = {1479-5876}, support = {25K22916//JSPS/ ; 25K03451//JSPS/ ; 18K15923//JSPS/ ; CREST JPMJCR19H2//Japan Science and Technology Corporation/ ; JPMJFR2017,FOREST//Japan Science and Technology Corporation/ ; Research Grant from The Chemo-Sero-Therapeutic Research Institute//The Chemo-Sero-Therapeutic Research Institute/ ; }, abstract = {BACKGROUND: Periodontitis is a complex polymicrobial disease driven by synergistic interactions within a dysbiotic oral community. Within this network, Porphyromonas gingivalis acts as a keystone pathogen that orchestrates the pathogenic transformation of the microbiota. Current broad-spectrum antimicrobials often disrupt the entire microbial ecosystem and release immunogenic lipopolysaccharides (LPS). We aimed to develop a targeted approach, Near-Infrared Photo-Antibacterial Targeting Therapy (NIR-PAT[2]), using an antibody-photosensitizer conjugate (IgY-IR700) to reduce P. gingivalis load within this polymicrobial complex and modulate the community profile.<br><br>METHODS: We evaluated the binding and bactericidal mechanism of NIR-PAT[2] in vitro compared to antimicrobial photodynamic therapy (aPDT), using scanning electron microscopy (SEM) and endotoxin assays. In vivo, a ligature-induced periodontitis mouse model was used to assess therapeutic effects on alveolar bone resorption and microbiome community structure (16&#xa0;S rRNA sequencing).<br><br>RESULTS: In vitro, NIR-PAT[2] eliminated P. gingivalis without affecting human cells. SEM analysis revealed a distinct mechanism: unlike aPDT, which caused bacterial disintegration, NIR-PAT[2] induced lethal transmembrane perforations while maintaining structural integrity. In parallel, endotoxin assays demonstrated that NIR-PAT[2] treatment significantly suppressed LPS release compared to aPDT. In vivo, NIR-PAT[2] treatment significantly inhibited alveolar bone resorption. Crucially, microbiome analysis demonstrated that NIR-PAT[2] did not merely eliminate the environment but induced a compositional shift toward a health-associated profile. By suppressing Porphyromonas, the treatment facilitated the partial restoration of commensal genera such as Streptococcus, disrupting the dysbiotic network.<br><br>CONCLUSIONS: This study suggests that NIR-PAT[2] functions as a "Near-Infrared Photo-Bacterialflora Modulation (NIR-PBAM)" technology. By targeting a keystone pathogen within the polymicrobial community, NIR-PBAM offers a strategy to partially restore microbial balance while presenting a potential advantage in limiting LPS release, thus overcoming the ecological disruption caused by conventional broad-spectrum antimicrobials.}, }
@article {pmid42231509, year = {2026}, author = {Sarhan, MS and Samadelli, M and Zink, A and Maixner, F}, title = {The Iceman's microbiome: unveiling millennia of microbial diversity and continuity.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42231509}, issn = {2049-2618}, support = {FESR1078-MummyLabs//European Regional Development Fund/ ; }, abstract = {BACKGROUND: The Iceman mummy, a 5300-year-old natural alpine glacier mummy, provides a unique opportunity to study ancient microbial ecosystems. However, disentangling the mummy's endogenous microbiome from modern environmental contaminants introduced during three decades of conservation remains a significant challenge.<br><br>RESULTS: By integrating culture-dependent and culture-independent approaches, including amplicon sequencing, shotgun metagenomics and de novo metagenomic assembly, as well as isolate-level genomics, we performed a comprehensive characterization of the Iceman's microbial landscape. We identified three distinct microbial drivers: endogenous post-mortem succession, ancient glacier-derived relicts, and modern anthropogenic introduction. Metagenomic analysis of internal tissues revealed anaerobic bacteria, including ancient gut taxa, including such as Romboutsia hominis, Clostridium moniliforme, Eubacterium sp., Ruminococcus bromii, Kineothrix sp., Treponema succinifaciens, Enterousia sp., and Huintestinicola butyrica. These taxa, characterized by ancient DNA (aDNA) damage profiles (C to T deamination frequency), show high similarity to ancestral, non-Westernized human gut communities, providing a rare baseline for Copper Age intestinal ecosystems. Conversely, we identified a shift in the external mycobiome, marked by the recent proliferation of psychrophilic yeasts, including Glaciozyma watsonii, Mrakia robertii, Phenoliferia glacialis, and Goffeauzyma sp. While internal bacterial communities remained stable, these external yeast populations showed increased relative abundance and reduced DNA damage signatures between 2010 and 2019, indicating active, modern colonization. Furthermore, strain-level analysis of Pseudomonas sp. 5C2 confirmed that specific environmental strains have successfully colonized the mummy, persisting across multiple tissue sites with minimal genetic divergence.<br><br>CONCLUSIONS: Our study demonstrates that the Iceman is not a static relic but a dynamic biological interface. The coexistence of ancient, endogenous gut microbes and modern, psychrophilic colonizers highlights the potential for ongoing microbial activity even at sub-zero temperatures. These findings underscore that maintaining strict environmental parameters is essential to prevent these specialized microbial communities from transitioning from latent persistence to active microorganisms. Video Abstract.}, }
@article {pmid42231528, year = {2026}, author = {Wang, W and Fortuna, R and Mayengbam, S and Seerattan, RA and Mu, C and Rios, JL and Abughazaleh, N and Vaghef Mehrabani, E and Noye Tuplin, EW and Hart, DA and Sharkey, KA and Herzog, W and Reimer, RA}, title = {Multiomics insights into the effects of prebiotics on physical function and metabolism in adults with obesity and knee osteoarthritis.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2679516}, doi = {10.1080/19490976.2026.2679516}, pmid = {42231528}, issn = {1949-0984}, abstract = {Knee osteoarthritis (OA) is a prevalent, painful, degenerative disease lacking effective disease-modifying drugs. The rise in obesity has increased the prevalence of metabolic OA, underscoring the need for effective management to delay or prevent knee replacement. Prebiotics confer improvement in physical function and metabolic health in adults with comorbid knee OA and obesity by unknown mechanisms. Here, we integrated metagenomic and metabolomic analyzes to investigate prebiotic fiber-linked mechanisms along the gut-knee axis. By reshaping the composition and function of the gut microbiota, prebiotics increased diet-derived carbohydrate availability, mitigated excessive host-glycan degradation and mucosal barrier disruption, reduced systemic inflammation and metabolic dysregulation, ultimately enhancing metabolic health and improving physical performance. In a diet-induced obese rat model, prebiotics reduced tibial cartilage degeneration and synovial membrane thickening, conferring protection against OA onset and progression through a common inflammatory pathway. Our findings provide mechanistic evidence supporting the therapeutic potential of prebiotic supplementation as a conservative management in humans and as a preventive approach for obesity-related knee OA in a preclinical rat model, mediated through the gut-joint axis.}, }
@article {pmid42231914, year = {2026}, author = {Lv, Y and Li, J and Xu, Z and Zhang, Y and Li, W and Kan, X and Dai, S and Lin, Y and Xu, X and Chen, W}, title = {Engineered skin commensal nanogels mitigate psoriasiform inflammation through dual regulation of cutaneous flora and host immunity.}, journal = {Materials today. Bio}, volume = {38}, number = {}, pages = {103267}, pmid = {42231914}, issn = {2590-0064}, abstract = {Psoriasis is a chronic inflammatory skin disorder characterized by immune dysregulation and alterations in the cutaneous microbiota. Current microbiome-targeted therapeutic strategies predominantly involve the topical delivery of live probiotics using hydrogel platforms. However, these approaches are hindered by limitations such as poor bacterial viability, transient colonization, and unresolved safety concerns, while often failing to address systemic immune dysfunction. To overcome these challenges, we developed nanogels derived from Staphylococcus epidermidis lysates via EDC/NHS crosslinking. The optimized formulation exhibited a uniform hydrodynamic diameter of 98.3 ± 30.2 nm and remained stable for up to 5 days without significant protein degradation. Leveraging their sub-100 nm size, these nanogels enabled multiple therapeutic mechanisms. First, they penetrated the epidermal barrier through psoriatic scales and were internalized by target cells, leading to suppressed keratinocyte hyperproliferation and reduced local inflammation. Second, they trafficked systemically via the cutaneous microvasculature, resulting in decreased activation of splenic dendritic cells (CD11c + CD80[+]) and normalization of the CD4+/CD8+ T-lymphocyte ratio. Concurrently, residual nanogels retained on the skin surface selectively inhibited the proliferation of Staphylococcus aureus while promoting the enrichment of commensal Staphylococcus species, thereby restoring microbial homeostasis and reinforcing barrier integrity. This strategy addresses key limitations of conventional live biotherapeutics by leveraging the enhanced biocompatibility of bacterial components and the multifunctional advantages of nanoscale delivery. It offers a synergistic and safe approach for effective psoriasis management.}, }
@article {pmid42231929, year = {2026}, author = {Mejía-Granados, DM and Kawasaki de Araújo, T and Malan-Müller, S and Oliveira Ribeiro de Aguiar Araújo, PA and Braz Dos Santos, LH and Yasuda, CL and Koutsodontis Machado Alvim, M and Carvalho, BS and Cendes, F and Lopes-Cendes, I}, title = {Intestinal microbial community assessment in patients with different forms of epilepsy and autoimmune encephalitis: An exploratory study.}, journal = {Gut microbes reports}, volume = {3}, number = {1}, pages = {2679348}, pmid = {42231929}, issn = {2993-3935}, abstract = {Despite the availability of antiseizure medications (ASMs), approximately one-third of patients with epilepsy remain refractory to treatment. Evidence suggests that the gut microbiota modulates central nervous system function through neuroimmune and metabolic pathways. We characterized the fecal microbiome of patients with epilepsy and autoimmune encephalitis (AE) using 16S rRNA sequencing. Ninety-six participants from a tertiary hospital in Brazil were included: mesial temporal lobe epilepsy (MTLE; n = 38), genetic generalized epilepsy (GGE; n = 11), AE (n = 10), and healthy controls (n = 37). Microbial community composition differed between treatment-responsive and refractory patients. Compared with responsive individuals (n = 16), refractory patients (n = 43) showed lower relative abundances of Agathobaculum, Bacteroides, Bilophila, and Coprobacter, and higher abundance of Guopingia. Dietary fiber intake was negatively associated with Enterocloster and Frisingicoccus. Riboflavin (vitamin B2) and niacin (vitamin B3) were positively associated with Schaalia and Hominimerdicola, respectively. Functional predictions indicated that valproic acid use and treatment responsiveness were associated with increased microbial potential for GABA synthesis and tryptophan degradation, and reduced potential for dopamine and histamine degradation. These findings link the gut microbiome to epilepsy subtype and treatment response.}, }
@article {pmid42232188, year = {2026}, author = {Shree Kumari, GR and Vaithilingam, M}, title = {Exploring the probiotic landscape in understanding postbiotics from indigenous bacteria isolated from the stool samples of a tribal population at Mulluvadi village, Tamil Nadu, India.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1817531}, pmid = {42232188}, issn = {1663-9812}, abstract = {BACKGROUND: Urbanisation has been associated with a decline in the diversity of the gut microbiome that could potentially limit access to functionally robust probiotic strains. In contrast, traditional tribal populations represent underexplored reservoirs of diverse microbiota with unique metabolic capabilities. In this study, isolated and functionally characterised culturable probiotic bacteria from the gut microbiomes of individuals from the Mulluvadi tribal community (Tamil Nadu, India), with a focus on their inferred postbiotic-producing potential.<br><br>METHODS: A total of 112 microbial isolates were obtained from the stool samples of 25 healthy individuals, from which 13 representative bacterial strains were shortlisted by sequential screening based on phenotypic and functional criteria. These isolates were evaluated for tolerance to gastrointestinal stress conditions (pH, bile salts, NaCl, and temperature), cell surface hydrophobicity, auto-aggregation, safety attributes, and functional properties, including antibacterial activity, exopolysaccharide production, protease activity, biofilm formation, and short-chain fatty acid (SCFA) production.<br><br>RESULTS: The 13 isolates, mainly comprising Lactiplantibacillus plantarum and Lacticaseibacillus rhamnosus, exhibited >70% survival under simulated gastric and biliary conditions, high levels of hydrophobicity (60%-80%), strong inhibition of pathogens (12-25&#xa0;mm), significant production of SCFAs, high levels of protease activity (15-20&#xa0;mm clearance), and marked membrane stabilising effects of human red blood cells (65%-82%). All isolates were non-haemolytic, negative for DNase production, and displayed safety profiles consistent with those of probiotics. In particular, L. plantarum and Heyndrickxia coagulans were identified as the most functionally potent strains.<br><br>CONCLUSION: Probiotic isolates from the gut microbiomes of a tribal population show remarkable postbiotic-producing capacity and potential functional relevance. These strains are promising candidates for further investigations toward the development of postbiotic-based functional formulations; however, their efficacies must be first established in animal and clinical trials and validated through additional in vivo and clinical studies for gut dysbiosis and other related disorders.}, }
@article {pmid42232211, year = {2026}, author = {Cheng, Z and Gao, L and Luo, D and Bi, C and Chen, Q and Chen, X}, title = {A prospective cohort study exploring salivary microbial predictors of white spot lesions during fixed orthodontic treatment.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2679805}, pmid = {42232211}, issn = {2000-2297}, abstract = {INTRODUCTION: White spot lesions (WSLs) are a common adverse outcome of fixed orthodontic treatment, prompting the search for salivary microbial predictors for early risk identification.<br><br>MATERIALS AND METHODS: Sixty-four patients undergoing fixed metal self-ligating orthodontic treatment were categorized into WSL and non-WSL groups based on lesion development after 12 months. Clinical indices (DI-S, CI-S, OHI-S, GI) and unstimulated whole saliva samples were collected at baseline and after 12 months. The salivary microbiome was analyzed using 16S rRNA gene sequencing.<br><br>RESULTS: The prevalence of WSLs was 54.7% at the patient level. Clinical indices did not differ significantly between groups. Although overall microbial community structure was similar at baseline, several taxa were enriched in patients who later developed WSLs, including Actinomyces, Rothia and Granulicatella. After 12 months, the WSL group showed reduced phylogenetic diversity and a microbial profile enriched in acidogenic and anaerobic taxa. Functional prediction indicated increased carbohydrate metabolism and fermentative pathways in WSL patients.<br><br>CONCLUSIONS: WSL development during fixed orthodontic treatment was associated with baseline salivary microbial differences and treatment-related ecological shifts. Salivary microbiome profiling may help identify patients at higher risk and support early risk stratification and preventive strategies in orthodontic care.}, }
@article {pmid42232608, year = {2026}, author = {Lopes, M and Vila Nova, C and Oliveira, RC and Schmitt, F and Mendes, F and Martins, D}, title = {Microbiome and Response to Therapy in Triple Negative Breast Cancer: A Systematic Review.}, journal = {Oncology research}, volume = {34}, number = {6}, pages = {4}, pmid = {42232608}, issn = {1555-3906}, abstract = {Objectives: Triple-negative breast cancer (TNBC) accounts for approximately 15% of all invasive breast cancers and is characterized by aggressive behavior, limited therapeutic options, and poor clinical outcomes. Due to the absence of hormone receptors and HER2 expression, systemic treatment relies predominantly on chemotherapy, which is associated with high rates of early recurrence and mortality. Emerging evidence suggests that alterations in the microbiome can contribute to TNBC progression and influence therapeutic response, particularly affecting the efficacy of chemotherapy and immunotherapy through immune-mediated mechanisms; however, its role in TNBC remains incompletely understood. This systematic review aims to explore the role of the microbiome in TNBC. It specifically aims to understand if the microbiome influences complete pathological response in TNBC. Methods: This systematic review was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. A comprehensive literature search was performed in PubMed and Cochrane databases. Fourteen eligible studies were included, encompassing preclinical and clinical evidence. Results: The findings indicate that both gut and tumor-associated microbiota significantly influence therapeutic response in TNBC, especially in the context of neoadjuvant chemotherapy (NACT) and immune checkpoint blockade (ICB). Higher microbial diversity and the presence of specific commensal taxa were consistently associated with enhanced antitumor immune activation, increased immune cell infiltration, and improved treatment efficacy. Conversely, antibiotic-induced dysbiosis was linked to reduced pCR rates and poorer clinical outcomes. Microbiome-modulating interventions demonstrated potential in restoring eubiosis and enhancing therapeutic responsiveness. Conclusions: Overall, the available evidence supports the microbiome as a promising biomarker and therapeutic target for optimizing treatment strategies and improving outcomes in TNBC.}, }
@article {pmid42232902, year = {2026}, author = {Lachnit, T}, title = {Nutrient-rich environments drive microbiome restructuring and mucus shedding in a coastal cnidarian.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1792133}, pmid = {42232902}, issn = {1664-302X}, abstract = {INTRODUCTION: Anthropogenic nutrient enrichment is increasing in coastal ecosystems, yet its effects on host-microbe interactions and animal fitness remain insufficiently understood. This study investigates how elevated dissolved nutrient availability and differing nutrient compositions influence microbiome structure and host responses in the sea anemone Nematostella vectensis.<br><br>METHODS: We experimentally enriched seawater with either a complex organic nutrient source or a protein-rich substrate. We then assessed resulting changes in microbiome composition, host behavior (including mucus shedding), and population growth.<br><br>RESULTS: Nutrient enrichment caused substantial restructuring of the host-associated microbiome, characterized by reduced diversity and increased dominance of fast-growing bacterial taxa. Community composition differed depending on nutrient type. Enriched conditions also triggered increased ectodermal mucus shedding, which physically removed surface-associated microbes. Copiotrophic taxa that proliferated under nutrient enrichment were disproportionately represented in shed mucus relative to whole polyps, suggesting spatial structuring of microbial associations with host surfaces. While this response limited microbial overgrowth, it imposed significant physiological costs, leading to reduced or negative population growth.<br><br>DISCUSSION: These findings demonstrate that nutrient enrichment alters host-associated microbiomes and identify mucus shedding as a host-mediated mechanism for microbial regulation. Although effective, this response carries substantial fitness costs, highlighting a trade-off between microbial control and host performance. This study provides mechanistic insight into how eutrophication may drive microbiome restructuring and impact host physiology in coastal cnidarians.}, }
@article {pmid42232906, year = {2026}, author = {Jin, Y and Zhu, J and Liao, D and Jin, X}, title = {From "spleen governing muscle" to gut microbiota: mechanisms of sarcopenic obesity in perimenopausal women.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1817839}, pmid = {42232906}, issn = {1664-302X}, abstract = {BACKGROUND: Sarcopenic obesity (SO) in perimenopausal women-characterized by the paradoxical coexistence of skeletal muscle loss and visceral adiposity-represents a complex metabolic challenge that conventional estrogen replacement therapies have failed to fully address. Emerging evidence from traditional Chinese medicine (TCM) suggests that the "spleen governing muscle" theory may offer a unique lens through which to understand this condition, with the gut microbiota serving as a critical mechanistic link between spleen deficiency and musculoskeletal deterioration.<br><br>OBJECTIVE: To systematically review the mechanisms linking spleen deficiency, gut microbiota dysbiosis, and sarcopenic obesity risk in perimenopausal women, integrating TCM theory with modern biomedical evidence.<br><br>METHODS: We synthesized findings from clinical observational studies, randomized controlled trials (RCTs), and mechanistic investigations examining the "spleen-gut-muscle" axis, with particular attention to studies employing 16S rRNA sequencing, metabolomics, and multi-omics approaches.<br><br>RESULTS: Spleen deficiency-manifesting as impaired transformation and transportation of nutrients-correlates with characteristic alterations in gut microbiota composition, including reduced diversity, elevated Firmicutes/Bacteroidetes ratios, and depletion of short-chain fatty acid (SCFA)-producing taxa. These microbial changes propagate systemic inflammation through lipopolysaccharide (LPS)-TLR4 signaling, activate muscle protein degradation via MuRF1 upregulation, and compromise insulin sensitivity through diminished GLP-1 secretion. Notably, TCM interventions-including herbal formulations (Sijunzi decoction, Buzhong Yiqi decoction), acupuncture, moxibustion, catgut embedding, and tuina massage-demonstrate potential to restore microbial homeostasis, increase SCFA production, and improve muscle mass and function. However, the evidence quality remains modest, with methodological limitations including inadequate blinding, small sample sizes, and short follow-up durations.<br><br>CONCLUSION: The "spleen-gut-muscle" axis represents a promising therapeutic target for perimenopausal sarcopenic obesity, bridging TCM theory with modern microbiome science. Nevertheless, current evidence is predominantly associative rather than causally definitive, derived largely from small-scale trials and preclinical models. Rigorous, large-scale RCTs with standardized TCM protocols, multi-omics endpoints, and extended follow-up are essential to establish efficacy and safety before microbiota-based TCM interventions can be recommended as adjunctive or standalone therapies.}, }
@article {pmid42232910, year = {2026}, author = {Oskolkov, N}, title = {Refining filtering criteria of Kraken family of tools for accurate taxonomic profiling of ancient metagenomic data.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1603339}, pmid = {42232910}, issn = {1664-302X}, abstract = {Taxonomic profiling is a key component of ancient metagenomic analysis, however it is also susceptible to false-positive identifications. In particular, taxonomic classification tools from the Kraken family, such as Kraken2 and KrakenUniq, are highly sensitive to the choice of filtering options. To address this issue, various filtering approaches have been proposed. In this study, I conduct a comprehensive benchmarking of different filtering strategies for Kraken family of tools using simulated microbial and environmental ancient metagenomic data. I evaluate these approaches based on the balance between sensitivity and specificity of ground truth reconstruction (F1-score), and propose an optimal thresholding strategy tailored to specific sequencing depths in ancient metagenomic datasets.}, }
@article {pmid42232978, year = {2026}, author = {Indolfi, C and Klain, A and Dinardo, G and Colosimo, S and Ferrara, S and Grella, C and Galdiero, M and De Filippis, A and Fiore, V and Miraglia Del Giudice, M}, title = {Association between Staphylococcus aureus colonization and clinical improvement in pediatric atopic dermatitis treated with dupilumab: a pilot study.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1836967}, pmid = {42232978}, issn = {2296-858X}, abstract = {BACKGROUND: Moderate-to-severe atopic dermatitis (AD) in children is characterized by impaired skin barrier function, type 2 inflammation, and frequent Staphylococcus aureus colonization, contributing to disease severity and risk of superinfection. Dupilumab, an anti-IL-4/IL-13 receptor monoclonal antibody, improves clinical outcomes in pediatric AD, but longitudinal data on culture-based skin and nasal microbial changes remain limited.<br><br>OBJECTIVE: To assess dupilumab efficacy in children with moderate-to-severe AD unresponsive to conventional therapy and to describe skin and nasal microbial colonization patterns at the 12-month time point compared with moderate AD receiving conventional topical therapy and healthy controls.<br><br>METHODS: Prospective observational study. Children aged 6-16&#x202f;years were enrolled in three groups: (a) moderate-to-severe AD starting dupilumab (assessments at baseline, 3, 6, and 12&#x202f;months); (b) moderate AD receiving conventional topical therapy not eligible for biologic therapy; and (c) age-matched healthy controls. Outcomes included Eczema Area and Severity Index (EASI), Children's Dermatology Life Quality Index (C-DLQI), and Peak Pruritus Numerical Rating Scale (NRS). At 12&#x202f;months, nasal and skin e-Swabs were cultured; isolates were identified by MALDI-TOF with antimicrobial susceptibility testing. Longitudinal changes were analyzed using the Friedman test (p&#x202f;<&#x202f;0.05).<br><br>RESULTS: Ten dupilumab-treated children (mean age 13&#x202f;years; 60% males) showed rapid and sustained improvement in C-DLQI (median 13.5 to 3 at 3&#x202f;months; 3.5 at 12&#x202f;months), EASI (24.5 to 5.65 at 3&#x202f;months, 1.2 at 12&#x202f;months), and pruritus (NRS 10 to 4.5 at 3&#x202f;months; 5.5 at 12&#x202f;months). No adverse events or discontinuations occurred. At 12&#x202f;months, nasal S. aureus colonization was detected in 2/10 dupilumab-treated patients versus 4/10 moderate AD receiving conventional topical therapy and 1/10 controls; skin S. aureus was absent in dupilumab-treated patients but present in 8/10 children with moderate atopic dermatitis receiving conventional topical therapy and 0/10 controls.<br><br>CONCLUSION: Dupilumab provides sustained clinical benefit and, in this cross-sectional assessment of a small pilot cohort, is associated with lower S. aureus colonization and the presence of commensal staphylococci in pediatric atopic dermatitis.}, }
@article {pmid42233016, year = {2026}, author = {Di Simone, N and Barnea, ER and Mueller, M}, title = {Editorial: Community series in the immunological role of the maternal microbiome in pregnancy, Volume II.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1872195}, doi = {10.3389/fimmu.2026.1872195}, pmid = {42233016}, issn = {1664-3224}, }
@article {pmid42233037, year = {2026}, author = {Celik, E and Bechara, FG and Stockfleth, E and Ocker-Serger, L and Abu Rached, N}, title = {Dietary patterns, metabolic pathways and metainflammation in hidradenitis suppurativa: a systematic review.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1830618}, pmid = {42233037}, issn = {1664-3224}, mesh = {Humans ; *Hidradenitis Suppurativa/metabolism/immunology/diet therapy ; *Metabolic Networks and Pathways ; *Inflammation/metabolism ; *Diet ; Diet, Mediterranean ; }, abstract = {BACKGROUND: Dietary factors have been suggested to influence inflammatory skin diseases; however, their role in the pathogenesis and clinical course of hidradenitis suppurativa (HS) remains insufficiently understood. Increasing evidence suggests that HS is a systemic immunometabolic disease characterized by chronic low-grade inflammation and metabolic comorbidities such as obesity, insulin resistance, and metabolic syndrome. Dietary patterns may therefore influence HS activity through metabolic and inflammatory pathways.<br><br>OBJECTIVE: To systematically evaluate available evidence on dietary patterns, nutritional interventions, and micronutrient status in hidradenitis suppurativa and to assess their associations with disease onset, disease severity, and underlying metabolic and inflammatory mechanisms.<br><br>METHODS: A systematic search was conducted in PubMed/Medline for studies published between 1985 and 2026, following PRISMA guidelines. Eligible study types included observational studies, interventional trials, and case-control or cross-sectional studies investigating dietary exposures or nutritional interventions in HS. Reference lists were screened for additional records.<br><br>RESULTS: Eleven studies met the inclusion criteria. Across observational cohorts, lower adherence to Mediterranean-style dietary patterns, higher glycaemic dietary patterns, and micronutrient deficiencies, particularly vitamin D and zinc, were generally associated with greater HS disease severity. Interventional evidence was limited. A small pilot study reported clinical improvement following a very low-calorie ketogenic diet, and yeast-exclusion diets were associated with symptom improvement in small patient cohorts. Evidence from bariatric surgery cohorts suggested that malabsorptive procedures and persistent micronutrient deficiencies may be associated with worsening HS in some patients. Overall, the available studies suggest potential links between diet and HS through metabolic, inflammatory, and microbiome-related pathways, although the evidence remains limited and heterogeneous.<br><br>CONCLUSION: Current evidence suggests that dietary habits and nutritional status may influence hidradenitis suppurativa through metabolic and inflammatory mechanisms. Although data remain heterogeneous and largely observational, promoting anti-inflammatory dietary patterns, optimizing micronutrient intake, and addressing obesity may offer supportive benefits alongside standard HS therapies. Further controlled studies are needed to establish causality.}, }
@article {pmid42233644, year = {2026}, author = {Dubin, CA and Zhao, C and Pollard, KS and Oskotsky, T and Golob, JL and Sirota, M}, title = {Expanding vaginal microbiome pangenomes via a custom MIDAS database reveals Lactobacillus crispatus accessory genes associated with cervical dysplasia.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0149825}, doi = {10.1128/msystems.01498-25}, pmid = {42233644}, issn = {2379-5077}, abstract = {The vaginal microbiome plays a central role in reproductive health. Vaginal microbiome dysbiosis is associated with many adverse reproductive health outcomes, but most studies have focused on associations at the species level. The potential contribution of intraspecies microbial variation, especially gene content differences across bacterial strains, remains underexplored in reproductive health contexts. The Metagenomic Intra-Species Diversity Analysis (MIDAS) framework enables such analyses, but depends on comprehensive reference databases. We constructed a MIDAS-compatible pangenome database from over 18,000 genomes in the Vaginal Microbiome Genome Collection (VMGC). Compared to the Genome Taxonomy Database (GTDB)-derived reference, the VMGC-derived database expanded the pangenomes of prevalent vaginal species, better capturing vaginal-specific intraspecies diversity. Applying this database to vaginal samples from a cervical dysplasia cohort, we identified 13 Lactobacillus crispatus accessory genes significantly associated with cervical dysplasia, including a HicAB toxin-antitoxin system, three transcriptional regulators, and three phage-derived genes. These findings highlight the utility of body site-specific reference resources and shotgun metagenomic sequencing for uncovering intraspecies microbial variation relevant to reproductive health.IMPORTANCEThe vaginal microbiome plays a critical role in reproductive health, and different bacteria from the same species can carry different genes that influence how the strains interact with the host and other microbes. These strain-level differences are often overlooked when microbiomes are analyzed only at the species level. Existing genomic reference databases are heavily biased toward gut and environmental bacteria, leaving the genetic diversity of vaginal microbes understudied. We built a specialized reference database from over 18,000 vaginal bacterial genomes that better reflects this diversity. We then applied this resource to quantify gene-level variation in vaginal samples from a cervical dysplasia cohort. Focusing on Lactobacillus crispatus, a prevalent and often beneficial vaginal species, we identified 13 genes that were more common in women with cervical dysplasia than in controls. This work demonstrates that body site-specific genomic resources are essential for uncovering strain-level bacterial differences relevant to reproductive health.}, }
@article {pmid42233652, year = {2026}, author = {Mehta, SD}, title = {Role of the penile microbiome in female sex partner risk of bacterial vaginosis and sexually transmitted infections: a narrative review.}, journal = {Clinical microbiology reviews}, volume = {}, number = {}, pages = {e0033125}, doi = {10.1128/cmr.00331-25}, pmid = {42233652}, issn = {1098-6618}, abstract = {SUMMARYThe penile microbiome (PMB) can be dominated by skin-associated bacteria (e.g., Corynebacterium, Staphylococcus, and Streptococcus) or by anaerobic bacteria that are associated with bacterial vaginosis (BV), and is influenced by male circumcision status, female partner vaginal microbiome (VMB), BV status, condom use, and antibiotic use. Penile bacteria that are associated with BV and genital mucosal inflammation are associated with men's risk of HIV and STIs. In the few studies that simultaneously evaluate the penile and vaginal microbiome in sex partners, specific taxa are highly correlated, with evidence for bi-directional transmissibility. BV-associated taxa in the PMB are associated with increased risk of BV and STIs in female sex partners. Emergent trials demonstrate that antimicrobial treatment in men can reduce penile anaerobic bacteria and female sex partner's risk of BV recurrence. However, data are lacking on factors influencing penile-vaginal bacterial exchangeability, the durability of bacterial exchange, and the conditions under which exchange may lead to increased risk of adverse outcomes in the index or partner. Optimal and non-optimal PMB have not been defined. Assessment of PMB composition and function across the life course is needed. Association of PMB with intrinsic host factors (genetics and endogenous hormones) is lacking; association with behavioral and lifestyle factors is limited. Addressing these gaps may lead to the development of assays to facilitate screening and monitoring after therapeutic interventions in men and female partners, or the development of therapeutics for optimizing PMB. Studies are needed to refine and develop new treatment and counseling guidelines for men and their sexual partners.}, }
@article {pmid42233654, year = {2026}, author = {Wang, W and Li, Y and Liang, Y and Wang, J and Zhang, Z and Zhang, Y and Xiao, C and Hao, H}, title = {Age-driven shifts of the camel gut microbiome and resistome in extensively reared dromedary camels.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0318325}, doi = {10.1128/spectrum.03183-25}, pmid = {42233654}, issn = {2165-0497}, abstract = {UNLABELLED: Camels are uniquely adapted to arid environments and are commonly raised in extensive grazing systems. The composition of their gut microbiome and antimicrobial resistance genes (ARGs) is expected to change with host development, but age-related patterns have not been well described. In this study, we analyzed fecal samples from juvenile (approximately 6 months old) and adult (6 years) dromedary camels kept under the same grazing management, with no recorded therapeutic antibiotic treatments during the study period. Shotgun metagenomic sequencing was used to profile bacterial communities, ARGs, and mobile genetic elements (MGEs). Juvenile camels showed lower alpha diversity and greater inter-individual variation than adults, and their gut communities were dominated by facultative anaerobes such as Escherichia and Streptococcus. Adult camels carried more stable, fiber-adapted communities enriched in Bacteroidaceae and Prevotellaceae. In parallel with these microbiome changes, the resistome also differed by age. Juveniles carried a wider range of ARGs, with higher contributions from multidrug efflux pumps and vancomycin resistance genes. Adults had a smaller and more concentrated set of ARGs, mainly β-lactamase and tetracycline resistance genes, together with lower ARG richness and diversity. MGEs also showed distinct age-related patterns: transposase genes were more common in juveniles, whereas insertion sequence-associated genes were more abundant in adults, suggesting age-specific routes of potential ARG mobility. Overall, these data indicate that maturation of the camel gut microbiome is accompanied by a reduction and focusing of the resistome and by a shift in the dominant types of MGEs. This study provides an age-stratified reference for ARG reservoirs and MGE-associated ARG mobility in camels studied under conditions with no recorded therapeutic antibiotic treatments and may be useful for future work on antimicrobial resistance in extensively managed livestock.<br><br>IMPORTANCE: Antimicrobial resistance is often studied in animals heavily exposed to antibiotics, leaving a gap in our understanding of its natural development. Camels, rarely treated with antibiotics, offer a unique model. By comparing juvenile and adult gut microbiomes, we found that early-life communities are diverse, unstable, and rich in mobile resistance genes, while adult communities are more stable and carry fewer mobile elements. These findings establish a natural baseline for how resistance genes emerge and settle without drug pressure, providing critical insights for One Health strategies aimed at limiting the spread of resistance in livestock and wildlife.}, }
@article {pmid42233658, year = {2026}, author = {Godoy-Vitorino, F and Vargas-Robles, D and Bolaños-Rosero, B and Pagán-Zayas, N and Cortés-Nazario, A and Wiggin, K and Allard, S and Romaguera, J and Gilbert, JA}, title = {Environmental fungi modulate the vaginal mycobiome and cervical disease progression in Hispanic women.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0005626}, doi = {10.1128/msystems.00056-26}, pmid = {42233658}, issn = {2379-5077}, abstract = {The vaginal mycobiome, though a minor component of the cervicovaginal ecosystem, plays a crucial role in reproductive health and disease. However, its composition and interactions with bacterial communities remain poorly understood, particularly among Hispanic women, who experience disproportionately high rates of human papillomavirus (HPV) infection and cervical cancer. We characterized the vaginal mycobiota across reproductive stages and examined its associations with cervical disease, HPV status, and bacterial community state types (CSTs) in 86 Hispanic participants from Puerto Rico using ITS1 amplicon sequencing. Amplicon sequence variants were inferred with QIIME2/DADA2 and taxonomically classified using the UNITE database, with diversity and discriminant taxa analyses applied to explore clinical and microbial associations. We detected 173 fungal species hypotheses, dominated by Candida albicans, Agaricomycetes sp., Scopuloides dimorpha, and Hortaea werneckii. While fungal composition did not differ significantly by reproductive stage, non-pregnant individuals exhibited greater inter-individual variability. Alpha diversity was reduced in high-grade squamous intraepithelial lesions compared with low-grade or normal cytology, and Candida parapsilosis prevalence was elevated in low-grade lesions. CST III, characterized by Lactobacillus iners dominance, showed greater dispersion variance than other CSTs. Collectively, these findings reveal a diverse vaginal mycobiome with stage- and disease-specific features and a notable contribution of environmental fungi that may influence cervical pathogenesis. This work provides foundational insight into cervicovaginal fungal ecology in a high-risk Hispanic population and highlights the importance of integrating bacteriome-mycobiome analyses in women's health research.IMPORTANCEThis study demonstrates that environmental fungi may play an important role in shaping the vaginal microbiome and influencing cervical disease progression in Hispanic women. While most prior research has focused on bacterial communities, our findings highlight fungi as significant yet underexplored contributors to reproductive health. By linking environmental fungal exposures to shifts in the vaginal mycobiome, this work expands understanding of how external factors may affect disease risk. These results underscore the need to include fungal communities in human microbiome research and support more comprehensive approaches to women's health. Ultimately, this study may inform improved risk assessment, prevention strategies, and the development of targeted interventions in diverse populations.}, }
@article {pmid42233676, year = {2026}, author = {Herzer, KR and Torres, CI and Krajmalnik-Brown, R and Delgado, AG}, title = {Environmental considerations and bioremediation applications of the metal-, nitrate-, and organohalide-respiring bacterium Trichlorobacter lovleyi (formerly Geobacter lovleyi).}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0056326}, doi = {10.1128/aem.00563-26}, pmid = {42233676}, issn = {1098-5336}, abstract = {Trichlorobacter lovleyi (formerly Geobacter lovleyi) is a gram-negative bacterium that can couple the oxidation of acetate or other small organic acids with the reduction of soluble and insoluble electron acceptors, such as chlorinated solvents, heavy metals, and nitrate. Evidence has shown that T. lovleyi plays a direct role in nitrogen, iron, and carbon cycling, and its versatile metabolism can be leveraged for environmental biotechnology applications. However, the contributions of T. lovleyi to treatment of contaminants at groundwater sites or electron transfer in bioelectrochemical systems have been largely overlooked. This minireview examines the genetic and metabolic features of T. lovleyi for dissimilatory reduction of nitrate to ammonium, extracellular electron, and organohalide-respiration, highlighting unique and conserved features relative to other genera in Geobacterales. We highlight applications of T. lovleyi in bioremediation of contaminated environments and identify knowledge gaps to fully leverage the metabolic potential of this bacterium. We feature T. lovleyi's ability to produce the important vitamin B12 cofactor and the syntrophic partnership it establishes with cobalamin-scavenging, obligate organohalide-respiring bacteria, particularly in environments where the concentration of chlorinated solvents poses toxicity challenges to the groundwater microbiome. We conclude that T. lovleyi has a meaningful, multi-faceted, but often neglected, contribution to groundwater and soil bioremediation. We hope this minireview will prompt researchers and bioremediation practitioners to more closely monitor T. lovleyi during reductive dechlorination enrichment efforts and bioremediation applications at sites contaminated with organohalogens, uranium, or nitrate.}, }
@article {pmid42234243, year = {2026}, author = {Ncir, WB and Abdelhedi, F and Keskes, LA}, title = {Gut microbiome-blood cholesterol crosstalk: towards personalized strategies for dyslipidemia.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {42234243}, issn = {1874-9356}, abstract = {Hypercholesterolemia is a major risk factor for cardiovascular diseases, influenced by both genetic predisposition and multifactorial acquired factors, including diet, lifestyle, obesity, type 2 diabetes, and gut microbiota dysbiosis. Accumulating evidence suggests that the gut microbiome plays a causal role in cholesterol metabolism through multiple complementary mechanisms, including bile acid transformation, modulation of hepatic and intestinal receptors (FXR, TGR5), production of short-chain fatty acids (SCFAs) that inhibit hepatic cholesterol synthesis and microbiol conversion of cholesterol into poorly absorbed coprostanol. Host genetic, dietary habits, and lifestyle shape gut microbiol composition, contributing to interindividual variability in lipid profiles and responses to lipid-lowering interventions.Dietary interventions, including polyphenols, phytosterols, L-theanine, and probiotics, can beneficially modulate gut microbial composition, enrich SCFA-producing taxa, and improve cholesterol homeostasis. Pharmacological agents, including statins and berberine, also interact with the gut microbiome, underscoring the bidirectional nature of host-microbiome-drug interactions. Human, animal and in vitro studies collectively support the importance of baseline microbial composition, host genetics, and lifestyle in determining treatment response.This review synthesizes current knowledge on gut microbiome alterations in hypercholesterolemia, their causal role in cholesterol metabolism, and the influence of host and environmental factors on interindividual variability in therapeutic responses. It further discusses dietary and pharmacological strategies targeting the gut microbiome to modulate lipid metabolism. A better understanding these complex interactions may enable the development of personalized, microbiome-based strategies for the prevention and management of hypercholesterolemia.}, }
@article {pmid42234268, year = {2026}, author = {Hoseini, R and Hoseini, Z and Heydarpour, B and Faraji, M}, title = {A systematic review of molecular signaling in the muscle-brain-gut axis: exercise-induced myokines and microbial metabolites as key mediators.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {42234268}, issn = {1573-4978}, abstract = {Exercise physiology is evolving from an organ-based framework toward a systems-level understanding, where molecular interactions between muscle, brain, and the gut microbiome critically influence performance and health. This review systematically examines the genetic, molecular, and cellular bases of this triad, with a focus on translational insights for disease prevention and human optimization. A systematic search of PubMed, Embase, and Web of Science was conducted up to October 2023 to identify studies exploring molecular pathways linking skeletal muscle, cognitive/affective function, and gut microbiota in exercise contexts. Inclusion criteria were original research articles investigating at least two components of the muscle-brain-gut axis. Exclusion criteria included non-English articles, conference abstracts, and studies without molecular data. The PRISMA 2020 guidelines were followed. The search strategy is detailed in Supplementary Material. Evidence was categorized into Grades 1 through 4 based on methodological rigor, omics integration, reproducibility, and translational relevance to human physiology and disease models. Analysis included 154 studies encompassing 987 molecular associations. Among these, 59 associations (Grades 1-2) provided robust evidence for genetically and functionally validated pathways, including myokine-mediated (e.g., irisin, BDNF) and microbially derived metabolites (e.g., SCFAs, tryptophan derivatives) that modulate neuroplasticity, mitochondrial function, inflammation, and HPA axis activity. Psychobiological factors influenced microbial composition, illustrating bidirectional gut-brain-muscle signaling. Most associations (n = 952) were limited by methodological variability or insufficient mechanistic depth. The integration of multi-omics platforms (metagenomics, metabolomics, proteomics) emerges as a key tool for personalized exercise interventions and biomarker discovery. This review synthesizes molecular evidence for the muscle-gut-brain axis as an integrative determinant of exercise responsiveness and disease resilience. We highlight genetic and metabolic pathways with diagnostic and therapeutic potential, aligning with the development of molecular tools for precision medicine. Future interdisciplinary research should leverage artificial intelligence and longitudinal omics to translate these mechanisms into targeted strategies for performance enhancement and disease prevention.}, }
@article {pmid42234685, year = {2026}, author = {Hu, J and Bao, G and Nawaz, M and Ma, W and Xing, N and Yuan, Y and Bao, L}, title = {Biomagnification in Trophic Transfer: Mechanisms of Trans-Trophic Toxicity from Co-Contamination of Aged NPs and TBP in a Soil-Rye-Armyworm System.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c01984}, pmid = {42234685}, issn = {1520-5851}, abstract = {The co-contamination of nanoplastics and organic pollutants poses a potential threat to agricultural ecosystems and food chain safety. To systematically reveal the individual and combined toxicity of aged carboxylated nanoplastics (NPs-COOH) and the flame retardant tributyl phosphate (TBP), as well as their transmission mechanisms along the food chain, this study established a "rye-armyworm" model. A multiscale investigation was conducted by integrating molecular docking, multiomics, and traditional toxicological methods. Results indicated that NPs-COOH and TBP form complexes via electrostatic and van der Waals interactions, synergistically enhancing their accumulation in rye roots and translocation into the vascular system. Combined exposure exerted synergistic toxicity on rye, manifested as inhibited photosynthesis, exacerbated oxidative stress, and significant deterioration in yield and nutritional quality. Transcriptomic and microbiome analyses further revealed that rye responds to the stress by systemically activating stress-response and detoxification metabolic pathways, accompanied by disruption of beneficial rhizospheric microbial communities. The pollutants were transferred along the food chain, with TBP undergoing biomagnification from rye to armyworm (BMF = 1.57), leading to growth inhibition, midgut structural damage, suppression of key detoxifying enzyme activities, and gut microbiota dysbiosis. This study elucidates the multidimensional ecological risks arising from the "vector effect" and synergistic toxicity of NPs-COOH and TBP in the soil-plant-insect system, providing further insights for a comprehensive assessment of the threats posed by such co-contamination to agricultural product safety and food chain health.}, }
@article {pmid42234773, year = {2026}, author = {Sakamachi, Y and Wiley, E and Trempus, CS and Jacobs, H and Solis, A and Johnson, CG and Meng, X and Hussain, S and Roselli, A and Lipinski, JH and O'Dwyer, DN and Randall, TA and Malphurs, J and Papas, B and Wu, BG and Li, Y and Kugler, MC and Mehta, S and Scappini, E and Thomas, SY and Li, JL and Zhou, L and Karmaus, PW and Lih, FB and Fessler, MB and McGrath, JA and Gibson, K and Kass, DJ and Gleiberman, A and Andrianova, E and Walts, A and Invernizzi, R and Molyneaux, PL and Yang, IV and Zhang, Y and Kaminski, N and Segal, LN and Schwartz, DA and Gudkov, AV and Garantziotis, S}, title = {Toll-like receptor 5 protects against murine lung fibrosis through reduced dysbiosis, and TLR5 deficiency is associated with human IPF.}, journal = {Science translational medicine}, volume = {18}, number = {852}, pages = {eadw1028}, doi = {10.1126/scitranslmed.adw1028}, pmid = {42234773}, issn = {1946-6242}, abstract = {Idiopathic pulmonary fibrosis (IPF) is a devastating pulmonary disease with no curative treatment other than lung transplantation that results from maladaptive responses to lung epithelial injury; however, the underlying mechanisms remain unclear, and treatment options are limited. Here, we showed that deficiency in the innate immune receptor toll-like receptor 5 (TLR5) is associated with IPF in humans and with increased susceptibility to bleomycin-induced pulmonary fibrosis in mice and that activation of lung epithelial TLR5 through a synthetic flagellin analog protected mice from experimental fibrosis. Mechanistically, epithelial TLR5 activation induced antimicrobial gene expression and ameliorated lung dysbiosis after injury. In contrast, TLR5 deficiency in mice and patients with IPF was associated with lung dysbiosis. Elimination of the microbiome in mice through administration of antibiotics abolished the protective effect of TLR5, and reconstitution of the microbiome by fecal microbiota transplantation rescued the observed phenotype. In conclusion, these studies revealed that TLR5 protects against pulmonary fibrosis through effects on the lung microbiota, providing insight into therapeutic approaches that may ultimately benefit patients with IPF.}, }
@article {pmid42235049, year = {2026}, author = {Prooyen, NV and Cho, M and Jiang, L and Rodgers, N and Varma, Y}, title = {Randomized Controlled Study of Bacteriophages in Acne Reveals Efficacy and Novel Mechanism for Promoting Long-Term Skin Health.}, journal = {Journal of drugs in dermatology : JDD}, volume = {25}, number = {6}, pages = {523-529}, doi = {10.36849/JDD.9346}, pmid = {42235049}, issn = {1545-9616}, mesh = {Humans ; *Acne Vulgaris/therapy/microbiology/diagnosis ; Double-Blind Method ; Male ; Female ; Adolescent ; Skin Microbiome ; Young Adult ; Adult ; Child ; Treatment Outcome ; *Bacteriophages ; *Salicylic Acid/administration &amp; dosage/therapeutic use ; *Phage Therapy/methods/adverse effects ; Skin/microbiology ; *Propionibacterium acnes/isolation &amp; purification ; }, abstract = {BACKGROUND: Acne is the most prevalent skin disease globally, with a significant burden and limited therapeutic innovation. Although it has a multifactorial etiology, Cutibacterium acnes (C acnes) overgrowth is a key factor in driving inflammation in acne. Bacteriophages are a novel mechanism that can specifically target C acnes and are found in greater abundance on healthy skin compared to acne-prone skin.<br><br>OBJECTIVES: To study the safety and efficacy of phages and salicylic acid (SA) in acne, and to analyze their mode of action and effect on microbiome diversity.<br><br>METHODS: A randomized double-blind placebo-controlled study was conducted on 90 participants for 8 weeks. Males and females 12 to 35 years old with mild to moderate acne were enrolled in placebo, phage, and phage + SA arms. Clinic visits at baseline, week 4, and week 8 collected safety data, VISIA imaging, lesion counts, IGA scores, and microbiome samples.<br><br>RESULTS: Phage treatment demonstrated an excellent safety profile. Participants in both phage and phage + SA arms showed significant improvement (P<0.05) over baseline at 8 weeks. Phage application resulted in a statistically significant (P<0.05) decrease of C acnes on the skin compared to placebo. Notably, phage use over 8 weeks significantly increased microbiome diversity, a marker of long-term skin health.<br><br>CONCLUSION: This study shows the potential of bacteriophages to be a highly promising modality with a unique mode of action for the treatment of acne. Beyond short-term lesion improvement, phage-induced enhancement of microbiome diversity suggests potential for durable, long-term skin health benefits. &amp;nbsp.}, }
@article {pmid42235053, year = {2026}, author = {Hornby, SB and Ly, YH and Obagi, ZA and Obagi, ZE and Stahl, CC and Woodin, FW}, title = {A Novel Retinoid and Salicylic Acid Topical Treatment for Moderate-Severe Acne.}, journal = {Journal of drugs in dermatology : JDD}, volume = {25}, number = {6}, pages = {558-561}, doi = {10.36849/JDD.9390}, pmid = {42235053}, issn = {1545-9616}, abstract = {BACKGROUND: Advances in biotechnology have enabled highly effective, site-specific topical therapies for skin disease. Particle-based delivery systems can be engineered with tailored physicochemical properties and surface modifications to optimize controlled drug release and skin targeting, potentially improving acne treatment outcomes.<br><br>OBJECTIVE: To evaluate the effectiveness and tolerability of a retinol plus site-specific salicylic acid-targeted bio-delivery system in 40 Fitzpatrick skin type I-VI patients with moderate-to-severe acne over 12 weeks.<br><br>RESULTS: Significant improvements were observed across multiple efficacy measures, including expert grading, microbiome analysis, visual imaging, and patient self-assessments. Investigator grading demonstrated a 27.8% reduction in inflamed pustules at 2 weeks and a 68.6% reduction at 12 weeks. Acne nodules improved by 61.1% at 2 weeks, with a 92.2% reduction by week 12. Post-inflammatory hyperpigmentation improved significantly beginning at week 2, with an overall 32.3% improvement at week 12. Microbiome analysis showed a 52% reduction in Cutibacterium acnes levels by week 12. Expert grading revealed no erythema by week 12 and no edema throughout the study period. Patients also reported no significant itching, burning, tingling, or stinging sensations during treatment.<br><br>CONCLUSION: Combination therapy with site-specific acne medication and retinol produced significant clinical improvement in acne and post-inflammatory hyperpigmentation while demonstrating excellent tolerability over 12 weeks. &amp;nbsp.}, }
@article {pmid42235133, year = {2026}, author = {Broadwell, NH and Lombardo, K and Kohn, TP and Wu, CQ and Kates, MR and Gearhart, JP and Bivalacqua, TJ}, title = {The effect of neonatal partial upper and lower urinary tract obstruction on the intestinal microbiome in a murine animal model.}, journal = {Journal of pediatric urology}, volume = {22}, number = {5}, pages = {106035}, doi = {10.1016/j.jpurol.2026.106035}, pmid = {42235133}, issn = {1873-4898}, abstract = {INTRODUCTION: The intestinal microbiome holds promise as a tool for prognostics, diagnostics, and interventions in patients with congenital anomalies of the kidney and urinary system. The goal was to characterize the neonatal rat intestinal microbiome in response to partial upper and lower urinary obstruction using 16S rRNA Illumina sequencing.<br><br>METHODS: Neonatal Sprague Dawley rats were operated on day three of life. Partial ureteral obstruction was performed in upper urinary tract obstruction (UUTO) via suture ligation. Partial urethral obstruction was created in lower urinary tract obstruction (LUTO) via clip-applier technique. The intestinal microbiome was evaluated via 16S rRNA gene amplicon sequencing. Alpha and beta diversity, single taxa abundance, and unique indicator species analysis was performed using R Statistical Software 4.2.0.<br><br>RESULTS: At 21 days post-operatively, body mass was higher in LUTO compared to UUTO (p = 0.003). Beta diversity clustered significantly between groups. LUTO had elevated Firmicutes:Bacteroidota ratios compared to UUTO (p = 0.014). A unique LUTO indicator was the absence of CAG-302 (p = 0.014). Lactobacillus_B was significantly downregulated in UUTO (p = 0.033). All unique indicators of UUTO derived from the Lachnospiraceae family.<br><br>CONCLUSION: This study evaluated the neonatal response of the gastrointestinal microbiome to urinary obstruction. LUTO resulted in high-risk microbiome profiles consistent with obesity and metabolic syndrome. UUTO rats had microbiome profiles consistent with CKD models, which modulate short chain fatty acids and uremic toxins. Such patterns in the intestinal microbiome may be used as a prognostic model to detect children at high-risk for organ damage secondary to obstructive uropathy.}, }
@article {pmid42235160, year = {2026}, author = {Lu, T and Chen, Y and He, Q and Zheng, B and Deng, D and Xiong, X}, title = {Gut bacterial species, serum metabolites, and serum cytokines associated with broodiness in chickens.}, journal = {Poultry science}, volume = {105}, number = {9}, pages = {107187}, doi = {10.1016/j.psj.2026.107187}, pmid = {42235160}, issn = {1525-3171}, abstract = {Increasing evidence suggests that the gut microbiota, serving as a "virtual endocrine organ", potentially modulates reproductive behavior in poultry via the gut-brain and gut-ovary axes. Broodiness in hens inhibits egg-laying activity and causes major economic losses in native chicken breeds, but its micro-physiological basis remains unclear. This study used shotgun metagenomic sequencing to delineate the cecal bacterial species associated with brooding status in Chinese Kangle chickens. We identified 34 cecal bacterial species exhibiting significantly varying abundances between the broodiness and control groups, including six species (e.g., Bacteroides sp. An51A and Phocaeicola barnesiae) that were significantly enriched in the broodiness group. Additionally, 28 species significantly enriched in the control group were screened. Among them, Subdoligranulum variabile and Oribacterium asaccharolyticum served as key biomarkers for distinguishing brooding status in Kangle chickens and were associated with functional shifts in the cecal microbiome. Non-targeted metabolomic analysis identified 17 differential metabolites, among which seven (e.g., (13E) -11a-hydroxy-9,15-dioxoprost-13-enoic acid and d-arabitol) were defined as metabolic markers of the broody state and were significantly associated with Subdoligranulum variabile and Oribacterium asaccharolyticum. In addition, our results suggest that serum cytokines, such as IFN-γ and IL-22, are potentially associated with the broody state and the alterations in both serum metabolites and the gut microbiota (e.g., Subdoligranulum variabile and Oribacterium asaccharolyticum). These findings provide a new insight into the mechanisms underlying reproductive behavior in poultry and offer a theoretical basis for alleviating broodiness through microecological interventions, thereby improving the reproductive efficiency of indigenous chicken breeds.}, }
@article {pmid42235180, year = {2026}, author = {Generali, D and Membrino, A and Fontana, A and Gattazzo, F and Strina, C and Milani, M and Cervoni, V and Caltavituro, A and Castagnetti, A and Del Bianco, S and Schettini, F}, title = {A mixed prebiotic/probiotic intervention (MBR-01) for the management of diarrhea during abemaciclib treatment of early breast cancer in postmenopausal patients: A single-center prospective case-control pilot study.}, journal = {Breast (Edinburgh, Scotland)}, volume = {88}, number = {}, pages = {104830}, doi = {10.1016/j.breast.2026.104830}, pmid = {42235180}, issn = {1532-3080}, abstract = {BACKGROUND: Adjuvant abemaciclib + endocrine therapy (ET) improves long-term outcomes in high-risk, hormone receptor-positive (HR+)/HER2-negative early breast cancer (eBC). However, treatment is frequently complicated by diarrhea, affecting adherence and quality-of-life (QoL). Increasing evidence suggests that abemaciclib-induced gastrointestinal toxicity may involve gut microbiota alterations. We conducted a prospective case-control pilot study evaluating the efficacy of MBR-01, a standardized prebiotic/probiotic formulation, in mitigating abemaciclib-induced diarrhea.<br><br>METHODS: We enrolled 20 postmenopausal patients with high-risk HR+/HER2-negative eBC considered unfit for adjuvant chemotherapy. Patients received abemaciclib&#xa0;+&#xa0;letrozole (control, n&#xa0;=&#xa0;10) or abemaciclib&#xa0;+&#xa0;letrozole&#xa0;+&#xa0;MBR-01 (experimental, n&#xa0;=&#xa0;10). The primary endpoint was the incidence and severity of diarrhea; secondary endpoints included treatment adherence, QoL assessments and exploratory baseline/week-12 microbiota characterization according to treatment arm.<br><br>TRIAL REGISTRATION NUMBER: ISRCTN11948182.<br><br>RESULTS: Diarrhea occurred in all patients. In the control group, diarrhea was predominantly grade 1 (50%) or grade 2 (40%), with one grade 3 event (10%). In the MBR-01 group, diarrhea frequency and severity were reduced by &#x223c;70% at the end of week-12; 90% of patients experienced only grade 1 diarrhea or none by week-12, and no grade &#x2265;3 events. Dose modification was only required in one control. Decrease in alpha-diversity and F.prausnitzii were associated with earlier diarrhea onset and longer duration; increase in E.coli correlated with higher grade events. MBR-01 supplementation seemed to preserve microbial diversity and limited E.coli expansion. QoL was significantly improved with MBR-01.<br><br>CONCLUSION: MBR-01 may effectively mitigate abemaciclib-induced diarrhea, likely through the achievement of stabilization of gut microbiota composition. Larger prospective studies are warranted to validate these preliminary findings.}, }
@article {pmid42235236, year = {2026}, author = {Das, A and Singh, D and Behera, RN and Sarangi, PP and Ambatipudi, K}, title = {Bovine milk fat globules containing probiotics enhance colonisation resistance, pathogen exclusion and macrophage modulation in simulated gut environments.}, journal = {Food chemistry}, volume = {521}, number = {}, pages = {149831}, doi = {10.1016/j.foodchem.2026.149831}, pmid = {42235236}, issn = {1873-7072}, abstract = {Probiotics are widely used to manage gastrointestinal disorders; however, their therapeutic effects have been limited by rapid transit and degradation in the gut. Milk fat globules (MFGs) have recently gained attention as a bio-carrier that can shield probiotics and enhance their functionality under gastrointestinal stress. The present study hypothesises that MFGs enhance the survival and functionality of probiotics (e.g., L. fermentum, L. mesenteroides) by supporting colonisation resistance and modulating host immune responses. MFGs+L. fermentum exhibited significantly higher exclusion of enteric pathogens (e.g., E. coli, S. enterica, S. flexineri, K. pneumoniae, and P. aeruginosa) and synergistically attenuated oxidative stress. Mass spectrometric analysis revealed adaptive shifts in pathways of amino-acid biosynthesis, peptidoglycan assembly, transporters, and metabolism. Flow cytometry-based marker analysis showed that MFG-containing L. fermentum downregulated inflammatory markers (CD11b, CD14) in macrophages, promoting a more balanced immune state. Collectively, these findings demonstrate that MFGs enhance probiotic resilience, gut microbiome, and immune modulation.}, }
@article {pmid42235313, year = {2026}, author = {Sun, Y and Li, L and Wang, Y and Hu, C and Zhao, Y and Deng, S and Pan, Y and Li, J and Huo, J and Zhu, F}, title = {Sophoraflavanone G alleviates ulcerative colitis in mice by reshaping the gut microbiome and restoring the Th17/Treg balance through the PI3K/AKT/NF-κB signaling pathway.}, journal = {International immunopharmacology}, volume = {184}, number = {}, pages = {116952}, doi = {10.1016/j.intimp.2026.116952}, pmid = {42235313}, issn = {1878-1705}, abstract = {Ulcerative colitis (UC) is characterized by diarrhea, bloody stool and a feeling of incomplete defecation. Sophoraflavanone G (SFG) is one of the main chemical components of Sophora flavescens Ait and possesses various pharmacological activities. This study aims to investigate the therapeutic efficacy of naturally derived SFG in alleviating dextran sulfate sodium (DSS)-induced UC and the underlying mechanisms. A mouse model of DSS-induced UC was created and treated with SFG, antibiotics (ABX) cocktail, or the AKT agonist SC79. Clinical symptoms and signs of UC were assessed. Expression levels of inflammatory factors, tight junction proteins, and mucin-2 (MUC-2) in colon tissues were detected. The underlying mechanism by which SFG relieved UC in mice was elucidated by RNA sequencing (RNA-Seq), network pharmacology, molecular docking and molecular dynamics simulation, and validated in mouse colon tissues. Furthermore, the effects of SFG in remodeling the gut microbiome and restoring the Th17/Treg balance were explored. The results showed that SFG significantly decreased the Disease Activity Index (DAI) score, alleviated bloody diarrhea, splenomegaly, and colon shortening in UC mice; it effectively suppressed the serum and colonic levels of inflammatory factors, and significantly upregulated the expression of tight junction proteins and MUC-2 in colon tissues. Furthermore, molecular studies demonstrated that SFG may bind to p110α to inhibit the PI3K/AKT/NF-κB signaling pathway and further regulate the Th17/Treg balance. Meanwhile, SFG restores the gut microbiome. In conclusion, this study confirms that SFG has a significant therapeutic effect on DSS-induced UC. The underlying mechanism may be partially attributed to the binding of SFG to p110α, which inhibits the PI3K/AKT/NF-κB pathway and further regulates the Th17/Treg balance; and restores the gut microbiome to alleviate UC. This research offers a novel natural candidate foundation for the clinical treatment of UC.}, }
@article {pmid42235388, year = {2026}, author = {Jiao, Y and Xu, L and Zhou, Y and Tang, L and Fu, J and Shi, Y and Li, J}, title = {Synergistic immobilization of lead and enhanced Solanum nigrum growth by phosphogypsum coupled with phosphate-solubilizing Bacillus megaterium: Roles of Pb mineral transformation and rhizosphere microbiome restructuring.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142539}, doi = {10.1016/j.jhazmat.2026.142539}, pmid = {42235388}, issn = {1873-3336}, abstract = {Phosphogypsum (PG), a gypsum-rich industrial by-product containing residual phosphate, has attracted increasing attention for lead (Pb) risk management in contaminated soils, yet its effects on Pb mobility, phytotoxicity, and rhizosphere processes remain insufficiently understood. Here, a PG-microbe coupled strategy was established by introducing the phosphate-solubilizing bacterium Bacillus megaterium (BM) to enhance Pb immobilization and support the growth of Solanum nigrum. Batch aqueous experiments showed that BM remained active in the presence of PG and improved Pb removal relative to abiotic PG, accompanied by pronounced Pb-P co-existence at the cell-mineral interface. In pot experiments, Pb stress severely inhibited plant growth and induced oxidative damage, whereas the combined PG-BM treatment restored biomass, alleviated cellular injury and increased glutathione levels. In the rhizosphere, PG-BM treatment elevated available P, Ca[2 +] , and SO4[2-] concentrations, altered dissolved organic matter composition, and restored key enzyme activities. The coupled treatment also shifted Pb from labile fractions to stable pools, increasing the combined proportion of oxidizable and residual fractions to 39.6%. X-ray diffraction analysis indicated enhanced formation of Pb phosphate minerals, including Pb3(PO4)2 and Pb5(PO4)3Cl, supporting Pb mineral transformation potentially associated with PG-BM coupling. High-throughput 16S rRNA sequencing revealed rhizosphere community restructuring under the PG-BM treatment, including the enrichment of genera such as Sphingomonas and Rhodanobacter, whereas PICRUSt2 and FAPROTAX indicated a distinct predicted functional shift. Overall, the PG-BM system reduced Pb phytotoxicity and promoted Pb stabilization under controlled pot conditions, although long-term stability and field-scale environmental safety require further validation.}, }
@article {pmid42235395, year = {2026}, author = {Li, Y and Zhu, T and Tao, C and Li, S and Cheng, H and Chen, W}, title = {Threshold-dependent control of ARG removal in global wastewater treatment plants: Molecular mechanisms of low-abundance functional genes deciphered via metagenomics and explainable AI.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142574}, doi = {10.1016/j.jhazmat.2026.142574}, pmid = {42235395}, issn = {1873-3336}, abstract = {Wastewater treatment plants (WWTPs) serve as critical barriers against the dissemination of antibiotic resistance genes (ARGs) from urban water environments to nature, yet the molecular mechanisms governing their biological removal remain poorly understood. By combining experimental metagenomic data from 19 Chinese WWTPs with additional data from 31 global WWTPs (50 WWTPs in total), an explainable machine learning (ML) framework was developed. The RFE-SHAP (Recursive Feature Elimination-SHapley Additive exPlanations) based on feature importance was applied to identify key biological features driving ARG removal. The study revealed that low-abundance microbial functional genes particularly those involved in DNA repair, energy metabolism, and quorum sensing exhibit threshold-dependent control over ARG attenuation. ML models (BFGs-GBDT) incorporating the RFE-SHAP-selected functional genes achieved exceptional predictive accuracy (R[2]test = 0.967), outperforming taxonomy-based models (average R[2]test = 0.805). Strikingly, these functionally critical genes, despite their low abundances (0.04 - 0.15%), exerted disproportionate influence on ARG removal efficiency, challenging the prevailing high-abundance-centric paradigm in WWTPs design. The findings not only elucidated the molecular mechanisms of ARG mitigation but also provided a predictive framework for precision engineering of microbial communities to enhance ARG elimination. This study advances wastewater treatment strategies from empirical ARG removal to mechanism-driven environmental risk control.}, }
@article {pmid42235419, year = {2026}, author = {Paeslack, N and Mimmler, M and Schulz, J and Kownatzki, J and Kollar, B and Melzow, F and Zamor, J and Dremova, O and Kuntic, M and Kiouptsi, K and Soshnikova, N and Mann, A and Kittner, JM and Daiber, A and Sommer, F and Reinhardt, C}, title = {Toll-like receptor 2 impacts small intestinal villus capillarization through epithelial dual oxidase 2.}, journal = {Redox biology}, volume = {95}, number = {}, pages = {104212}, doi = {10.1016/j.redox.2026.104212}, pmid = {42235419}, issn = {2213-2317}, abstract = {The microbiota shapes postnatal gut development and physiology. In the small intestine, epithelial-to-endothelial crosstalk governs the microbiota-induced remodeling of villus capillary networks essential for nutrient transport. The intestinal epithelial enzyme dual oxidase 2 (DUOX2), an established regulator of the microbiome-host interaction, exerts microbicidal functions through the generation of reactive oxygen species. However, its role in intestinal vascular development remains poorly understood. Here, we demonstrate a Toll-like receptor 2 (TLR2)-dependent regulatory pathway controlling DUOX2 expression that influences villus vascularization in the small intestine. Mice globally lacking DUOX2 activity exhibited a notable reduction in vascularization in the small intestine, accompanied by alterations in gut microbial community structure. Conversely, mice with an intestinal epithelial-specific deficiency of TLR2 displayed an increase in villus vascularization along with elevated expression levels of DUOX2. Notably, DUOX2 expression was strongly upregulated in intestinal epithelial biopsies from patients with Crohn's disease. Similarly, inflammatory conditions induced by dextran sulfate sodium (DSS) treatment in mice resulted in increased epithelial Duox2 expression accompanied by enhanced villus vascularization. Together, our findings suggest a microbiota-TLR2-DUOX2 signaling axis in intestinal epithelial cells that promotes villus vascularization. This mechanism links microbial sensing in the intestinal epithelium to structural remodeling of the villus microvasculature during homeostasis and inflammation.}, }
@article {pmid42235462, year = {2026}, author = {Yang, D and Gong, X}, title = {Association between vitamin D status and bacterial vaginosis in non-pregnant women of reproductive age: a systematic review and meta-analysis.}, journal = {European journal of obstetrics, gynecology, and reproductive biology}, volume = {324}, number = {}, pages = {115208}, doi = {10.1016/j.ejogrb.2026.115208}, pmid = {42235462}, issn = {1872-7654}, abstract = {BACKGROUND: Bacterial vaginosis (BV) is the most common vaginal dysbiosis in women of reproductive age, and vitamin D (VD) has been implicated in mucosal immune regulation. However, the relationship between VD deficiency (VDD) and BV remains inconclusive, with prior reviews limited by inclusion of pregnant populations and incomplete literature coverage.<br><br>OBJECTIVE: To systematically evaluate the association between VD status and BV in non-pregnant women of reproductive age, and to assess the effect of VD supplementation on BV outcomes.<br><br>METHODS: PubMed, Embase, Cochrane Library, Web of Science, and CNKI were searched from inception through January 2025. Observational studies and intervention trials reporting VD status and BV outcomes in non-pregnant reproductive-age women were eligible. Random-effects meta-analysis with restricted maximum likelihood (REML) estimation and Hartung-Knapp adjustment was performed. Heterogeneity was assessed using I[2] and Cochran Q statistics. Subgroup and sensitivity analyses were pre-specified by geographic region, VDD cutoff, BV diagnostic method, and risk of bias.<br><br>RESULTS: Thirteen studies (9 observational, 4 interventional) met inclusion criteria. Among observational studies (7 entries from 5 studies; n&#xa0;=&#xa0;6,862), the pooled odds ratio (OR) for BV with VDD was 1.00 (95% CI: 0.71-1.42; I[2]&#xa0;=&#xa0;63.9%; prediction interval: 0.66-1.53), indicating no overall association. Substantial geographic heterogeneity was observed: the single Iranian study showed a strong positive association (OR&#xa0;=&#xa0;4.34), whereas Western (OR&#xa0;=&#xa0;0.96) and African (OR&#xa0;=&#xa0;1.01) studies were null. Among intervention studies (4 studies; n&#xa0;=&#xa0;281), VD supplementation was associated with a non-significant trend toward reduced BV persistence (pooled RR&#xa0;=&#xa0;0.68; 95% CI: 0.28-1.63; I[2]&#xa0;=&#xa0;85.7%). However, excluding the sole null US trial revealed a consistent protective effect across three non-US studies (RR&#xa0;=&#xa0;0.47; 95% CI: 0.37-0.60; I[2]&#xa0;=&#xa0;0%). GRADE certainty of evidence was very low for both outcomes.<br><br>CONCLUSIONS: The VDD-BV relationship is population-dependent. In VDD-prevalent populations, both observational and intervention evidence suggested an association: VD supplementation reduced BV persistence in the Iran subgroup (RR&#xa0;=&#xa0;0.45, I[2]&#xa0;=&#xa0;0%). In the limited US data available, no such association was detected, although this finding may not generalize to all Western populations. These findings support targeted VD supplementation for women with documented deficiency rather than universal use, though GRADE certainty is very low and confirmatory RCTs are needed.}, }
@article {pmid42235504, year = {2026}, author = {Tian, C and Guo, X and Wang, D and Chen, Q and Shen, H and Li, X and Liu, C and Qi, Y and Chen, Y and Wang, L and Wang, Y and Cao, Y and Liu, Y and Yin, H and Chen, Y and Gu, X and Jiang, C and Tang, L and Xie, C and Ding, Q}, title = {Uric acid promotes dietary lipid absorption through microbiome and metabolomic remodeling via a liver-gut endocrine axis.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.05.005}, pmid = {42235504}, issn = {1934-6069}, abstract = {Hyperuricemia closely correlates with obesity, yet high uric acid (UA) is largely viewed as a consequence or biomarker of obesity rather than a causal driver. Integrating human clinical analyses with animal studies, we redefine UA as a liver-derived endocrine regulator that drives obesity by modulating gut ecology. UA remodels the gut microbiota, selectively depleting Lactobacillus johnsonii by disrupting peptidoglycan synthesis. This depletion reduces microbial phenyllactic acid (PLA)-a metabolite produced by L. johnsonii lactate dehydrogenase that we identify as an endogenous suppressor of intestinal peroxisome proliferator-activated receptor alpha (PPARα) signaling. Consequently, PPARα disinhibition upregulates fatty acid transporters, accelerating lipid absorption and promoting obesity. Leveraging human genetic data, we pinpoint lysine acetyltransferase 5 (TIP60) as a master regulator of hepatic UA production. Hepatic TIP60 ablation lowers UA, restoring the L. johnsonii-PLA axis and conferring obesity resistance. These findings establish a UA-driven liver-gut axis and nominate TIP60 inhibition as a dual-target therapy for obesity and hyperuricemia.}, }
@article {pmid42235902, year = {2026}, author = {Salehi, M and Gottardo, A and Russo, TDB and Bonventre, G and Incorvaia, L and Gristina, V and Trecciola, MC and Galvano, A}, title = {Gut Microbiome Dysbiosis and Cancer: A Systematic Review on the Emerging Role of Probiotics in Oncology.}, journal = {Critical reviews in oncology/hematology}, volume = {}, number = {}, pages = {105416}, doi = {10.1016/j.critrevonc.2026.105416}, pmid = {42235902}, issn = {1879-0461}, abstract = {OBJECTIVE: To evaluate the role of probiotic supplementation in cancer patients and its clinical effects.<br><br>ELIGIBILITY CRITERIA: English-written clinical trials, pooled-, or meta-analyses of clinical trials assessing probiotic treatments in cancer patients.<br><br>INFORMATION SOURCES: PubMed, Scopus, and Web of Science databases up to September 2025.<br><br>Narrative synthesis of included studies, stratified by assessed outcomes.<br><br>INCLUDED STUDIES: 3 clinical trials, 1 in vivo study followed by a clinical trial, 2 meta-analyses and 1 pooled analysis.<br><br>SYNTHESIS OF RESULTS: Across chemotherapy settings, probiotic supplementation was associated with a reduction in clinically relevant diarrhea, with the most consistent signal for severe diarrhea and for selected subgroups (e.g., patients with colostomy during irinotecan-based therapy). Meta-analytic evidence also supported improvements in other gastrointestinal (GI) symptoms (nausea/vomiting, bloating, anorexia). In surgical oncology, perioperative probiotics/synbiotics were associated with faster GI functional recovery and favorable recovery-related markers in individual trials, while pooled randomized evidence in colorectal surgery indicated fewer postoperative infections and shorter length of stay; effects on anastomotic leak were inconsistent. Controlled clinical studies did not report probiotic-strain invasive infections, although rare serious events have been described in broader evidence.<br><br>LIMITATIONS OF EVIDENCE: Heterogeneity in study designs, formulations, and outcome definitions; limited reporting of resource-utilization outcomes and adverse-event attribution; few large-scale trials; scarce direct oncologic efficacy endpoints.<br><br>INTERPRETATION: Probiotics appear to be a promising adjunct for supportive care in selected cancer pathways, particularly for GI toxicity and perioperative outcomes. Strain-defined, adequately powered trials with harmonized endpoints are needed to inform guideline-ready use.}, }
@article {pmid42236101, year = {2026}, author = {Borghi, E and Tassi, L and d'Orsi, G and Uzzau, S and Pivari, F and Ricci, E and Longoni, G and Mingarelli, A and Previtali, R and Berardi, R and De Diego, L and Vigano', I and Olivotto, S and Compierchio, E and Veggiotti, P and Canevini, MP and Vignoli, A}, title = {Microbiota-gut-brain axis and treatment resistance in epilepsy: a multicentre prospective study protocol (CARE).}, journal = {BMJ open}, volume = {16}, number = {6}, pages = {e111607}, doi = {10.1136/bmjopen-2025-111607}, pmid = {42236101}, issn = {2044-6055}, abstract = {INTRODUCTION: Approximately one-third of people with epilepsy (PWE) experience resistance to treatment, including pharmacological therapies, epilepsy surgery, vagus nerve stimulation (VNS) and dietary interventions such as the ketogenic diet (KD). Emerging evidence suggests that the gut microbiota may influence seizure susceptibility and treatment response through the microbiota-gut-brain axis, potentially contributing to treatment resistance. The MiCrobiota-gut-brain Axis in Resistant Epilepsy project investigates how gut microbial features and associated host epigenetic signatures affect clinical outcomes in PWE undergoing diverse treatment strategies.<br><br>METHODS AND ANALYSIS: This is a multicentre, prospective, longitudinal study involving four clinical centres in Italy and one self-financing partner. Participants aged 3-50 years will be enrolled and stratified into four intervention cohorts: newly diagnosed drug-na&#xef;ve epilepsy scheduled to start anti-seizure medications, focal drug-resistant epilepsy (DRE) undergoing epilepsy surgery, DRE receiving VNS, and DRE initiating KD. Clinical assessments (including body mass index calculation, self-reported monthly seizure count, dietary evaluation, quality of life scale and gastrointestinal symptoms scale), electroencephalography, MRI and biological sample collection (stool and blood) will be obtained at baseline and longitudinally at two or three timepoints over a 12-month observation period. Gut microbiota changes over time will be assessed via metagenomics (using 16S ribosomal RNA sequencing) and metaproteomics; the associated host DNA methylation profiles will be obtained from blood using Illumina EPIC arrays. Primary endpoints include identification of microbial or host methylation changes predictive of therapeutic response (ie, reduction from baseline in monthly seizure count) to the intervention. Data will be analysed using multivariate models and mixed-effect regression. Further, omics data and corresponding metadata will be integrated using multi-omics approaches to identify molecular signatures biomarkers predictive of treatment response and prognosis in PWE.<br><br>ETHICS AND DISSEMINATION: The study received ethical approval from the Research Ethic Board (Comitato Etico Territoriale Lombardia 3, ID 4896 - parere numero 4896_17.07.2024_N_bis). All participants or their legal guardians will provide written informed consent. Results will be disseminated through peer-reviewed publications, conference presentations or lay summaries targeting patient organisations.<br><br>TRIAL REGISTRATION NUMBER: ClinicalTrials.gov Identifier NCT07010445, registered on 2 May 2025.}, }
@article {pmid42236126, year = {2026}, author = {Goudman, L and Vandeputte, D and Forget, P and Demuyser, T and Moens, M}, title = {Gut microbiome profiles in patients with nociceptive pain, neuropathic pain, and pain-free controls: a case-control study.}, journal = {Regional anesthesia and pain medicine}, volume = {}, number = {}, pages = {}, doi = {10.1136/rapm-2026-107796}, pmid = {42236126}, issn = {1532-8651}, abstract = {OBJECTIVE: Gut microbiota have been implicated in pain modulation through immune, inflammatory, and neurobiological pathways, yet whether distinct gut microbial signatures differentiate nociceptive from neuropathic low back pain remains unclear.<br><br>METHODS AND ANALYSIS: In this longitudinal study, we profiled the gut microbiome of individuals with nociceptive low back pain (n=10), neuropathic low back pain (n=10), and pain-free controls (n=10) at baseline and after 3&#x2009;months. Pain patients were resampled following standard-of-care treatment, while controls were resampled to capture background temporal variation. Gut microbial profiles were characterized using 16S rRNA gene (V4) sequencing. Alpha diversity was analyzed using mixed-effects models, beta diversity using Bray-Curtis, weighted UniFrac, and centered log-ratio-Euclidean distances, and differential abundance using Analysis of Compositions of Microbiomes with Bias Correction 2 (ANCOM-BC2).<br><br>RESULTS: Entropy-based alpha-diversity indices did not differ between groups or over time. Richness-based metrics suggested a possible reduction in the neuropathic-dominant group in pairwise contrasts after rarefaction, although omnibus group effects did not reach conventional statistical significance. Overall microbial community structure did not differ between pain groups and controls, and no population-specific or population-by-time effects were detected at the genus or amplicon sequence variant level.<br><br>CONCLUSION: Together, these findings indicate that gut microbiome differences across chronic pain phenotypes are subtle, characterized mainly by changes in low-abundance taxa rather than broad community shifts, underscoring limitations of microbiome-based stratification in chronic pain and the need for larger, integrative studies.}, }
@article {pmid42236487, year = {2026}, author = {Apjok, G and Sári, T and Méhi, O and Asbóth, A and Barna, L and Sala, D and Gróf, I and Vásárhelyi, BM and Juhász, S and Pál, C and Horváth, P and Migh, E and Schneider, G and Hill, C and Deli, M and Shkoporov, A and Kintses, B}, title = {Prevalent gut phages encode modular adhesins mediating epithelial binding and endoplasmic reticulum trafficking.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-74031-x}, pmid = {42236487}, issn = {2041-1723}, support = {9262//European Molecular Biology Organization (EMBO)/ ; 220646/Z/20/Z//Wellcome Trust (Wellcome)/ ; }, abstract = {Bacteriophages are crucial components of the human microbiome and hold promise as therapeutic agents. Yet, their physical interactions with mammalian cells remain poorly understood. Here, we developed a high-throughput platform to identify phages that adhere to epithelial layers and the proteins that mediate this interaction. The identified phages encode immunoglobulin (Ig)-like domain-containing proteins that, when displayed on a non-adherent phage, confer epithelial binding and internalization in vitro, and increased phage retention in the mouse gut in vivo. Phages encoding these adhesins are among the most abundant and prevalent human gut phages, including crAss-like phages and myoviruses closely related to the recently proposed Flandersviridae family. Domain sequence variation alters epithelial interaction profiles, and internalized phages traffic to the endoplasmic reticulum through the Golgi apparatus, suggesting access to non-degradative internalization pathways. These findings reveal widespread phage-human interactions in the human viral community, with potential impacts on health and implications for next-generation phage therapeutics.}, }
@article {pmid42236502, year = {2026}, author = {Bansal, S and Chaudhary, R and Bansal, N and Bishnoi, M and Kondepudi, KK and Chopra, K}, title = {Fructooligosaccharide supplementation ameliorates gut associated metabolic dysregulation in estrogen-deprived rats via targeting oxidative stress, inflammation, apoptosis, and gut microbiome.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-50101-4}, pmid = {42236502}, issn = {2045-2322}, support = {ANRF/ECRG/2024/001702/LS//Anusandhan National Research Foundation (ANRF), Prime Minister Early Career Research Grant (PMECRG) Program/ ; }, abstract = {Estrogen is a key regulatory hormone that maintains metabolic and gut homeostasis by modulating immune responses, microbial composition, and energy balance. However, estrogen deficiency is strongly associated with gut associated metabolic dysregulation (GAMD), characterised by increased oxidative stress, systemic inflammation, and altered gut microbiome (GM). Prebiotic compounds such as fructooligosaccharide (FOS) have shown potential in modulating gut and metabolic health. This study aimed to assess the therapeutic potential of FOS supplementation in restoring GAMD in estrogen-deprived rats. To induce GAMD, female Sprague-Dawley rats were bilaterally ovariectomized (OVX) and fed FOS for 28 days to restore the gut and associated metabolic functions. At the end, various physiological, anthropometric, and adiposity markers were assessed. Further, oxidative stress, inflammation, apoptosis, and histopathological parameters were evaluated in the colon and liver. Furthermore, gut mucosa, tight junction gene (TJG), and GM were also analysed. OVX rats fed FOS (50 &amp; 100 mg/kg) for 28 days showed recovery of basic physiological, anthropometric, and adiposity markers. There was also a substantial reduction in apoptosis, inflammation, and oxidative stress in both the colon &amp; liver. Additionally, gut mucosa, TJG, and GM were restored. Histopathological examinations revealed improved gut integrity (mucosal layer &amp; goblet cells) and liver health (healthy hepatocytes). FOS ameliorates the postmenopausal GAMD by targeting oxidative stress, inflammation, and GM. Therefore, FOS may be a promising candidate for preventing postmenopausal complications in clinical settings.}, }
@article {pmid42236717, year = {2026}, author = {Chen, Y and Feng, J and Lü, P and Zhou, D and Wei, Y and Jing, T and Zheng, Z and Raza, W and Qi, D and Zhang, M and Zhao, Y and Li, K and Wang, W and Cheng, X and Xie, J}, title = {Streptomyces sesquiterpenes elicit 10-HCA secretion and recruit disease-suppressive microbiota to enhance banana Fusarium wilt resistance.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73928-x}, pmid = {42236717}, issn = {2041-1723}, abstract = {Plant-beneficial microbe interactions are vital for enhancing soil-borne disease resistance, largely through the assembly of a disease-suppressive microbiome. However, the mechanisms governing these interactions remain elusive. Here, we establish an interaction model between banana and Streptomyces yongxingensis sp. nov. 2-11. We demonstrate that strain Sy2-11 suppresses banana Fusarium wilt (BFW) by recruiting a protective rhizosphere microbiome. Furthermore, we identify sesquiterpenes (aristolene and ledene), produced by strain Sy2-11, as key signaling molecules that trigger banana roots to biosynthesize 10-hydroxycapric acid (10-HCA). Interestingly, 10-HCA specifically enriches beneficial Bacillus spp., which is essential for the suppression of BFW. This effect is validated by synthetic communities (SynComs) and chemotaxis-deficient mutants of Bacillus velezensis. Our findings reveal a previously unreported mechanism that differs from conventional plant-microbe interactions, whereby Streptomyces, acting as a beneficial elicitor, releases sesquiterpene signals to trigger 10-HCA secretion in banana plants, thereby orchestrating the assembly of a rhizosphere microbiome that suppresses BFW. These findings provide a promising strategy for rhizosphere micro-ecological regulation and sustainable soil-borne disease control, with significant potential for advancing sustainable agriculture.}, }
@article {pmid42221783, year = {2026}, author = {Mingat, SX and Ehara, T and Izumi, H and Ejima, R and Mitsuyama, E and Nakamura, H and Miyaji, K and Xiao, JZ}, title = {Synbiotic effects of 2'-fucosyllactose and Bifidobacterium longum subsp. infantis M-63 in fermented human fecal communities.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1744839}, pmid = {42221783}, issn = {2296-861X}, abstract = {BACKGROUND/OBJECTIVES: Human milk oligosaccharides (HMOs) are the third most abundant solid component of human milk. HMOs are selectively utilized by infant-type human-residential bifidobacteria (HRB), resulting in the formation of a gut microbiota dominated by bifidobacteria and the production of health-beneficial metabolites, such as acetate and aromatic lactic acids (ALAs), in breastfed infants. HMOs play key roles in infant health by acting as prebiotics, preventing infections, and regulating the immune system. However, the prevalence of HMO-utilizing bifidobacteria in the gut microbiota of infants and young children varies greatly between countries and regions, with some infants and children containing none.<br><br>METHODS: We used a pH-controlled single-batch fermenter to model the human gut microbiota and evaluated whether HMOs provide infants or young children having or lacking bifidobacteria with HMO-utilizing ability with any physiological benefits. We conducted fecal fermentation with 2'-fucosyllactose (2'-FL), with or without supplementation with a probiotic HRB strain (Bifidobacterium longum subsp. infantis M-63).<br><br>RESULTS: 2'-FL alone did not significantly increase the relative abundance of bifidobacteria or the production of acetate and ALAs during fecal fermentation of infants and young children. Conversely, 2'-FL&#x202f;+&#x202f;M-63 significantly increased bifidobacteria and promoted acetate and ALA production in the fecal fermentation of both infants and young children.<br><br>CONCLUSION: Health benefits from 2'-FL may be restricted by inter-individual and age-dependent differences in gut microbiota response. Supplementation with a probiotic HRB with high HMO-utilizing ability could overcome this restriction. Our findings provide insights into the development of formulas for infants and young children.}, }
@article {pmid42221821, year = {2026}, author = {Bischof, F and Krumbholz, P and Kleinau, G and Scheerer, P and Stäubert, C}, title = {Comparative analysis reveals molecular adaptation of mammalian HCA2 to microbial metabolites.}, journal = {iScience}, volume = {29}, number = {6}, pages = {116030}, pmid = {42221821}, issn = {2589-0042}, abstract = {Metabolite-sensing G protein-coupled receptors (GPCRs), such as hydroxycarboxylic acid receptor 2 (HCA2), translate endogenous and microbial signals into physiological responses, regulating metabolism and immunity, yet the extent of HCA2 functional diversification across mammals remain unclear. Here, comparative pharmacology, metabolomics, evolutionary analysis, and structural mapping of mammalian HCA2 orthologs reveal extensive functional diversification across mammals, especially in odd-toed ungulates. Notably, African rhinoceros HCA2 exhibits multiple HCA3-like substitutions, resulting in loss of responsiveness to HCA2 agonists and increased sensitivity to HCA3-specific ligands. Positive selection analyses and metabolomic profiling of fecal extracts implicate microbiome-derived metabolites, particularly phenylpropionic and trans-cinnamic acid, as potential drivers of this adaptive shift. Mutagenesis experiments identified key amino acid substitutions in extracellular and transmembrane regions that modulate ligand potency and efficacy. These findings demonstrate that mammalian HCA2 receptors have undergone lineage-specific molecular evolution shaped by host-microbe metabolic interactions, highlighting how ecological contexts drive receptor adaptation and functional diversification.}, }
@article {pmid42221840, year = {2026}, author = {Ju, K and Shan, Y and Pan, L}, title = {Functional Recovery After Chemotherapy- and Radiotherapy-Induced Gastrointestinal Injury: Mechanisms, Clinical Assessment, and Management.}, journal = {International journal of general medicine}, volume = {19}, number = {}, pages = {610529}, pmid = {42221840}, issn = {1178-7074}, abstract = {Chemotherapy- and radiotherapy-induced gastrointestinal injury is a common complication of cancer treatment and may present with diarrhea, abdominal pain, urgency, bloating, rectal bleeding, and reduced oral intake. Although many cases improve after treatment completion, some patients develop persistent or late bowel dysfunction that impairs nutrition, treatment tolerance, daily functioning, and quality of life. Conventional terms such as toxicity, mucositis, and enteritis are clinically useful, but they do not fully capture the problem of incomplete functional recovery. We propose a practical recovery-oriented framework that operationalizes meaningful recovery across four interconnected domains: structural recovery, barrier recovery, clinical recovery, and patient-centered recovery. Using this framework, we summarize the acute-to-chronic clinical spectrum of luminal gastrointestinal injury, examine mechanisms of failed recovery, review clinical assessment and management, and discuss emerging strategies including biomarker-guided monitoring, microbiome-directed interventions, organoid-based platforms, and regenerative therapies. Current care remains largely supportive and symptom-centered. A recovery-oriented model may improve clinical decision-making by integrating symptom trajectory, nutritional status, treatment tolerance, patient-reported burden, and selected biological signals to better monitor and restore gastrointestinal function.}, }
@article {pmid42221959, year = {2026}, author = {Wen, Y}, title = {Gut microbiota-derived tryptophan metabolites: molecular mechanisms, nutritional strategies and implications for swine health.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1807477}, pmid = {42221959}, issn = {2297-1769}, abstract = {Tryptophan, an essential amino acid, has nutritional value. Beyond that, it is an important signaling molecule that connects the gut microbiota with host physiology. While host-mediated pathways are well-characterized, the microbiota-driven indole pathway has emerged as a major modulator of host homeostasis. Commensal bacteria metabolize unabsorbed tryptophan into indole-3-propionic acid (IPA), indole-3-lactic acid (ILA) and other bioactive indole derivatives. These bioactive indole derivatives can act as ligands for aryl hydrocarbon receptor (AhR) and pregnane X receptor (PXR). This review makes a summary of the main tryptophan metabolic pathways. It also elucidates the molecular mechanisms by which microbial metabolites derived from tryptophan restore the integrity of the intestinal barrier, maintain immune homeostasis, and modulate host metabolism. Building on this, we discuss nutritional strategies, such as dietary patterns and probiotic interventions, and their potential to modulate tryptophan metabolism. Using pigs as a translational model, we summarize the potential applications of these metabolites in alleviating weaning stress and improving growth performance. This review focuses on tryptophan metabolism and provides a theoretical basis for microbiome interventions and precision nutrition strategies in swine production.}, }
@article {pmid42222135, year = {2026}, author = {Gabriel, PO and Velasco-Cruz, C and Randall, JJ}, title = {Host genotype and environment shape rhizosphere and root microbiome composition of pecan rootstocks.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1778537}, pmid = {42222135}, issn = {2813-4338}, abstract = {The rhizosphere and root-associated microbiomes play a crucial role in nutrient acquisition, stress tolerance, and overall plant performance. However, little is known about how microbial communities assemble and shift across environments in pecan (Carya illinoinensis). In this study, we compared the bacterial and fungal community compositions in the roots and rhizosphere of four pecan clonal rootstocks (NMU03, NMU04, NMU05, and NMU155) cultivated under greenhouse conditions, as well as their subsets that were subsequently transplanted to the field. Amplicon sequencing of 16S rRNA and ITS regions revealed significant differences in microbial diversity and taxonomic composition across environments and genotypes. Bacterial assemblages in greenhouse roots were typically dominated by a few families (e.g., Burkholderiaceae, Rhodanobacteraceae, and unclassified taxa). In contrast, field samples exhibited broader taxonomic distributions, with families such as Xanthobacteraceae, Haliangiaceae, and Geminicoccaceae emerging as dominant members. Fungal OTU abundance was consistently higher than bacterial abundance across all genotypes, likely reflecting mutualistic associations with mycorrhizal fungi, such as those in the Elaphomycetaceae family. Interestingly, Aspergillaceae dominated greenhouse and field fungal communities, suggesting ecological adaptability and potential contributions to plant stress tolerance. Comparisons with earlier greenhouse studies revealed that while some signature core microbiome members were retained following transplantation from the greenhouse to the field, the abundance of others decreased, highlighting successional shifts in community structure driven by environmental transitions. Together, these findings demonstrate the dynamic, genotype and environment-specific structuring of pecan microbiomes and highlight the importance of microbiome-informed breeding strategies to improve plant-microbe associations under variable growth conditions among pecan breeders.}, }
@article {pmid42222136, year = {2026}, author = {Crippen, TL and Kim, D and Swiger, SL and Anderson, RC}, title = {Protist community sites and structure under two barn management systems at a commercial dairy.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1803341}, pmid = {42222136}, issn = {2813-4338}, abstract = {INTRODUCTION: Investigations into the location and load of protists in the environment arounddairies are scarce but are essential to maintaining the health of livestock.Moreover, the design of dairy barns has fluctuated over the decades to maximizecattle health and milk production without regard to influences on environmentalmicrobiomes. Beyond cost, the major emphasis of barn design is the managementof appropriate temperature and comfort for cattle. However, there havebeen no corresponding investigations into whether these design changes affect protist communities within barns.<br><br>METHODS: In this study, community shotgun metagenomic analysis was used to define the spatial composition and relative abundance of protist communities from 118 samples of manure, lagoons, troughs, and house and stable flies at a commercial dairy implementing two free-stall management systems: flow-through and cross-vent. Sequence reads were mapped to the CosmosID database. Viability was not assessed; therefore, results reflect DNA detection only not viability or disease occurrence.<br><br>RESULTS: The protist composition differed significantly between dairy components. Ecological findings showed that troughs and lagoons harbored high protist diversity, including the possible pathogen Neobalantidium coli and potential carriers Paramecium biaurelia and Acanthamoeba. Manure had the lowest protist diversity. Stable flies carried more protist taxa than house flies. Both fly species uniquely carried the non-pathogenic alveolate parasite Hammondia hammondi. The water mold plant pathogen Pseudoperonospora cubensis was identified in all sample types. Of the total relative abundance of protists, 2.10% were amoebas, 7.63% alveolate parasites, 62.71% water molds, 23.31% ciliates, 1.74% foraminifera, and 2.50% diatoms.<br><br>DISCUSSION: These results describe preliminary spatial overlaps and possible avenues of dissemination, providing a basis for assessing appropriate management systems and identifying protist reservoir sites within dairy operations.}, }
@article {pmid42222207, year = {2026}, author = {Colussi-Pelaez, E}, title = {Histamine Intolerance Through a Functional Medicine Lens: A Systems-Based Review.}, journal = {Integrative medicine (Encinitas, Calif.)}, volume = {25}, number = {2}, pages = {86-88}, pmid = {42222207}, issn = {1546-993X}, }
@article {pmid42222260, year = {2026}, author = {Alfaro-García, RG and Vargas-Mejía, P and Patiño-Conde, V and Rebollar, EA and Guerrero-Analco, JA and Vega-Arreguín, J and Reverchon, F and Méndez-Bravo, A}, title = {Phytophthora root rot induces compositional and functional changes in avocado rhizosphere bacterial communities.}, journal = {FEMS microbes}, volume = {7}, number = {}, pages = {xtag025}, pmid = {42222260}, issn = {2633-6685}, abstract = {Understanding how plant pathogens modulate the rhizosphere microbiota is essential to integrated disease management. Here, the compositional and functional shifts in the avocado rhizosphere bacteriome induced by Phytophthora cinnamomi were assessed to identify bacterial taxa enriched in the symptomatic condition and elucidate the microbial functions modulated by the infection. Metabarcoding and metatranscriptomics analyses revealed that Phytophthora root rot (PRR) induced compositional shifts in bacterial communities, leading to the enrichment of members of MND1, RB41, and Nitrospira. Functional analysis showed that this enrichment might be due to the release of nutrients following root rot, as carbohydrate metabolism was stimulated in rhizobacterial communities of infected trees. Moreover, the relative abundance of transcripts from genes associated with stress response and cell signaling increased in some of the most active genera in the rhizosphere of PRR-symptomatic trees, suggesting their potential to mitigate the adverse effects of infection. These findings highlight the need to combine compositional and functional microbiome data to differentiate between taxa attracted by nutrient release and those contributing to the plant defense. The interactions of beneficial bacterial taxa with the pathogen should be further studied, as they may constitute promising biocontrol agents.}, }
@article {pmid42222261, year = {2026}, author = {Wassermann, B and Kögl, I and Gokul, JK and Wicaksono, WA and Schweitzer, M and Korsten, L and Berg, G}, title = {Diversity and selected functional traits of microbiota associated with traditional dried plant foods from South African informal markets.}, journal = {FEMS microbes}, volume = {7}, number = {}, pages = {xtag026}, pmid = {42222261}, issn = {2633-6685}, abstract = {Traditional plant-based products provide nutritional benefits and support cultural heritage; however, their sale in urban informal markets raises potential food safety considerations. We characterized the microbiota of five traditional dried plant products (baobab, masau, nyii, dinawa, and lude) obtained from three informal markets in South Africa (n = 51 samples) using 16S rRNA gene sequencing and quantitative real-time PCR; bacterial isolates (n = 87) were further evaluated using selected phenotypic assays. Bacterial abundance and composition varied across products and vendors. Baobab exhibited the highest microbial richness (1460 ASVs) but relatively low bacterial loads (10[6] 16S rRNA gene copies g[-1]), whereas dried leafy greens showed the lowest richness (470 ASVs) but the highest bacterial abundance (10[9] copies g[-1]). Across products, higher bacterial diversity correlated with genera such as Bifidobacterium and Prevotella, while higher bacterial abundance correlated with genera such as Salmonella, Vibrio, and Acinetobacter. Notably, health implications of detected taxa cannot be inferred from genus-level identification based on 16S rRNA gene sequencing. Phenotypic traits observed among selected isolates included growth in the presence of several antibiotics (particularly sulfadiazine and ampicillin), protease activity, and inhibition of indicator strains under laboratory conditions. Overall, traditional dried plant foods harbor diverse microbial communities shaped by plant characteristics and vendor-related practices, highlighting the importance of improved handling and drying practices.}, }
@article {pmid42222391, year = {2026}, author = {Jiang, S and Du, Z and Wang, Y and Ma, H and Ma, Z and Wang, X}, title = {Dynamic changes and clinical significance of the gut microbiota and serum metabolites in breast cancer onset, progression and chemotherapy intervention.}, journal = {Frontiers in oncology}, volume = {16}, number = {}, pages = {1795317}, pmid = {42222391}, issn = {2234-943X}, abstract = {OBJECTIVE: Alterations of the gut microbiota and host metabolic reprogramming are closely associated with the development of breast cancer and the treatment response; however, integrated studies of the gut microbiota and metabolome spanning the transition from benign breast disease (BBD) to malignancy and the postchemotherapy phase remain limited. This study aims to systematically characterize the dynamic changes in the "gut microbiota-serum metabolome-breast tumor" axis from benign breast disease (BBD) to breast cancer (BC) and postchemotherapy breast cancer (PCBC) and to evaluate its potential value in diagnosis and disease monitoring.<br><br>METHODS: We enrolled 295 female participants, who were divided into a BBD group (n = 83), a BC group (n = 100), and a PCBC group (n = 88), and included 24 paired fecal samples from the same patients that were collected before and after chemotherapy. Fecal samples underwent 16S ribosomal RNA (rRNA) sequencing, while serum samples underwent an liquid chromatography-high-resolution mass spectrometry (LC-MS/MS) based nontargeted metabolomic analysis; we compared differences in gut microbiota diversity, taxonomic composition, and functional predictions across groups and screened for differentially abundant metabolites and enriched metabolic pathways. In a subset of patients with paired multiomics data (BBD n=19, BC n=31, and PCBC n=34), Spearman's correlation analysis, multiomics principle component analysis (PCA)/partial least squares-discriminant analysis (PLS-DA), and random forest models were employed to integrate the microbiota and metabolic features.<br><br>RESULTS: Cross-sectional remodeling of the gut microbiome structure occurred. The &#x3b1; diversity of the gut microbiota was similar across the three groups (BBD, BC, and PCBC); however, the &#x3b2; diversity analysis based on the weighted UniFrac distance revealed the significant separation of the microbial community structure among the three groups. At the taxonomic level, the BBD group was significantly enriched with beneficial commensal bacteria that produce short-chain fatty acids (e.g., Faecalibacterium and Roseburia); in contrast, the BC group shifted toward the enrichment of inflammation- or tumor-associated genera (e.g., Blautia, Fusobacterium, Sneathia, and Prevotella), while the PCBC group further accumulated various opportunistic pathogens (such as Phocaeicola, Sutterella, Enterococcus, and Chlamydia). As the disease progressed and chemotherapy was administered, the microbiome gradually shifted from a "metabolic protective" state to an "inflammatory/pathogenic" state. The characteristics of the dynamic remodeling of serum metabolomic profiles were identified. Nontargeted metabolomics revealed more than 3,000 metabolites, and the multivariate analysis indicated significant heterogeneity in the metabolomic profiles associated with malignant transformation and those measured before and after chemotherapy. In the BC group, energy, amino acid, and lipid metabolism were significantly disrupted, and widespread metabolite depletion was observed; however, in the postchemotherapy PCBC group, adaptive pathways such as estrogen, bile acid, and drug metabolism were activated, and persistent abnormalities in purine/nucleotide, carbon, and multiple amino acid metabolism were detected. Overall, the serum metabolic network underwent a dynamic remodeling process, transitioning from homeostasis to severe disruption and then to partial reconstruction following treatment. Among these changes, the differentially abundant metabolites torsemide, cortolone-3-glucuronide, and trimethylselenonium all had area under the curve (AUC) values greater than 0.75 in distinguishing between different disease stages and chemotherapy statuses, demonstrating their good potential as biomarkers. Interaction networks and multiomics predictive models of the "gut-metabolism-tumor" axis were established. Multiomics association networks revealed a systemic shift in gut-metabolism interaction patterns from a steady state characterized by "probiotic-energy/amino acid and polyphenol metabolism coupling" during the benign phase to a new steady state dominated by "proinflammatory/opportunistic pathogens-lipid reprogramming, exogenous metabolite metabolism, and oxidative stress." A multiomics classification model based on random forests demonstrated that the combined analysis of the gut microbiota and serum metabolite profiles exhibited exceptional efficacy in distinguishing between the BBD, BC, and PCBC groups. It identified a cluster of strongly associated features characterized by anaerobic gram-positive cocci, Lactobacillus-associated microbiota, and their paired metabolites, providing an important molecular fingerprint for clinical assessment.<br><br>CONCLUSIONS: This study integrates gut microbiome and serum metabolomic data to reveal that during the progression of benign breast lesions to breast cancer and throughout chemotherapy, the "gut microbiota-host metabolism-breast tumor" axis transforms from a state characterized by commensal depletion, the expansion of opportunistic pathogens, and reprogramming of energy/lipid metabolism to a persistent metabolic signature associated with drug metabolism and the activation of oxidative stress pathways. The integrated multiomics model helps characterize the biological differences across various stages of breast disease. The identified characteristic bacterial genera and metabolite combinations provide preliminary theoretical clues for the future exploration of microbiome-related mechanisms in breast cancer and for auxiliary assessments.}, }
@article {pmid42222592, year = {2026}, author = {O'Shea, KM and Brooks, E and Polmear-Swendris, N and Slack, IF and Smith, JA and Gordon, A and Aquino, DM and Gern, JE and Khurana Hershey, GK and Johnson, CC and Wilkowski, J and Hines, J and Lukacs, NW and Schuler, CF and Baker, JR}, title = {The Michigan Sibling Immunity Birth Study (M-SIBS): Study design protocol for a unique food allergy birth cohort.}, journal = {The journal of allergy and clinical immunology. Global}, volume = {5}, number = {4}, pages = {100721}, pmid = {42222592}, issn = {2772-8293}, abstract = {BACKGROUND: Food allergy is a rapidly escalating public health concern, yet the biologic pathways that link early-life exposures with disease onset remain poorly defined. No existing food-allergy birth cohort has yet paired criterion-standard oral food challenges with comprehensive, family-wide multiomics profiling.<br><br>OBJECTIVE: The Michigan Sibling Immunity Birth Study (M-SIBS) was established to elucidate early-life genetic and environmental interactions that drive disease. By enrolling entire families, including atopic siblings, the study leverages shared genetics, perinatal sampling, and household exposures to identify modifiable factors in food allergy development.<br><br>METHODS: M-SIBS is a prospective birth cohort at the University of Michigan that will enroll 1000 infants who have a first-degree relative with atopic disease. Mothers are recruited prenatally along with biologic fathers and siblings. Infants are then followed through 36 months of life. Extensive longitudinal phenotyping includes (1) serial skin prick and serum-specific IgE testing to the 9 most common food allergens at designated intervals; (2) standardized oral food challenges to confirm any positive result; (3) biospecimen collection at specified time points prebirth and postbirth; and (3) validated clinical, psychosocial, and environmental surveys administered longitudinally. It is designed to integrate genomic, epigenomic, transcriptomic, metabolomics, and microbiome data into a single multiomics framework across the family unit.<br><br>CONCLUSIONS: M-SIBS integrates criterion-standard clinical diagnostics for food allergy with family-based multiomics to generate an unprecedented data set on the earliest drivers of food allergy.}, }
@article {pmid42222691, year = {2026}, author = {L'Orphelin, JM and Morice, C and Gardères, J and Chopin, S and Lucas, C and Bouchet, C and Bailly-Caillé, B and Da Silva-Dias, V and Mourad, N and Jouandet, M and Akroun, J and Acher, A and Dompmartin, A and Parienti, JJ}, title = {Sensoriality of emollient creams: can sensory experience compromise blinding in trials?.}, journal = {Skin health and disease}, volume = {6}, number = {3}, pages = {250-258}, pmid = {42222691}, issn = {2690-442X}, abstract = {BACKGROUND: Regular application of emollients, particularly those that enhance the skin's acid mantle and promote ceramide production, can help restore skin barrier integrity, reduce inflammation and prevent disease flares. These emollients not only protect the skin, but also modulate on the skin microbiome, which has become a cornerstone in disease management. Sensory properties, such as texture, appearance and the sensation of freshness, are critical factors influencing patient perception, treatment adherence and product efficacy.<br><br>OBJECTIVES: To test, a controlled study involving 120 participants, the ability of consumers to recognize emollient creams based solely on sensory characteristics to ensure that sensory stimuli from emollients cannot be a source of unblinding in a clinical trial involving topical corticosteroids.<br><br>METHODS: We conducted a double-blind quantitative assessment in a controlled environment involving 120 healthy volunteers who were regular users of moisturizing creams, of whom 50% were classified as 'na&#xef;ve' users and 50% as 'connoisseurs'. The creams under investigation (n = 4) were placed in identical bottles and evaluated in monadic sequence according to a Latin square experimental design.<br><br>RESULTS: There were no significant statistical differences in overall appearance, shine or transparency between the four emollients. Only 6% of consumers recognized Neutraderm, 8% La Roche-Posay, 6% Avene and 4% Uriage (i.e. figures below any recognition by chance). Overall, we report a satisfaction rate of almost 60% for the topicals used (from 45% up to 64%).<br><br>CONCLUSIONS: This finding supports the feasibility of conducting blinded clinical trials on the emollients used in this study as sensory cues are unlikely to compromise the blinding.}, }
@article {pmid42222730, year = {2026}, author = {Rahim, M and Lawrence, B and Ganga, G}, title = {Indole-3-acetic acid production by endophytic consortia from red ginger lily (Alpinia purpurata (Vieill.) K. Schum) and its application in plant growth promotion.}, journal = {Physiology and molecular biology of plants : an international journal of functional plant biology}, volume = {32}, number = {5}, pages = {1041-1053}, pmid = {42222730}, issn = {0971-5894}, abstract = {UNLABELLED: Indole-3-acetic acid (IAA) is a widely studied plant hormone, produced by plants and microorganisms like bacteria and fungi, which regulates plant growth and development. The current study was conducted to investigate the IAA production by endophytes isolated from Alpinia purpurata (Vieill.) K. Schum (red ginger lily), a medicinally and ornamentally important rhizomatous plant whose endophytic microbiome remains largely unexplored, particularly with respect to phytohormone production. This study assembled an effective IAA producing consortium, confirming IAA production by LC MS and evaluated its plant growth promotion potential by seed-germination assays, hydroponics, tissue culture, and field trials. A total of fifty morphologically distinct bacteria were obtained, whose IAA production ranged from 17.75 ± 0.02 to 257.35 ± 0.77 µg/mL. Three strains, Agrobacterium radiobacter, Pseudomonas psychrophila, and Lysinibacillus macroides, were used to form a microbial consortium that produced more IAA (320.77 ± 02 µg/mL) than the individual isolates. IAA was confirmed to be present in the sample at 0.442 µg/mL with a typical retention period by LC MS analysis. When compared to untreated controls, plant growth assessments showed improved rhizome yield (70.8%), shoot development (41.7%), leaf characteristics (45.6%), and seed germination (50%). This is the first study to report on IAA production by endophytic bacteria derived from Alpinia purpurata, resulting in the formation of a functionally compatible microbial consortium that produces biologically active IAA, validated by LC-MS/MS, and shown to promote germination and plant growth in tissue culture, hydroponic, and field environments.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-026-01745-z.}, }
@article {pmid42222738, year = {2026}, author = {Park, JH and Chung, J and Lee, HJ and Na, HS}, title = {Comparison of 16S rRNA gene amplicon and whole-genome shotgun metagenomic sequencing for subgingival oral microbiome profiling.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2679807}, pmid = {42222738}, issn = {2000-2297}, abstract = {BACKGROUND: Periodontitis is a chronic inflammatory disease driven by a dysbiotic subgingival microbiome. While 16S rRNA gene amplicon sequencing is widely used, whole-genome shotgun (WGS) metagenomics is increasingly applied for higher taxonomic and functional resolution.<br><br>OBJECTIVE: The aim of this study was to directly compare 16S rRNA gene amplicon (V1-V2) sequencing and WGS metagenomic sequencing using matched subgingival plaque samples from patients with periodontitis.<br><br>METHODS: Subgingival plaque samples from 28 patients with periodontitis were analyzed using both 16S rRNA gene amplicon (V1-V2) sequencing and WGS metagenomics. Taxonomic composition, microbial diversity, differential abundance and functional analysis were compared across platforms.<br><br>RESULTS: WGS generated markedly higher read counts than 16S rRNA gene amplicon but showed wide variability in non-human reads, whereas 16S rRNA gene amplicon yielded a consistent proportion of non-chimeric reads. High taxonomic overlap was observed at the phylum level but declined at higher taxonomic ranks. WGS preferentially detected taxa such as Actinomyces, Corynebacterium and Olsenella, while the 16S rRNA gene amplicon more frequently captured Saccharibacteria (TM7) and low-abundance taxa. Core genera, including Rothia, Neisseria and Cardiobacterium showed comparable abundance patterns across platforms. When patients were grouped depending on probing pocket depth (PPD), LEfSe analysis resulted in platform-specific enrichment patterns. Functional analyses revealed shared central pathways, such as pyruvate metabolism, while 16S-based PICRUSt2 emphasized reductive and degradative pathways and WGS-based HUMAnN highlighted oxidative and biosynthetic pathways. Notably, WGS-based functional profiles were strongly influenced by microbial read depth.<br><br>CONCLUSIONS: This comparative analysis demonstrates that 16S rRNA gene amplicon (V1-V2) sequencing and WGS both robustly capture core subgingival microbial signatures. While WGS provides higher species-level and functional resolution, the resolution was strongly constrained by microbial read depth in host-rich subgingival samples. These findings provide practical guidance for selecting appropriate sequencing strategies and optimizing sample preparation when designing WGS-based periodontal microbiome studies.}, }
@article {pmid42223229, year = {2026}, author = {Miao, S and Liu, W and Li, Y and Gu, R and Wang, Y}, title = {Mapping the Research Landscape of Gut Microbiota in Autoimmune Eye Diseases: A Bibliometric Analysis and Knowledge Evolution Study.}, journal = {Ocular immunology and inflammation}, volume = {}, number = {}, pages = {1-14}, doi = {10.1080/09273948.2025.2606819}, pmid = {42223229}, issn = {1744-5078}, abstract = {PURPOSE: This study aims to systematically analyze and map the research landscape of gut microbiota in autoimmune eye diseases through comprehensive bibliometric analysis.<br><br>METHODS: We retrieved 261 relevant publications from the Web of Science Core Collection (2010-2024) and analyzed them using CiteSpace, VOSviewer, and biblioshiny.<br><br>RESULTS: The results reveal three distinct developmental phases: initial exploration (2010-2015), emerging growth (2016-2020), and rapid expansion (2021-2024). International collaboration analysis identified the United States and China as leading contributors, with strong European research clusters. Core research themes centered on gut microbiota-host immune system interactions, inflammatory pathways, and disease-specific microbial signatures. Temporal analysis demonstrated evolution from fundamental studies to mechanistic investigations and therapeutic applications. Citation analysis identified landmark studies that established gut-eye axis mechanisms and pathogenic processes. Analysis of research hotspots revealed increasing focus on personalized medicine approaches, multi-omics integration, and microbiome-based therapeutics.<br><br>CONCLUSION: This study provides a comprehensive overview of the field, identifies research frontiers, and proposes future research directions, namely, methodological advancement, mechanistic understanding, and clinical translation.}, }
@article {pmid42223258, 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 = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0028826}, doi = {10.1128/spectrum.00288-26}, pmid = {42223258}, issn = {2165-0497}, 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 2 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.<br><br>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&#xb0;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 {pmid42223272, year = {2026}, author = {Borton, MA and Oliverio, AM and Narrowe, AB and Villa, JA and Rinke, C and Hoyt, DW and Liu, P and McGivern, BB and Bechtold, EK and Ellenbogen, JB and Daly, RA and Smith, GJ and Angle, JC and Flynn, RM and Freiburger, AP and Louie, KB and Stemple, B and Northen, TR and Henry, C and Miller, CS and Morin, TH and Bohrer, G and Wrighton, KC}, title = {Mapping the soil microbiome functions shaping wetland methane emissions.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0068025}, doi = {10.1128/msystems.00680-25}, pmid = {42223272}, issn = {2379-5077}, abstract = {Accounting for only 8% of Earth's land cover, freshwater wetlands remain the foremost contributors to global methane emissions. Yet the microorganisms and processes underlying methane emissions from wetland soils remain poorly understood. Over a five-year period, we surveyed the microbial membership and in situ methane measurements from over 700 samples in one of the most prolific methane-emitting wetlands in the United States. We constructed a catalog of 2,502 metagenome-assembled genomes (MAGs), with more than half of the 70 bacterial and archaeal phyla sampled containing novel lineages. Integration of these data with 133 soil metatranscriptomes provided a genome-resolved view of the biogeochemical specialization and versatility expressed over wetland soil spatial and temporal gradients. Centimeter-scale depth differences best explained patterns of microbial community structure and transcribed functionalities, even more than land cover or temporal information. Moreover, while extended flooding restructured soil redox, this perturbation failed to reconfigure the transcriptional profiles of methane-cycling microorganisms, contrasting with theoretically expected responses to hydrological perturbations. Co-expression analyses, coupled with depth-resolved methane measurements, revealed the metabolisms and trophic structures most predictive of methane hotspots. Mapping the spatiotemporal transcriptional patterns on this compendium of biogeochemically classified soil-derived genomes begins to untangle the microbial carbon, energy, and nutrient processing contributing to wetland methane production.IMPORTANCESoil microbial ecology is increasingly recognized as essential to climate mitigation, but realizing its full potential requires shifting from static genome inventories to dynamic assessments of microbial activity. This study shows that methane-cycling microbes exhibit stable, depth-stratified expression patterns, even in response to major redox and flooding shifts, undermining assumptions that water-table manipulations common in wetland management can alone reduce methanogenesis. Instead, methane cycling is shaped by spatially organized, transcriptionally active networks involving not only methanogens but also methanotrophs, fermenters, and iron reducers. These findings expose the limitations of genome-only models and highlight the need for soil diagnostics that capture in situ activity. Together, we provide a foundation for developing activity-based microbiome tools, embedding microbial functions into Earth system models, and designing interventions that move beyond "single-lever" strategies and instead work with the structure and dynamics of microbial communities as complex, layered systems.}, }
@article {pmid42223530, year = {2026}, author = {Pokharel, SK and Walsh, S and Shehata, N and Ahearne, A and Belin, D and Larson, B and Tabor, B and Wall, D and Stevens, DC}, title = {Predator avoidance promotes inter-bacterial symbiosis with myxobacteria in polymicrobial communities.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag140}, pmid = {42223530}, issn = {1751-7370}, abstract = {Myxobacteria are predatory soil bacteria with the largest known bacterial genomes, rich in biosynthetic gene clusters for specialized metabolites. Despite their ecological importance as potential keystone taxa in soil food webs, there is a disconnect between laboratory-isolated myxobacteria and abundant Myxococcota detected in environmental metagenomic studies. Here, we report the isolation and characterization of stable myxobacterial swarm consortia from rhizospheric soil, consisting of myxobacteria associated with novel Microvirga species. Using metagenomic sequencing, we assembled metagenome-assembled genomes (MAGs) for four consortia, revealing phylogenetically distinct yet stably associated bacterial partnerships. Comparative genomics identified evidence of horizontal gene transfer, including acyl-homoserine lactone (AHL) synthases and ankyrin repeat (ANKYR) proteins shared between consortium members, and genome-scale metabolic modeling predicted complementary auxotrophies. Time-lapse microscopy revealed that Archangium exhibited reduced predation toward its Microvirga companion (0.7% predation rate) compared to non-symbiotic Myxococcus xanthus (14.9% predation rate) but maintained robust predatory capacity against Escherichia coli prey. These findings indicate that predation avoidance and metabolic complementarity can drive stable inter-bacterial symbiosis in predatory myxobacterial communities, providing foundational insights into previously overlooked myxobacterial partnerships that may be prevalent in natural soil ecosystems.}, }
@article {pmid42223629, year = {2026}, author = {Bahar, A and Khazaei, M and Tahmasebi, H}, title = {The complex of gut microbial metabolites and sex hormones in Alzheimer's disease.}, journal = {Seminars in immunopathology}, volume = {48}, number = {1}, pages = {}, pmid = {42223629}, issn = {1863-2300}, mesh = {Humans ; *Alzheimer Disease/metabolism/etiology ; *Gonadal Steroid Hormones/metabolism ; *Gastrointestinal Microbiome ; Animals ; Disease Susceptibility ; Dysbiosis ; Blood-Brain Barrier/metabolism ; }, abstract = {Alzheimer's Disease (AD) is a progressive neurodegenerative disorder with a complex pathophysiological mechanism and a marked sex difference in prevalence and disease severity, with women being more affected and showing a more aggressive disease course. Recent studies indicate that a complex interplay among gut microbiota (GM), their metabolites, and sex hormones is a crucial factor in AD pathogenesis. In this review, we attempted to synthesize current studies to critically discuss the tripartite interplay among GM, sex hormones, and the brain in AD. Firstly, we discuss the role of the microbiota-gut-brain axis in AD pathogenesis with a focus on how gut dysbiosis contributes to neuroinflammation, disruption of the blood-brain barrier (BBB), and accumulation of pathological proteins. Then, we discuss the mechanistic roles of various GM-derived metabolites in AD pathogenesis, with a focus on the two-edged role of SCFAs and their derivatives, the neuroactive role of tryptophan and its derivatives, and the modulatory roles of bile acids and trimethylamine N-oxide. Finally, we discuss a novel concept, the "microgenderome," referring to the bidirectional interplay between sex hormones and GM, and how GM regulates sex hormone levels through unique enzymatic functions termed the "estrobolome" and a newly proposed "testobolome."}, }
@article {pmid42223784, year = {2026}, author = {Moghaddam, NA and Mohabbat, A and Jigheh, MP and Mahboubi, A and Ravanlo, ZZ and Shanehbandi, D and Shokri, S and Baghi, HB}, title = {The interplay between HPV, vaginal microbiota and host immunity in cervical carcinogenesis.}, journal = {Discover oncology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12672-026-05169-9}, pmid = {42223784}, issn = {2730-6011}, abstract = {Cervical cancer (CC) remains a major global health challenge, largely driven by persistent infection with high-risk human papillomavirus (HPV) genotypes. Emerging evidence suggests that the interplay between HPV, the vaginal microbiota (VM), and host immune responses critically influences viral persistence and disease progression. In particular, dysbiotic VM marked by reduced Lactobacillus dominance and increased prevalence of anaerobic bacteria such as Gardnerella, Sneathia, Prevotella, and Atopobium-can impair HPV clearance, promote chronic inflammation, and facilitate progression from cervical intraepithelial neoplasia (CIN) to invasive carcinoma. Understanding these tripartite interactions offers opportunities for novel preventive and therapeutic strategies, including microbiome modulation, immunotherapy, and gene editing. This review highlights the potential of microbiome-targeted interventions to enhance immune responses against HPV and reduce the burden of CC, although the underlying causal mechanisms require further investigation in prospective studies.}, }
@article {pmid42223828, year = {2026}, author = {J, G and Ranganathan, N and A S, V and Chopra, H}, title = {Targeting Type 2 and Non-type 2 Asthma: Emerging Biologics and Personalized Strategies.}, journal = {Current allergy and asthma reports}, volume = {26}, number = {1}, pages = {}, pmid = {42223828}, issn = {1534-6315}, mesh = {Humans ; *Asthma/immunology/drug therapy/therapy ; *Precision Medicine/methods ; *Biological Products/therapeutic use ; *Anti-Asthmatic Agents/therapeutic use ; Cytokines/antagonists &amp; inhibitors ; Th2 Cells/immunology ; }, abstract = {PURPOSE OF REVIEW: Asthma continues to pose a serious global health issue affecting billions of people and causing significant morbidity. It is immunologically heterogeneous disease, classified as Type 2 (Th2/ILC2-mediated, eosinophilic) or Type 1 (Th1-mediated, neutrophilic, steroid-resistant) inflammation. This review aims to evaluates current biologic therapies, emerging strategies, and challenges in asthma management and highlights the challenges and future directions in personalized asthma management.<br><br>RECENT FINDINGS: Current biologics for Type 2 asthma like anti-IgE (omalizumab), anti-IL-5 (mepolizumab, reslizumab, benralizumab), anti-IL-4/IL-13 (dupilumab) and anti-TSLP (tezepelumab) were effectively controlling severe eosinophilic asthma. Emerging therapies for Type 1 and mixed phenotypes include anti-TNF-&#x3b1; agents, CXCR2 antagonists, IL-17 blockers, JAK-STAT inhibitors and microbiome-based approaches and upstream epithelial cytokine-targeting therapies such as anti-TSLP agents. Dual or broad-spectrum strategies, such as bispecific antibodies and endotype-guided biologic selection offer more targeted interventions. Despite these advances, challenges persist regarding high costs, limited accessibility, absence of robust biomarkers, and potential risks of immunosuppression. Biologics have transformed severe Type 2 asthma management, but effective treatments for Type 1 and steroid-resistant asthma remain limited. Future directions involve multi-omics, machine learning and gene therapy to optimize personalized therapy and develop inclusive strategies for the diverse inflammatory endotypes.}, }
@article {pmid42223880, year = {2026}, author = {Li, J and Liu, Y and Jia, L}, title = {The Role of Lacticaseibacillus Rhamnosus in Periodontitis Management: From Microecological Regulation to Clinical Application.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {42223880}, issn = {1867-1314}, support = {82571088//the National Nature Science Foundation of China/ ; 82101009//the National Nature Science Foundation of China/ ; 2024-1-2141//Capital's Funds for Health Improvement and Research/ ; G202532300//Beijing High-Level Innovation and Entrepreneurship Talent Support Program young backbone talent projects/ ; L242122//Beijing Natural Science Foundation/ ; YSP20200904//Beijing Stomatological Hospital, Capital Medical University Young Scientist Program/ ; }, abstract = {Periodontitis is a chronic inflammatory disease caused by dysbiosis of the periodontal microbiome, threatening both oral and systemic health. Current prevention and treatment strategies for periodontitis mainly rely on mechanical therapy, with antibiotics used as supplements. However, limitations of mechanical therapy and increasing antibiotic resistance have prompted the exploration of new adjunctive strategies. Probiotic therapy, particularly Lacticaseibacillus rhamnosus (L. rhamnosus), formerly known as Lactobacillus rhamnosus, has emerged as a promising approach due to its ability to modulate periodontal microecology. L. rhamnosus exerts therapeutic effects by inhibiting pathogens, modulating immune responses, and promoting tissue repair. L. rhamnosus has been applied in various forms for the adjuvant treatment of periodontitis and numerous clinical trials have confirmed its safety and effectiveness, indicating broad potential for application. Nevertheless, current clinical studies still face challenges such as unclear strain-specific effects and a lack of standardized administration protocols. Future research should investigate the mechanisms of different strains and evaluate targeted interventions in diverse patient populations to advance the clinical use of probiotic therapies.}, }
@article {pmid42224056, year = {2026}, author = {Paiva, BR and Schultz, J and Modolon, F and Brito, JS and Ribeiro-Alves, M and Rosado, AS and Cardozo, LFMF and Mafra, D}, title = {Intestinal microbiota profile and inflammation in patients undergoing hemodialysis: a comparison between the Southern and Southeastern regions of Brazil.}, journal = {Jornal brasileiro de nefrologia}, volume = {48}, number = {3}, pages = {e20250097}, pmid = {42224056}, issn = {2175-8239}, mesh = {Humans ; Male ; *Renal Dialysis ; Brazil ; Female ; *Inflammation/microbiology/blood/etiology ; Middle Aged ; *Gastrointestinal Microbiome ; *Renal Insufficiency, Chronic/therapy/microbiology/blood ; Feces/microbiology ; }, abstract = {INTRODUCTION: Exogenous lifestyle factors, such as different cultures, diets, and geo-graphic location, can alter the microbiota in patients with chronic kidney disease (CKD), which is closely related to inflammation. However, few studies have examined how these factors influence the composition of the microbiota. Thus, the objective of this study was to characterize and compare the intestinal microbiota profile and inflammation in CKD patients undergoing hemodialysis (HD) in the Southern and Southeastern regions of Brazil.<br><br>METHODS: Blood and stool samples were obtained from two groups of HD patients: one from the city of Blumenau (Southern region) and the other from the city of Rio de Janeiro (Southeastern region). Fecal DNA was extracted, and the V4 region of the bacterial 16S ribosomal RNA gene was sequenced. The fecal microbiome was analyzed using bioinformatic tools. Plasma concentrations of IL-6 and TNF-&#x3b1; were evaluated by ELISA.<br><br>RESULTS: Thirty patients were included in the study, with 14 individuals residing in the Southern region (group S) [50% male, 58 (13.5) years of age] and 16 individuals residing in the Southeastern region (group SE) [47.1% male, 57 (19) years of age]. The &#x3b1;- and &#x3b2;-diversity indices of the intestinal microbiota did not differ significantly between the groups. However, patients from the Southern region had higher plasma TNF-&#x3b1; (p = 0.008) and IL-6 (p = 0.003) levels than those from the Southeastern region.<br><br>CONCLUSION: Although HD patients with CKD residing in the Southern and Southeastern regions present similar intestinal microbial patterns, patients from the Southern region had higher concentrations of inflammatory markers.}, }
@article {pmid42224283, year = {2026}, author = {Correale, J and Marrodan, M and Piedrabuena, MA and Soman, K and Farez, MF and Baranzini, SE}, title = {Microbiome-derived metabolites from vitamin B2 and B9 pathways modulate MAIT cells from multiple sclerosis patients.}, journal = {Multiple sclerosis (Houndmills, Basingstoke, England)}, volume = {}, number = {}, pages = {13524585261447695}, doi = {10.1177/13524585261447695}, pmid = {42224283}, issn = {1477-0970}, abstract = {BACKGROUND: Mucosal-associated invariant T (MAIT) cells recognize microbial vitamin B2 and B9 metabolites via MR1 and have been implicated in multiple sclerosis (MS). How patient-specific gut microbiota shape human MAIT-cell pathogenicity at the clonal level remains unknown.<br><br>MATERIAL AND METHODS: We generated 62 MAIT-cell clones from relapsing-remitting multiple sclerosis (RRMS) patients and 50 from healthy controls (HCs). Clones were stimulated with riboflavin- or folate-pathway metabolites, paraformaldehyde-fixed patient-matched gut bacterial isolates, or interleukin (IL)-12/IL-18. Activation markers, cytokine secretion, cytotoxicity, and competitive MR1-ligand inhibition were assessed. Intestinal permeability was evaluated using I-FABP, LBP, GLP-2, and fecal &#x3b1;-1-antitrypsin.<br><br>RESULTS: MS-derived MAIT clones showed markedly enhanced activation, increased interferon-gamma (IFN-&#x3b3;), IL-17, and granulocyte-macrophage colony-stimulating factor (GM-CSF) secretion, and greater cytotoxicity compared with HCs when stimulated with riboflavin-producing taxa isolated from the same patients. Importantly, several responses diverged from predictions based on murine models and genomic inference, including mixed cytokine profiles and graded competitive inhibition by folate-derived ligands. These findings highlight species-specific differences in MR1 ligand handling and MAIT-cell activation. Activation required uptake of intact bacteria and acid-dependent MR1 loading. MS patients exhibited significant intestinal barrier dysfunction, linking dysbiosis to systemic MAIT-cell hyperactivation.<br><br>CONCLUSION: At clonal resolution, this study demonstrates that patient-specific microbial metabolism, MR1-ligand competition, and epithelial barrier disruption cooperate to amplify MAIT-cell pathogenicity in MS, revealing human-specific mechanisms not predicted by animal models.}, }
@article {pmid42224874, year = {2026}, author = {Kenzi, M and Benbernou, M and Khelifa, H and Tbahriti, HF}, title = {Machine learning-based prediction of antibiotic resistance gene distribution in agricultural soils under different climate change scenarios.}, journal = {The Science of the total environment}, volume = {1042}, number = {}, pages = {181905}, doi = {10.1016/j.scitotenv.2026.181905}, pmid = {42224874}, issn = {1879-1026}, abstract = {Antibiotic resistance genes (ARGs) in agricultural soils represent a major public health concern, as climate change is believed to augment their dissemination and abundance. Understanding the impact of future climate change scenarios on ARG abundance is essential to implement predictive and proactive One Health strategies. In this study, a total of 2301 soil samples from 67 countries across six continents were compiled from three global metagenome databases, namely NCBI SRA, MG-RAST, and JGI IMG/M. Six machine learning models, namely LightGBM, XGBoost, Random Forest, Support Vector Machines, Deep Neural Networks, and Logistic Regression, were used to predict ARG distribution patterns in agricultural soils, and their performance was evaluated using stratified 10-fold cross-validation with metrics such as AUC-ROC, precision, recall, F1 score, and Matthews Correlation Coefficient. WorldClim 2.1 and CMIP6 models were used to project ARG distribution under three Representative Concentration Pathway scenarios, namely RCP 2.6, RCP 4.5, and RCP 8.5, for the years 2050 and 2070. The LightGBM model achieved the best predictive performance, with an AUC-ROC of 0.957 (95% CI: 0.951-0.963), substantially higher than that of the other models, while the Deep Neural Networks model achieved an AUC-ROC of 0.891. The LightGBM model demonstrated high stability across cross-validation folds, with minimal fold-to-fold variance, defined as the standard deviation of AUC-ROC scores across the 10 folds (SD = 0.008). SHAP feature importance analysis identified soil temperature, pH, and organic carbon content as the top three factors influencing ARG relative abundance, with SHAP values of 0.342, 0.287, and 0.251, respectively. Annual precipitation and soil moisture level were also identified as significant contributors to ARG distribution. SHAP dependency plots revealed critical thresholds for ARG relative abundance, with a sharp increase observed independently when soil temperature exceeds 18 °C and when soil pH drops below 6.5. Furthermore, a non-linear accelerating increase in ARG abundance risk was observed as climate change intensity worsened across scenarios. Projections for future climate change scenarios indicate a potential 34.7% increase in high-risk ARG zones by the year 2070, with the largest changes expected in South Asia, Sub-Saharan Africa, and Mediterranean regions. Paired t-tests revealed significant differences in performance among all models (p < 0.001). These findings demonstrate that gradient-boosting methods such as LightGBM outperform deep learning approaches for ARG prediction from soil microbiome data, offering higher accuracy and interpretability. As climate change is projected to increase ARG risks in a non-linear manner, the development of climate-adaptive agricultural practices and global surveillance systems is urgent. This framework provides actionable risk-mapping tools to support precision farming and region-specific policy interventions within the One Health approach.}, }
@article {pmid42224947, year = {2026}, author = {Alake, SE and Ice, JA and Orphan, J and Adedigba, P and Islam, P and Hatter, B and Lu, P and Perez, L and Olawale, F and Butcher, JT and Knotts, TA and Wozniak, KL and Lin, D and Chowanadisai, W and Smith, BJ and Lucas, EA}, title = {Pinto bean supplementation prevents vascular dysfunction by modulating the gut microbiome in an interleukin-10-dependent manner in mice fed an atherogenic diet.}, journal = {Nutrition research (New York, N.Y.)}, volume = {151}, number = {}, pages = {120-133}, doi = {10.1016/j.nutres.2026.05.001}, pmid = {42224947}, issn = {1879-0739}, abstract = {The risk of cardiovascular disease increases under gut inflammatory conditions, but the underlying mechanism remains unclear. Pinto bean (PB) consumption reportedly increases the ileal expression of the anti-inflammatory cytokine interleukin (IL)-10. We investigated the effects of PB supplementation on inflammatory signature and vascular endothelial function in mice. We hypothesize that the effect of PB is mainly mediated by IL-10. Eight-week-old female mice from a C57BL/6 J background were randomized to groups in a 2 × 3 design, with genotype (Il10[+]/[+], WT or Il10[-]/[-], KO) and diets (AIN-93 M [CON] diet, atherogenic diet with 36.5% fat kcal and 1% cholesterol [Ath], or Ath diet + 5% PB, wt/wt [Ath+PB]) as factors. Gut microbiota composition, fecal short-chain fatty acids (SCFAs), ileal T-cell populations, inflammatory markers, and vascular endothelial function were examined. In WT mice, PB supplementation preserved gut microbial diversity and maintained fecal butyrate concentrations compared with atherogenic diet alone (P< .05), while sustaining the relative abundance of SCFA-producing taxa (Alistipes, Roseburia). These microbial changes were accompanied by an increased proportion of ileal regulatory T cells (P < .001) and preserved acetylcholine-induced, endothelium-dependent vasodilation (P < .05). In contrast, IL-10 KO mice exhibited impaired endothelial function and reduced microbial diversity irrespective of diet, and PB supplementation did not significantly improve vascular or immune outcomes. Overall, PB supplementation was associated with preserved vascular endothelial function and favorable microbiota and immune profiles in WT but not IL-10-deficient mice, suggesting these dietary benefits require intact IL-10 signaling.}, }
@article {pmid42224959, year = {2026}, author = {Das, R and Baldi, A and Pasricha, SR and Thompson, LM and Díaz-Artiga, A and Grajeda, LM and McCracken, JP and Jesser, K and Waller, L and Freeman, MC and Clasen, T and Sinharoy, SS}, title = {Upper respiratory microbiome composition and associations with air pollution and infant respiratory health: a longitudinal study in Guatemala.}, journal = {International journal of hygiene and environmental health}, volume = {276}, number = {}, pages = {114843}, doi = {10.1016/j.ijheh.2026.114843}, pmid = {42224959}, issn = {1618-131X}, abstract = {The early-life composition and maturation of the upper respiratory microbiome, and their associations with environmental exposures and respiratory health, remain poorly characterized. We collected nasopharyngeal (NP) and oropharyngeal (OP) samples (n = 257) from a cohort of 114 Guatemalan infants at birth and six months between February and August 2019. We analyzed their NP and OP microbiomes using 16S rRNA gene sequencing and examined associations with air pollution and respiratory outcomes during the first year of life. Results show that NP and OP microbiomes exhibited distinct developmental trajectories, with NP diversity declining and OP diversity increasing by six months, accompanied by age-related compositional restructuring. Taxonomic succession was anatomically site-specific; NP communities matured toward lower alpha diversity with facultative dominance, whereas OP communities showed anaerobic enrichment and rising alpha diversity, yielding stable, differentiated airway communities. Neither alpha nor beta diversity was consistently associated with WHO IMCI (Integrated Management of Childhood Illness) pneumonia (both severe and non-severe), cough, or hypoxemia, except for higher NP alpha diversity at birth, which predicted increased odds of fast breathing episodes (Shannon: adjusted OR = 4.81, 95% CI: 1.80, 7.46 &amp; inverse Simpson: aOR = 1.20, 95% CI: 1.04, 1.43). Higher NP Bacteroidota relative abundance at birth was associated with lower odds of subsequent WHO IMCI pneumonia (aOR: 0.003, 95% CI 0.001-0.02; FDR = 0.10). Higher personal PM2.5 exposure at 3 months was associated with differential NP microbiome composition at 6 months, including lower Firmicutes abundance (β = -0.53; 95% CI: -0.82, -0.25; FDR = 0.17) and higher Prevotella abundance (β = 3.21; 95% CI: 1.90, 4.51; FDR = 0.08), consistent with PM2.5 acting as an ecological stressor that may predispose to airway dysbiosis. These findings reveal coordinated but site-specific patterns of microbial maturation in early infancy and suggest that predictable age-related shifts in community composition, together with both environmental exposures, shape upper airway microbial communities with implications for respiratory health.}, }
@article {pmid42225162, year = {2026}, author = {Wu, G and Wang, Z and Tsigkou, K and Vrieze, J and Angelidaki, I}, title = {A stress-response-recovery framework integrating microbial life-history strategies for stressed anaerobic digestion.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135055}, doi = {10.1016/j.biortech.2026.135055}, pmid = {42225162}, issn = {1873-2976}, abstract = {Anaerobic digestion (AD) is a mature biotechnology; however, its operational stability remains constrained by the limited predictability of microbial responses to environmental stress. In this review, stressed AD systems are defined as microbial ecosystems in which one or more environmental stressors disrupt microbial functioning, reduce microbial growth and survival, and drive deterministic and/or stochastic shifts in the AD microbiome, thus impacting process performance. For stressed AD, this review proposes a unifying stress-response-recovery framework integrating microbial life-history strategies. Specifically, stress acts as an ecological filter that suppresses stress-sensitive microorganisms while selecting stress-tolerant ones. During the response phase, system resilience can be achieved through multiple forms of microbial plasticity, including spatial reorganization (e.g., granulation), metabolic rerouting (e.g., shifts from acetoclastic methanogenesis to syntrophic acetate oxidation), and alternative electron-transfer pathways such as direct interspecies electron transfer. Importantly, recovery does not necessarily ensure a return to the original community structure; instead, it is governed by functional redundancy, microbial memory, and ecological hysteresis, often resulting in alternative stable states with reconfigured metabolic networks while preserving methane production. Collectively, these insights provide complementary ecologically informed management strategies, highlighting the potential of strategy-based monitoring, microbiome engineering, and targeted interventions to enhance system resilience. By integrating ecological theory with engineering practice, this review advances the understanding of AD stress and provides a framework for designing more robust and adaptable anaerobic systems.}, }
@article {pmid42225178, year = {2026}, author = {Wilczynski, W and Musiałowski, M}, title = {Chronic effects of the organoarsenicals adamsite and triphenylarsine on the intestinal microbiota of Danio rerio.}, journal = {Environmental toxicology and pharmacology}, volume = {}, number = {}, pages = {105051}, doi = {10.1016/j.etap.2026.105051}, pmid = {42225178}, issn = {1872-7077}, abstract = {Organoarsenicals, including the chemical warfare-related adamsite and triphenylarsine (TPA), are contaminants of emerging concern in aquatic environments. While the chronic effects of these compounds on zebrafish (Danio rerio) survival, growth, and other toxicological endpoints have been characterized, the role of gut microbiota in host responses remains unclear. Here, we investigated the effects of 28-day sublethal exposure to adamsite (0.05, 0.15, 0.20, 0.25μg/L) and TPA (0.73, 0.17, 1.88, 3.00, 4.80μg/L) on the intestinal microbiota of zebrafish. Microbiota composition and predicted function were assessed using 16S rDNA sequencing and PICRUSt2. Adamsite caused concentration-dependent microbial diversity loss and substantial shifts in community composition, as well as predicted function, consistent with its high toxicity. In contrast, TPA induced only minor changes, with microbial diversity maintained and functional potential retained, reflecting the comparatively lower toxicity. These findings highlight the gut microbiota as a responsive target of organoarsenical toxicity, supporting microbiome-aware ecotoxicological risk assessment.}, }
@article {pmid42225253, year = {2026}, author = {Singh, L and Bhullar, G and Shaik, S and Ganesh, V and Kesani, H and Rai, M}, title = {Gut Feeling: Microbiota as a Hidden Regulator of Hypertension.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {101623}, doi = {10.1016/j.tjnut.2026.101623}, pmid = {42225253}, issn = {1541-6100}, abstract = {Emerging evidence identifies the gut microbiota as a key regulator of blood pressure through its role in metabolizing dietary substrates into bioactive compounds that influence vascular, immune, and neurohumoral pathways. This review synthesizes recent mechanistic, preclinical, and clinical evidence linking gut microbial dysbiosis to hypertension, with particular emphasis on nutrition-dependent microbial metabolism and its translational implications. Experimental studies demonstrate that depletion of short-chain fatty acid (SCFA)-producing bacteria and enrichment of pro-inflammatory and trimethylamine-producing taxa contribute to endothelial dysfunction, immune activation, and renin-angiotensin-aldosterone system dysregulation. Fecal microbiota transplantation (FMT) and germ-free animal models provide causal evidence that hypertensive microbiota can directly elevate blood pressure. Human multi-omics and metabolomic studies further show that microbial functional capacity and metabolite production, rather than taxonomic composition alone, are strongly associated with hypertensive phenotypes and therapeutic responsiveness. Importantly, dietary interventions, including high-fiber diets, resistant starch, and the Dietary Approaches to Stop Hypertension (DASH) diet, modulate microbial composition and enhance SCFA production, providing a mechanistic basis for their antihypertensive effects. Microbiota-drug interactions have also emerged as a novel determinant of antihypertensive treatment efficacy. Collectively, these findings support a metabolite-centered framework in which diet-microbiota interactions influence blood pressure regulation. Targeting the gut microbiota through nutritional and microbiome-based strategies represents a promising adjunctive approach for hypertension prevention and personalized management. However, large-scale longitudinal and interventional human studies are needed to establish causality and optimize microbiota-targeted therapies.}, }
@article {pmid42225474, year = {2026}, author = {Bao, W and Li, G and Ding, Y and Wang, Y}, title = {Harnessing the gut microbiome for MASLD management: opportunities and challenges.}, journal = {Science bulletin}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.scib.2026.05.017}, pmid = {42225474}, issn = {2095-9281}, }
@article {pmid42226086, year = {2026}, author = {Ravi, SSN and Pipinos, A and Insley, N and Kaur, C and Kan, J and Heller, W and H Smith, A and Zinati, G and Richie, J and Bais, H}, title = {Exploring the role of ergothioneine and mycorrhizal fungi in shaping the wheat soil microbiome.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00913-8}, pmid = {42226086}, issn = {2524-6372}, abstract = {BACKGROUND: The association between plants and soil microbes is critical for both soil and plant health. Introducing beneficial microbial inoculants, such as arbuscular mycorrhizal fungi (AMF), can enhance the uptake of nutrients and compounds in plants including ergothioneine (ERGO), a well-known antioxidant and anti-inflammatory compound that humans must obtain through diet. However, little is known about how ERGO and inoculated AMF influence ERGO uptake in plants or affect soil microbiome composition, including bacteria, archaea, and fungi. This study investigates the interaction between soil-applied ERGO and AMF inoculation in plant-microbe symbioses to assess (1) whether these treatments increase ERGO content in the staple crop wheat (Triticum aestivum), and (2) how they alter soil microbiome structure.<br><br>RESULTS: Combined treatment with ERGO and AMF significantly increased wheat (Triticum aestivum) biomass and ERGO accumulation in roots and shoots. This co-treatment also led to higher bacterial diversity in rhizosphere. PERMANOVA analysis confirmed that both AMF and AMF/ERGO treatments significantly influenced microbiome composition, particularly bacterial communities. Indicator species analysis showed enrichment of Thioalkalivibrio, Chlorobi bacterium, Planctomycetes (Planctomycete A-2) and Candida subhashi,&#xa0;Paecilomyces zollerniae under ERGO and AMF/ERGO treatments.<br><br>CONCLUSIONS: Overall, the data show that plants can readily take up ERGO from the soil, with or without AMF, and that both ERGO and AMF amendments reshape soil microbiome communities. These findings highlight the broader role of ERGO and AMF in connecting soil microbiome to plant and human nutrition, a link that warrants further investigation.}, }
@article {pmid42226305, year = {2026}, author = {Grundler, F and Ducarmon, QR and Holley, A and Knufinke, M and Strathmeyer, S and Heelemann, S and Geyer, R and Martínez-Téllez, B and MacArthur, MR and Zeller, G and Wilhelmi de Toledo, F and Mesnage, R}, title = {Health benefits of a five-day at-home modified fasting program: a randomised controlled trial.}, journal = {Genome medicine}, volume = {18}, number = {1}, pages = {}, pmid = {42226305}, issn = {1756-994X}, support = {ALTF 1030-2022//EMBO postdoctoral fellowship/ ; RYC2022-036473-I//MCIN/AEI/10.13039/501100011033/ ; }, mesh = {Humans ; Female ; *Fasting ; Adult ; Male ; Blood Pressure ; Weight Loss ; Metabolomics ; Middle Aged ; Biomarkers ; }, abstract = {BACKGROUND: Fasting is one of the most cost-effective methods to improve cardiometabolic health. We tested a 5-day hypocaloric (~ 600 kcal/day) and ketogenic, modified fasting program (MFP) in a two-arm randomised controlled trial, where sixty-four healthy subjects were randomised to MFP or control group.<br><br>METHODS: We randomly assigned 64 participants to a group receiving the MFP or to a group of participants who were told to continue with their usual eating behaviour and lifestyle (control group). The changes in blood pressure and body weight were considered as primary endpoints. Secondary outcomes included ketosis, glucose and lipid metabolism, inflammatory markers, antioxidant capacity and well-being. Biological pathways and metabolic processes were explored with nuclear magnetic resonance blood metabolomics and gut metagenomics analyses. Outcomes were assessed at baseline, end of the MFP, after food reintroduction, and one month later.<br><br>RESULTS: MFP participants (n&#x2009;=&#x2009;32) experienced weight loss compared to controls (-&#x2009;0.52&#x2009;&#xb1;&#x2009;0.03&#xa0;kg vs.&#x2009;-&#x2009;0.03&#x2009;&#xb1;&#x2009;0.02&#xa0;kg, p&#x2009;<&#x2009;0.001). Changes in blood pressure caused by the MFP were non-significant at the end of the fasting period. However, blood pressure was significantly reduced following food reintroduction (systolic: -0.56&#x2009;&#xb1;&#x2009;0.12 mmHg vs.&#x2009;-&#x2009;0.16&#x2009;&#xb1;&#x2009;0.12 mmHg, p&#x2009;<&#x2009;0.05 and diastolic: -0.36&#x2009;&#xb1;&#x2009;0.08 mmHg vs.&#x2009;-&#x2009;0.01&#x2009;&#xb1;&#x2009;0.08 mmHg, p&#x2009;<&#x2009;0.01). Serum biochemistry showed the MFP reduced glucose levels and coagulation factors. The MFP also significantly increased physical well-being. Blood metabolomics revealed a significant decrease in chronic inflammation markers. Shotgun metagenomics of the gut microbiome showed significant changes in relative abundance of 11 bacterial species and in the genomic repertoire of 52 carbohydrate-active enzymes (CAZymes), reflecting an increase in families metabolising host-derived glycan substrates. None of these differences in gut microbiome and blood metabolome were shown to be statistically different from the control group one month after the intervention. Comparing MFP effects with a previous cohort's 5-day prolonged fasting showed similar metabolic changes.<br><br>CONCLUSIONS: This MFP is safe and transiently improves cardiometabolic health and physical well-being in healthy individuals.<br><br>CLINICAL TRIAL REGISTRATION: This trial was prospectively registered at ClinicalTrials.gov (NCT05821660) on 6 April 2023 prior to the start of patient recruitment.}, }
@article {pmid42226423, year = {2026}, author = {Xu, Q and Zhang, X and Tian, H and Yang, X and Zhang, J and Li, H and Ma, Z and Zhang, D and Huang, K and Zhang, Y and Zhao, Y and Li, X and Zhao, L and Cheng, J and Xu, D and Li, F and Weng, X and Wu, W and Wang, W}, title = {Integrating rumen microbiome and host metabolome to investigate feed conversion ratio across different fattening stages in Hu sheep.}, journal = {Animal bioscience}, volume = {}, number = {}, pages = {}, doi = {10.5713/ab.260317}, pmid = {42226423}, issn = {2765-0189}, abstract = {OBJECTIVE: Feed conversion ratio (FCR) is a crucial economic trait in animal breeding and management and is also of great significance for environmental sustainability. This study aimed to investigate the potential regulatory mechanisms of FCR in sheep by integrating rumen microbiota and host metabolome through multi-omics analysis.<br><br>METHODS: FCR data were collected from 127 male Hu sheep. Extreme individuals were selected for rumen metagenomic and serum metabolomic analyses to identify key factors driving FCR across early and late fattening stages.<br><br>RESULTS: Bacteroides, Prevotella, and other genera were identified as dominant taxa in the rumen across both stages, suggesting their involvement in FCR regulation. Notably, Nocardia tengcongensis differed significantly between the highest FCR values (HF) and lowest FCR values (LF) groups at different stages, indicating its potential as a predictive biomarker of feed efficiency. Functional analysis revealed that the pentose phosphate pathway (M00004) and lysine biosynthesis via the succinyl-DAP pathway (M00016) were enriched in the LF group, whereas the methanogenesis pathway (M00357) was significantly enriched in the HF group, indicating increased methane production. Thirteen metabolites consistently differed between HF and LF across fattening stages and may serve as predictive biomarkers. In addition, the abundance of Prevotella and Bacteroides increased over time and showed significant correlations with key metabolites.<br><br>CONCLUSION: These findings suggest strong interactions between rumen microbiota and host metabolites that may collectively influence FCR, providing new insights into microbial and metabolic regulation of feed efficiency and a theoretical basis for optimizing feeding strategies in sheep.}, }
@article {pmid42226511, year = {2026}, author = {Schindler, JC and Pillai, GV and Raffay, TM and Viswanath, SE and Seth, P}, title = {Computational Quantification of Peristalsis in Preclinical Mouse Models Using Smartphone Videography.}, journal = {Neurogastroenterology and motility}, volume = {38}, number = {6}, pages = {e70353}, doi = {10.1111/nmo.70353}, pmid = {42226511}, issn = {1365-2982}, support = {1R01CA280981-01A1/CA/NCI NIH HHS/United States ; 1U01CA294415-01A1/CA/NCI NIH HHS/United States ; 1R01NR019585-01A1/NR/NINR NIH HHS/United States ; 1R01EB037526-01/EB/NIBIB NIH HHS/United States ; 1I01BX006439-01//Veterans Affairs Biomedical Laboratory Research and Development Service/ ; //Northeast Ohio Renal Research Innovation Award/ ; F30-ES03527/NH/NIH HHS/United States ; T32-GM007250/NH/NIH HHS/United States ; T32-GM152319/NH/NIH HHS/United States ; R01-HL172894/HL/NHLBI NIH HHS/United States ; R01-DK128347/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Peristalsis/physiology/drug effects ; Mice ; *Smartphone ; *Video Recording/methods ; Gastrointestinal Motility/physiology ; Gastrointestinal Transit/physiology ; Mice, Inbred C57BL ; Gastrointestinal Microbiome/physiology ; }, abstract = {BACKGROUND: A number of diseases and medical interventions affect gastrointestinal motility. However, quantitative methods for measuring effects on peristalsis in live animals are uncommon, cumbersome, and lack standardization.<br><br>METHODS: Here we present a new computational method for quantifying gut peristalsis in preclinical mouse models that requires only a video taken using a mobile phone camera. Our analytical pipeline processes the videographic data to track motion as it correlates to gastrointestinal transit.<br><br>RESULTS: This method is compatible with different mouse models (such as conventionally housed and germ-free), gut microbiome compositions, and can further be used to screen the impact of drugs on gut motility, which we demonstrate using methacholine as an example. Quantitative peristalsis measurements after methacholine treatment of conventionally housed and germ-free mice with or without reconstitution of their gut microbiomes demonstrate that our analytical method can detect and quantify changes in peristalsis driven not only by endogenous acetylcholine signaling but also by colonic anatomy and the microbiome.<br><br>CONCLUSION: We envision that our computational tool will find uses in preclinical drug or mouse model screenings and forms the cornerstone to expand this methodology to other non-gastrointestinal applications.}, }
@article {pmid42226580, year = {2026}, author = {Ahmed, MT and Majumdar, S and Noman, AA and Alam, MJ and Alam, MJ}, title = {Identification of Key Microbial Signatures Associated With Breast Cancer: Machine Learning-Based Approaches Using Gut Microbiome Data.}, journal = {Cancer medicine}, volume = {15}, number = {6}, pages = {e72008}, doi = {10.1002/cam4.72008}, pmid = {42226580}, issn = {2045-7634}, mesh = {Humans ; Female ; *Breast Neoplasms/microbiology ; *Machine Learning ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/genetics ; Predictive Learning Models ; *Bacteria/genetics/classification ; Middle Aged ; Case-Control Studies ; Random Forest ; }, abstract = {BACKGROUND: Breast cancer (BC) is one of the most common types of cancer incidence and mortality rates among women all over the world. Limitations in existing diagnostic methods, especially in low- and middle-income countries, require novel, noninvasive biomarkers. A complex and modifiable ecosystem, the gut microbiome has become a potential origin of such biomarkers because it has a systemic influence on host immunity, metabolism, and regulation of hormones. This study explores the gut microbiome alterations associated with BC and evaluates machine learning (ML) models to predict disease status based on 16S rRNA gene sequencing data of Ghanaian cohort (520 BC patients, 442 healthy controls).<br><br>RESULTS: Following high-quality sequence processing with QIIME2 and DADA2, alpha and beta diversity analyses showed a lower microbial richness and different community structures in BC patients (PERMANOVA, p&#x2009;=&#x2009;0.001). Random Forest-based feature selection was used to find the top 20 discriminative genera, which were used to train 10 supervised ML algorithms. Ensemble models, particularly Random Forest, achieved the highest performance in predictive models (mean across 100 folds: AUC&#x2009;=&#x2009;0.78, accuracy&#x2009;=&#x2009;0.70), indicating strong discriminative potential. The results of SHAP analysis provided clear pictures of how specific microbes influence BC risk. We identified several risk-associated genera, notably Bacteroides, Lachnoclostridium, Parasutterella, and Tannerellaceae, whereas Coprococcus, Romboutsia, Ruminococcus, and Prevotella were associated with lower BC risk.<br><br>CONCLUSION: This study reveals a clear shift in the gut microbiome community structure among BC patients. We identified specific bacterial genera that act as either elevated or decreased disease risk. These findings not only highlight the power of machine learning models for noninvasive risk prediction but also provide a foundation for novel microbiome-based diagnostic strategies.}, }
@article {pmid42226885, year = {2026}, author = {Wang, S and Wikle, CK and Micheas, AC and Welch, JLM and Starr, JR and Lee, KH}, title = {Inference for Stationary Log-Gaussian Cox Point Processes using Bayesian Deep Learning: Application to Human Oral Microbiome Image Data.}, journal = {Spatial statistics}, volume = {73}, number = {}, pages = {}, pmid = {42226885}, issn = {2211-6753}, support = {R01 GM126257/GM/NIGMS NIH HHS/United States ; R21 DE026872/DE/NIDCR NIH HHS/United States ; }, abstract = {It is common in nature to see aggregation of objects in space. Exploring the mechanism associated with the locations of such clustered observations can be essential to understanding the phenomenon, such as the source of spatial heterogeneity, or comparison to other event generating processes in the same domain. Log-Gaussian Cox processes (LGCPs) represent an important class of models for quantifying aggregation in a spatial point pattern. However, implementing likelihood-based Bayesian inference for such models presents many computational challenges, particularly in high dimensions. In this paper, we propose a novel likelihood-free inference approach for LGCPs using the recently developed BayesFlow approach, in which invertible neural networks are employed to approximate the posterior distribution of parameters of interest. BayesFlow is a neural simulation-based method based on "amortized" posterior estimation. That is, after an initial training procedure, fast feed-forward operations allow rapid posterior inference for any data within the same model family. Comprehensive numerical studies validate the reliability of the framework and show that BayesFlow achieves substantial computational gain in repeated application, especially for two-dimensional LGCPs. We demonstrate the utility and robustness of the method by applying it to two distinct oral microbial biofilm images.}, }
@article {pmid42226891, year = {2026}, author = {Gong, Q and Ding, K and Lou, W and Wang, J and Bian, G}, title = {Associations Between Social Jetlag and Gut Microbiome Profiles in Adolescents.}, journal = {Nature and science of sleep}, volume = {18}, number = {}, pages = {603131}, pmid = {42226891}, issn = {1179-1608}, abstract = {BACKGROUND: The microbiota-gut-brain axis plays a vital role in health, with growing evidence linking SJL to the gut microbiome. In this study, the relationship between self-reported SJL and gut microbiome composition is evaluated in an adolescent population.<br><br>METHODS: A total of 120&#xa0;healthy adolescents (69 females, 51 males; mean age 12.69&#xb1;0.65 years) were included. We investigated the associations of self-reported SJL with gut microbial &#x3b1;-diversity, the Firmicutes/Bacteroidetes (F/B) ratio, specific bacterial taxa, and functional gene diversity.<br><br>RESULTS: Participants had an average SJL of 0.87&#xb1;0.73&#xa0;h, with 25.0% experiencing SJL &#x2265;2&#xa0;h/d. Although continuous SJL was negatively correlated with &#x3b1;-diversity at the family level (Shannon and Simpson indices, all P<0.05), no significant differences were found between the SJL <2 and &#x2265;2&#xa0;h/d groups. Several taxa across multiple taxonomic levels (e.g. Bacteroidia and Bacteroidales) were associated with SJL (P<0.05). Differential abundance was observed for multiple families and genera between these two SJL groups. After FDR correction (q&#x2264;0.05), only the glutamate dehydrogenase gene gdh_K00262 was significantly enriched in the high SJL group (q=0.05).<br><br>CONCLUSION: SJL is associated with shifts in functionally relevant gut taxa, rather than a global ecological restructuring, in adolescents. Future work is needed to decipher the mechanisms of this microbiome-SJL interaction and its health significance.}, }
@article {pmid42227044, year = {2026}, author = {Singh, VK and Gupta, P and Jain, SK and Matreja, PS}, title = {The gut-brain axis in Alzheimer's and Parkinson's diseases: a systematic review of microbiota-derived biomarkers and novel therapeutic approaches.}, journal = {Journal of clinical and experimental neuropsychology}, volume = {}, number = {}, pages = {1-16}, doi = {10.1080/13803395.2026.2673084}, pmid = {42227044}, issn = {1744-411X}, abstract = {BACKGROUND: The altered gut microbiota substantially impacts the onset and progression of Alzheimer's disease (AD) and Parkinson's disease (PD), the two most widely studied neurodegenerative conditions. Microbiome-derived metabolites have been increasingly associated with disease onset, progression, and therapeutic targets in neurodegenerative disorders. Exploring the diagnostic and therapeutic implications of gut microbiome-derived biomarkers is critical to advancing our understanding and management of neurodegeneration.<br><br>METHODOLOGY: We systematically reviewed both clinical and preclinical studies published from 2010 to 2025. Studies examining gut microbiota composition, microbial-derived metabolites, or therapeutic interventions targeting the gut microbiome were included. Identification of gut microbiome alterations, discovery of microbial or metabolite-based biomarkers, association with disease onset or progression, and/or therapeutic effects on cognitive, neurological, or inflammatory outcomes were evaluated.<br><br>RESULT: Short-chain fatty acids(SCFAs) such as butyrate and acetate were found to be noninvasive biomarkers in patients with Alzheimer's disease (AD), mild cognitive impairment (MCI), and Parkinson's disease (PD). Lower SCFA levels correlated with cognitive decline. Diagnostic accuracy improved when SCFA combinations were used, with AUCs ranging from 0.75 to 0.87. Trimethylamine N-oxide(TMAO) levels showed inconsistent associations, with both elevated and reduced levels linked to disease risk. Therapeutic approaches targeting gut microbiota, including probiotics, prebiotics, dietary changes, and fecal microbiota transplantation, demonstrated cognitive benefits and modulation of gut-brain signaling pathways.<br><br>CONCLUSION: Overall, gut-derived biomarkers offer a promising avenue for early diagnosis and novel therapeutic approaches in AD and PD, while acknowledging that evidence in other neurodegenerative diseases remains limited through modulation of the gut-brain axis.}, }
@article {pmid42227074, year = {2026}, author = {Akinsuyi, OS and Ojeda, A and Xhumari, J and Ruggles, JV and Santos de Freitas, A and Roesch, LFW}, title = {Host transcriptional signatures associated with microbial sequence signals reveal age-related decline in intestinal homeostasis.}, journal = {Future microbiology}, volume = {}, number = {}, pages = {1-15}, doi = {10.1080/17460913.2026.2682676}, pmid = {42227074}, issn = {1746-0921}, abstract = {AIMS: To characterize age-associated alterations in intestinal barrier homeostasis by integrating host transcriptomic profiles and mucosa-associated microbial sequence signals recovered from human colonic biopsy RNA-seq datasets.<br><br>MATERIALS AND METHODS: We performed an integrative host-microbiome metatranscriptomic analysis of human colonic biopsies from adults aged 20 to >70&#x2009;years (n&#x2009;=&#x2009;238). RNA-seq libraries from four public datasets were analyzed using DESeq2, GSEA, Ingenuity Pathway Analysis (IPA), and SAHMI for differential expression, pathway enrichment, and microbial profiling.<br><br>RESULTS: Aging was associated with progressive transcriptional remodeling of the intestinal barrier. Key epithelial genes regulating differentiation (GATA5), extracellular matrix (ECM) turnover (MMP9, ADAMTS4), and lipid metabolism (FABP6, LRP2, LPA) showed age-dependent dysregulation, accompanied by elevated chemokine and cytokine signaling (CXCL1, CCL19, IL17A, IL22). Pathway analyses identified enrichment of IL-17 and ECM-cytokine signaling, consistent with chronic inflammatory activation. Parallel microbial profiling revealed a shift from butyrate-producing commensals (Faecalibacterium, Roseburia, Bifidobacterium) toward mucolytic and pro-inflammatory taxa (Ruminococcus torques, Acidaminococcus intestini, Bacteroides ovatus).<br><br>CONCLUSIONS: This study supports a continuum model of immune, structural, and microbial remodeling associated with aging. The findings highlight mucosal host-microbe interactions as potential therapeutic targets for preserving epithelial resilience and promoting healthy aging.}, }
@article {pmid42227124, year = {2026}, author = {Akimova, NI and Alekseeva, MG and Bekker, OB and Danilenko, VN}, title = {[Toxin-Antitoxin Systems: Formation of Genetic Networks of Human Microbiome Bacteria and Prospects for Application].}, journal = {Molekuliarnaia biologiia}, volume = {60}, number = {2}, pages = {248-265}, doi = {10.7868/S3034555326020049}, pmid = {42227124}, issn = {0026-8984}, abstract = {Toxin-antitoxin systems are modules consisting of genes that encode a stable toxin and a labile antitoxin. These systems are found in the genomes of most bacteria and archaea species. At present, eight types of toxin-antitoxin systems are distinguished. They perform a variety of functions in bacterial cells, the most important of which is adaptation to environmental stress. This review focuses on various types of toxin- antitoxin systems, their functions, and the mechanisms regulating interactions between the main components. These systems are described in detail for Bifidobacterium bifidum, Bifidobacterium longum, Lacticaseibacillus rhamnosus, and Mycobacterium tuberculosis. Furthermore, promising applications of toxin-antitoxin systems in biotechnology and infectious disease therapy are described.}, }
@article {pmid42227171, year = {2026}, author = {Rodriguez-Cisneros, C and Agashe, A and Chaudhury, R and Daniel, K and Hewedy, OA and Maric, A and Hartman, S}, title = {Anticipate, acclimate, recuperate and remember: How spatiotemporal signal integration controls flooding stress resilience in plants.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/erag262}, pmid = {42227171}, issn = {1460-2431}, abstract = {Flooding is a major abiotic stress that restricts terrestrial plant growth and survival. A plant tissue's ability to avoid or sustain critical oxygen deprivation (hypoxia) and subsequent re-oxygenation damage is vital for its survival. Submergence triggers rapid ethylene and hypoxia signalling that in turn control acclimation responses, promoting plant resilience. Interestingly, an extensive range of additional environmental and internal factors were shown to influence these canonical signalling pathways associated with flooding acclimation and tolerance. Here, we discuss how such integrative ethylene- and hypoxia-dependent signalling enables plants to anticipate and prepare for potential flooding-induced hypoxia stress, fine-tune acclimation according to the environmental and internal metabolic context, and effectively orchestrate re-oxygenation responses. Furthermore, plants naturally experience environmental stress manifold throughout their lives, which may lead to long-term morphological adaptations and the encoding of stress memory to promote survival against sequential stressors.}, }
@article {pmid42227223, year = {2026}, author = {Pérez-Ortega, S and Ortiz-Álvarez, R and Wierzchos, J and Blázquez, M and Gérault, A and de Los Ríos, A}, title = {Exploring the lichenization continuum through the marine tripartite symbiosis of Collemopsidium pelvetiae.}, journal = {American journal of botany}, volume = {}, number = {}, pages = {e70210}, doi = {10.1002/ajb2.70210}, pmid = {42227223}, issn = {1537-2197}, abstract = {PREMISE: Symbioses between lichen-forming fungi and brown algae (phaeophytes) are extremely rare. We investigated the interactions between the marine fungus Collemopsidium pelvetiae and its two photosynthetic partners, the brown alga Pelvetia canaliculata and a cyanobacterial symbiont to address questions on symbiosis biology, lichenization, and the diversity of fungal-photosynthetic associations in marine environments.<br><br>METHODS: We combined light microscopy, fluorescence microscope in structural illumination microscopy mode (SIM), and transmission electron microscopy (TEM) to characterize thallus architecture, symbiont interfaces, and ultrastructural interactions. Amplicon-based 16S rRNA sequencing profiled cyanobacteria and heterotrophic bacteria from two regions (northern Spain and Brittany, France).<br><br>RESULTS: Collemopsidium pelvetiae had distinct interactions with its two photosynthetic partners and with heterotrophic bacteria. Interactions with Pelvetia canaliculata were restricted to the region beneath the perithecia, where hyphae penetrated the outer amorphous cell-wall layer, without any evident host defense response. In contrast, the interaction with cyanobacteria involved the formation of intracellular haustoria, which ultimately lead to the death of the cyanobionts, suggesting a controlled parasitic relationship or a transitional stage toward lichenization. Unexpectedly, C. pelvetiae also produced haustorium-like projections into heterotrophic bacterial cells, a structure not previously reported in lichen symbioses. Microbiome analysis identified Pleurocapsa as the most likely cyanobiont genus associated with C. pelvetiae and revealed consistent heterotrophic bacterial communities, suggesting a species-specific assemblage.<br><br>CONCLUSIONS: This marine tripartite symbiosis involves distinct interaction modes, challenging strict lichen definitions. We propose that lichen symbioses form a multidimensional continuum of strategies rather than a single mutualistic model.}, }
@article {pmid42227270, year = {2026}, author = {Medeiros, MJ and Schoville, S and Price, DK and Yew, JY}, title = {Microbiome Structure of Endemic Hawaiian Drosophila Is Shaped More by Habitat Than Host Identity.}, journal = {Molecular ecology}, volume = {35}, number = {11}, pages = {e70417}, doi = {10.1111/mec.70417}, pmid = {42227270}, issn = {1365-294X}, support = {2025669//National Science Foundation/ ; P20GM125508/NH/NIH HHS/United States ; P20GM139753/NH/NIH HHS/United States ; 19CON-95452//Hawai'i Community Foundation/ ; }, mesh = {Animals ; Hawaii ; *Drosophila/microbiology/genetics ; *Ecosystem ; *Microbiota/genetics ; Phylogeny ; Fungi/classification/genetics ; Bacteria/classification/genetics ; }, abstract = {The Hawaiian Drosophila radiation exemplifies rapid adaptation and species diversification. Many factors have been attributed to these phenomena, including allopatry, sexual selection, and ecological specialization. In recent years, the microbiome has come to the forefront as an important driver of adaptation that is capable of facilitating host survivorship, enhancing resilience to local environmental challenges, and enabling the use of different dietary resources. To determine the factors that contribute to microbiome community variation in natural populations, we conducted a survey of bacterial and fungal communities from over 500 wild flies collected from across six islands of the Hawaiian archipelago. These samples represent a breadth of host plant specializations, habitats, lifestyles and endemicity. Our findings reveal that microbiome variation is largely driven by abiotic factors including elevation, temperature, rainfall, and evapotranspiration, but is not strongly constrained by phylogenetic relatedness. Identical species inhabiting three separate locations exhibited different microbiomes. By contrast, distantly related species inhabiting the same site had more similar microbiomes. The microbiomes of endemic species also differ from recently introduced invasive Drosophila in terms of diversity, composition, and predicted function. Given the myriad roles of the microbiome in nutrition, reproduction, and mate choice, these results provide a foundation for determining the roles of the microbiome in the ecological divergence of Hawaiian Drosophila.}, }
@article {pmid42227352, year = {2026}, author = {Pérez-Carrasco, V and Uroz-Torres, D and Soriano-Lerma, A and Soriano, M and García-Salcedo, JA and Arias-Moliz, MT}, title = {Association Between the Root Canal Microbiome and Apical Lesion Size: An Observational Shotgun Metagenomic Study.}, journal = {International endodontic journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/iej.70190}, pmid = {42227352}, issn = {1365-2591}, support = {//European Society of Endodontology/ ; }, abstract = {AIM: The aim was to characterize the taxonomic and functional composition of the microbiome involved in primary endodontic infections and to evaluate their association with the periapical lesion size using shotgun metagenomic sequencing.<br><br>METHODOLOGY: Samples from primary root canal infections diagnosed with apical periodontitis were analysed with shotgun sequencing. Samples were classified according to the lesion size as small (<&#x2009;3&#x2009;mm) or large (>&#x2009;7&#x2009;mm). The bacterial DNA copies in each group were quantified by qPCR. Taxonomic and functional annotations were made using Bracken/Kraken2 and HUMAnN3 software. Species richness, Shannon, Simpson and Pielou indices were used to measure alpha diversity. The similarity of the bacterial communities between study groups was evaluated by Principal Coordinate Analysis based on Bray-Curtis distances. The ALDEx2 package was used to infer the differences between species, and the edgeR package for KEGG pathways. For all statistical analyses, p&#x2009;<&#x2009;0.05 was considered as significant.<br><br>RESULTS: A total of 49 samples were analysed, 27 with small lesions and 22 with large lesions. Species richness and Shannon indices showed differences between both groups, whereas no differences were seen according to Simpson and Pielou indices. A different community composition (PERMANOVA, p&#x2009;=&#x2009;0.0019) was observed between the two groups. Three species were significantly enriched in the large lesion samples, Filifactor alocis, Lachnospiraceae bacterium oral taxon 500 and Olsenella uli, while three others were enriched in small lesion samples, Acinetobacter baumannii, Acinetobacter pittii and Cutibacterium acnes. Functionally, benzoate, flavonoid and steroid degradation, the sphingolipid signalling pathway and proteasome function were enriched in samples with large lesions. Monoterpenoid biosynthesis, phospholipase D signalling, the sulphur relay system and staurosporine biosynthesis were enriched in small lesions.<br><br>CONCLUSIONS: Teeth with large periapical lesions harbour greater bacterial loads and exhibit a more diverse microbial community than those with small lesions. Differences in species-level taxonomic composition were observed between both groups. Functionally, large lesions are enriched in pathways associated with immune evasion and pro-inflammatory activity, whereas small lesions are characterized by pathways related to apoptosis, metabolic adaptation and anti-inflammatory processes. These findings suggest that lesion severity is also shaped by the functional potential of the microbiome to modulate host inflammation.}, }
@article {pmid42227372, year = {2026}, author = {Zhang, X and Liu, G and Yan, Z}, title = {Global Research Trends in Innate Lymphoid Cells in the Gut and Kidney: A Bibliometric and Visual Analysis.}, journal = {Endocrine, metabolic &amp; immune disorders drug targets}, volume = {}, number = {}, pages = {}, doi = {10.2174/0118715303409659251128095655}, pmid = {42227372}, issn = {2212-3873}, abstract = {INTRODUCTION: Innate lymphoid cells (ILCs), critical immune regulators in mucosal tissues, maintain tissue homeostasis, modulate inflammation, and drive immune defense. While their roles in gut and kidney biology are increasingly studied, global research trends and focal points in this field remain largely uncharacterized.<br><br>METHOD: Using the Web of Science Core Collection (2004-2024), we analyzed 6,835 articles on gut- and kidney-associated ILCs. Bibliometric tools (VOSviewer, CiteSpace) were employed to evaluate publication trends, collaborations, institutional contributions, author influence, journal profiles, and keyword patterns to identify research priorities.<br><br>RESULT: Annual publications surged from 2004 to 2024, peaking at 622 in 2024. The U.S. (2,145 articles), China (1,539), and Germany (679) dominated output, with Harvard Medical School and Inserm as leading institutions. Gregory F. Sonnenberg and David Artis were the most-cited authors. Key journals included Frontiers in Immunology, Immunity, and Journal of Immunology. Research hotspots centered on inflammatory mechanisms (e.g., inflammatory bowel disease), immunotherapy, and ILC-microbiome crosstalk. Emerging trends emphasized tumor microenvironment interactions, as highlighted by keyword burst analysis.<br><br>CONCLUSION: This study underscores the therapeutic potential of ILCs in inflammation and cancer within the gut and kidney, advocating for interdisciplinary collaboration to advance mechanistic and clinical research.}, }
@article {pmid42227379, year = {2026}, author = {Md Sabudin, SNS and Das, S and Mohamad Umbaik, NA and Md Zin, SR}, title = {Microbiome and Its Association with Diseases of the Ear, Nose and Pharynx.}, journal = {Endocrine, metabolic &amp; immune disorders drug targets}, volume = {}, number = {}, pages = {}, doi = {10.2174/0118715303427717251222184941}, pmid = {42227379}, issn = {2212-3873}, abstract = {INTRODUCTION: The microbiome refers to the entire community of microorganisms, including bacteria, fungi, viruses, their genes, and the environment that surrounds them. The microbiome is found in the gut, skin, and the oral and nasal cavities, and is an important interface between the human body and the environment outside. Notably, the ear, nose, and throat or pharynx microbiome remains poorly studied. Therefore, the present review discusses the association of the microbiome with various diseases of the ear, nose, and pharynx.<br><br>METHODS: The literature was obtained by conducting a comprehensive search of the PubMed, Scopus, Web of Science, and Google Scholar databases, followed by screening the abstracts for relevance. The selected articles were then retrieved for deeper exploration.<br><br>RESULTS: This review highlights the disturbance of the balance of the microbiome, which is referred to as dysbiosis, that may be the cause of various diseases in the body.<br><br>DISCUSSION: We also discuss various microorganisms found in the ear, nose, and pharynx and their link with related diseases and brain health.<br><br>CONCLUSION: The microbiome is important for the better health of the human body as it modulates the immune system. Accordingly, a better understanding of its interaction with the host may lead to advances in drug design.}, }
@article {pmid42227474, year = {2026}, author = {Yang, F and Zhu, Z and Wang, Y and Qin, Y and Yue, H}, title = {Lung-Brain Axis Mechanisms of Cognitive Dysfunction in Long COVID.}, journal = {CNS &amp; neurological disorders drug targets}, volume = {}, number = {}, pages = {}, doi = {10.2174/0118715273421593251202095722}, pmid = {42227474}, issn = {1996-3181}, abstract = {Cognitive dysfunction, characterized by memory impairment, attentional deficits, and executive dysfunction, represents a critical clinical manifestation in post-acute sequelae of COVID-19 that significantly compromises patients' quality of life. The lung-brain axis, as a bidirectional regulatory network connecting the respiratory system to the central nervous system, interacts through neural circuits, humoral pathways, and microbial pathways, and may play a central role in the cognitive impairments occurring in long COVID (LC). This paper systematically reviews the multidimensional pathways of the lung-brain axis and their pathological mechanisms in the cognitive impairment of LC, including direct viral neuroinvasion during the acute phase, chronic injury triggered by viral persistence, immune homeostasis dysregulation, hypoxaemia, microbiome disruption, and renin- angiotensin system imbalance. It then explores clinical intervention strategies based on the lungbrain axis, integrating supportive treatments, such as oxygen therapy, exercise therapy, and cognitive training, with treatments targeting the lung-brain axis, including antiviral drugs, immunomodulation, probiotics, and neuromodulation techniques. It is also suggested that future research should favour the integration of multi-omics technologies and the development of individualised therapeutic targets.}, }
@article {pmid42227762, year = {2026}, author = {Mulisa, G and Zhao, J and Lelissa, G and Ademola-Popoola, IJ and Diaz Huemme, AM and Weyrich, LS and Mihret, A and Gemechu, T and Bane, A and Pero-Gascon, R and De Boevre, M and De Saeger, S and Abebe, T and Bisanz, JE}, title = {Multi-cohort comparative analysis of salivary microbiotas reveals rural Ethiopians harbor a distinct composition correlated with lower esophageal cancer prevalence.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0023226}, doi = {10.1128/msystems.00232-26}, pmid = {42227762}, issn = {2379-5077}, abstract = {Esophageal cancer (EC) results in high mortality due to difficulty in early diagnosis, particularly in low- and middle-income countries, including the African EC belt typified by high prevalence, early onset, and poor prognosis. While the precise etiological factors remain unknown, emerging data suggest links to the oral microbiota. In this study, we conducted a secondary analysis using V4 16S rRNA sequencing from a cross-sectional study of treatment-naive, newly diagnosed EC patients (N = 103) and healthy controls (N = 108) residing in agricultural regions of Ethiopia. We report that the salivary microbiota in the healthy Ethiopian controls is highly diverse, forming two functionally distinct community clusters differing in diversity, composition, and absolute abundance. Microbiota composition was associated with sex and alcohol consumption, but not age. Comparisons against groups from geographically distinct populations representing Tanzania, Uganda, Venezuela, and the United States (N = 641) showed that cluster 2 resembled other East African populations, while cluster 1 was unique to the Ethiopian cohort. Both EC subtypes, esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma, were associated with a loss of microbial diversity and an increased probability of having a cluster 2 microbiota (adjusted OR = 2.9 [95% CI 1.5-5.9]). Classifiers trained to discriminate healthy and EC samples were further validated on two external EC cohorts from China (N = 161). Models trained on the Ethiopian cohort could predict disease status in an external cohort of mid- and late-stage ESCC from China (AUROC = 0.70 ± 0.03 [mean ± SD]), demonstrating the generalization of microbial features of ESCC across populations.IMPORTANCERecent reports in North America and China have correlated oral microbiota composition with esophageal cancer, although the translation of this knowledge into the African esophageal cancer belt is hampered by a lack of data on the oral microbiota of East Africans and limited cross-cohort comparative analyses validating the utility of these biomarkers. We report that the human salivary microbiota is a meaningful biomarker of later-stage esophageal cancer that transcends geography and ethnicity and may provide utility for large-population screening. A lower-diversity and lower-abundance salivary microbiota correlated with esophageal cancer warrants further investigation to understand the role of oral microbes in mediating carcinogenesis.}, }
@article {pmid42228016, year = {2026}, author = {Putelo, AM and Bajgai, S and Poblete, MK and Guido, G and Perusina Lanfranca, M and He, Q and Raihan, T and Hatzinger, CN and Mirani, A and Kolli, SH and Lank, DS and Feng, TY and McGinty, MT and Miagkov, U and Pilehvari, A and You, W and Harris, TE and Rutkowski, MR}, title = {Commensal Dysbiosis Alters Primary Bile Acid Signaling to Drive Mammary Gland Inflammation and Breast Tumor Dissemination.}, journal = {Cancer research}, volume = {}, number = {}, pages = {}, doi = {10.1158/0008-5472.CAN-25-4466}, pmid = {42228016}, issn = {1538-7445}, abstract = {Breast cancer is the most commonly diagnosed malignancy and a leading cause of cancer-related mortality. Hormone receptor-positive (HR+) tumors represent the most prevalent metastatic subtype, and early dissemination remains a major clinical challenge. Commensal dysbiosis, defined as an inflammatory gut microbiome with low biodiversity, promotes metastasis by inducing mammary gland inflammation. Here, we investigated systemic mechanisms governing dysbiosis-induced metastasis. Metabolomic profiling revealed elevated primary bile acids (BAs) in the dysbiotic fecal microbiome. Sequestration and supplementation approaches demonstrated that, beyond driving metabolic disease and mammary gland inflammation, primary BAs orchestrated enhanced HR+ tumor dissemination via a prostaglandin E2 (PGE2)-dependent pathway. Analysis of The Cancer Genome Atlas (TCGA) showed that BA, insulin resistance, and PGE2 gene signatures associated with reduced survival in patients with HR+ tumors. In complementary analyses using the Epic Cosmos electronic health record database, bile acid sequestrant use was associated with longer restricted mean survival time among patients with metastatic disease. Together, these findings reveal that commensal dysbiosis-associated loss of microbial BA metabolism elevates primary BAs and promotes HR+ metastatic progression through PGE2 signaling.}, }
@article {pmid41992382, year = {2026}, author = {Cuteri, V and Preziuso, S and Li, Y and Laus, F}, title = {Fecal virome at the human-animal interface: a one health perspective on an uncharted frontier.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {41992382}, issn = {2524-4671}, abstract = {The exponential growth of the human population and associated intensifications in animal farming, pet ownership, and habitat anthropisation have dramatically increased human-animal interactions. Global livestock production now exceeds 24 billion animals annually, and pet ownership has risen to over 70% of households in many developed nations, creating unprecedented interfaces for viral exchange. This heightened contact has multiplied opportunities for zoonotic and reverse-zoonotic transmission, as tragically exemplified by the SARS-CoV-2 pandemic. The fecal virome—defined as the totality of viral nucleic acids in the gastrointestinal tract—represents a crucial, yet largely unexplored, pathway for such exchanges. While the bacterial microbiome’s role is increasingly recognized, the virome’s composition, dynamics, and transmissibility between co-habiting humans and animals remain poorly characterized. This review compiles current evidence on the fecal virome of key domestic animals (equines, livestock, pets) and their human contacts under the “One Health” framework. We critically evaluate methodological approaches—from targeted PCR to viral metagenomics—and highlight the discovery of novel viruses and identification of zoonotic agents through metagenomic approaches. Critically, we identify significant knowledge gaps, including the absence of definitive evidence for contemporary cross-species transmission versus shared ancestry or convergent evolution. We propose a strategic research agenda focused on longitudinal studies of human-animal cohorts, standardized metagenomic methodologies, and functional analyses of the virome. Elucidating the fecal virome at this interface is paramount for developing proactive surveillance strategies to predict and prevent the next emerging viral disease.}, }
@article {pmid42217383, year = {2026}, author = {Kong, T and Du, Z and Zhou, J and Zheng, Z and Zhang, J and Zhang, S and Jiang, F and Sun, X and Huang, W and Zhang, R and Li, F and Lin, W and Lan, X and Cao, Y and Yan, G and Sun, W}, title = {Assimilatory sulfate reduction potential in the plastisphere microbiome is linked to plastic mineralization in sulfur-rich mining-impacted river sediments.}, journal = {Water research}, volume = {303}, number = {}, pages = {126182}, doi = {10.1016/j.watres.2026.126182}, pmid = {42217383}, issn = {1879-2448}, abstract = {Microbial communities colonizing plastic surfaces are shaped by environmental factors, yet the role of sulfur in plastisphere assembly and plastic fate remains poorly understood. Here, we collected plastic debris from sulfur-rich, mining-impacted river sediments to characterize plastisphere microbiomes and evaluate their potential roles in plastic transformation. Paenibacillus spp. were identified as core plastisphere members, and their distribution was strongly associated with total sulfur concentrations. Metagenomic binning suggested that Paenibacillus harbored genomic potential associated with plastic transformation/mineralization and sulfate assimilation. An isolate of Paenibacillus provided further laboratory-based evidence that sulfate amendment may support plastic mineralization, although the precise in situ mechanism remains to be clarified. Because both the metagenome-assembled genome and the isolate genome encoded an almost complete assimilatory sulfate reduction pathway but lacked a complete dissimilatory sulfate reduction pathway, the observed sulfate depletion is more conservatively interpreted as sulfate uptake coupled with assimilatory sulfate reduction and subsequent sulfur assimilation into biomass rather than canonical sulfate respiration. Together, these findings suggest that sulfate availability and assimilatory sulfur metabolism may represent underappreciated controls on plastic turnover in sulfur-rich environments by supporting plastic-associated carbon transformation. This study links plastic-carbon fate to local sulfur cycling and provides new insight into microplastic persistence in sulfur-rich aquatic ecosystems.}, }
@article {pmid42217765, year = {2026}, author = {Li, L and Wei, J and Deng, Y and Yu, J and Wei, X and Wang, W and Chen, J and Wei, J and Yuan, T and Tan, H and Wu, Z and Jiang, J}, title = {The First Toxicological Assessment of Copper Exposure in Cipangopaludina cathayensis: Integrative Insights from Gut Microbiota and Hepatopancreas Responses.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128436}, doi = {10.1016/j.envpol.2026.128436}, pmid = {42217765}, issn = {1873-6424}, abstract = {Copper (Cu) is an essential trace element for biological organisms; however, excessive levels beyond biological tolerance can induce significant toxicity. Cipangopaludina cathayensis is a widely distributed freshwater gastropod in China and an important aquaculture species, yet information regarding its toxic responses to Cu exposure remains limited. In this study, the 96 h LC50 (median lethal concentration) of Cu for C. cathayensis was determined to be 0.150 mg/L, with a calculated safety concentration of 0.015 mg/L. Based on these values, 20% and 30% of the LC50 were selected as exposure concentrations for a 14-day experiment. Under Cu exposure, gut microbial α-diversity significantly increased, the Firmicutes/Bacteroidota ratio markedly decreased, potentially beneficial genera such as Bacteroides declined, whereas potentially pathogenic taxa including Aeromonas became enriched. Cu exposure induced infiltration of inflammatory cells and structural disruption of the intestinal mucosal layer, while the hepatopancreas exhibited vacuolation and tubular lumen dilation. The antioxidant defense system was severely impaired, as indicated by reduced SOD, CAT, and GSH levels and elevated MDA accumulation. Regarding metabolic responses, Cu exposure disrupted standard metabolism, with both oxygen consumption and ammonia excretion significantly reduced. Functional analyses of the gut microbiome and hepatopancreas metabolome revealed inhibited carbohydrate metabolism pathways. In contrast, lipid metabolism pathways were upregulated-although Cu exposure may disrupt normal lipid metabolic functions-possibly suggesting a compensatory strategy to meet energy demands under Cu stress. Additionally, the upregulation of protein (amino acid) metabolism-related pathways likely contributes to tissue repair processes.}, }
@article {pmid42217961, year = {2026}, author = {Dash, HR and Das, S}, title = {Investigative leads and individualization through forensically relevant human commensal microbiome.}, journal = {Advances in applied microbiology}, volume = {133}, number = {}, pages = {91-112}, doi = {10.1016/bs.aambs.2026.04.001}, pmid = {42217961}, issn = {0065-2164}, mesh = {Humans ; *Microbiota ; *Forensic Microbiology/methods ; *Bacteria/genetics/classification/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; }, abstract = {The advent of high-throughput DNA sequencing technology has facilitated the rapid and explicit analysis of human microbiome. Microbiome analysis from the crime scene provides definitive evidence of human contacts and/or their body fluids. Besides, personalized microbiome is strongly influenced by the geographic, lifestyle, ethnic and other environmental factors. The role of microbiome analysis in the prediction of post-mortem time interval has been widely established. Forensic Microbiome Database has featured a catalogue of varied group of microorganisms in different parts of the body which might provide a crucial piece of evidence in identification of body-fluids. Though the forensically relevant human microbiome analysis faces significant challenges both from technological and data related issues, this field holds significant promise in generating investigative leads and subsequent identification of an individual in the post-DNA profiling era. The proposed chapter describes the various aspects of human microbiome in forensics use and its challenges in its practical application in various forensic scenarios.}, }
@article {pmid42218054, year = {2026}, author = {Daniel, N and Papadimitriou, N and Chatziioannou, AC and Jenab, M and Mayén, AL and Keski-Rahkonen, P and Fedirko, V and Hassan, MM and Hughes, DJ}, title = {Genetically predicted gut bacteria, circulating bacteria-associated metabolites and liver cancer: A Mendelian randomisation study.}, journal = {Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.dld.2026.05.008}, pmid = {42218054}, issn = {1878-3562}, abstract = {BACKGROUND AND AIMS: Recent data suggest a role for the gut microbiome in the development of hepatocellular carcinoma. We investigated associations of gut microbiome abundances and concentrations of circulating bacteria-associated metabolites with hepatocellular carcinoma using Mendelian randomisation.<br><br>METHODS: Two-sample Mendelian randomisation was conducted using summary statistics from release 11 of FinnGen (609 cases and 473,046 controls) and The North American Hepatocellular Cancer Epidemiology Consortium (1872 cases and 2907 controls). Inverse variance-weighted analyses were performed as well as several sensitivity analyses.<br><br>RESULTS: In the FinnGen analyses, acetoacetate, ascorbate and asparagine were nominally associated with decreased risk. Alanine, hippuric acid and taurocholic acid were nominally associated with increased risk. The Barnesiella, Catenibacterium, Enterorhabdus and Eubacterium oxidoreducens genera were nominally associated with increased risk. Escherichia-Shigella was nominally associated with decreased risk. In the North American Hepatocellular Cancer Epidemiology Consortium analyses, the circulating bacteria-associated metabolites taurochenodeoxycholic acid and threonate were nominally associated with decreased risk. Five genera were nominally associated with increased risk; Eubacterium rectale group, Hungatella, Sellimonas and the unknown genus 1000005472.<br><br>CONCLUSION: These results, based on genetically predicted gut microbiome characteristics and circulating gut bacteria-related metabolite concentrations, suggest a putative causal role in hepatic carcinogenesis.}, }
@article {pmid42218119, year = {2026}, author = {Fessler, JL and Olm, MR and Engleman, EG and Sonnenburg, JL}, title = {Integration of donor microbiota following FMT correlates with anti-PD-1 response in melanoma.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73465-7}, pmid = {42218119}, issn = {2041-1723}, support = {R21CA290426//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; }, abstract = {Fecal microbiota transplantation (FMT) has shown promise in improving anti-PD-1 therapy in melanoma, but the underlying microbial features remain poorly defined. We performed a strain-resolved metagenomic meta-analysis across three independent FMT plus anti-PD-1 melanoma trials (n = 41). Across cohorts, therapeutic benefit was linked to successful integration of donor microbiota, rather than increased diversity or engraftment of specific species. Responders acquired more donor-derived strains, exhibited greater post-FMT similarity to their donor, and maintained a more stable microbiome. Following FMT, non-responders' microbiomes showed greater taxonomic instability, larger fluctuations in estimated microbial load, and increased abundance of pathogen-associated secretion system genes, whereas responders showed enrichment for microbial functions involved in community-level metabolism and communication. Finally, shifts in tumor-infiltrating immune profiles tracked with clinical outcomes and microbiome changes. Together these findings highlight that distinct patterns of microbiome restructuring, including stable community transitions and altered functional capacity, are associated with anti-PD-1 response following FMT.}, }
@article {pmid42218210, year = {2026}, author = {Maqami, M and Khalili, B and Shariatmadari, H}, title = {Interactive roles of mineralogy, microbial community composition and litter quality in regulating organic matter turnover.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-49740-4}, pmid = {42218210}, issn = {2045-2322}, abstract = {Soils are often treated as chemically defined reactors, yet the physical architecture of minerals, organic inputs, and microbiomes jointly shapes where and how carbon turns over. We used a factorial microcosm experiment to test how clay mineralogy (fibrous palygorskite vs. swelling bentonite), clay content (0-20%), calcium carbonate (7.5-15%), litter quality (recalcitrant wheat vs. labile alfalfa), and microbiome origin (native soil vs. a synthetic fungi + bacteria consortium) interact to control respiration kinetics and microbial biomass carbon over 90 days. Clay type and amount acted as primary filters: increasing clay generally raised cumulative mineralized C, but palygorskite produced higher C0, faster mineralization (higher k or lower t0, steeper n), and stronger late-stage biomass recovery than bentonite, indicating a colonizable, catalytic habitat rather than a purely protective matrix. Litter chemistry modulated this filter: N-rich alfalfa shifted the system toward facilitation, with rapid, high-amplitude mineralization and large biomass peaks, whereas high-C:N wheat slowed mineralization, increased sensitivity to clay content, and emphasized protection and diffusion limitation. Microbiome composition added a third control: native communities generated higher cumulative C loss but lower rate constants, while the synthetic consortium drove faster mineralization and higher biomass on palygorskite. Calcium carbonate acted as a tuner, enhancing C0, k and biomass in wheat systems and shifting mineralization timing in alfalfa systems. Together, these results support a hierarchical framework where mineral pore architecture sets the habitat filter, litter quality and microbial traits determine its exploitation, and Ca availability adjusts the balance between facilitation and protection.}, }
@article {pmid42218218, year = {2026}, author = {Zhu, G and Yang, G}, title = {Multikingdom microbiome-based machine learning enables multiple sclerosis diagnosis.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01030-7}, pmid = {42218218}, issn = {2055-5008}, support = {32571054 and 82371350//National Natural Science Foundation of China/ ; C7014-24GF//Research Grant Council of the Government of Hong Kong SAR/ ; Institute Digital Medicine internal grant (9229501-13-YG)//City University of Hong Kong/ ; }, abstract = {Emerging evidence suggests a role for the gut bacteria in the pathogenesis of multiple sclerosis (MS); however, the role of other microorganisms and their diagnostic potential for MS remain poorly explored. Here, we analyzed large-scale metagenomic data derived from fecal samples (discovery cohort n = 1152; total n = 1306 across 3 geographically diverse cohorts). Subsequently, we utilized multikingdom gut microbiome data to develop machine learning models to distinguish MS patients from healthy controls. Our analysis identified distinct microbiome alterations, revealing 90 bacterial, 3 fungal, 2 viral species, 119 KEGG orthology genes, and 17 metabolic pathways significantly associated with MS. Machine learning models integrating multikingdom taxonomic and functional features achieved the area under the receiver operating characteristic curves (AUCs) of 0.977 for males and 0.978 for females. On external validation datasets, the ensemble models yielded AUCs of 0.813 in males and 0.745 in females, while the 30-marker models reached AUCs of 0.849 and 0.763, respectively. Notably, the accuracy of the model was associated with Faecalibacterium spp. and L-methionine biosynthesis pathways, which were less abundant in MS patients. Collectively, our findings highlight the potential application of multikingdom and functional gut microbiome markers as non-invasive biomarkers for MS.}, }
@article {pmid42218309, year = {2026}, author = {Sedaghat-Rostami, E and Yang, L and Vats, A and Paudyal, B and Briggs, E and Carr, BV and Freimanis, G and Ruedas-Torres, I and Downing, T and Rollier, C and Marougka, K and De Haan, CAM and Mehat, J and La Ragione, R and Muir, A and Richard, AC and Van Reeth, K and Salguero, FJ and Gerner, W and Tchilian, E}, title = {Pathogen-specific immune responses might underlie divergent outcomes of coronavirus and influenza infection in the natural porcine host.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-10400-y}, pmid = {42218309}, issn = {2399-3642}, abstract = {Coronaviruses and influenza A viruses are major respiratory pathogens with pandemic potential. Using pigs as a translational large-animal model, we compare the virulence, pathogenesis, and immune responses to porcine respiratory coronavirus (PRCV) and pandemic H1N1 2009 influenza virus (pH1N1). Here we show that PRCV induces higher viral load and prolonged viral shedding, stronger systemic and mucosal T cell activation, expansion of memory B cells, and distinct nasal microbiome changes. In contrast, pH1N1 results in rapid neutralising antibody production, robust Tfh and germinal centre B cell responses, and broader early nasal microbial diversity. Transcriptional responses to PRCV and pH1N1 infection start with the activation of shared interferon-stimulated genes but later diverge as pathways involving stromal-immune interactions and vascular integrity shapes lung pathology and subsequent immune responses. These findings demonstrate fundamental differences in coronavirus and influenza virus-host interactions and establish the pig as a powerful comparative model for studying respiratory virus pathogenesis and immunity.}, }
@article {pmid42218386, year = {2026}, author = {Guo, S and Liu, J and Zheng, H and Wu, X}, title = {Nipple aspirate fluid as a proximal breast liquid biopsy platform: advancing precision risk management in breast cancer.}, journal = {Clinical proteomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12014-026-09612-5}, pmid = {42218386}, issn = {1542-6416}, support = {WJ2025M107//the Scientific Research Project of Hubei Provincial Health Commission/ ; Grant No.2023AFB493//the Natural Science Foundation of Hubei Province, China/ ; Grant No. HBCHBCC&#x2011;A02//the National Key Clinical Specialty Construction Project Fund of the Breast Center, Hubei Cancer Hospital/ ; 2024HBCHYN11//the Scientific Research Projects of Hubei Cancer Hospital/ ; EWT [2023] 65, Oncology//the Hubei Province Medical Youth Top Talent Project/ ; 2025HBCHHHRC005//the Talent Project of Hubei Cancer Hospital/ ; 2025HBCHLHRC002//the Talent Project of Hubei Cancer Hospital/ ; 2025HBCHYN24//the Scientific Research Project of Hubei Cancer Hospital/ ; 320.6750.2024&#x2011;21&#x2011;5 and 320.6750.2025&#x2011;21&#x2011;13//the Wu Jieping Fund Project/ ; CXPJJH123001&#x2011;2320//the Hubei Chen Xiaoping Science and Technology Development Foundation Youth Science Special Fund/ ; 2022SWZX09//the Subject of Biomedical Research Center of Hubei Cancer Hospital/ ; CTYC002//the 2024 Chutian Talents Program Special Fund/ ; }, abstract = {BACKGROUND: Current breast cancer (BC) risk management relies primarily on imaging and blood‑based liquid biopsies. However, these approaches are constrained by morphological blind spots, limited sensitivity for early lesions, and an inability to directly capture the biology of the ductal microenvironment where most tumors originate. There is a pressing need for novel strategies that provide direct, local insight into breast tissue risk.<br><br>MAIN BODY: This review repositions nipple aspirate fluid (NAF) as a proximal, breast-specific liquid biopsy platform. Emerging evidence demonstrates that NAF, obtained by nipple aspiration from non-lactating breasts and not limited to cases of spontaneous nipple discharge, originates from a functionally autonomous ductal microenvironment and provides rich multi-omics information, including proteins, metabolites, epigenetic alterations, extracellular vesicles, inflammatory/oxidative mediators, microbiome-associated signals, and other local regulatory readouts, rather than simply representing a filtrate of blood. We summarize the biological foundations of NAF and its multi-omics landscape, highlighting its potential in three key clinical scenarios: (1) molecular risk stratification for pathologic nipple discharge, (2) individualized biological risk profiling in women with high-risk or dense breasts, and (3) proximal monitoring of treatment response and microenvironmental dynamics in patients with diagnosed BC.<br><br>CONCLUSION: Although standardization and prospective validation remain essential challenges, the development of robust collection protocols, integration of multi&#x2011;omics data, and execution of well&#x2011;designed clinical trials could enable NAF to shift BC management from a paradigm of "early detection" toward one of "precision risk insight and intervention," ultimately aiming to improve patient outcomes and net benefit.}, }
@article {pmid42218533, year = {2026}, author = {Kim, W and Kim, JE and Hong, YS and Hwang, DW and Kim, J and Lee, JS and Shin, JH and Kim, TW and Nagarkar, D and Byrd, A and Sung, CO and Kim, SY}, title = {Dynamics of tumor ecosystems and microbiome in response to neoadjuvant ABFOLFOX treatment in patients with unresectable colorectal cancer with liver metastasis.}, journal = {Genome medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13073-026-01680-4}, pmid = {42218533}, issn = {1756-994X}, support = {ASA-1 project//This work was supported by the imCORE Network on behalf of F. Hoffmann-La Roche (ASA-1 project)./ ; }, abstract = {BACKGROUND: This study aims to explore the effects of neoadjuvant atezolizumab, bevacizumab, leucovorin, 5-fluorouracil, and oxaliplatin (ABFOLFOX) in patients with unresectable colorectal liver metastases (CRLM), focusing on the molecular dynamics of tumor ecosystems (TE) of CRLM and their impact on treatment outcomes.<br><br>METHODS: The study comprises two cohorts with CRLM tissue samples analyzed with RNA sequencing and immunohistochemical staining: cross-sectional cohort A (n&#x2009;=&#x2009;60, CRLM treated with or without neoadjuvant chemotherapy) and prospectively registered cohort B (n&#x2009;=&#x2009;20 with serial sampling and treated with ABFOLFOX). Shotgun metagenomic sequencing was performed for stool samples from cohort B.<br><br>RESULTS: Durable disease control (PFS&#x2009;&#x2265;&#x2009;24 months) was observed in 35% (7/20) of patients receiving ABFOLFOX. Analysis revealed a progressive increase in the immunogenic microenvironment within CRLM tissues upon the addition of therapeutic agents, specifically bevacizumab, and the most significant TE changes in CRLM were observed in those treated with ABFOLFOX in cohort B. The monocyte lineage was significantly associated with benefit from ABFOLFOX. Good responders exhibited improved immune response and notable activation of the SP140 transcription factor regulon. Moreover, microbiome analysis revealed that high abundance of Prevotella was positively correlated with good response and enhanced immune environment within the tumor. Causal mediation analysis suggested that the gut microbiome partially links the ABFOLFOX treatment response to the tumor microenvironment.<br><br>CONCLUSIONS: ABFOLFOX enhances the TE immune profile of CRLM, which is further augmented by the gut-liver axis characterized by Prevotella abundance, and can induce durable disease control in a subgroup of patients.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov, NCT03698461. May 08, 2019 (prospectively registered).}, }
@article {pmid42218547, year = {2026}, author = {Ji, S and Xia, J and Yang, Z and Liu, S and Zhang, X and Liu, X and Hao, Y and Wang, W and Long, S and Li, S}, title = {Mechanism of a polyherbal mixture alleviates calf diarrhea: an integrated network pharmacology, metabolomics, and microbiome study.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42218547}, issn = {1674-9782}, support = {No. 2022YFD1301001//National Key R&amp;D Program of China/ ; No. ZDYF2023XDNY067//Key Research and Development Projects in Hainan Province/ ; }, abstract = {BACKGROUND: Calf diarrhea represents a prevalent and serious challenge in dairy farming. While medicinal plants demonstrate considerable potential for preventing calf diarrhea within antibiotic-free farming systems, their active components and mechanisms remain poorly characterized. The objective of this study was to investigate a polyherbal mixture (PM; including Crataegus pinnatifida, Callicarpa nudiflora Hook. &amp; Arn., Mallotus apelta (Lour.) Müll.Arg., Amomum villosum Lour., Centella asiatica (L.) Urban, and Alpinia oxyphylla Miq.) supplemented to preweaning calves from d 4 to 60, utilizing an integrated approach combining network pharmacology, metabolomics, and microbiomics.<br><br>RESULTS: Dietary supplementation with 40&#xa0;g/d of PM significantly decreased the occurrence of diarrhea (P&#x2009;<&#x2009;0.05), increased monocyte levels (P&#x2009;<&#x2009;0.05), and improved jejunal villus height (P&#x2009;<&#x2009;0.05). Network pharmacology predicts that IL6, EGFR, SRC, TP53, and CCND1 are key targets, while acacetin, chrysin, tectochrysin, dihydroartemisinic acid, and lysionotin may be potential active constituents. The serum metabolome revealed that PM supplementation significantly enriched the steroid hormone biosynthesis. At the same time, PM altered the gastrointestinal microbiota, increasing the abundance of bacteria such as Mediterranea massiliensis, Prevotella denticola, and Duncaniella freteri in the rumen and Clostridium nexile in feces, while decreasing the abundance of Blautia producta, Vescimonas fastidiosa, and Alistipes putredinis in feces (P&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: Collectively, these findings suggest that PM supplementation alleviated calf diarrhea by remodeling serum steroid hormone biosynthesis and improving ruminal and fecal microbiota composition. Acacetin, chrysin, tectochrysin, dihydroartemisinic acid, and lysionotin may be potential active components.}, }
@article {pmid42218556, year = {2026}, author = {Li, F and Xu, X and Zhou, M and Du, S and He, Z and Xia, Z and Chen, Q and Li, J and Tang, S and Zhong, W and Xu, J}, title = {Longitudinal dynamics of gut microbiota and mycobiota in pneumonia-derived sepsis: evidence of taxonomic stability and trans-kingdom network reorganization.}, journal = {Gut pathogens}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13099-026-00838-0}, pmid = {42218556}, issn = {1757-4749}, support = {81970464//National Natural Science Foundation of China/ ; 201903010064, 202201011066//Science and Technology Program of Guangzhou/ ; 2022A1515011248, 2022A1515011855//National Natural Science Foundation of Guangdong Province/ ; }, abstract = {BACKGROUND: Gut microbial dysbiosis has been implicated in sepsis-related organ dysfunction. However, the longitudinal dynamics of the gut microbiota and mycobiota-and particularly their cross-kingdom ecological organization-in pneumonia-derived sepsis remain incompletely understood.<br><br>METHODS: Patients with pneumonia-derived sepsis were prospectively enrolled. Fecal samples and clinical data (SOFA scores and inflammatory markers) were collected on Day 1 and Day 7. Gut bacterial and fungal communities were profiled using 16&#xa0;S rRNA and ITS1 sequencing. Longitudinal and outcome-stratified analyses were performed. Trans-kingdom co-occurrence networks and module-based topological analyses were constructed, and associations with clinical parameters were explored.<br><br>RESULTS: Global analyses indicated relative compositional stability in the gut microbiota and mycobiota between Day 1 and Day 7, with no significant differences in alpha or beta diversity. The dominant bacteria were Bacillota, Bacteroidota, and Pseudomonadota at the phylum level, and Enterococcus, Bacteroides, and Escherichia-Shigella at the genus level; Escherichia-Shigella showed a decreasing trend and Bacteroides an increasing trend, though neither reached statistical significance (Padj&#x2009;>&#x2009;0.05). Ascomycota dominated the fungal community, with Candida, Fusarium, and Oligophagozyma as the core genera, with no obvious temporal shifts. However, outcome-based stratification revealed that fungal Chao1 richness increased significantly post-treatment, specifically in the bad-outcome group (P&#x2009;<&#x2009;0.05). The most notable findings emerged from the trans-kingdom interactome. In the favorable-outcome group, a specific modular configuration (ModM1) was identified post-treatment, containing four microbiota hubs (Parabacteroides, Mediterraneibacter, Serratia, and Enterococcus). While the aggregate abundance of ModM1 lacked clinical correlation, its hub genus, Mediterraneibacter-a prevalent anaerobe-showed a negative association with PCT and TNF-&#x3b1;. Additionally, the fungal-integrated ModM8 showed a potential positive association with IL-8. Conversely, the bad-outcome group showed a lack of such hub-anchored coordination.<br><br>CONCLUSIONS: In this small exploratory cohort, early pneumonia-derived sepsis appeared to exhibit relative taxonomic stability but subtle reorganization of cross-kingdom ecological connectivity. Microbial shifts appeared to manifest primarily as changes in network embedding rather than abundance. These observations provide exploratory insights that require further validation regarding topological integration, especially fungal involvement in inflammatory modules, for understanding host-microbiome interactions in critical illness. Larger longitudinal studies are warranted.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov, NCT04525677, registered on 14 July 2020.}, }
@article {pmid42218569, year = {2026}, author = {Gavillet, H and Hatfield, LR and Hardman, M and Marsh, R and Einarsson, GG and Thornton, CS and Parkins, MD and Duckers, J and Bomberger, JM and Hilliam, Y and Lee, SE and Lord, RW and Jones, A and Horsley, A and Daniels, TWV and Teneback, CC and Rivett, DW and van der Gast, C}, title = {Remodelling of cystic fibrosis respiratory microbiota in response to extended elexacaftor-tezacaftor-ivacaftor therapy.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02440-7}, pmid = {42218569}, issn = {2049-2618}, abstract = {BACKGROUND: Cystic fibrosis (CF) has profoundly changed since the introduction of CF Transmembrane Conductance Regulator modulator therapies (CFTRmt), a class of medications that improve function of the CFTR protein encoded by certain CF-causing gene mutations. Amongst these, the triple combination therapy elexacaftor-tezacaftor-ivacaftor (ETI) has been the most impactful and widely used to date. Given chronic respiratory infection and concomitant inflammation is the leading cause of morbidity and early mortality for the majority in CF, what is not certain are the long-term effects of ETI therapy on the respiratory microbiota and pathogens embedded within. Here, we assessed the effects of ETI CFTRmt over 3 years on the respiratory microbiota, using sputum and cough swab samples, from a multi-centre cohort of 276 adults with CF (awCF) from 6 CF centres in the UK, USA, and Canada, and compared to a non-CF healthy cohort.<br><br>RESULTS: Using Kruskal-Wallis analyses with post hoc Dunn's tests, Wilcoxon signed-rank tests, and PERMANOVA analyses with Bonferroni correction, we determined that respiratory microbiota characteristics (diversity, dominance, and composition) became decreasingly like those of awCF pre-ETI and remodelled to align more with the healthy cohort, where canonical CF pathogens increasingly became less ecologically important in terms of their distributions and abundances across awCF with increased duration on therapy. However, the on-ETI microbiota was impeded from becoming fully 'healthy' due to continued antibiotic exposure and irreversible lung damage experienced by awCF. Specifically, we found that azithromycin, an antibiotic widely used principally for its immunomodulatory benefits, was associated with adverse effects on the respiratory microbiota nullifying the observed positive effects of ETI treatment. Our results indicated that when administered alongside ETI therapy, azithromycin contributed to a pre-ETI microbiota dysbiosis and enabled enhanced persistence of emblematic CF pathogens.<br><br>CONCLUSIONS: The highly anticipated introduction of ETI CFTRmt has greatly changed the course of CF for many people living with this inherited disease. Here, we find that ETI CFTRmt enabled positive remodelling of the respiratory microbiota towards a healthy-like state. However, azithromycin appeared to impede total remodelling, making it an ideal candidate for evaluation for discontinuation in the CFTRmt era. While traditional pathogens become less ecologically important, the potential evolution and emergence of virulent strains should be investigated. Additionally, the impacts and implications of ETI therapy on the understudied fungal microbiota should also be explored. Video Abstract.}, }
@article {pmid42218700, year = {2026}, author = {Zhang, Y and Wang, Y and Yang, Y and Mei, H and Liu, X and He, Y and Qin, S and Feng, B}, title = {Gut-Liver Axis Failure in Critical Alcohol-Associated Liver Disease: From ICU Secondary Hits to Microbiome-Targeted Therapy.}, journal = {Mediators of inflammation}, volume = {2026}, number = {1}, pages = {e3968719}, doi = {10.1155/mi/3968719}, pmid = {42218700}, issn = {1466-1861}, support = {82460373//National Natural Science Foundation of China/ ; 82560382//National Natural Science Foundation of China/ ; HZ (2025) 312//Zunyi Science and Technology Bureau, China/ ; HZ (2023) 366//Zunyi Science and Technology Bureau, China/ ; HZ (2025) 172//Zunyi Science and Technology Bureau, China/ ; QZYY-2024-137//Guizhou Administration of Traditional Chinese Medicine/ ; gzwkj2024-310//Guizhou Provincial Health Commission/ ; MTyk2024-55//Kweichow Moutai Hospital Research Project/ ; HZ202411//Traditional Chinese Medicine Hospital of Zunyi Medical and Pharmaceutical College/ ; }, mesh = {Humans ; Intensive Care Units ; *Liver Diseases, Alcoholic/therapy/microbiology/metabolism ; *Liver/metabolism ; *Gastrointestinal Microbiome/physiology ; Animals ; Intestinal Barrier Function ; Fecal Microbiota Transplantation ; Dysbiosis ; }, abstract = {Alcohol-associated liver disease (ALD) can progress to critical illness phenotypes requiring intensive care, including severe alcohol-associated hepatitis, acute decompensation, and alcohol-associated acute-on-chronic liver failure (ACLF). In these patients, short-term outcomes are driven less by the burden of fibrosis alone than by systemic inflammation, immune dysfunction, infection, and multiorgan failure. At the core of this process is gut-liver axis failure, which links alcohol-induced dysbiosis and intestinal barrier disruption to microbial translocation, hepatic innate immune activation, and systemic inflammatory amplification. In the intensive care unit (ICU), secondary hits such as broad-spectrum antibiotics, acid suppression, parenteral nutrition, shock, sedatives or opioids, and mechanical ventilation may further exacerbate these mechanisms and disturb microbial ecology and barrier integrity. Microbiome-targeted therapies (probiotics, postbiotics, and fecal microbiota transplantation) are biologically plausible. However, current evidence is mainly derived from non-ICU or relatively stable ALD populations. Therefore, their use in critically ill patients requires strict safety boundaries, including severe barrier disruption, invasive devices, uncontrolled infections, and profound immune dysfunction. This narrative review synthesizes the pathophysiological continuum from gut barrier failure to systemic inflammation and multiorgan dysfunction in critical ALD, with particular emphasis on ICU-specific secondary hits, safety-aware microbiome modulation, and future phenotype-informed precision strategies.}, }
@article {pmid42218826, year = {2026}, author = {Kao, CS and Chien, LC and Hsieh, FI and Chao, HJ and Kallawicha, K and Chen, YH and Wang, YL and Wu, CD and Jiang, CB}, title = {Integrating urban land-use characteristics and heavy metal exposure in assessing pediatric gut microbiota: Implications for environmental management.}, journal = {Integrated environmental assessment and management}, volume = {}, number = {}, pages = {}, doi = {10.1093/inteam/vjag092}, pmid = {42218826}, issn = {1551-3793}, abstract = {Early-life exposure to environmental pollutants poses a critical risk to pediatric health, yet few studies have integrated chemical contaminants with urban land-use characteristics to assess their combined associations with the developing gut microbiome. In this study, we evaluated the associations between fecal heavy metal (HM) concentrations and residential land-use cover area (measured as area-based metrics within specific buffers), as well as gut microbial composition and predicted functional pathways, in 78 preschool children from the greater Taipei area. Using Bayesian kernel machine regression (BKMR), we characterized nonlinear and interactive exposure-response relationships. Elevated fecal cadmium (Cd) levels were significantly and positively associated with increased abundance of Bacteroides (q = 0.02), while nominal positive associations were observed with Klebsiella and Veillonella. Fecal lead (Pb) showed a suggestive positive association with Phocaeicola (q = 0.07). Crucially, residential land-use features modified these associations: increased gas station coverage was linked to lower Bacteroides and Veillonella levels but higher Klebsiella abundance, whereas green-space coverage was positively associated with Veillonella. The BKMR model highlighted synergistic negative associations between fecal Cd and gas station area coverage within a 1500-m residential buffer on Veillonella and Bacteroides, suggesting that the spatial distribution of physical urban infrastructure may be linked to the apparent effects of chemical contaminants on the gut microbiota. These environmental contaminants were further associated with alterations in predicted microbial functional pathways involved in energy metabolism, secondary metabolite biosynthesis, and genetic information processing. These findings suggest that children's gut health may be associated with a complex interplay of urban chemical and structural factors. Our results underscore the need for science-informed urban management and health-protective zoning, which may inform strategies such as optimizing land-use cover area of gas stations near residential areas and increasing urban greenery to mitigate environmental risks during critical developmental windows.}, }
@article {pmid42218921, year = {2026}, author = {Guo, F and Fu, W and Topalović, O and Zhang, Q and Li, K and Li, H and Qing, X}, title = {Genomic insights into nematode microbiomes reveal novel endosymbionts Rickettsiella.}, journal = {Molecular phylogenetics and evolution}, volume = {223}, number = {}, pages = {108650}, doi = {10.1016/j.ympev.2026.108650}, pmid = {42218921}, issn = {1095-9513}, abstract = {BACKGROUND: Bacterial endosymbionts are key drivers of invertebrate ecology and evolution. While the diversity and functional role of the nematode microbiome remain poorly explored.<br><br>METHODOLOGY: We reconstructed and characterized 108 metagenome-assembled genomes from 10 published and 15 newly sequenced nematode genomes.<br><br>PRINCIPAL FINDINGS: We report the first evidence of Rickettsiella in nematodes and discovered novel endosymbionts Cardinium and Wolbachia in plant-parasitic nematodes. The nematode microbiome is enriched with genes for carbohydrate metabolism and the biosynthesis of essential amino acids and vitamins, indicating a potential primary role in host nutrition. Notably, mobile genetic elements like prophages and insertion sequences (IS) are widespread and carry passenger genes involved in vitamin biosynthesis, suggesting horizontal gene transfer facilitates metabolic adaptation. Genomic reduction in the nematode Rickettsiella lineage, reveals extensive gene loss, particularly in amino acid biosynthesis. Crucially, we find no evidence of purifying selection on its residual nutritional pathways, and thus cannot clearly support a mutualistic role for this association.<br><br>CONCLUSION: Our findings expand the known host range of major endosymbiont groups and reveal a spectrum of symbiotic relationships in nematodes, from putative mutualism driven by nutritional supplementation to associations with neutral or parasitic traits, shaped by pervasive horizontal gene transfer and reductive genome evolution.}, }
@article {pmid42219028, year = {2026}, author = {Fan, X and Xiao, X and Tan, D and Yu, B and Chen, D and He, J and Luo, J and Luo, Y and Yan, H and Wang, J and Wu, A and Wang, Q and Wang, H and Mao, X}, title = {Host-targeted apple pectic oligosaccharides repair intestinal barrier in colitis via HSP90β/miRNA/CORO2A axis.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2026.05.057}, pmid = {42219028}, issn = {2090-1224}, abstract = {INTRODUCTION: While functional oligosaccharides alleviate inflammatory bowel disease (IBD), their mechanisms conventionally attributed to gut microbiota modulation. The direct, host-targeted regulatory pathways of apple pectic oligosaccharides (APOS) remain elusive.<br><br>OBJECTIVES: This study aimed to elucidate the host-directed parallel mechanism by which APOS restores intestinal epithelial barrier integrity and immune homeostasis during colitis.<br><br>METHODS: We integrated multi-omics analysis, biophysical binding validation, and a dextran sulfate sodium (DSS)-induced rat colitis model. Mechanistic dependency was validated via in vivo miRNA rescue and in vitro (IEC18 and human Caco-2) models using dual-luciferase assays and bidirectional genetic manipulation.<br><br>RESULTS: APOS (200&#x202f;mg/kg) significantly ameliorated colitis severity. Mechanistically, APOS directly bound to the N-terminal pocket of membrane HSP90&#x3b2; on intestinal epithelial cells. This interaction inhibited the release of miR-148a-5p and miR-216a-3p, thereby de-repressing their shared downstream target, the cytoskeletal regulator CORO2A. CORO2A restoration re-anchored junctional networks (ZO-1, AJAP1 and GJA1) and suppressed Th1/Th17-driven cytokine storms. Crucially, exogenous miRNA supplementation in vivo completely abolished APOS-mediated barrier protection despite maintaining a restored microbiome, confirming the indispensable role of this host-directed pathway.<br><br>CONCLUSION: Operating synergistically with microbial modulation, APOS functions as a highly potent (Human Equivalent Dose 11.35&#x202f;mg/kg), host-directed therapeutic. By engaging the HSP90&#x3b2;/miRNA/CORO2A axis to rebuild the physical defense line, this study conceptualizes a novel framework for precision nutritional intervention in IBD.}, }
@article {pmid42219044, year = {2026}, author = {Shil, S and Datta, SP and Banerjee, D and Paul, S and Khatua, A and Chowdhury, J and Koner, GS and Das, AK and Mukherjee, A and Karmakar, UK and Haldar, S and Debnath, A}, title = {Hypervariable region-specific detection of an avian gut pathobiont in multi-primer 16S rRNA metagenomics: the V9 region identifies Gallibacterium anatis undetected by conventional V3-V4 approaches.}, journal = {Journal of microbiological methods}, volume = {246}, number = {}, pages = {107565}, doi = {10.1016/j.mimet.2026.107565}, pmid = {42219044}, issn = {1872-8359}, abstract = {Hypervariable region (V-region) selection critically determines which taxa are resolved in 16S rRNA amplicon surveys, yet most commercial poultry gut microbiome studies rely on the V3-V4 primer pair optimised for Illumina short-read platforms. The Ion GeneStudio S5 Prime with multi-primer 16S chemistry simultaneously amplifies six variable regions (V2, V3, V4, V67, V8, V9) from a single library, providing an unprecedented opportunity to benchmark region-specific taxonomic resolution in the same sample set without inter-library bias. 29 commercial broiler caecal samples (HEALTHY n = 10; DISEASED n = 19) were analysed per-V-region on the Ion GeneStudio S5 Prime using the Ion 16S Metagenomics Kit, yielding 46,542 classified reads distributed across six V-regions. From a total sequencing depth of 342,716-1,358,797 reads per sample. Independent ASV-level validation was performed using QIIME2 v2024.10 DADA2 (738 ASVs, SILVA 138), confirming all primary findings. V3 contributed the highest read volume (14,818 reads, 31.8%) and resolved the most genera (52 unique). V9 contributed the fewest reads (2831, 6.1%) but the highest number of region-exclusive genera (11), including the avian pathobiont Gallibacterium anatis. Critically, 121 of 220 total G. anatis reads (55%) were recovered exclusively via V9 primers; zero G. anatis reads were detected by V3 across all 29 samples.". In a parallel differential abundance analysis, G. anatis was the most significantly enriched taxon in diseased caecal microbiota (DESeq2 padj = 1.45 × 10[-6]), a finding that would have been entirely missed by a conventional V3-V4 workflow. In silico analysis of one of the samples from this set, found G. anatis (GenBank PX986441.1) confirmed absence of the 341F primer binding site. Mean sequence identity was uniformly high across all regions (98.74-99.05%), confirming that V9 underperformance is a coverage rather than quality issue. These findings demonstrate significant primer bias in single-region 16S workflows applied to poultry gut microbiome research, with direct implications for diagnostic assay design and pathobiont surveillance programmes.}, }
@article {pmid42219426, year = {2026}, author = {Jäkel, J and Ludwig, J and Hüning, B and Felderhoff-Müser, U and Härtel, C}, title = {Intersectionality of early developmental risks and resilience after preterm birth.}, journal = {Molecular and cellular pediatrics}, volume = {13}, number = {1}, pages = {}, pmid = {42219426}, issn = {2194-7791}, abstract = {The period from conception through preschool age represents a critical developmental window for both microbiome and brain. During this time, several modifiable factors may influence development via the gut-brain axis, including the mode of delivery, exposure to antibiotics, maternal nutrition, breastfeeding, and sensitive, emotionally responsive caregiving. Infants born preterm (<37 weeks gestation) face numerous challenges that can perturb their developing gut microbiome as well as neurobehavioral trajectories. Biological and medical risks are exacerbated by stressful social context conditions. Understanding the complex mechanisms shaping the gut-brain axis and identifying modifiable protective factors is key to help define specific target groups and critical windows for individualized prevention of adverse outcomes after preterm birth. Today, a large knowledge gap exists on (a) how gut, brain, and behavioral development interact over time, and (b) which social and modifiable factors are key drivers of this interaction that could be harnessed for treatment and intervention. Translational research on the gut-brain axis after preterm birth is critically needed. Future studies should consider intentional sampling for variation in social factors such as level of education and immigrant background to identify populations that are susceptible to microbiome modifications and provide more evidence of how interventions might optimize long-term outcomes.}, }
@article {pmid42219523, year = {2026}, author = {Magory Cohen, T and Bodner, L and Turjeman, S and Sharon, E and Cohen, A and Bouchebti, S and Tikhonov, E and Koren, O and Levin, E}, title = {Gut microbiome mediates an evolutionarily conserved social behavior in eusocial insects.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {42219523}, issn = {2524-4671}, support = {1538/18//Israel Science Foundation/ ; }, abstract = {UNLABELLED: The gut microbiome is increasingly recognized as a key mediator of social behavior and division of labor in eusocial insects. In some species, trophallactic interactions facilitate nutrient exchange between larvae and adults, creating social interdependency. However, the role of gut bacterial symbionts in this process remains unclear. Here, we investigated the relative contributions of host identity, environment, and trophallactic interactions to gut microbiome assembly in two social wasp species, Vespa orientalis and Vespula germanica, using a cross-fostering, common garden experiment. Newly emerged workers and early-instar larvae were reciprocally exchanged and reared under controlled conditions. High-throughput 16S rRNA gene sequencing and functional inference revealed limited variation across treatments in worker gut communities, mainly shaped by shared environment, indicating stability and environmental dominance. Conversely, larval gut microbiomes were highly plastic, influenced by both larval species and the identity of their nursing workers, highlighting the impact of social interactions. Functional profiles reflected caste-specific roles: workers harbored microbiomes enriched for antimicrobial and detoxification pathways, while larvae microbiomes were enriched in metabolic functions for protein digestion and development. These findings demonstrate that metabolic division of labor in eusocial wasps is supported by life stage-specific microbial communities and functions and maintained by social interactions, positioning the gut microbiome as a key contributor to the maintenance of eusociality.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00560-x.}, }
@article {pmid42219628, year = {2026}, author = {Osuji, IE and Akanmu, AO and Babalola, OO}, title = {Bacterial Diversity and Functional Dynamics in the Soybean (Glycine max L.) Rhizosphere Under Different Organic Fertilisation.}, journal = {Environmental microbiology reports}, volume = {18}, number = {3}, pages = {e70370}, doi = {10.1111/1758-2229.70370}, pmid = {42219628}, issn = {1758-2229}, support = {CRP/ZAF22-93//International Centre for Genetic Engineering and Biotechnology/ ; }, mesh = {*Glycine max/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Soil Microbiology ; Manure/analysis/microbiology ; Animals ; *Fertilizers/analysis ; Cattle ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Biodiversity ; Soil/chemistry ; Poultry ; *Microbiota ; DNA, Bacterial/genetics ; }, abstract = {Soybean (Glycine max L.) is a globally important legume for oil and protein production, yet its responses to specific organic fertilisation practices remain insufficiently understood. Organic amendments such as cattle dung and poultry manure are sustainable alternatives to inorganic fertilisers, but their effects on the soybean rhizosphere microbiome remain poorly characterised. This study investigated microbial community structure and functional diversity under poultry manure and cattle dung treatments. Rhizospheric soils were collected from treated plots, untreated controls and bulk soil and then subjected to physicochemical analysis. DNA extracted from samples was analysed using 16S rRNA gene sequencing on the Illumina NovaSeq 6000 platform, with data processed in QIIME 2 (v2019.1). Poultry manure increased available phosphorus (28%) and calcium (19%), while cattle dung enhanced potassium (22%) and magnesium (17%). Microbial community composition shifted significantly, with poultry manure promoting copiotrophic taxa such as Burkholderia and Cupriavidus and cattle dung enriching decomposers including Paenibacillus and Treponema. Alpha diversity was highest in poultry manure (Shannon index 6.2) and bulk soil (6.0) and lowest in cattle dung (5.1). Functional predictions indicated retention of core metabolic pathways, suggesting functional redundancy. Overall, organic fertilisation reshapes microbial communities while maintaining essential functions, supporting sustainable soybean cultivation.}, }
@article {pmid42219690, year = {2026}, author = {Zhu, P and Yuan, X and Wang, X and Shi, Y}, title = {Application of Nano Silica Is Associated With Enhanced Wheat Resistance to Fusarium Crown Rot via Regulation of Metabolic Pathways and Soil Microbial Community.}, journal = {Environmental microbiology}, volume = {28}, number = {6}, pages = {e70343}, doi = {10.1111/1462-2920.70343}, pmid = {42219690}, issn = {1462-2920}, support = {SDAIT0107//Shandong Modern Agricultural Technology &amp; Industry System/ ; SDNYXTTG-2023-30//Agricultural Major Technology Collaborative Promotion Plan Project in Shandong Province/ ; }, mesh = {*Triticum/microbiology ; *Fusarium/physiology ; *Soil Microbiology ; *Silicon Dioxide/pharmacology ; Metabolic Networks and Pathways/drug effects ; *Microbiota/drug effects ; *Plant Diseases/microbiology/prevention &amp; control ; *Disease Resistance/drug effects ; Lignin/metabolism ; *Nanoparticles ; }, abstract = {Nano silica (NS) has promising agricultural applications, yet its effects and mechanisms in enhancing wheat resistance to Fusarium crown rot (FCR) caused by Fusarium pseudograminearum (FP) remain underexplored. Here, we conducted a pot experiment with 200 mg/L NS, integrating soil metagenomics, plant physiology, and metabolomics to investigate this process. Soil metagenomic analysis revealed that NS was associated with reshaped microbial community structure and distinct functional pathway variations (GO/KEGG annotations). In wheat, NS treatment was linked to activated fructose/mannose metabolism and phenylpropanoid biosynthesis, increasing SOD and POD activities by 14.5% and 169.9% and reducing MDA content by 37.0%. It was also associated with upregulated lignin-related enzymes (PAL, C4H, and 4CL) and their encoding genes, thus promoting lignin accumulation, enhancing stem strength, and restoring cellulose content. Our findings suggest a potential dual mechanism: NS-associated soil microbiome changes coincide with improved plant antioxidant capacity and defence gene expression, reinforcing stem integrity to alleviate FCR, providing new insights for eco-friendly FCR management.}, }
@article {pmid42219697, year = {2026}, author = {Liang, S and Strodl, E and Barron, L and Bambling, M and Vitetta, L}, title = {Associations Between Microbial Depletion and Autonomic Dysregulation in Binge-Eating Disorder.}, journal = {The International journal of eating disorders}, volume = {}, number = {}, pages = {}, doi = {10.1002/eat.70139}, pmid = {42219697}, issn = {1098-108X}, abstract = {OBJECTIVE: The interplay between the gut microbiome and autonomic nervous system remains unexplored in binge-eating disorder (BED). We aimed to explore specific microbial alterations in BED and examine their potential association with cardiac vagal tone as a distinct bio-behavioral phenotype.<br><br>METHOD: Women with BED and co-occurring major depressive disorder (BED+MDD; n&#x2009;=&#x2009;19) were compared to strictly matched controls with MDD alone (n&#x2009;=&#x2009;38) to isolate BED-specific effects. We analyzed the gut microbiome via 16S rRNA sequencing and assessed cardiac vagal tone using short-term heart rate variability (specifically normalized high-frequency power, HFnu). Nutritional intake was analyzed to explore diet-microbiome interactions.<br><br>RESULTS: While global diversity did not differ between groups, differential abundance analysis identified lower relative abundance of several fermentative taxa, including Catenibacterium, Acidaminococcus, Pediococcus, Fusobacterium, Megasphaera, and Prevotella in the BED group. Notably, a cross-system association emerged exclusively in the BED group: the depletion of Pediococcus was strongly correlated with reduced vagal tone (HFnu; p&#x2009;=&#x2009;0.003) and specific micronutrient patterns. This relationship was absent in the MDD-only controls.<br><br>DISCUSSION: Our findings demonstrate a BED-specific link between the depletion of the fermentative guild, autonomic instability, and dietary energy intake. This linked state may reflect a physiological response to the acute substrate surges characteristic of binge-eating, potentially compromising gut-brain axis homeostasis. Future research incorporating direct measures of binge behavior and luminal environment is required to validate whether these microbial patterns represent a causal mechanism or a reproducible physiological marker of the disorder.}, }
@article {pmid42219768, year = {2026}, author = {Liu, X and Chen, T and Qin, X and Han, M and Zhang, X and Zhou, J and Li, P}, title = {Simplified synergistic rhizosphere bacterial consortia enhance the antagonistic activities against Ralstonia solanacearum and improve plant health.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-10-25-2115-RE}, pmid = {42219768}, issn = {0191-2917}, abstract = {The rhizosphere microbiota plays a vital role in plant stress resistance and pathogen suppression. Bacterial wilt, caused by Ralstonia solanacearum, leads to significant economic losses in a wide variety of crops. The utilization of native microbial consortia has emerged as a promising strategy for combating this disease. In this study, we assembled a synthetic microbial consortium (Co-4) from rhizosphere bacteria with demonstrated antagonistic activity, comprising four strains of Bacillus sp., Heyndrickxia sp., Franconibacter sp., and Pseudomonas sp. Transcriptome analysis of tomato plants treated with Co-4 revealed significant alterations in gene expression, particularly in carbohydrate and energy metabolism, as well as translation processes. These changes correlated with enhancements in various plant growth traits, including height, stem thickness, biomass, leaf area, photosynthetic rate, and root development. Furthermore, two simplified consortia, SynCom1 (Bacillus, Heyndrickxia, Franconibacter) and SynCom2 (Franconibacter, Pseudomonas), exhibited augmented antagonistic properties against R. solanacearum compared to their individual constituent strains. Using SynCom2 as a model, we demonstrated that its synergistic interactions resulted in increased biofilm formation, motility, biomass production, cross-feeding interactions, and volatile organic compounds (VOC) emissions, all of which likely contribute to disease suppression and enhanced plant defense. This study highlights the potential of simplified synthetic consortia for managing bacterial wilt through cooperative microbial functions, presenting an effective and environmentally sustainable biocontrol strategy.}, }
@article {pmid42220059, year = {2026}, author = {Ren, R and Li, X and Li, H and Cao, Z and Hou, M and Zhao, C and Lou, N and Hu, S and Li, Y and Ma, Q and Li, Y and Fan, Y and Zhao, K and Zhao, K and Qiu, D and Gong, F and Li, Z and Liu, H and Ma, X and Wang, X and Yin, D}, title = {Resistant Peanut Genotype Reprograms Rhizosphere Metabolism to Enhance Bacterial Wilt Suppression.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e75910}, doi = {10.1002/advs.75910}, pmid = {42220059}, issn = {2198-3844}, support = {U22A20475//National Natural Science Foundation of China (NSFC)-Henan United Fund/ ; 264000510007//Zhongyuan Scholars in Henan Province/ ; 221111110500//Key Scientific and Technological Project of Henan Province/ ; HARS-22-05-G1//Key Scientific and Technological Project of Henan Province/ ; 262102111109//Key Scientific and Technological Project of Henan Province/ ; 242102111154//Key Scientific and Technological Project of Henan Province/ ; 30501308/111//Special Fund for Young Talents in Henan Agricultural University/ ; }, abstract = {Bacterial wilt caused by Ralstonia solanacearum compromises the yield and quality of peanut (Arachis hypogaea L.). While rhizosphere microbiome-assisted defense is known, how resistant plant genotypes orchestrate this process remains unclear. Here, we integrate multi-omics analyses of resistant and susceptible peanut genotypes to uncover a genotype-specific defense mechanism. The resistant genotype selectively recruits beneficial bacteria (e.g., Kosakonia and Frankia), which coincides with activated salicylic acid (SA)-dependent systemic acquired resistance (SAR). Crucially, we identify keystone rhizosphere metabolites (including betaine, arginine, and SA) that are positively correlated with both beneficial microbiome assembly and SAR gene expression, establishing a self-reinforcing defense loop. Leveraging these insights, we develop a prebiotic formulation that enhances beneficial microbial recruitment and stimulates SAR. Field trials demonstrate that the prebiotics reduce bacterial wilt incidence from 84.2% to 5.0% and increase yield by 12.9%-20.3%. Collectively, our study reveals a synergistic microbiome-immune co-regulation mechanism in peanut and delivers a translatable solution for sustainable disease management.}, }
@article {pmid42220213, year = {2026}, author = {Sayol-Altarriba, A and Aira, A and Martín-López, E and Villasante, A and Albarracín, R and Faneca, J and Pitart, C and Roca, I and Casals, G and Marco, S and Villanueva-Cañas, JL and Casals-Pascual, C}, title = {Metabolic Screening of Gut Microbiota by Fourier-Transform Infrared Spectroscopy.}, journal = {ACS infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1021/acsinfecdis.6c00128}, pmid = {42220213}, issn = {2373-8227}, abstract = {Short-chain fatty acids (SCFAs) are bacterial metabolites with crucial roles in host homeostasis and immune system modulation. Given their benefits, they have been proposed as markers of healthy microbiota. However, accurate SCFA quantification typically requires gas chromatography coupled with mass spectrometry (GC-MS), which is time-consuming, expensive, and requires specialized personnel and equipment, limiting its routine use for stool quality assessment in clinical contexts. In this initial feasibility study, we explored the use of Fourier transform infrared (FT-IR) spectroscopy as a rapid metabolic screening approach for stool samples. Analysis of SCFA-associated spectral windows enhanced discrimination between healthy and dysbiotic stool samples with Clostridioides difficile infection using principal component analysis. FT-IR is not intended to replace GC-MS for precise SCFA quantification but rather to provide a rapid screening of metabolically relevant differences. Although additional validation is still needed, the present study provides a robust proof-of-concept demonstrating the feasibility of applying FT-IR spectroscopy to clinical stool samples. Combined with the widespread availability of this technology in most hospitals, these advantages highlight its potential for future development as a tool for routine screening in clinical laboratories.}, }
@article {pmid42220281, year = {2026}, author = {de Bruijn, CMA and Oorthuys, AOJ and Zeevenhooven, J and Davids, M and Levels, JHM and Vlieger, AM and Herrema, H and Nieuwdorp, M and Benninga, MA}, title = {Feasibility and efficacy of fecal microbiota transplantation in adolescents with refractory irritable bowel syndrome: A randomized clinical pilot trial.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1002/jpn3.70459}, pmid = {42220281}, issn = {1536-4801}, support = {//Stichting Dioraphte/ ; //For Wis(h)dom Foundation/ ; 09150182010020/ZONMW_/ZonMw/Netherlands ; 015.017.050//Aspasia Premium/ ; }, abstract = {OBJECTIVES: To assess the feasibility and efficacy of fecal microbiota transplantation (FMT) in adolescents (16-21 years) with refractory irritable bowel syndrome (IBS).<br><br>METHODS: Randomized controlled pilot trial. Thirty-two patients were included and randomized to receive two allogeneic or autologous FMTs. At baseline and after 6 weeks, two allogeneic or autologous FMTs were administered via a nasoduodenal tube. Feasibility outcomes included dropout rate. Clinical efficacy was evaluated by the proportion of responders (&#x2265;50 points reduction in total score of the IBS severity-scoring-system) at 12, 24, and 48 weeks follow-up. Secondary outcomes included health-related quality of life (QoL), depression and anxiety scores, and school/work absenteeism.<br><br>RESULTS: One patient (3%) withdrew after randomization, due to lack of effect after the first FMT. Response rates 12 weeks after allogeneic and autologous FMTs were 40% and 38% (p&#x2009;=&#x2009;0.886). At 24 weeks, significantly more patients responded after allogeneic FMTs (60% vs. 25% autologous, p&#x2009;=&#x2009;0.048), without significant differences at 48 weeks (60% vs. 50%, p&#x2009;=&#x2009;0.576). Total QoL score was significantly better after allogeneic than autologous FMTs at 12, 24, and 48 weeks (p&#x2009;=&#x2009;0.028, p&#x2009;=&#x2009;0.007, p&#x2009;=&#x2009;0.011). In the allogeneic FMTs group, school/work absenteeism was 7% at 24 weeks (vs. 41% autologous, p&#x2009;=&#x2009;0.037).<br><br>CONCLUSIONS: Allogeneic FMTs were feasible and resulted in high response rates and better QoL compared to autologous FMTs. These results provide preliminary evidence for the use of allogeneic FMTs in adolescents with refractory IBS.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov identifier: NCT03074227 (https://clinicaltrials.gov/study/NCT03074227?id=NCT03074227&amp;rank=1).}, }
@article {pmid42220507, year = {2026}, author = {Wei, F and Nakahara, Y and Isobe, J and Igarashi, Y and Saito, H and Murakami, S and Kondo, T and Himuro, H and Kouro, T and Matsui, T and Wada, S and Tsunoda, T and Yoshimura, K and Sasada, T}, title = {Gut microbiome functional pathways outperform taxonomic profiles in predicting immune checkpoint inhibitor response in non-small cell lung cancer: an interpretable machine learning approach with SHAP.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1832317}, pmid = {42220507}, issn = {1664-3224}, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/drug therapy/microbiology/mortality/immunology ; *Immune Checkpoint Inhibitors/therapeutic use ; *Lung Neoplasms/drug therapy/microbiology/mortality/immunology ; *Gastrointestinal Microbiome/drug effects ; *Machine Learning ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Aged ; Treatment Outcome ; Predictive Learning Models ; Feces/microbiology ; }, abstract = {INTRODUCTION: Lung cancer remains the leading cause of cancer mortality worldwide, with non-small cell lung cancer (NSCLC) accounting for the majority of cases. Although immune checkpoint inhibitors (ICIs) have transformed the therapeutic landscape of NSCLC, clinical responses remain highly variable. Emerging evidence implicates the gut microbiome in modulating the outcomes of ICI treatment; however, most studies to date have focused on taxonomic composition rather than microbial functional capacity. This study aimed to systematically compare the predictive value of taxonomic versus functional gut microbiome features across multiple ICI-related outcomes.<br><br>METHODS: Pretreatment fecal samples from 77 Japanese patients with NSCLC receiving ICIs were profiled using 16S rRNA sequencing. Six feature sets, comprising three taxonomic (family, genus, and species) and three functional (KEGG Orthology, Enzyme Commission, and MetaCyc pathways), were assessed using permutational multivariate analysis of variance for their association with clinical outcomes, including treatment response, irAEs, progression-free survival, and overall survival. Machine-learning models were subsequently developed based on MetaCyc pathway features to predict treatment response, with nested internal and external validation to ensure robustness and SHapley Additive exPlanations (SHAP) analysis for model interpretability.<br><br>RESULTS: Of all the feature sets tested, the functional profiles derived from the MetaCyc pathways exhibited the strongest association with the RECIST-defined response. A four-pathway signature, comprising PWY-4984 (urea cycle), SALVADEHYPOX-PWY (adenosine nucleotide degradation), OANTIGEN-PWY (O-antigen biosynthesis in E. coli), and PWY-5088 (L-glutamate degradation VIII to propanoate), achieved robust predictive performance, substantially outperforming any single feature. SHAP analysis confirmed that the primary drivers of responder classification were pathways involved in nitrogen metabolism and short-chain fatty acid biosynthesis.<br><br>CONCLUSIONS: In this study, gut microbial functional profiles consistently outperformed taxonomic features in predicting ICI response in patients with NSCLC. These findings suggest that metabolic pathway-based signatures may capture functional microbiome-host interactions more effectively and hold greater promise as translatable, safer targets for precision intervention, particularly through metabolite-oriented strategies.}, }
@article {pmid42220515, year = {2026}, author = {Yang, Q and Liu, C and Wang, Q and An, J and Cai, Y}, title = {Infection-driven proliferative phase impairment in chronic wounds: a mechanistic framework for precision regenerative therapy.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1803023}, pmid = {42220515}, issn = {1664-3224}, mesh = {Humans ; *Wound Healing ; Animals ; Biofilms ; Chronic Disease ; *Wound Infection/therapy/microbiology/pathology/immunology ; Regeneration ; *Regenerative Medicine/methods ; Cell Proliferation ; *Wounds and Injuries/therapy ; }, abstract = {Chronic wounds represent a major clinical challenge characterized by persistent failure of tissue repair, a phenomenon that cannot be fully explained by infection and inflammation alone. Emerging evidence indicates that wound-associated microbial communities establish stable pathogenic ecosystems that specifically disrupt the proliferative phase of healing, the critical stage responsible for cellular expansion, angiogenesis, and extracellular matrix reconstruction. Here, we propose the conceptual framework of infection-driven proliferative phase impairment (IDPPI), which describes a pathological state in chronic wounds wherein sustained microbial pathogenic activities continuously compromise host regenerative programs. We synthesize current evidence showing that coordinated virulence factor deployment, biofilm persistence, and host immune-metabolic dysregulation converge to induce proliferative arrest. They do so through direct cellular injury, suppression of repair-related signaling pathways, and disruption of cell-cycle control. This integrated pathogenic cascade ultimately locks wounds into a state of low-efficiency or arrested regeneration. Building on this mechanistic framework, we outline a sequential, targeted therapeutic paradigm encompassing three interconnected levels: targeted suppression of virulence and biofilm functions, restoration of immune-metabolic homeostasis within the wound microenvironment, and spatiotemporally controlled promotion of regeneration using responsive biomaterials and cell-free regenerative strategies. Rather than prioritizing non-selective microbial eradication, this approach emphasizes functional disarmament of pathogenic ecosystems and reactivation of host proliferative capacity. Finally, we discuss how advances in spatial multi-omics, biomimetic human-relevant models, artificial intelligence, and real-time sensing technologies can enable dynamic assessment and adaptive intervention, supporting a paradigm shift in chronic wound management from static staging toward feedback-guided (closed-loop), mechanism-informed regenerative medicine. IDPPI is presented as an integrative framework that reorders causality by placing infection-driven disruption of proliferative repair execution as the proximal failure mode.}, }
@article {pmid42220946, year = {2026}, author = {Hassan, EH and Zaghloul, W and Ahmed, SM and Ghozi, AM and Abdelwahab, IA}, title = {Study of the gut microbiome profile in full-term infants with necrotizing enterocolits.}, journal = {World journal of clinical pediatrics}, volume = {15}, number = {2}, pages = {112551}, pmid = {42220946}, issn = {2219-2808}, abstract = {BACKGROUND: Necrotizing enterocolitis (NEC) is a severe gastrointestinal disease that primarily affects preterm. Recently, cases with similar clinical manifestations have been observed in full-term infants without Hirschsprung's disease. Dysbiosis suggested to have role in development of NEC.<br><br>AIM: To compare the gut microbiome composition between full term infants with NEC and healthy controls and to evaluate the impact of feeding sources on microbial diversity.<br><br>METHODS: Ten full term infants with NEC and six matched healthy breastfed control infants were enrolled in the study. Triplicate stool samples were collected from the enrolled infants. Genomic DNA was isolated and subjected to polymerase chain reaction analysis.<br><br>RESULTS: Bacteroidetes and Bacteroides were more abundant in control infants than in NEC cases, although the differences were statistically insignificant (P = 0.118 and P = 0.147, respectively), with large and moderate effect sizes. Bifidobacteria levels were significantly greater when a relaxed threshold (P &#x2264; 0.1) was used in both the control and NEC breastfed groups than in the NEC formula-fed group (P = 0.098). Additionally, alpha diversity was significantly reduced at the 0.1 level in NEC patients, especially among formula-fed infants (P = 0.094).<br><br>CONCLUSION: Full-term Egyptian infants with NEC exhibit reduced microbial diversity and alterations in bacterial abundance, supporting a potential link between dysbiosis and NEC. Feeding practices, particularly breastfeeding, appear to influence the gut microbiome profile regardless of NEC status. Although Bacteroidetes and Bacteroides did not reach statistical significance, their effect sizes suggest a need for further investigation into their roles in NEC pathogenesis in full-term infants.}, }
@article {pmid42220947, year = {2026}, author = {Sintusek, P and Klomkliew, P and Visedthorn, S and Phutthawong, K and Noicharoen, T and Soontornsook, A and Tran, DL and Payungporn, S}, title = {Distinct early gut microbiota patterns by delivery mode within 100 hours of birth.}, journal = {World journal of clinical pediatrics}, volume = {15}, number = {2}, pages = {117841}, pmid = {42220947}, issn = {2219-2808}, abstract = {BACKGROUND: Disruptions in the early-life gut microbiome have been reported to be associated with various health conditions. However, few studies have investigated the establishment of the gut microbiota in the immediate postnatal period.<br><br>AIM: To characterize the gut microbiota of neonates within the first 100 hours after birth.<br><br>METHODS: A total of 512 healthy neonates born at a tertiary hospital were enrolled in this study. Stool samples were collected between March 2024 and December 2024 and categorized by delivery mode and stool collection time. Microbiota diversity and composition were assessed using full-length 16S rDNA sequencing. Stool samples from 140 neonates with predominant breastfeeding were analyzed.<br><br>RESULTS: Of the 140 neonates, 70 (50%) were female, 66 (47.1%) were delivered by vaginal delivery (VD), 74 (52.9%) were delivered by cesarean section (CS), and 87 (62.1%) were firstborn. The time of stool collection ranged from 13.2 minutes to 109.82 hours. A significant difference in the time of stool collection was observed between CS and VD neonates (43.0 hours; 95%CI: 35.8-50.1 vs 32.4 hours; 95%CI: 27.8-36.9; P = 0.016). Gut microbiota analysis revealed that CS was associated with higher alpha diversity (Chao1 and Shannon indices; P < 0.001) and beta diversity (P < 0.001). A reduction in the gut microbiota diversity was observed 48 hours after birth (P < 0.001). Escherichia coli predominated in the VD samples. Bifidobacterium species, including Bifidobacterium longum, Bifidobacterium pseudocatenulatum, and Bifidobacterium bifidum, emerged significantly 48 hours after birth. CS neonates exhibited a higher relative abundance of skin- and environmental-associated taxa, including Staphylococcus, Streptococcus, and Pseudomonas, and markedly reduced colonization by Bifidobacterium species despite predominant breastfeeding.<br><br>CONCLUSION: Despite predominant breastfeeding, CS neonates showed reduced colonization by Bifidobacterium and a greater abundance of skin- and environment-associated taxa within the first 100 hours of life. These findings indicate that delivery mode can be a key determinant of early microbial assembly and highlight the need for targeted strategies to support the establishment of beneficial microbiota in CS-delivered infants.}, }
@article {pmid42220960, year = {2026}, author = {Al-Beltagi, M and Saeed, NK and El-Sawaf, Y and Bediwy, AS and Elbeltagi, R}, title = {Early-life gastrointestinal inflammation and the developing brain: Unravelling the pathways to long-term cognitive dysfunction.}, journal = {World journal of clinical pediatrics}, volume = {15}, number = {2}, pages = {117843}, pmid = {42220960}, issn = {2219-2808}, abstract = {The gut-brain axis (GBA) is a complex, bidirectional communication network critical to integrating central nervous system functions with gastrointestinal (GI) health. This review examines how disruptions to the GBA during the critical early-life developmental window - a period of rapid neurogenesis and microbial colonization - contribute to long-term neurocognitive and psychiatric vulnerabilities. Evidence from animal models demonstrates that early-life stress, antibiotics, and infection induce sustained neuro-inflammation and alter microglial function, leading to long-term behavioral and cognitive impairments in adulthood. Human studies corroborate these findings, revealing that severe early GI insults, such as necrotizing enterocolitis, confer a high risk (40%) of global neurodevelopmental impairment and specific attention deficits. Chronic inflammatory conditions similarly impact the central nervous system: A high burden of early severe enteric infection is an independent risk factor for diminished intelligence quotient (IQ) and executive function, while conditions like celiac disease and inflammatory bowel disease are associated with persistent deficits in attention, processing speed, memory, and executive function. These clinical outcomes are strongly linked to systemic inflammation [elevated interleukin-6, kynurenine-to-tryptophan (Kyn:Trp) ratio], micronutrient deficiencies (iron, vitamin B12, folate), and structural white matter changes in the brain. Furthermore, chronic GI disease imposes a significant psychiatric burden, with high comorbidity of anxiety and depression often mediating poor health-related quality of life, particularly in pediatric inflammatory bowel disease. The findings underscore the necessity for a shift in clinical practice: Chronic GI disease in early life must be recognized as a red flag for neurocognitive risk. We advocate for a multidisciplinary approach encompassing early neurodevelopmental follow-up for high-risk groups and routine screening for cognitive and emotional comorbidities. Future research must focus on long-term prospective cohorts, identifying precise mechanistic biomarkers (metabolomics, microbiome signatures), and conducting interventional trials targeting the GBA to mitigate these long-term functional consequences.}, }
@article {pmid42221001, year = {2026}, author = {Yuan, HX and Yin, ZT and Wang, LH and Ma, L and Liu, Y and Ju, YL and Yue, B}, title = {Age-stratified management of pediatric perianal abscesses: a proposed framework integrating the "Developmental Healing Axis".}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1789225}, pmid = {42221001}, issn = {2296-2360}, abstract = {Pediatric perianal abscesses represent a frequent yet underrecognized condition that poses diagnostic and therapeutic challenges due to tissue fragility and age-dependent healing dynamics. This review synthesizes current evidence on the epidemiology, pathophysiology, and management of pediatric perianal abscesses to provide a conceptual basis for clinical decision-making. Surgical interventions such as incision and drainage offer rapid symptom relief but may increase the risk of fistula formation, particularly in older children. In contrast, conservative strategies including antibiotic therapy and observation are often effective in infants and young children, reflecting their superior regenerative capacity. Age-related differences in immune response, microbiota composition, and glandular anatomy contribute to variations in disease progression and healing outcomes. By integrating data from recent studies and clinical guidelines, this review highlights the importance of individualized, age-specific management to optimize recovery, minimize recurrence, and prevent fistula development. Furthermore, it identifies gaps in current evidence and underscores the need for standardized treatment protocols and future research into predictive and microbiome-related factors influencing disease course.}, }
@article {pmid42221002, year = {2026}, author = {Kolluru, S and Liao, N and Haase, K and Foley, O and Cherkasskiy, L and Tauseef, A}, title = {Epidemiological trends in infant mortality related to necrotizing enterocolitis.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1825909}, pmid = {42221002}, issn = {2296-2360}, abstract = {INTRODUCTION: Necrotizing enterocolitis (NEC) is the leading cause of gastrointestinal morbidity and mortality among infants in the neonatal intensive care unit. With an overall prevalence of 1%, NEC is found in about 11% of infants with very low birthweights (VLBW) and 22% in infants of extremely low birthweights. A disease of prematurity, NEC has a multifactorial pathogenesis involving a combination of feeding regimens, gut microbiome, and birth weight. This study aims to elucidate the demographic factors associated with NEC- mediated infant mortality, with the goal of guiding future research into disease diagnosis and management.<br><br>METHODS: The CDC WONDER database was queried to collect data on mortality from NEC of infants <1 year old between 1999 and 2023. Data was stratified by sex, race/ethnicity, urbanization status, and census region. Crude mortality rate (CMR) was determined, and Joinpoint analysis was conducted to identify significant changes in mortality trends.<br><br>RESULTS: Overall NEC-related CMR decreased slightly between 1999 and 2023. CMR was higher in males than females throughout the study period, though mortality decreased slightly in the male population. When stratified by race, Non-Hispanic (NH) Black or African American patients had the highest overall CMR, followed by Hispanic or Latino and NH White patients, respectively. Regionally, the South had the highest CMR across the four studied census regions, though Southern mortality decreased over the study period. The West reported the lowest mortality from NEC and was the only census region with reported increase in CMR. In both urban and rural areas, mortality initially increased before a subsequent decrease throughout the study period.<br><br>DISCUSSION: This study builds on prior research efforts into mortality trends in NEC to highlight the disproportionate mortality burden associated with NEC faced by certain groups, including males, NH Black of African American patients, and patients from the Southern United States. Further research into the implications of different socioeconomic determinants of health and biomarker variability by demographic cohort can guide more effective diagnostic and management strategies.}, }
@article {pmid42221078, year = {2026}, author = {Gaspary, JFP and Lopes, LFD and Gaspary, FP and Lopes, EG and Edgar, AL and Camara, EP and Camara, AG}, title = {Stabilized adaptive states in microbiome-human integrated physiology: reframing health and chronic disease as symbiotic biological states.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1824897}, pmid = {42221078}, issn = {2296-858X}, abstract = {BACKGROUND: Modern medicine has achieved remarkable precision in identifying molecular mechanisms and developing targeted interventions. However, a persistent clinical paradox remains: many chronic conditions-including metabolic, autoimmune, neuropsychiatric, and oncological disorders-exhibit long-term stability, resistance to guideline-concordant treatment, and recurrent trajectories. Despite extensive mechanistic characterization, the organizational basis of this stability remains insufficiently explained.<br><br>CONCEPTUAL GAP: In acute contexts such as infection and environmental intoxication, organisms can remain internally coherent while temporarily prioritizing non-host biological demands. This state-based perspective, however, has rarely been extended to chronic disease. At the same time, microbiome research has demonstrated that human physiology operates within a multigenomic system, in which exogenous gene repertoires contribute substantial metabolic and signaling capacity. Epigenetic research further indicates that repeated ecological exposures can progressively stabilize adaptive biological states over time.<br><br>PROPOSED FRAMEWORK: We propose a conceptual framework in which health and disease are interpreted as stabilized adaptive states emerging from hierarchical signal integration within a multigenomic human system. In this model, chronic pathology reflects coherent but constrained regulatory configurations, rather than simple dysregulation or isolated system failure. Central to this interpretation is membrane-level decisional architecture, which governs signal routing, threshold modulation, and downstream transcriptional responses across tissues.<br><br>IMPLICATIONS: This framework reorganizes existing evidence into a systems-level interpretation of chronic disease stability, providing a basis for generating testable hypotheses regarding state transitions, responsiveness to perturbation, and restoration of physiological flexibility. Rather than introducing new therapeutic doctrines, the model aims to clarify how biological systems stabilize over time and how such stabilization may be investigated within existing experimental paradigms.<br><br>https://www.crd.york.ac.uk/PROSPERO/view/CRD420261295889, CRD420261295889; https://www.crd.york.ac.uk/PROSPERO/view/CRD420261295945, CRD420261295945.}, }
@article {pmid42221101, year = {2026}, author = {Chai, J and Gui, W and Zhang, J and He, W and Li, Q}, title = {Anti-diabetic retinopathy molecular mechanism of Dihuang Yinzi: insights from network pharmacology, metabolomics, and microbiome analysis.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1793936}, pmid = {42221101}, issn = {2296-858X}, abstract = {BACKGROUND: Diabetic retinopathy (DR) represents a major microvascular complication arising from diabetes mellitus, characterized by multifactorial pathogenesis encompassing genetic, metabolic, and microbial components. While Dihuang Yinzi (DHYZ), a traditional Chinese herbal formulation, exhibits therapeutic promise for DR management, the precise mechanistic underpinnings warrant further investigation. This research sought to elucidate critical target genes, metabolic compounds, and microbial species implicated in DHYZ's therapeutic action against DR.<br><br>METHODS: We constructed a murine DR model and procured biological specimens from 18 animals distributed across three experimental cohorts (control, disease model, and DHYZ-treated groups, n = 6 per group) for metabolomic profiling and microbiome characterization. Candidate genes emerged from overlapping DHYZ-associated targets with DR-linked genes. Through six computational algorithms within the cytoHubba plugin, we pinpointed pivotal target genes. Molecular docking studies examined binding affinity between essential target proteins and bioactive constituents. Metabolomic and microbiome datasets underwent differential expression analysis to enumerate candidate metabolites and microbial taxa, respectively. Finally, Spearman correlation-based integrative omics analysis distinguished critical metabolites and key microbial species.<br><br>RESULTS: We identified 110 candidate genes and five key target genes (STAT3, IL6, TNF, ESR1, and IL1B). Molecular docking analysis revealed strong binding interactions between ESR1 and six corresponding active compounds, with the highest binding affinity observed for naringenin. Additionally, metabolomic analysis identified 50 candidate metabolites, and microbiome analysis revealed 24 candidate microbes. Spearman correlation analysis further pinpointed 30 key metabolites and 18 key microbes.<br><br>CONCLUSION: This study elucidates five key target genes, 30 key metabolites, and 18 key microbes through which DHYZ may exert its therapeutic effects in DR. These findings provide valuable insights and a foundational reference for understanding the multi-omics mechanism of DHYZ in the treatment of diabetic retinopathy.}, }
@article {pmid42221399, year = {2026}, author = {Al Jnainati, M and Govindarajan, A and Tyagi, S and Iltaf, M and Al Jnainati, J and Ayoub, M and Shadab, HA}, title = {Harnessing Microbiome Therapy to Treat Metabolic Syndrome.}, journal = {AACE endocrinology and diabetes}, volume = {13}, number = {3}, pages = {463-472}, pmid = {42221399}, issn = {3050-9157}, abstract = {BACKGROUND/OBJECTIVE: Metabolic syndrome, a global health crisis marked by insulin resistance, obesity, and dyslipidemia, necessitates novel therapeutic approaches beyond conventional symptom management. Emerging research highlights the gut microbiome as a pivotal modulator of metabolic health, with dysbiosis-characterized by reduced microbial diversity and proinflammatory shifts-implicated in disease pathogenesis. This review synthesizes evidence from preclinical and clinical studies on microbiome-targeted therapies, including fecal microbiota transplantation, designer probiotics, and synbiotics, which aim to restore microbial balance and ameliorate metabolic dysfunction.<br><br>CASE REPORT: This review synthesizes evidence from preclinical and clinical studies on microbiome-targeted therapies, including fecal microbiota transplantation, designer probiotics, and synbiotics, which aim to restore microbial balance and ameliorate metabolic dysfunction.<br><br>DISCUSSION: Fecal microbiota transplantation transfers beneficial microbiota to enhance insulin sensitivity, while probiotics and synbiotics modulate inflammation, strengthen gut barrier integrity, and stimulate metabolic regulators like glucagon-like peptide-1 and short-chain fatty acids. Mechanistically, these therapies mitigate systemic inflammation, improve glucose/lipid homeostasis, and reduce intestinal permeability linked to endotoxin translocation. Clinical trials report improved glycemic control, lipid profiles, and weight management, underscoring their multitargeted potential. However, challenges such as donor variability, lack of standardized protocols, and long-term safety concerns hinder widespread application. Personalized approaches, informed by machine learning and microbial biomarkers, alongside innovations in Clustered Regularly Interspaced Short Palindromic Repeats-based engineering and encapsulation technologies, may address these limitations.<br><br>CONCLUSION: Despite promising outcomes, rigorous large-scale trials and interdisciplinary collaboration are essential to validate efficacy, optimize delivery, and ensure ethical compliance. In conclusion, microbiome therapies represent a paradigm shift in treating metabolic syndrome by targeting root causes, yet translating preclinical success into clinical practice demands further innovation and evidence-based standardization.}, }
@article {pmid42221477, year = {2025}, author = {Ceylan, A and Saçaklı, P and Özgenç Çınar, &#xd6; and Ramay, MS and Ahsan, U and Harijaona, JA and Bayraktaroğlu, AG and Manghebati, F and Calik, A}, title = {Effect of supplemental dietary phytogenic blends on growth performance, jejunal histomorphometry, and jejunal immunity of broiler chickens.}, journal = {Archives animal breeding}, volume = {68}, number = {1}, pages = {13-26}, pmid = {42221477}, issn = {2363-9822}, abstract = {This study evaluated the effects of two phytogenic blends on broiler performance, intestinal histomorphology, CD4[+] (cluster of differentiation) and CD8[+] T-cell numbers, and mRNA abundances of several cytokines in broilers. For this purpose, a total of 300 Ross 308 male broiler chicks that were 1 d old were randomly allocated to five experimental groups. The control group was fed a basal diet without any additives, and there were two phytogenic supplement groups (blend A, mainly comprising extracts of Thymus vulgaris and Filipendula ulmaria, and blend B, consisting of Ginkgo biloba and Silybum marianum) with two dosage regimens each (100 and 200 mg kg[-1] (denoted A100 and A200) and 100 and 300 mg kg[-1] (B100 and B300) of the diet, respectively). Over the total growing period, body weight gain and feed intake were unchanged among the groups, although phytogenic blend B showed a dose-dependent improvement in feed conversion ratio. Both phytogenic blends did not affect carcass characteristics. Jejunal morphology (villus height, crypt depth, and their ratio) was modified depending on both the composition and the dosage levels of the selected phytogenics. Also, both phytogenic blends linearly increased the CD4[+] and CD8[+] T-cell numbers in the jejunum. Moreover, no major treatment effects were observed on mRNA abundances of cytokines (IL-1 β , IL-6, and TNF α). However, across the two phytogenic additives employed, a positive linear dose response in IL-1 β abundance was noted on day 21 in broilers fed phytogenic blend B. Overall, dietary phytogenic blend B improved the intestinal health and growth performance of chickens compared to blend A. Further studies are suggested to elucidate the effects of the tested phytogenic blends on gut microbiome and on oxidative stress in broiler chickens.}, }
@article {pmid42221478, year = {2026}, author = {Agranyoni, O and Yolken, RH and Johnson, SB and Volk, H and Sabunciyan, S}, title = {Comparing saliva collection and DNA extraction methods for saliva-based microbiome profiling.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1809075}, pmid = {42221478}, issn = {1664-302X}, abstract = {AIMS: Mounting preclinical evidence demonstrates the importance of the human microbiome in health and disease. Saliva presents a particularly appealing medium for microbiome research due to its non-invasive collection and the availability of extensive biobanked samples across various conditions. However, methodological challenges remain- particularly regarding sample storage and the variability introduced by different nucleic acid extraction kits, which can exhibit selective affinities for certain bacterial taxa. In this study, we systematically compared multiple saliva collection and DNA extraction methods to optimize protocols for 16S rRNA-based microbiome profiling. Our approach incorporated rigorous quality control measures, including the analysis of water controls, differential abundance testing, and correlation analyses across groups, to identify the most reliable and reproducible methods for salivary microbiome characterization.<br><br>METHODS AND RESULTS: We compared four commercially available kits for at-home saliva collection to determine their effectiveness at preserving the salivary microbiome following 1&#x202f;week of storage at room temperature (RT). We also compared three commercially available DNA extraction kits marketed for salivary microbiome characterization. We discovered that the DNA extraction kit used significantly impacted the microbiome composition. One week of incubation in the preservative solution shifted the bacterial composition of the saliva. Additionally, we demonstrated that contaminants in the environment and kits reagents may be increased during the incubation period, posing a significant challenge.<br><br>CONCLUSION: Our work demonstrates the feasibility of, and provides a framework for, microbiome characterization in saliva that applies to clinical and population-based studies. Our findings indicate that saliva microbiome studies using different extraction kits may introduce systematic biases, which should be accounted for when comparing results across studies. Using the same nucleic acid collection and extraction kits in various experiments is essential for reproducibility due to their different affinity to specific bacteria and contamination rates.}, }
@article {pmid42221488, year = {2026}, author = {Kang, Z and Zhang, S and Jiao, Z and Wang, X and Wei, Y and Wang, R and Chang, Y and Wang, N}, title = {Genomic and microecological insights into the biocontrol mechanisms of Bacillus velezensis BER1 against rice sheath blight.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1836902}, pmid = {42221488}, issn = {1664-302X}, abstract = {Rice sheath blight is a major fungal disease threatening global rice production, causing substantial yield losses and lacking effective resistant cultivars. In this study, we systematically evaluated the biocontrol efficacy of Bacillus velezensis BER1 against rice sheath blight and elucidated its underlying mechanisms from three complementary perspectives: strain genomics, plant immune responses, and the phyllosphere microbiome. Genome analysis revealed that BER1 harbors 22 secondary metabolite biosynthetic gene clusters, including those encoding natural products such as fengycin and bacillaene with broad-spectrum antifungal and antibacterial activities. Application of BER1 reduced disease severity to 35.4%, outperforming conventional chemical treatment, and significantly induced the expression of rice immune-related genes (e.g., NH1 and PR1a), accompanied by increased activities of defense enzymes such as POD and PAL. 16S rRNA amplicon sequencing further showed that BER1 markedly increased the relative abundance of Bacillus in the phyllosphere while suppressing potential pathogenic taxa, and enriched functional pathways associated with secondary metabolite biosynthesis, particularly polyketide-related pathways. Compared with chemical intervention, BER1 maintained microbial community stability through ecological niche competition and sustained metabolic activity, thereby reducing pathogen risk. Collectively, these findings provide quantitative evidence supporting BER1 as a promising green and sustainable biocontrol agent against rice sheath blight and highlight the potential of microecology-based strategies for plant disease management.}, }
@article {pmid42221489, year = {2026}, author = {Zhu, W and Guo, L}, title = {Advances in vulvovaginal candidiasis research: a comprehensive review from epidemiology, diagnosis, treatment to resistance mechanisms.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1811011}, pmid = {42221489}, issn = {1664-302X}, abstract = {Vulvovaginal candidiasis (VVC), predominantly caused by Candida albicans, is one of the most common vaginal infections in women of reproductive age. Its clinical management has become increasingly complex due to the rising prevalence of non-albicans Candida infections, escalating azole resistance, and the challenge of biofilm formation. This review systematically summarizes recent advances in VVC research, with a focus on evolving epidemiology, innovations in diagnostics, current and emerging therapies, and an in-depth analysis of resistance mechanisms. Key molecular pathways underpinning antifungal resistance-including biofilm development, efflux pump overexpression, target-site gene mutations, and alterations in transcriptional regulators-are examined. The findings of this review support several actionable strategies for future practice. First, routine use of molecular diagnostics (PCR, MALDI-TOF MS) is essential for species identification and resistance detection, enabling a shift from empirical to precision-based therapy. Second, antifungal susceptibility testing should be interpreted with attention to vaginal pH conditions, and non-azole alternatives (boric acid, nystatin, ibrexafungerp, oteseconazole) should be prioritized when azole resistance is confirmed or suspected. Third, emerging approaches-including biofilm-disrupting agents, probiotic microbiome modulation, and nanotechnology-enhanced drug delivery-offer promising adjunctive and preventive strategies, particularly for recurrent VVC. By integrating these contemporary findings, this review provides a translational framework to optimize diagnosis, guide therapeutic decision-making, and inform future research priorities in VVC management. Notably, several novel agents-including ibrexafungerp and oteseconazole-have already received FDA approval and are entering clinical practice, with multiple ongoing trials evaluating boric acid, probiotics, and novel oral antifungals, underscoring the accelerating translation of mechanism-informed therapies into patient care.}, }
@article {pmid42221491, year = {2026}, author = {Sufi, F}, title = {Editorial: Generative AI and large language models in microbial evolution, resistance mechanisms, and antimicrobial drug discovery.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1848209}, doi = {10.3389/fmicb.2026.1848209}, pmid = {42221491}, issn = {1664-302X}, }
@article {pmid42221502, year = {2026}, author = {Xia, Q and Xin, J and Mu, Y and Li, M and Yao, J and Xiao, X and Wang, X and Gang, X}, title = {Therapeutic potential of natural compounds from medicinal and food homology substances targeting gut microbiota in lipid metabolism disorders.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1809114}, pmid = {42221502}, issn = {1664-302X}, abstract = {Dyslipidemia contributes to chronic diseases such as non-alcoholic fatty liver disease (NAFLD), type 2 diabetes (T2DM), and obesity. Emerging evidence highlights gut dysbiosis as a key driver of abnormal lipid metabolism. This review examines how natural bioactive compounds from medicinal and food homology (MFH) substances regulate lipid metabolism by modulating the gut microbiome. It summarizes evidence on the modification of the microbiota-lipid metabolism axis by natural compounds from MFH substances and discusses the limitations of applications and their promise for preventing and treating metabolic diseases. By capitalizing on these microbiota-mediated effects, natural compounds may serve as a beneficial natural resource for adjusting lipid metabolism.}, }
@article {pmid42221503, year = {2026}, author = {Alia, K and Khan, H and Muzaffar, H and Perveen, N and Alrashedi, S and Al Dhaheri, Y and Waheed, Y and Alam, MT and Naseem, M and Muhammad, K}, title = {Gut dysbiosis and microbial metabolites in atopic dermatitis: implications for immune regulation along gut-skin axis.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1829876}, pmid = {42221503}, issn = {1664-302X}, abstract = {Atopic dermatitis (AD) is a multifactorial skin disorder characterized by immune dysregulation, impaired epidermal barrier, and strong microbial imbalance. Although genetic susceptibility and environmental triggers are established AD drivers, growing evidence highlights the gut skin axis as an important but underexplored AD pathogenesis factor. Gut microbiota dysbiosis, loss of short-chain fatty acid (SCFA)-producing bacteria, and altered metabolite profiles, such as tryptophan derivatives and secondary bile acids, have been linked to systemic immune imbalance and skin inflammation. However, the precise mechanism by which gut microbial alterations influence cutaneous immunity remains unclear. This review synthesizes recent advances from clinical and experimental studies to delineate how the gut microbiota and their metabolites shape the immune response, regulate the integrity of the epithelial barrier, and modulate AD severity. By integrating emerging insights into early-life microbial colonization, metabolite-mediated immune programming, and therapeutic interventions, including prebiotics, probiotics, and microbial-derived metabolites, the current gaps and the translational potential of targeting the gut- skin axis. The knowledge consolidated here advances our understanding of AD beyond skin-focused perspectives and highlights new avenues for microbiome-based preventive and therapeutic strategies.}, }
@article {pmid42221532, year = {2026}, author = {Mishra, AK and Mishra, A and Vikal, A and Singh, H and Y Thajudeen, K and Khan, G and Ahmed, MM}, title = {Fecal microbiota transplant and its usefulness in hepatic disorders: a systematic review.}, journal = {Therapeutic advances in gastroenterology}, volume = {19}, number = {}, pages = {17562848261452504}, pmid = {42221532}, issn = {1756-283X}, abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is an emerging therapeutic approach aimed at restoring gut microbial balance through the transfer of stool from healthy donors. It has gained significant attention for its role in managing gut dysbiosis-associated disorders, particularly hepatic diseases.<br><br>OBJECTIVE: This systematic review evaluated the therapeutic efficacy and clinical potential of FMT in the management of liver-related conditions, including recurrent Clostridium difficile infection (CDI), non-alcoholic fatty liver disease, liver cirrhosis, and hepatic encephalopathy.<br><br>DESIGN: A systematic review of existing literature was conducted to assess the clinical outcomes, mechanisms, and challenges associated with FMT in hepatic disorders.<br><br>DATA SOURCES AND METHODS: Relevant studies were identified from peer-reviewed scientific databases, focusing on clinical trials, observational studies, and experimental research investigating the role of FMT in gut dysbiosis and liver disease. Data were analyzed to evaluate efficacy, underlying mechanisms, and safety considerations.<br><br>RESULTS: FMT demonstrated high efficacy in recurrent CDI, with cure rates exceeding 80%-90%. In hepatic disorders, FMT was associated with improved microbial diversity, enhanced gut barrier integrity, and reduced systemic inflammation, contributing to better liver function and clinical outcomes. However, variability in donor selection, potential safety risks, and regulatory limitations remain significant challenges.<br><br>CONCLUSION: FMT represents a promising therapeutic strategy in hepatology, underscoring the critical role of the gut-liver axis. Advances such as synthetic microbiota and personalized microbiome-based therapies may further optimize its safety and efficacy, paving the way for innovative, microbiome-centered interventions in liver disease management.}, }
@article {pmid42221580, year = {2026}, author = {Zhang, W and Wu, S and Shen, L and Peng, P and Li, R and Zheng, Q and Jia, X and Liu, Q and Liu, Y}, title = {Identification and evaluation of gut microbiome as non-invasive biomarkers for early lung adenocarcinoma from a multi-center study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1813261}, pmid = {42221580}, issn = {2235-2988}, mesh = {Aged ; Female ; Humans ; Male ; Middle Aged ; *Adenocarcinoma of Lung/diagnosis/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Biomarkers ; China ; *Gastrointestinal Microbiome ; *Lung Neoplasms/diagnosis/microbiology ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; }, abstract = {OBJECTIVE: This study aims to characterize the GM in LUAD patients and develop and validate a GM-based diagnostic model for LUAD.<br><br>METHODS: In this prospective, randomized, multi-center study, the GM was characterized, and an LUAD classifier was developed using a training cohort of 175 early-stage LUAD patients and 107 healthy controls. The model was further validated in a test cohort, two independent external cohorts from Jiangsu and Hainan, and an advanced LUAD cohort. Additional ML models were also developed and compared to assess their predictive performance.<br><br>RESULTS: LUAD patients exhibited reduced microbial diversity and significantly altered microbial composition compared to healthy controls. The phylum Verrucomicrobia and 13 genera, including Enterococcus and Akkermansia, were more abundant in the LUAD group, while 5 phyla, such as Fusobacteria and Cyanobacteria, and 17 genera, including Lactobacillus and Weissella, were enriched in the control group. Using random forest (RF), eight operational taxonomic units were identified as the optimal subset, achieving an area under the curve (AUC) of 0.998 in the training cohort and maintaining high accuracy in the test cohort (AUC&#xa0;=&#xa0;96.9%). The model also demonstrated robust performance in two independent cohorts from Jiangsu (AUC&#xa0;=&#xa0;97.6%) and Hainan (AUC&#xa0;=&#xa0;82.9%), with strong diagnostic potential for advanced LUAD. Among five common models, the RF model exhibited the highest diagnostic accuracy.<br><br>CONCLUSIONS: This study provides a comprehensive characterization of the gut microbiome in LUAD and develops a diagnostic model based on microbial biomarkers, which is validated across regionally diverse cohorts, highlighting its potential as a reliable and non-invasive screening tool for LUAD.}, }
@article {pmid42221589, year = {2026}, author = {Song, D and Gao, H and Wang, T and Wei, Q and Liu, A and Ren, J}, title = {Gut microbiota dysbiosis-induced chronic inflammation as a driver of atherosclerosis: cellular crosstalk and host-microbe interactions.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1789194}, pmid = {42221589}, issn = {2235-2988}, mesh = {*Dysbiosis/complications/microbiology ; Humans ; *Atherosclerosis/etiology/microbiology ; *Gastrointestinal Microbiome ; *Inflammation/microbiology ; Animals ; *Host Microbial Interactions ; Fecal Microbiota Transplantation ; Methylamines/metabolism ; Intestinal Barrier Function ; Fatty Acids, Volatile/metabolism ; }, abstract = {Gut microbiota dysbiosis is increasingly recognized as an upstream contributor to chronic low-grade inflammation and atherosclerosis (AS). Disruption of microbial homeostasis may impair intestinal barrier integrity, increase exposure to pro-inflammatory microbial products and metabolites, and reduce protective metabolites such as short-chain fatty acids (SCFAs), thereby activating innate immune signaling and sustaining vascular inflammation. Current evidence indicates that gut dysbiosis promotes atherosclerosis mainly through three interconnected processes: metabolite imbalance, barrier dysfunction with microbial translocation, and systemic immune reprogramming. Clinical studies have linked gut-derived biomarkers, particularly trimethylamine N-oxide (TMAO) and lipopolysaccharide (LPS)-related signals, to atherosclerotic burden and adverse cardiovascular outcomes, while experimental studies using fecal microbiota transplantation, probiotics, antibiotics, and gene-deficient models support a contributory role of the gut-immune-vascular axis. Emerging interventions, including dietary modulation, pharmacological repurposing, and microbiome-targeted therapies, may attenuate gut-derived chronic inflammation and offer new strategies for AS prevention and treatment. However, heterogeneity across studies and the limited causal evidence in humans warrant cautious interpretation. Overall, gut dysbiosis-driven chronic inflammation represents a biologically meaningful and potentially modifiable pathway in atherosclerosis.}, }
@article {pmid41873129, year = {2026}, author = {Alcheva, A and Jensen, JA and Hatsukami, DK and Stepanov, I}, title = {Changes in the Oral Microbiota after Switching from Smoking to Exclusive e-Cigarette Use in an 8-Week Product-Switching Trial.}, journal = {Cancer prevention research (Philadelphia, Pa.)}, volume = {19}, number = {6}, pages = {369-379}, doi = {10.1158/1940-6207.CAPR-25-0244}, pmid = {41873129}, issn = {1940-6215}, support = {U19 CA157345/CA/NCI NIH HHS/United States ; U01 DA045523/DA/NIDA NIH HHS/United States ; //Masonic Cancer Center, University of Minnesota (MCC)/ ; P30 CA-077598//National Cancer Institute (NCI)/ ; }, mesh = {Humans ; Female ; *Microbiota/genetics ; Male ; *Mouth/microbiology ; Adult ; *Electronic Nicotine Delivery Systems/statistics &amp; numerical data ; Cross-Sectional Studies ; *Vaping/adverse effects ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; *Smoking/adverse effects ; Bacteria/isolation &amp; purification/genetics/classification ; }, abstract = {UNLABELLED: Cross-sectional data indicate that the oral microbiota differs between people who smoke or use e-cigarettes, suggesting potential as a research tool in product-switching trials, as a biomarker of product use status and/or long-term health effects. However, its sensitivity to short-term product switching remains unclear. We examined a subset of participants in an 8-week product-switching study who were asked to switch from smoking to exclusive e-cigarette use and had oral cells collected (n = 58). Using available biomarker data, we determined that 12 achieved complete switching and 46 engaged in dual use. A subgroup of participants in the same study who continued exclusive smoking (n = 20) was included for reference. Oral microbiota profiles were characterized at baseline and at the end of the study (week 8) using 16S rRNA gene sequencing targeting the V3 to V4 hypervariable regions on an Illumina MiSeq platform. Participants who switched to exclusive e-cigarette use had a significant decrease in alpha diversity (Shannon index) at week 8 compared with baseline smoking (P = 0.02), and their beta diversity at week 8 differed from those who engaged in dual use or continued exclusive smoking (r2 = 0.04; P = 0.014). They also showed increased abundances of proinflammatory genera (Streptococcus, Veillonella, Haemophilus, Fusobacterium), whereas dual users had decreased abundances of several commensal genera, including Lactobacillus, Limosilactobacillus, and Neisseria. Our findings indicate that the oral microbiota may serve as a sensitive tool for detecting and interpreting changes in tobacco-related exposures, and potentially for monitoring product use compliance in clinical studies of product switching.<br><br>PREVENTION RELEVANCE: By analyzing the oral microbiome, individuals' tobacco use status could be assessed, and the impact of interventions, such as switching to e-cigarettes, on reducing tobacco exposure could be evaluated. This information can inform tobacco cessation programs, risk stratification, and personalized prevention strategies for individuals at higher risk for tobacco-related cancer.}, }
@article {pmid41875284, year = {2026}, author = {Neuman, H and Shitrit, A and Turjeman, S and Koren, O}, title = {From Womb to Weaning: Microbial Signals That Shape the Developing Brain.}, journal = {Developmental neuroscience}, volume = {}, number = {}, pages = {1-13}, doi = {10.1159/000551712}, pmid = {41875284}, issn = {1421-9859}, abstract = {BACKGROUND: The gut microbiota plays a vital role in shaping brain development through complex bidirectional communication within the microbiota-gut-brain axis. Emerging evidence highlights neural, immune, endocrine, metabolic, and epigenetic pathways by which gut microbes influence neurodevelopmental processes.<br><br>SUMMARY: This review synthesizes current knowledge on the temporal dynamics of gut colonization and brain maturation. Drawing on mechanistic insights from animal models, we emphasize the central role of the maternal microbiota and particularly, microbially derived metabolites that cross the feto-placental barrier and shape fetal brain development. We also discuss molecular and cellular targets of microbial influence, implications for neurodevelopmental disorders, and potential therapeutic strategies.<br><br>KEY MESSAGES: Understanding these interactions opens new avenues for early-life interventions aimed at optimizing neurodevelopments and preventing neuropsychiatric conditions.}, }
@article {pmid42212655, year = {2026}, author = {Torres-Morales, J and Giacomini, JJ and Chen, T and Voorhis, A and Kauffman, KM and Dewhirst, FE and Borisy, GG and Mark Welch, JL}, title = {Pangenomes of the human oral microbiome.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0026126}, doi = {10.1128/mra.00261-26}, pmid = {42212655}, issn = {2576-098X}, abstract = {We announce the release of 579 pangenomes derived from 8,115 genomes curated by the Human Oral Microbiome Database, capturing shared and variable gene content across oral microbial taxa. This openly accessible resource supports both online and offline exploration, enabling systematic studies of microbial function, evolution, and community structure.}, }
@article {pmid42212684, year = {2026}, author = {Liu, J and Zhao, P and Jiang, D and Li, S and Jin, C and Xu, D and Wang, X and Chen, Y and Tang, B and Qu, X}, title = {Decoding the microbiome: artificial intelligence-targeted gut microenvironment breakthroughs in personalized cancer therapy.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2672791}, doi = {10.1080/19490976.2026.2672791}, pmid = {42212684}, issn = {1949-0984}, mesh = {Humans ; *Precision Medicine/methods ; *Artificial Intelligence ; *Gastrointestinal Microbiome ; *Tumor Microenvironment ; *Colorectal Neoplasms/microbiology/therapy/diagnosis ; Multiomics ; Animals ; }, abstract = {The gut microbiome functions as a key regulator of tumorigenesis and progression, thereby modulating tumor development and treatment outcomes (including chemoresistance, immunotherapy efficacy, and adverse effects) through its influence on the immune microenvironment and metabolite-mediated signaling pathways. Recent advances in multiomics technologies (metagenomics, metabolomics, and transcriptomics) have generated large-scale, comprehensive, and heterogeneous datasets whose complexity exceeds the capabilities of manual analysis, thus necessitating the implementation of artificial intelligence-based approaches. This review systematically examines the crucial role of the gut microbiome in tumorigenesis, with particular emphasis on colorectal cancer (CRC), specifically addressing its utility as a diagnostic and prognostic biomarker. Furthermore, building upon existing applications of artificial intelligence (AI) in microbiome research and cancer diagnosis and treatment, this review presents an AI-driven precision intervention framework and delineates personalized treatment strategies.}, }
@article {pmid42212695, year = {2026}, author = {Hughes, SM and Frenkel, LM}, title = {The HIV Reservoir in the Female Reproductive Tract.}, journal = {American journal of reproductive immunology (New York, N.Y. : 1989)}, volume = {95}, number = {6}, pages = {e70262}, doi = {10.1111/aji.70262}, pmid = {42212695}, issn = {1600-0897}, mesh = {Female ; Humans ; *HIV Infections/virology/drug therapy/immunology ; *Genitalia, Female/virology ; *HIV-1/physiology ; Animals ; }, abstract = {Antiretrovirals can prevent the spread of replicating HIV within the host and decrease the virus in plasma to levels undetectable in clinical assays, and in genital secretions to untransmissible levels. However, during effective treatment with antiretrovirals, infectious HIV persists lifelong because the virus integrates into the host's DNA, and these proviruses are replicated within the host's DNA when the infected host cells proliferate. Cells with infectious virus that persist during antiretroviral therapy (ART), the HIV reservoir, are spread throughout the body, including the female reproductive tract (FRT). HIV-infected cells have been detected at multiple sites in the FRT, and the virus is shed in FRT secretions; however, less is known about the FRT reservoir than about other sites in the body. The FRT consists of the ovaries, fallopian tubes, uterus, cervix, and vagina. This collection of diverse tissues has several unique features: squamous and columnar epithelia, hormone production and regulation, cyclical changes, a unique microbiome, and exposure to sexual activity. Given these unique features, it cannot be assumed that infected cells located in the FRT will respond to curative therapeutic interventions in the same manner as infected cells elsewhere in the body. Thus, it is imperative to increase our understanding of the features of the HIV reservoir in the FRT. Here, we review data on the viral reservoir and shedding in the FRT and relate it to strategies to cure HIV infection.}, }
@article {pmid42212696, year = {2026}, author = {Zhao, F and An, R and Yu, S and Ma, Y and Liu, W and Sheng, C and Xie, X and Zhang, J}, title = {Fusobacterium nucleatum in cancer: Interactions with microbiota, tumour colonisation and cancer progression.}, journal = {Clinical and translational medicine}, volume = {16}, number = {6}, pages = {e70704}, doi = {10.1002/ctm2.70704}, pmid = {42212696}, issn = {2001-1326}, support = {82172362//National Natural Science Foundation of China/ ; 81800023//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Neoplasms/microbiology ; *Fusobacterium nucleatum/pathogenicity ; *Microbiota/physiology ; Disease Progression ; Tumor Microenvironment ; }, abstract = {BACKGROUND: Growing evidence from multi-cancer cohort studies has positioned the oral pathobiont Fusobacterium nucleatum (F. nucleatum) as an emerging microbial contributor to cancer progression. Increased intratumoral abundance of F. nucleatum has been reported in colorectal, breast, esophageal, pancreatic, oral, and gastric cancers and is frequently associated with adverse clinicopathological features, treatment resistance, metastatic behavior, and poor prognosis. Advances in microbiome profiling, spatial analysis, and single-cell technologies have begun to reveal how F. nucleatum colonizes tumors and interacts with host cells and tumor-associated microbial communities.<br><br>MAIN BODY: This review summarizes current evidence regarding the tumor-associated activities of F. nucleatum, with emphasis on its routes of tumor entry, spatiotemporal colonization patterns, adhesion- and glycan-dependent tropism, polymicrobial niche formation, and crosstalk with cancer cells and immune components. We discuss how F. nucleatum promotes oncogenic signaling, inflammatory amplification, genomic and epigenetic reprogramming, epithelial-mesenchymal transition, metastatic dissemination, immune evasion, and therapy adaptation. Particular attention is given to its context-dependent effects on chemotherapy, radiotherapy, and immunotherapy responses, as well as emerging strategies aimed at detecting or selectively targeting intratumoral F. nucleatum.<br><br>CONCLUSION: F. nucleatum represents both a biomarker-associated organism and a potentially modifiable component of the tumor microenvironment. Defining its strain-level heterogeneity, spatial ecology, and therapy-specific functions will be essential for translating microbiome-guided precision oncology from mechanistic insight into clinical application.<br><br>KEY POINTS: F. nucleatum colonises tumours through mucosal translocation, adjacent-tissue migration and hematogenous dissemination. It promotes cancer progression via adhesion, inflammation, immune evasion, epigenetic remodelling and metastasis. Its effects on therapy response are tumour-context dependent. Microbiome-guided targeting may enable precision oncology.}, }
@article {pmid42212786, year = {2026}, author = {Zielińska, K and Pantiukh, K and Łabaj, PP and Kosciolek, T and Org, E}, title = {A large-scale comparative metagenomic analysis of short-read sequencing platforms indicates high taxonomic concordance and functional analysis challenge.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0171425}, doi = {10.1128/msystems.01714-25}, pmid = {42212786}, issn = {2379-5077}, abstract = {UNLABELLED: Driven by the increasing scale of microbiome studies and the rise of large, continuously expanding population cohorts, the volume of sequencing data is growing rapidly. As such, ensuring the comparability of data generated across different sequencing platforms has become a pressing concern in efforts to uncover robust links between the microbiome and human health. In this study, we conducted a comprehensive comparison of taxonomic and functional profiles from 1,351 matched human gut microbiome sample pairs, sequenced using both the MGISEQ-2000 (MGI) and NovaSeq 6000 (Illumina NovaSeq) platforms. Taxonomic profiles showed high concordance within and between platforms: 96.44% ± 5.96% of species were shared between MGI-MGI pairs, and 92.07% ± 5.20% were shared between MGI and NovaSeq pairs. The proportion of platform-specific species was low, at 3.42% for MGI-MGI comparisons and 5.89% for MGI-NovaSeq comparisons. No significant differences in Shannon diversity were observed for either within-platform or between-platform comparisons. However, functional profiles revealed notable discrepancies between platforms, which were attributed to differences in pre-sequencing protocols.<br><br>IMPORTANCE: Our findings demonstrate robust taxonomic comparability between MGI and NovaSeq platforms, while revealing systematic functional differences that should be carefully considered in cross-platform metagenomic studies.}, }
@article {pmid42212790, year = {2026}, author = {Zielińska, K and Pantiukh, K and Org, E and Łabaj, PP and Kosciolek, T}, title = {Moving from a taxonomic to a functional perspective in global microbiome analysis requires optimizing multiplexing ratios.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0014426}, doi = {10.1128/msystems.00144-26}, pmid = {42212790}, issn = {2379-5077}, abstract = {Next-generation sequencing has revolutionized microbiome research, yet the transition from taxonomic to functional profiling remains a major technical challenge. While marker gene sequencing provides a widely accessible ecological view, it often lacks the resolution for actionable insights. This perspective argues that shifting to whole metagenomic sequencing is essential for mapping functional potential, such as antimicrobial resistance, and metabolic pathways. However, we identify a critical bottleneck: excessive multiplexing. High multiplexing ratios reduce the number of unique molecules per sample, leading to high duplication rates and the stochastic dropout of low-abundance genes. We demonstrate that functional profiles are far more sensitive to these library complexity issues than taxonomic ones. We recommend prioritizing total sequencing depth and reducing multiplexing to ensure sufficient unique coverage. Additionally, adopting long-read or hybrid architectures is vital for providing the genomic context necessary for strain-level resolution. These optimizations are prerequisites for robust global microbiome synthesis and translational science.}, }
@article {pmid42212815, year = {2026}, author = {Jiang, H and Zhang, H and Ding, X and Wang, Y and Wu, C and Peng, A and Cao, D and Wang, J and Zeng, W and Zhu, F}, title = {Association of gut microbiota and inflammatory markers with enteral nutrition intolerance in patients with early-stage moderate-to-severe intracerebral hemorrhage.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0313825}, doi = {10.1128/spectrum.03138-25}, pmid = {42212815}, issn = {2165-0497}, abstract = {UNLABELLED: Enteral nutrition intolerance (ENI) is a common and challenging complication in patients with moderate-to-severe intracerebral hemorrhage (msICH). Emerging evidence suggests that gut microbiota is vital for host immune regulation and nutrient metabolism. However, the relationship between intestinal microbial alterations, inflammatory responses, and ENI in patients with early-stage msICH (emsICH) remains poorly understood. Therefore, this study aimed to explore these associations. A total of 100 patients with emsICH were enrolled in this study, including 50 with ENI and 50 without ENI (NENI). The gut microbiota composition was assessed using 16S ribosomal RNA gene sequencing, and the relationships between microbial profiles, systemic inflammatory indicators, and ENI status were systematically analyzed. Patients with ENI exhibited significantly reduced alpha diversity and distinct microbial structure when compared to those with NENI. Linear discriminant analysis effect size identified 19 differentially abundant taxa, with pathogenic genera, including Enterococcus and Finegoldia, enriched in patients with ENI. However, beneficial short-chain fatty acid-producing genera, such as Subdoligranulum and Faecalibacterium, were enriched in patients with NENI. A six-genus biomarker panel demonstrated a strong predictive power for ENI (area under the curve = 0.812). Functional phenotype analysis revealed an increased abundance of Gram-negative and facultative anaerobic bacteria in patients with ENI. Moreover, ENI-associated genera were positively correlated with blood inflammatory indicators, whereas NENI-associated taxa exhibited negative correlations. The analysis of the Kyoto Encyclopedia of Genes and Genomes pathways suggested that several essential physiological pathways in ENI were disturbed, with upregulation of inflammation-related signaling pathways (e.g., Jak-STAT and MAPK) and downregulation of pathways involved in metabolism (particularly in energy metabolism). Gut microbiota dysbiosis in patients with emsICH is strongly associated with ENI and systemic inflammation. Specific microbial signatures may serve as non-invasive biomarkers for ENI risk assessment. These findings shed light on gut microbiota-associated inflammation and the ENI axis and offer a theoretical basis for microbiota-targeted and nutritional interventions in neurocritical care.<br><br>IMPORTANCE: Enteral nutrition intolerance (ENI) is a frequent and serious complication in patients with moderate-to-severe intracerebral hemorrhage (ICH). Our study demonstrates that ENI is strongly associated with gut microbiota imbalance, characterized by an overrepresentation of inflammation-promoting bacteria and a loss of beneficial short-chain fatty acid-producing taxa. This microbial shift was closely linked to heightened systemic inflammation, providing new insights into the gut-inflammation-ENI axis in neurocritical illness. By identifying specific bacterial signatures, our findings suggest that stool-based microbial assessment may serve as a noninvasive tool for early risk prediction and highlight the potential of microbiota-targeted strategies to improve nutritional management and outcomes in patients with ICH.}, }
@article {pmid42212825, year = {2026}, author = {Wang, X and Wang, X and Xu, S and Zheng, J and Pang, Y and Cheng, T and Han, R and Zhao, W and Huang, Z}, title = {Lactobacillus shapes LPS-reservoir modules within the gut microbiota to mitigate atrial fibrillation.}, journal = {mBio}, volume = {}, number = {}, pages = {e0074126}, doi = {10.1128/mbio.00741-26}, pmid = {42212825}, issn = {2150-7511}, abstract = {Atrial fibrillation (AF) is the most prevalent clinical arrhythmia, associated with numerous complications, elevated morbidity and mortality rates, and limited therapeutic interventions, which have been confirmed to be related to the intestinal microbiota. However, there is currently limited research on the interaction between gut microbiota and AF. Herein, we integrated the largest Chinese gut microbiota cohort (n = 355) related to AF to date and identified a marked microbial imbalance in AF patients, characterized primarily by a significant reduction in Lactobacillus abundance. Using a rat model, we validated the role of Lactobacillus in lowering intestinal lipopolysaccharide (LPS) levels and alleviating host inflammation and AF-related symptoms. Mechanistically, microbial network analysis revealed that Lactobacillus promotes the formation of "LPS-reservoir modules," enhancing microbial community stability and reducing free LPS levels, thereby mitigating AF pathogenesis. These findings offer novel insights into the complex interplay among gut microbiota, LPS, and cardiovascular diseases.IMPORTANCEAF is a common heart rhythm disorder with limited treatment options. While emerging evidence links AF to the gut microbiome, the exact mechanisms remain poorly understood. Here, we analyzed a large cohort of AF patients and discovered a significant depletion of Lactobacillus in their gut microbiota. Using an animal model, we demonstrated that replenishing Lactobacillus reduces systemic inflammation and alleviates AF symptoms. Mechanistically, Lactobacillus promotes the formation of stable microbial networks. This enhanced stability prevents massive bacterial death and turnover, thereby reducing the release of free LPS into the environment. This work is highly significant as it decodes a vital link between gut stability and cardiovascular health, suggesting that Lactobacillus-based probiotics could serve as an innovative strategy for managing AF.}, }
@article {pmid42212959, year = {2026}, author = {Teh, TRD and Jimenez, NR and Herbst-Kralovetz, MM}, title = {Sequencing the genome of Lactobacillus iners strain SPIN 2503V10-D for improved quality and completeness.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0147725}, doi = {10.1128/mra.01477-25}, pmid = {42212959}, issn = {2576-098X}, abstract = {We sequenced and annotated the genome of Lactobacillus iners SPIN 2503V10-D, a human vaginal isolate previously sequenced as a reference genome for the Human Microbiome Project, to refine its existing genomic data.}, }
@article {pmid42213059, year = {2026}, author = {Zhuang, Y and Huang, Z and Liu, S and Xu, Y and Hou, G and Gao, D and Chen, T and Ma, B and Jiang, W and You, J and Li, M and Wang, W and Li, S and Cao, Z}, title = {Early life nutritional imbalance impairs colonic epithelial regeneration through gut microbiota dysbiosis and metabolic suppression.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag135}, pmid = {42213059}, issn = {1751-7370}, abstract = {Childhood malnutrition represents a major global health burden that extends beyond caloric deficiency to include dietary imbalance. The early-life gut microbiome functions as a dynamic ecosystem whose structure and metabolic output are intimately linked to host development, yet how nutritional imbalance disrupts this ecosystem and its integration with the host remains poorly understood. Using an isocaloric but nutrient-imbalanced diet in a mouse model, we recapitulated chronic growth stunting and identified a systemic syndrome comprising growth retardation, oxidative stress, and immunosuppression. Gut microbiota dysbiosis was established as the central mediator of these pathological manifestations. Integrated multi-omics analyses revealed that nutritional imbalance compromised microbial community structure and function, reducing diversity and ecological stability whereas disrupting metabolic activity-particularly short-chain fatty acid (SCFA) production. Through single-cell RNA sequencing of colonic epithelium, we demonstrated that these microbial perturbations suppressed host energy metabolism and inhibited the Wnt/β-catenin signaling pathway in regenerative epithelial cells. This resulted in the downregulation of key stem cell regulators LGR5 and ASCL2, ultimately impairing epithelial renewal and manifesting as reduced crypt depth. Our findings reveal a microbiota-dependent mechanism linking dietary imbalance to impaired host development, demonstrating how nutritional stress disrupts gut microbial structure and metabolic output, ultimately compromising epithelial regeneration. This work highlights the importance of considering the gut microbiome as an ecosystem whose homeostasis is fundamental to early-life health.}, }
@article {pmid42213076, year = {2026}, author = {Gan, B and Yang, C and Jia, C and Wang, K and Chen, J and Ding, S and Zhao, J}, title = {Microbiome-mediated polyphosphate accumulation enhances the resilience of sponge holobionts to future climate scenarios.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag128}, pmid = {42213076}, issn = {1751-7370}, abstract = {Ocean warming is threatening the stability of marine ecosystems, yet the mechanisms underlying the resilience of foundational species like sponges remain poorly understood. Polyphosphate (PolyP), a key player in marine phosphorus burial, is hypothesized to play an important role in sponge stress adaptation. Here, we demonstrated that microbiome-mediated PolyP dynamics were closely associated with sponge adaptation to thermal stress. Field investigation of three sponge species (Spongia sp., Tedania sp., Haliclona simulans) revealed marked interspecific differences in PolyP accumulation, with Spongia sp. maintaining the highest PolyP levels. Strong seasonal fluctuations in sponge PolyP content, peaking in June and reaching a minimum in January, correlated with ambient temperature. We found that this variation was regulated by ppk1 gene expression levels rather than by altering the microbial composition. The ppk1-harboring microbial assemblages exhibited host specificity, and phylogenetic analysis uncovered sponge-specific clades of ppk1 genes. Laboratory warming experiments further confirmed the functional link: under acute heat stress, both the ppk1 gene of the symbiotic microorganisms and the inorganic pyrophosphatase (ppa) gene in the host were upregulated in Spongia sp. PolyP likely provide an energy source for the host, maintaining holobiont stability and leading to low mortality. Conversely, H. simulans, with limited PolyP supply, ultimately suffered 100% mortality. Our results establish a link whereby sponge-associated microbes, via ppk1 expression, modulate PolyP accumulation to support host oxidative phosphorylation and mitigate thermal stress. This microbiome-mediated physiological pathway contributes to our understanding of sponge climate resilience, offering new functional insights into holobiont persistence in a warming ocean.}, }
@article {pmid42213079, year = {2026}, author = {Krupkin, H and Padhi, EM and Nachun, D and Kain, J and Long, JZ and Montgomery, SB}, title = {Genomics-Informed Approach Identifies Which Cell Types Regulate the Metabolome.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btag330}, pmid = {42213079}, issn = {1367-4811}, abstract = {Metabolism occurs in a cell type-specific manner, but which cells regulate metabolite levels remains unclear. Here, we integrate some of the largest metabolite quantitative trait loci datasets, TOPMed and UK Biobank, with one of the most extensive single-cell RNA sequencing resources, Tabula Sapiens. This integration allows us to identify cell types that regulate metabolites body-wide. We find hepatocytes are the primary regulatory cell type for most metabolites, associating with 385/410 (94%) metabolites for whom an association is found. Additionally, our multi-gene approach reveals more metabolite associations with beta cells compared to those identified using a single-gene approach. For example, we identify novel metabolite-cell type associations, such as the association between phenylpropanoic acid and beta cells, this metabolite that was previously thought to be regulated by the microbiome.}, }
@article {pmid42213186, year = {2026}, author = {Zhai, Y and Wang, D and Li, Z and Cui, T and Zhang, R and Liu, Y and Liu, H and Liu, S}, title = {Analysis of salivary metabolites and microbial characteristics in patients with dental fluorosis.}, journal = {Clinical oral investigations}, volume = {30}, number = {6}, pages = {}, pmid = {42213186}, issn = {1436-3771}, support = {No. YQZD2023060//the Anhui Province Key Cultivation Project for Excellent Young Teachers in Universities/ ; No. 2025byyfyjq04//the First Affiliated Hospital of Bengbu Medical University Science Fund for Outstanding Young Scholars/ ; No. LH250304001//the Longhu Project of Bengbu Medical University/ ; No. BYYFY2022TD001//the high-level scientific and technological innovation team of the First Affiliated Hospital of Bengbu Medical University/ ; }, mesh = {Humans ; *Saliva/microbiology/metabolism/chemistry ; *Fluorosis, Dental/microbiology/metabolism ; Female ; Male ; RNA, Ribosomal, 16S ; *Microbiota ; Multiomics ; Case-Control Studies ; Adult ; Dental Caries/microbiology/metabolism ; *Metabolome ; }, abstract = {OBJECTIVES: This study aimed to characterize specific alterations in the salivary microbiome and metabolome associated with dental fluorosis (DF), using dental caries (DC) as a comparative pathology.<br><br>MATERIALS AND METHODS: A multi-omics analysis was performed on saliva samples from 99 individuals with DF, 100 with DC, and 100 healthy controls (HC). Lipidomic profiling and 16S rRNA gene sequencing were integrated, and the resulting datasets were analyzed using multivariate statistical approaches and correlation analyses.<br><br>RESULTS: Clear separation was observed in both the molecular and microbial profiles of saliva among the DF, DC, and HC groups. The DF group showed significantly higher levels of LPA (18:4) and 15-oxoETE, along with enrichment of Enterobacter, Alloprevotella, Leptotrichia, Aggregatibacter, Klebsiella, Selenomonas, Peptostreptococcus, Peptostreptococcaceae_[XI][G-5], Actinomyces graevenitzii, Prevotella pallens, Leptotrichia buccalis, Desulfobulbus sp._HMT_041, Prevotella intermedia, Ruminococcaceae_[G-1] bacterium_HMT_075, and Peptostreptococcus stomatis. However, the core microbial taxa and the identified differential metabolites showed only weak correlations.<br><br>CONCLUSIONS: The salivary microbiome and lipidomic profiles in individuals with DF differed significantly from those observed in both caries patients and healthy controls. The core microbial taxa and differential metabolites identified in the DF group were associated with various systemic diseases and inflammatory processes, respectively.<br><br>CLINICAL RELEVANCE: The salivary multi-omics signatures identified in this study provide new insights into the potential long-term health risks associated with dental fluorosis.}, }
@article {pmid42213296, year = {2026}, author = {Girna, I and Kuban-Jankowska, A and Jakubczyk-Slabicka, A and Kosiński, A and Gruchała, M and Górska-Ponikowska, M}, title = {The Gut-Oral-Skin-Heart Microbiota Axis and Oxidative Stress: Where Have We Been and Where Are We Going.}, journal = {Dermatology and therapy}, volume = {}, number = {}, pages = {}, pmid = {42213296}, issn = {2193-8210}, support = {ST-46\ST-85//Medical University of Gdansk/ ; ST 01-10026/0010448/01/182//Medical University of Gdansk/ ; }, abstract = {Scientific interest in the relationship between cardiovascular disease and the human microbiome has grown substantially in recent years, with particular emphasis placed on the gut microbiota. Emerging evidence suggests, however, that distinct microbial niches-including the skin, oral cavity, and gut-may interact to influence cardiovascular homeostasis through shared pathogenic pathways, most notably oxidative stress and systemic inflammation. Intestinal dysbiosis has been strongly linked to the increased production of microbial metabolites such as trimethylamine N-oxide, which promotes endothelial dysfunction, oxidative imbalance, and atherogenesis. The oral microbiome has similarly been implicated in cardiovascular pathology through mechanisms encompassing chronic low-grade inflammation, transient bacteremia, and direct vascular colonization by pathogenic species. The contribution of the skin microbiome to cardiovascular risk remains less well defined; nevertheless, chronic inflammatory dermatoses-psoriasis in particular-have been consistently associated with elevated cardiovascular risk, a relationship potentially mediated by systemic immune dysregulation and oxidative stress. This review synthesizes current evidence on the gut-oral-skin-cardiac microbiome axis, underscoring the central role of oxidative stress as a convergent pathogenic mechanism and examining potential therapeutic implications. A more comprehensive understanding of these interconnected systems may inform the development of novel, microbiome-targeted strategies for the prevention and management of cardiovascular disease.}, }
@article {pmid42213326, year = {2026}, author = {Asia, LK and Sebigi, TW and Loots, DT and Mason, S and Jansen van Vuren, E and Williams, ME}, title = {Metabolomics of HIV in the Modern cART Era.}, journal = {Advances in experimental medicine and biology}, volume = {1507}, number = {}, pages = {109-137}, pmid = {42213326}, issn = {0065-2598}, mesh = {Humans ; *HIV Infections/drug therapy/metabolism/virology/immunology ; *Metabolomics/methods ; *HIV-1/drug effects/metabolism ; *Metabolome/drug effects ; *Anti-HIV Agents/therapeutic use ; Metabolic Reprogramming ; Lipid Metabolism/drug effects ; }, abstract = {HIV remains a global health challenge, affecting millions of individuals worldwide. While combination antiretroviral therapy (cART) significantly reduces viral loads to undetectable levels, it does not eradicate the virus completely, and a compromised host immune system persists. Traditionally, HIV-1 research has largely focused on elucidating the mechanisms of viral replication, characterising host immune responses, specifically inflammation, and developing effective antiretroviral therapies. However, comparatively less emphasis has historically been placed on understanding the metabolic alterations associated with HIV-1 infection. Metabolomics, a powerful tool that provides a functional understanding of the systemic metabolic changes induced by HIV and cART, is increasingly recognised for its potential to reveal the complex interplay between chronic inflammation, metabolic reprogramming, and long-term health outcomes. This chapter explores the critical metabolic pathways disrupted by HIV infection in the modern cART era, focusing on amino acid, glucose, microbiome, and lipid metabolism. Using metabolomic profiling, this chapter highlights persistent immunometabolic dysfunctions in people living with HIV, highlighting pathways of comorbidity risk and offering insights into therapeutic interventions to improve patient outcomes in the modern cART era.}, }
@article {pmid42213391, year = {2026}, author = {Gao, Z and Yang, X and Nie, M and Shi, S and Yuan, G and Li, X and Zhang, Y and Liu, D}, title = {Blautia Coccoides CML164 Improved Lipid and Energy Metabolism in Broiler Chickens Via Gut Microbiota Pathways.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {42213391}, issn = {1867-1314}, support = {2022YFD1300400//National Key Research and Development Program of China/ ; }, abstract = {The probiotic potential of Blautia coccoides CML164, a novel acetate-producing strain isolated from the poultry gut, was systematically evaluated for its ability to modulate lipid and energy metabolism in broilers via gut microbiota-mediated pathways. Supplementation with Blautia coccoides CML164 significantly reshaped the cecal microbiome, enriching beneficial short-chain fatty acid (SCFA)-producing bacteria such as Phocaeicola vulgatus, Parabacteroides distasonis, and members of Prevotellaceae, while concurrently increasing cecal acetate concentration in broiler chickens. These microbial changes were accompanied by improved mitochondrial function, enhanced hepatic fatty acid oxidation (upregulation of PPARα, ACOX1), and suppression of lipogenic genes (SREBP1, PPARγ), leading to reduced abdominal fat deposition and improved serum lipid profiles without compromising growth performance in broilers. The study demonstrates that Blautia coccoides CML164 functions as an effective probiotic by orchestrating gut microbiota composition and promoting SCFA production, thereby activating host metabolic pathways that mitigate lipid accumulation. Our findings highlight the critical role of microbial intervention in regulating energy homeostasis and offer a promising strategy for leveraging probiotics to enhance metabolic health in poultry production.}, }
@article {pmid42213471, year = {2026}, author = {George, M and Negi, L and Maan, M}, title = {A Gutsy Move? Microbiome Reset With Fecal Microbiota Transplant Brings Remarkable Turnaround in Severe Alcohol-Associated Hepatitis: A Case Report.}, journal = {Gastroenterology nursing : the official journal of the Society of Gastroenterology Nurses and Associates}, volume = {49}, number = {3}, pages = {163-178}, pmid = {42213471}, issn = {1538-9766}, }
@article {pmid42213482, year = {2026}, author = {Wienholts, K and Petersen, AE and van Helsdingen, CPM and Talboom, K and Davids, M and de Wilt, JHW and de Jonge, WJ and Tanis, PJ and Hompes, R and Derikx, JPM and , }, title = {Perioperative faecal microbiome dynamics in patients undergoing rectal cancer surgery in the IMARI-trial.}, journal = {BJS open}, volume = {10}, number = {3}, pages = {}, pmid = {42213482}, issn = {2474-9842}, support = {//Dutch Cancer Society/ ; //B. Braun Surgical, S. A and Stryker European Operations B.V/ ; }, mesh = {Humans ; *Rectal Neoplasms/surgery/microbiology ; *Feces/microbiology ; Male ; Female ; Ileostomy ; *Gastrointestinal Microbiome ; Aged ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Colorectal Surgical Procedures ; Perioperative Period ; Decontamination/methods ; }, abstract = {BACKGROUND: The gut microbiome influences health by regulating metabolism, modulating the immune system, and protecting against pathogens. Surgical interventions, antibiotics, and dietary changes can disrupt this balance. In rectal cancer surgery, the perioperative microbiome's role in selective digestive decontamination and ileostomy formation remains underexplored. This manuscript aimed to investigate perioperative microbiome dynamics in patients undergoing rectal cancer surgery, focusing on the impact of selective digestive decontamination and ileostomy.<br><br>METHODS: This study was part of the IMARI-trial. Faecal samples were collected before surgery and faecal or ileostomy samples on postoperative day 4. Microbial composition and diversity were assessed using 16S ribosomal RNA sequencing; alpha and beta diversity analyses were stratified by time point, ileostomy status, and selective digestive decontamination administration.<br><br>RESULTS: Of the 246 enrolled in the IMARI-trial, 214 patients were analysed. Postoperative samples showed significantly lower alpha diversity than preoperative samples, indicating reduced microbial richness and evenness across groups. Beta diversity analyses revealed distinct clustering between pre- and postoperative samples, with surgery explaining the largest variance in microbial composition (R2 = 15.6%; P < 0.001). Ileostomy status (R2 = 9.6%; P < 0.001) and selective digestive decontamination administration (R2 = 3.1%; P = 0.002) also contributed significantly. Notable taxonomic shifts included increased postoperative abundances of Enterococcus and Klebsiella, alongside reduced Firmicutes genera, particularly in ileostomy samples.<br><br>CONCLUSION: Surgery and perioperative factors induce significant, early microbiome alterations, favouring facultative anaerobes over obligate anaerobes. Although selective digestive decontamination selectively modulates specific taxa, its overall impact on diversity appears less pronounced than surgery and ileostomy status. These findings underscore the need for studies linking perioperative microbiome trajectories to clinical endpoints and for evaluating microbiome-informed perioperative strategies, including antibiotic stewardship, diet, or microbial therapeutics, in rectal cancer care.}, }
@article {pmid42213775, year = {2026}, author = {Yuan, K and Lian, Y and Huang, P and Cao, F and Yang, X and Lu, Y and Ding, X and Wang, L and Yang, H and Ye, Z and Chen, Q and Fu, J and Yuan, S and Fan, Y and Cai, S and Du, D and Ren, J and Zhang, X and Xu, H}, title = {Integrative analysis reveals intra-tumoral microbial enterotypes shape host transcriptomes in colorectal cancer.}, journal = {Cell reports}, volume = {45}, number = {6}, pages = {117413}, doi = {10.1016/j.celrep.2026.117413}, pmid = {42213775}, issn = {2211-1247}, abstract = {The intratumor microbiome and host gene regulation are key contributors to colorectal cancer (CRC), yet their interactions remain unclear. To investigate the interplay between intra-tumoral microbe and host gene, we analyzed paired tumor and normal tissues from 31 patients. Integrated multi-omics analysis identified 4,197 significant bacteria-gene correlation pairs involving 30 bacterial taxa. Patient stratification based on these associations reveals two distinct molecular subgroups characterized by unique microbial signatures and immune profiles. In a mouse model, Bacteroides fragilis alters the tumor immune microenvironment, promoting myeloid-derived suppressor cell (MDSC)-mediated CXCL signaling that impaired CD8[+] T cell activation and promotes exhaustion. B. fragilis directly promotes CXCL2 expression and ROS production in MDSCs, which subsequently drives CD8[+] T cell exhaustion and immune evasion. These findings reveal that intra-tumoral microbiota influence host transcriptomes and immune modulation in CRC, supporting microbiome-based molecular stratification and offering insights into potential microbiota-targeted therapies.}, }
@article {pmid42214204, year = {2026}, author = {Cookson, AL and Collis, RM and Soni, A and Srey, F and Muirhead, RW}, title = {Fencing off critical source areas reduces faecal contamination and reshapes microbial communities in agricultural headwater catchments.}, journal = {The Science of the total environment}, volume = {1041}, number = {}, pages = {181867}, doi = {10.1016/j.scitotenv.2026.181867}, pmid = {42214204}, issn = {1879-1026}, abstract = {Agricultural headwater catchments are critical sources of microbial contamination to surface waters, yet the effectiveness of mitigation practices in these small, dynamic systems is not well defined. A paired-catchment experimental design was used to assess the effects of permanent fencing of critical source areas (CSAs) in ephemeral streams within deer-grazed pastures. Faecal, soil, and freshwater samples were collected over four years, comprising two years of baseline monitoring and two years following mitigation. Viable Escherichia coli concentrations were measured in faeces, soil and water alongside high-resolution microbiome profiling and microbial source tracking. Microbiomes of freshly voided faeces were dominated by anaerobic taxa (Bacteroidia, Clostridia and Spirochaetia) which were significantly reduced (p < 0.001) in aged faeces and replaced by aerotolerant Actinobacteria, Alphaproteobacteria and Gammaproteobacteria (p < 0.001). Fencing reduced E. coli concentrations in CSA soils by 87.4% (p < 0.0001) and by 47.0% (p = 0.041) in storm event flows, with the strongest effects in water during baseflow conditions with a 60.6% (p < 0.0004) reduction in E. coli. Freshwater microbial alpha diversity increased in the treated catchment, while soil microbiomes remained stable. Beta diversity analyses indicated distinct shifts in freshwater communities after the permanent fenced treatment, but shifts in the CSA soil microbiomes after fencing were not observed. Source tracking indicated reduced CSA soil contributions (p < 0.001), with a greater relative influence of aged faeces during storm events (p < 0.0001). These results demonstrate that fencing off CSAs can lower faecal inputs and alter aquatic microbial communities. Culture-based and sequencing approaches provided complementary insights into contamination patterns, linking observed reductions in E. coli concentrations to changes in microbial diversity and community structure. This work highlights how mitigation targeting CSAs can influence both water quality and freshwater microbiomes, and underscores the value of integrating traditional monitoring with molecular methods in evaluating agricultural management practices.}, }
@article {pmid42214348, year = {2026}, author = {Debrah, MA and Awuah, MB and Koh, A and Ramsey, J}, title = {Complete genome sequence of Escherichia Siphophage Serwaa.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0122225}, doi = {10.1128/mra.01222-25}, pmid = {42214348}, issn = {2576-098X}, abstract = {Escherichia coli 4s is a Gram-negative bacterium of the equine gastrointestinal tract microbiome. Here, we report the complete genome of 4s siphophage, Serwaa. The Serwaa genome is 62,144 bp with 42 of 85 proteins assigned a predicted function. Serwaa shares the highest similarity with other Nonagviruses.}, }
@article {pmid42214354, year = {2026}, author = {Kumar, G and Pagano, SS and Cavanaugh, N and Hudson, AO and Savka, MA}, title = {Whole genome sequencing of three cloacal bacterial isolates from migratory birds.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0021626}, doi = {10.1128/mra.00216-26}, pmid = {42214354}, issn = {2576-098X}, abstract = {We report the whole-genome sequences of three bacterial isolates from the cloaca of migratory songbirds. Among these, Kluyvera cryocrescens and Stenotrophomonas rhizophila are known as opportunistic human pathogens. In contrast, Pseudomonas mandelii is a psychrotrophic bacterium that is generally considered non-pathogenic.}, }
@article {pmid42214368, year = {2026}, author = {Karmarkar, B and Dhotre, D}, title = {Harnessing gut microbiome enzymes: Segatella copri and Stenotrophomonas maltophilia prolyl peptidases degrade gliadin peptides and improve epithelial barrier function in a celiac disease model.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0321425}, doi = {10.1128/spectrum.03214-25}, pmid = {42214368}, issn = {2165-0497}, abstract = {UNLABELLED: Celiac disease (CeD) is an autoimmune enteropathy triggered by gluten-derived peptides that resist gastrointestinal digestion, notably the proline-rich 33-mer and 11-mer gliadin epitopes. Here, we describe a rational, metagenome-based strategy to identify gut microbiome-derived prolyl peptidases capable of degrading these immunogenic peptides. Integrating metagenomic mining with structure-based in silico screening, we identified two novel enzymes PSP692 from Segatella copri and PSP464 from Stenotrophomonas maltophilia. Recombinant expression, purification, and characterization confirmed their activity under physiologically relevant conditions: PSP692 efficiently degrades the 33-mer at pH 6, while PSP464 targets the 11-mer at pH 4. Functional assays using CaCo-2 cell line, both in bi- and tri-dimensional assays, demonstrated that degradation of gliadin peptides by PSP692 and PSP464 significantly restored the expression of tight junction proteins (ZO-1 and occludin), reduced IL-6 secretion, and improved barrier integrity. These findings establish a foundational strategy for the discovery of microbiome-derived glutenases and provide both a compelling case and a methodology for data-driven discovery of functional enzymes that degrade immunogenic gliadin peptides, with translational potential as adjunct therapies in CeD and gluten-related disorders.<br><br>IMPORTANCE: Celiac disease affects 1.4% of the global population, and, as of date, a gluten-free diet (GFD) is the only therapy available. Adherence to GFD is difficult, and inadvertent exposure to gluten still occurs. To address this, various approaches are utilized to develop adjuvant therapies. These include recombinant enzymes that, to date, have been discovered by serendipity. We have outlined and validated a method to identify enzymes with potential from metagenomic data, which will also be validated experimentally.}, }
@article {pmid42214386, year = {2026}, author = {Sun, H and Dulencin, A and Kirn, TJ and Vo, J and Liachko, I and Rao, D and Manzano-Santana, J and Patel, E and Looi, C and Horton, DB and Barrett, E and Weidner, M and Bachmann, G and Panettieri, RA and Connor, BA and Rogova, M and Nagy-Szakal, D and Couto-Rodriguez, M and Kotwal, S and Wu, Q and Simon, J and Blaser, MJ and Dominguez Bello, MG}, title = {Autologous fecal microbiota transplantation restores the infant gut microbiome and metabolome after antibiotics: a case report.}, journal = {mBio}, volume = {}, number = {}, pages = {e0071126}, doi = {10.1128/mbio.00711-26}, pmid = {42214386}, issn = {2150-7511}, abstract = {UNLABELLED: Antibiotic exposure during infancy disrupts gut microbiome assembly during a critical developmental window. Strategies to restore these ecosystems remain limited. In the REPAIR trial (NCT06609980), eight infants were followed longitudinally; two received amoxicillin for otitis media, and one subsequently underwent autologous fecal microbiota transplantation (aFMT) using stool collected prior to antibiotic exposure. Shotgun metagenomics, Hi-C-assisted resistome profiling, and untargeted metabolomics were performed on samples collected before and after antibiotics. Amoxicillin treatment was associated with displacement of community structure, enrichment of antibiotic resistance genes (ARGs), and altered fecal metabolites, including short-chain fatty acids, bile acids, acylcarnitines, bilirubin derivatives, tricarboxylic acid (TCA) cycle metabolites, and amino acids. In the non-restored infant, microbiota composition and ARG profiles remained persistently altered during follow-up, accompanied by sustained metabolic divergence. In contrast, the aFMT-treated infant demonstrated convergence toward pre-antibiotic community structure, directional restructuring of ARG carriers -including reduction of β-lactam and tetracycline resistance genes- and metabolite profiles trending toward the pre-antibiotic baseline across analytical platforms. Although limited to a case-based comparison, these findings provide integrated ecological and functional evidence that aFMT may promote recovery following antibiotic perturbation during early-life microbiome development and support the rationale for larger controlled clinical trials.<br><br>IMPORTANCE: Antibiotic exposure in early life disrupts the developing gut microbiome during a critical window of host-microbe interaction. However, the extent to which these disturbances resolve naturally, or can be actively reversed, remains unclear. In this study, we use longitudinal sampling in infants to examine microbiome recovery following antibiotics, with and without autologous fecal microbiota transplantation (aFMT). We show that antibiotic exposure leads to coordinated disruptions in microbial composition, antibiotic resistance genes, and metabolic profiles. While partial recovery spontaneously occurs over time, faster and more extensive restoration toward the pre-antibiotic state is observed following aFMT. These findings provide insight into the ecological dynamics of microbiome reassembly in early life and highlight the potential of using controlled perturbations to understand microbiome resilience.<br><br>CLINICAL TRIALS: This study is registered with ClinicalTrials.gov as NCT06609980.}, }
@article {pmid42214402, year = {2026}, author = {Logan, J and Martin, K and Gillespie, L and McConnachie, A and Lee, WN and Burhan, H and Brown, T and Faruqi, S and Jackson, DJ and Kurukulaaratchy, R and Mansur, AH and Saralaya, D and Fowler, SJ and Patel, P and Brown, J and Lordan, J and Siddiqui, S and Smith, SJ and Shah, PA and Haldar, K and Megremis, S and Harrison, SA and Brown, R and Nelson, C and Mistry, V and Brown, V and Chalmers, JD and Djukanovic, R and Pavord, ID and Heaney, LG and Brightling, CE and Chaudhuri, R}, title = {Asthma exacerbation profile of benralizumab for severe eosinophilic asthma (the BenRex study): a multicentre, prospective cohort study.}, journal = {The Lancet. Respiratory medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/S2213-2600(26)00096-2}, pmid = {42214402}, issn = {2213-2619}, abstract = {BACKGROUND: Benralizumab, an interleukin-5 receptor α antagonist, depletes blood eosinophils, reducing exacerbations of severe asthma by approximately 50% versus placebo. In this study, we aimed to characterise mechanisms underlying exacerbations occurring on benralizumab.<br><br>METHODS: BenRex, a multicentre, prospective cohort study, recruited participants meeting national licensing criteria for benralizumab for asthma. The study was conducted in 15 UK severe asthma centres. After collecting baseline data, open-label benralizumab was administered for 12-18 months. At exacerbation, participants attended for medical review before initiating treatment, fractional exhaled nitric oxide (FeNO), spirometry, asthma control questionnaire, and blood and sputum sampling.<br><br>FINDINGS: Between Sept 30, 2019, and April 23, 2024, 121 exacerbation events were assessed in 156 individuals. 90 participants (58%) were female and 66 (42%) were male; 147 (94%) of participants identified as White. Median blood eosinophil counts at exacerbation were 0 (IQR 0-0) cells per &#x3bc;L. Airway neutrophilia was present in 55% of exacerbations where sputum was available (27/49). Median C-reactive protein (CRP) increased from 3&#xb7;00 mg/L (1&#xb7;00-6&#xb7;00) at baseline to 9&#xb7;00 mg/L (3&#xb7;00-17&#xb7;00) at exacerbation (p=0&#xb7;0067). Clinically relevant viral pathogens were seen in eight (20&#xb7;5%) of 39 sputum samples; although viruses were detected in 22 (56&#xb7;4%) of 39 samples. Influenza A, metapneumovirus, and rhinovirus were the most common viral pathogens (each found in 2 [5&#xb7;1%] of 39 samples). New acquisition of Moraxella catarrhalis (3 [13&#xb7;6%] of 22), Haemophilus influenzae (4 [18&#xb7;2%] of 22), and Streptococcus pneumoniae (2 [9&#xb7;1%] of 22) occurred. DNA-neutrophil elastase complexes (p=0&#xb7;0080) and azurocidin-1 (p=0&#xb7;012) concentrations rose from baseline to exacerbation. FeNO was &#x2265;50 parts per billion in 56 (50&#xb7;5%) of 111 assessed exacerbations and was associated with reduced odds of bacterial detection. FeNO did not correlate with CRP or sputum neutrophils.<br><br>INTERPRETATION: Our findings suggested that eosinophilic inflammation is not involved in exacerbations when a patient is being treated with benralizumab. Airway neutrophilia, viral pathogens, and alteration of the sputum microbiome point to infection as the most prominent causes of exacerbations. This observation should improve precision management of asthma exacerbations occurring despite treatment with benralizumab.<br><br>FUNDING: AstraZeneca.}, }
@article {pmid42214537, year = {2026}, author = {Wang, K and Li, C and Mohamed, K and Mohamed, AF and Nagaoka, K and Li, C and Shen, D}, title = {Intratracheal Lactobacillus rhamnosus attenuates poultry-house PM2.5-induced lung inflammation in broilers by remodeling the pulmonary microbiota-metabolite axis.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128449}, doi = {10.1016/j.envpol.2026.128449}, pmid = {42214537}, issn = {1873-6424}, abstract = {Fine particulate matter (PM2.5) in intensive farming systems is a bioaerosol mixture that poses severe risks to respiratory health; however, the role of the lung microbiome in PM2.5-induced toxicity and its potential as a therapeutic target remain poorly understood. Here, we investigated the pulmonary toxicity of poultry-house PM2.5 and evaluated the protective efficacy of intratracheal Lactobacillus rhamnosus (L. rhamnosus) administration in a broiler model. Exposure to PM2.5 caused significant lung pathological injury, oxidative stress, and inflammatory responses. Integrative analysis of 16S rRNA gene sequencing and untargeted metabolomics revealed that PM2.5 disrupted the pulmonary microecology, depleting commensal Lactobacillus while enriching opportunistic pathogens (Escherichia-Shigella), which coincided with a marked suppression of tryptophan metabolism. Strikingly, L. rhamnosus intervention reversed this dysbiosis and specifically restored the levels of indole derivatives, particularly indole-3-lactic acid (ILA). Correlation analysis further demonstrated that elevated ILA levels were strongly associated with reduced pro-inflammatory cytokines and improved antioxidant capacity, suggesting a strong correlation between L. rhamnosus administration, the reinstatement of microbiota-derived tryptophan metabolites, and respiratory protection. Collectively, our findings provide the evidence that identifying and restoring key microbial metabolites offers a potent remediation strategy against environmental bioaerosol-induced respiratory injury.}, }
@article {pmid42214560, year = {2026}, author = {Xue, M and McShane, C and Kim, J and Khorasaniha, R and Leibovitzh, H and Shao, J and Chen, R and Jeong, S and Madsen, KL and Griffiths, AM and Walters, TD and Steinhart, AH and Dieleman, LA and Huynh, HQ and Panaccione, R and Aumais, GL and Bitton, A and Mack, D and Jacobson, K and Bressler, B and Marshall, JK and Moayyedi, P and Plotkin, L and Dotan, I and Bernstein, CN and El-Matary, W and Hyams, JS and Otley, A and Lee, SH and Turner, D and Armstrong, H and Croitoru, K and ,  and Turpin, W}, title = {β-Glucan and Inulin Estimated Intake Are Associated With Reduced Risk of Crohn's Disease, Improved Gut Barrier and Systemic Inflammation Markers, and Multi-Omic Signatures in a High-Risk Cohort.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2026.05.006}, pmid = {42214560}, issn = {1528-0012}, abstract = {BACKGROUND &amp; AIMS: The cause of Crohn's Disease (CD) remains unclear; however evidence suggests fiber intake may play a role. We aimed to investigate the association between intake of total fiber and select fermentable fiber subtypes and future risk of CD in an at-risk population.<br><br>METHODS: The Genetic, Environmental, Microbial Project prospectively followed asymptomatic first-degree relatives of individuals with CD. Habitual intake of total fiber and select fiber subtypes was estimated from baseline food frequency questionnaires and biologic samples were collected. Incident CD was confirmed during follow-up. Cox proportional hazards models estimated hazard ratios (HRs) for CD. Associations between fiber subtype intake and urinary fractional excretion of lactulose-mannitol ratio (LMR), C-reactive protein (CRP), gut microbiota (16S rRNA sequencing), and serum proteomics (Olink&#xae;) were evaluated using multivariable regression models.<br><br>RESULTS: During a median follow-up of 8.5 years of 3,314 FDRs, 94 developed CD. Higher &#x3b2;-glucan (HR 0.70, 95% CI 0.54-0.92) and inulin (HR 0.68, 95% CI 0.49-0.96) intake were associated with lower CD risk. Associations were strongest in those with higher baseline relative abundance of Erysipelotrichaceae UCG-003, but weaker with higher Colidextribacter. Higher &#x3b2;-glucan and inulin intake were associated with lower LMR, lower abundance of pathobionts (Ruminococcus torques and Lachnoclostridium), and lower concentrations of inflammation- and barrier-related proteins, including CRP, TREM-1, OSM, and MMP-9.<br><br>CONCLUSIONS: Higher estimated &#x3b2;-glucan and inulin intake was associated with preserved gut barrier function, lower systemic inflammatory markers and lower CD risk which was modified by the microbial context. These findings support microbiome-informed dietary strategies and intervention trials for CD prevention.}, }
@article {pmid42214632, year = {2026}, author = {Wei, B and Mao, T and Ijiti, GO and Zhang, G and Yang, H and Jiao, Q and Niu, C}, title = {Gut microbiota-mediated recycling of residual nitrogen in black soldier fly larval frass.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135001}, doi = {10.1016/j.biortech.2026.135001}, pmid = {42214632}, issn = {1873-2976}, abstract = {Black soldier fly larvae-based waste bioconversion systems generate frass containing substantial residual and excreted nitrogen, limiting overall nitrogen use efficiency. This study evaluates a microbiome-based strategy to enhance nitrogen recovery from black soldier fly larvae frass and redirect residual nitrogen into larval biomass. Using surface-sterilized larvae, targeted supplementation with gut-derived bacteria, and [15]N-labelled urea tracing, nitrogen transfer from frass into larval biomass was quantified. Among eight isolated gut bacterial strains, Providencia rettgeri, Proteus mirabilis, and Citrobacter freundii showed the strongest individual effects on larval growth and nitrogen assimilation. A defined consortium of these strains consistently outperformed single-strain treatments, increasing larval dry mass and total nitrogen content by up to 49% and 58%, respectively. Isotopic analysis confirmed enhanced incorporation of urea-derived nitrogen into larval tissues, while residual nitrogen in frass was reduced by 29% relative to conventional rearing. Genomic analysis and urease inhibition experiments further demonstrated that bacterial urease activity underpins this enhanced nitrogen recycling. While demonstrated on a model substrate, the findings highlight potential adaptability to complex industrial wastes pending further validation. Targeted gut microbiome engineering via a urease-active consortium offers a biologically precise route to improve nitrogen use efficiency in insect bioconversion systems.}, }
@article {pmid42214718, year = {2026}, author = {Li, D and Wang, J and Chong, H and Song, Y and Zhang, P and Zhang, D and Xiao, H}, title = {Changes in gut microbiota of Loxostege sticticalis (Lepidoptera:Pyralidae) at different diapause stages.}, journal = {Journal of insect physiology}, volume = {}, number = {}, pages = {105008}, doi = {10.1016/j.jinsphys.2026.105008}, pmid = {42214718}, issn = {1879-1611}, abstract = {Loxostege sticticalis, belonging to the family Pyralidae in the order Lepidoptera, is a major migratory pest in the agro-pastoral ecotone of Eurasia, which can survive harsh winters and food shortages through diapause. Although gut microbiota have been shown to play a crucial role in insect environmental adaptation, their succession patterns and functions during diapause in L. sticticalis remain unclear.. This study used 16S rRNA sequencing to analyze the succession patterns of the gut microbiota in L. sticticalis at the prediapause (PD), diapause (D1, D3, and D5, diapause for 1, 3, and 5 months), and post-diapause quiescence (PDP) stages. The results showed that the gut microbiota underwent significant dynamic reorganization during diapause maintenance: diversity is at lowest in the PD stage, however, it rapidly recovered, and eventually stabilized during diapause stage. Bacteroidetes was the dominated the initial community, while Actinobacteriota abundance gradually increased with the extension of diapause and became the dominant bacteria during the PDP stage. Functional predictions showed that the bacteria related to lipid and amino acid metabolism, likely helping the host accumulate energy to cope with starvation during diapause; while at the PDP stage, the microbiome was enriched in taxa that contribute to nitrogen cycling, likely assisting in the recycling of endogenous nitrogen to support the upcoming pupation and metamorphosis. In conclusion, L sticticalis actively changes the proportion of gut bacteria to store and release energy, and to promote nitrogen absorption. Gut bacteria facilitate host adaptation to environmental stress via metabolic compensation, revealing synergistic insect-microbe adaptation during diapause. This study provides a theoretical foundation for new, eco-friendly pest control strategies.}, }
@article {pmid42214864, year = {2026}, author = {Wasnik, S and Cheng, S and Zhao, X and Keang, K and Zhang, H and Cross, JS}, title = {Tire wear particle and leachate induce oxidative stress and reshape the rice rhizosphere soil system: Multi-omics evidence of tissue-specific phytotoxicity.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142458}, doi = {10.1016/j.jhazmat.2026.142458}, pmid = {42214864}, issn = {1873-3336}, abstract = {Tire wear particles (TWPs) are an emerging environmental contaminant of global concern, yet their impacts on terrestrial systems remain poorly characterized. This study investigated the phytotoxic effects of TWPs and tire leachate (TL) on rice paddy seedlings through an integrated analysis of soil properties, microbial diversity, and plant physiology. Rice seedlings were exposed to environmentally relevant concentrations (0.1-10 g/kg soil) and TL solution (1-100%) for 28 days. Results revealed contrasting dose-response patterns: while low concentrations stimulated growth, high-dose TP significantly inhibited development and altered photosynthetic pigments concentrations. Root tissues exhibited substantial oxidative stress, characterized by significant malondialdehyde (MDA) accumulation. High-throughput 16S rRNA sequencing showed a restructuring of the soil microbial community, with TL exposure shifting dominant taxa toward phyla associated with the degradation of complex organic compounds. Structural integration via partial least squares path modeling (PLS-PM) achieved a Goodness of Fit (GoF) of 0.67, confirming a robust statistical link between tire-derived contamination and biological decline. Crucially, targeted metabolomics revealed tissue-specific metabolic reprogramming. Roots showed greater sensitivity than leaves, marked by the accumulation of stress-related amino acids (e.g., proline and GABA) and the depletion of key TCA cycle intermediates (e.g., malic and succinic acid). This indicated a metabolic shift from primary growth toward oxidative defense and energy compensation. These findings demonstrate that tire-derived contaminants pose a significant risk to the soil-plant-microbe system, highlighting root oxidative health and metabolic stability as critical endpoints for assessing the impact of traffic-related pollution on terrestrial productivity.}, }
@article {pmid42214935, year = {2026}, author = {Ayaz, M and Wenjing, L and Deng, M and Li, L and Song, K}, title = {Warming-acidification synergy amplifies plastisphere-mediated nitrous oxide emissions.}, journal = {Journal of environmental management}, volume = {410}, number = {}, pages = {130079}, doi = {10.1016/j.jenvman.2026.130079}, pmid = {42214935}, issn = {1095-8630}, abstract = {Climate warming, acidification, and plastic pollution converge to create unrecognized feedback in the nitrogen cycle. Here, we demonstrate that these anthropogenic pressures synergistically amplify emissions of nitrous oxide (N2O), from plastic waste in a lake ecosystem. A factorial mesocosm study reveals that combined warming (28 °C) and acidification (pH 6.0) synergistically enhance N2O emissions from plastic substrates by accelerating nitrogen transformations, depleting ammonium and nitrate while transiently accumulating nitrite. This response is governed by polymer type, with the plastisphere assembled on polylactic acid (PLA) sustains significantly higher (up to 78%) emissions than on polyethylene (PE). A significant temperature and acidification interaction (p < 0.001) confirms synergism, with the combined effect exceeding additivity by 132 μg N g[-1] MLVSS h[-1] for PLA and 36.2 μg N g[-1] MLVSS h[-1] for PE. Bacterial-dominated communities produce the highest N2O (1182.9 μg N g[-1] MLVSS h[-1] from PLA at pH 6.0 and 28 °C), while acetylene inhibition corroborates this trend, with PLA emissions 49% higher than PE. Mechanistically, the synergy reassembles the plastisphere microbiome into efficient, cooperative networks, enriching keystone N2O-producing denitrifiers (e.g., Thauera (Aminoaromatica MZ1T), Pseudomonas Stutzeri) and enhancing electron transfer efficiency. This community shift creates a decisive genetic constriction, upregulating the nirS gene while suppressing the N2O-reducing nosZ gene. Our findings position plastic waste as a climate-sensitive biogeochemical reactor, creating feedback between plastic pollution and anthropogenic climate forcing.}, }
@article {pmid42215009, year = {2026}, author = {Shidara, S and Desai, KM and Mizoguchi, T}, title = {LepR[+] skeletal stem/progenitor cells in craniofacial tissues.}, journal = {Journal of oral biosciences}, volume = {68}, number = {4}, pages = {100791}, doi = {10.1016/j.job.2026.100791}, pmid = {42215009}, issn = {1880-3865}, abstract = {BACKGROUND: Leptin receptor (LepR)[+] stromal cells are widely recognized as skeletal stem/progenitor cells (SSPCs) in the bone marrow that generate osteolineage cells, and contribute to skeletal homeostasis under steady-state conditions and tissue repair. By expressing representative niche factors, including stem cell factor and C-X-C motif chemokine ligand 12, LepR[+] SSPCs function as key microenvironmental components of the hematopoietic stem cell (HSC) niche. Over the past decade, genetic cell-labeling studies have identified LepR[+] SSPCs in craniofacial tissues, including in the periodontal ligament and alveolar bone marrow, where they differentiate into osteoblasts and cementoblasts.<br><br>HIGHLIGHT: Emerging evidence indicates that periodontal LepR&#x202f;[+]&#x202f;cells contribute to orthodontic remodeling, periodontal repair, and extraction socket healing. Independent SSPC populations may coexist with LepR[+] SSPCs in oral tissues and contribute in parallel to tissue homeostasis. Periodontal LepR[+] cells also express HSC niche-associated factors, suggesting their possible role in the regulation of local immune and hematopoietic environments. Because oral tissues are continuously exposed to mechanical forces and the oral microbiome, LepR[+] SSPCs in the oral environment may function through unique regulatory mechanisms that influence skeletal homeostasis and hematopoiesis.<br><br>CONCLUSION: In this review, current knowledge regarding LepR[+] SSPCs in periodontal tissues is summarized, and their emerging roles in skeletal maintenance, tissue repair, and hematopoietic regulation is discussed. Further elucidation of the regulatory mechanisms governing these cells will advance understanding of oral skeletal and hematopoietic biology, and may provide new insights into oral health and regenerative strategies.}, }
@article {pmid42215125, year = {2026}, author = {Wu, T and Sun, S and Zhu, Z and Zhu, G and Tang, S and Wang, Z and Luo, F and Chen, X and Zhang, L and Xu, Y}, title = {Rind-core microbial niche differentiation at centimeter-scale modulates the sensory quality of solid-state high-temperature Daqu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {238}, number = {}, pages = {119456}, doi = {10.1016/j.foodres.2026.119456}, pmid = {42215125}, issn = {1873-7145}, mesh = {Fermentation ; *Hot Temperature ; *Food Microbiology/methods ; *Taste ; *Microbiota ; *Alcoholic Beverages/microbiology/analysis ; *Wine/microbiology/analysis ; Bacteria/metabolism ; Hydrogen-Ion Concentration ; }, abstract = {High-temperature Daqu (HTD) is a vital microbial starter for Moutai-flavor Baijiu, providing the essential enzymes and flavor precursors required for fermentation. However, restricted mass and heat transfer during the solid-state process drive pronounced spatial heterogeneity across the Daqu brick, yet how this niche differentiation modulates HTD quality remains elusive. In this study, we analyzed a comprehensive dataset (n = 134) spanning 12 production batches, performing centimeter-scale characterization of physicochemical properties and microbial succession in both high-quality and ordinary-quality HTD. Our results showed that while whole-sample analysis failed to detect differences between high-quality and ordinary-quality Daqu, spatial partitioning revealed that ordinary-quality rind had significantly lower acidity than high-quality rind during the early fermentation stage (S1, days 9-12), with no difference in the core. Furthermore, significant microbial differentiation was observed between the rind and core of HTD, with this spatial divergence occurring at an accelerated rate in ordinary-quality samples during fermentation. Redundancy analysis (RDA) and laboratory validation further confirmed that these micro-ecological variations were primarily driven by gradients in acidity and water content Our study highlights the importance of considering centimeter-scale microbial heterogeneity, providing insight into its relationship with microbial succession rates and how these factors contribute to the final quality of HTD.}, }
@article {pmid42215186, year = {2026}, author = {Palanisamy, V and Bosilevac, JM and Wang, R and Chitlapilly Dass, S}, title = {Microbial transcriptional dynamics of beef-processing drain biofilm models revealed by enrichment-based metatranscriptomics.}, journal = {Food microbiology}, volume = {139}, number = {}, pages = {105096}, doi = {10.1016/j.fm.2026.105096}, pmid = {42215186}, issn = {1095-9998}, mesh = {*Biofilms/growth &amp; development ; Cattle ; Animals ; *Bacteria/genetics/isolation &amp; purification/classification ; *Microbiota/genetics ; *Red Meat/microbiology ; Gene Expression Profiling ; Transcriptome ; Food Handling ; Food Microbiology ; }, abstract = {Microbial biofilms in beef-processing facilities represent persistent reservoirs of foodborne pathogens and spoilage organisms, posing significant risks of cross-contamination of meat products. Floor-drains, as nutrient-rich convergence points within processing environments, are particularly conducive to multi-species biofilm formation. While previous studies have characterized the taxonomical composition and functional potential of drain microbial communities, their transcriptional activities remain largely unexplored. To address this gap, we developed a metatranscriptomic approach to study the transcriptional dynamics of drain-associated microbiomes in beef-processing facilities using enrichment-derived drain biofilm models (hereafter referred to as biofilm models). Floor drain swab samples were collected from hotbox and cooler areas of nine beef-processing plants in 2019 and 2021, and subjected to laboratory enrichment under processing-relevant ecological conditions prior to RNA extraction and sequencing. Metatranscriptomic analysis revealed a core set of highly transcriptionally active genera, including Pseudomonas, Carnobacterium, Acinetobacter, and Brochothrix, in the biofilm models. Functional profiling indicated high expression (Σlog10TPM >3.5) of key biofilm-associated functions such as cell adhesion, exopolysaccharide biosynthesis, bacterial chemotaxis, and quorum sensing (QS), suggesting potential biofilm formation, migration and microbial communication. In comparing biofilm models developed from samples collected in 2019 and 2021, a significant upregulation of genes associated with biofilm formation were identified in 2021-derived communities, suggesting differences in transcriptional responses under identical enrichment conditions between microbial communities originating from the two sampling periods. Transcriptional activity of antimicrobial resistance (AMR) genes was also detected, particularly those associated with tolerance to quaternary ammonium compounds (QACs), the predominant sanitizers used in food-processing environments. The biofilm models employed in this study may introduce selection bias relative to the native drain community. However, by using drain-derived inocula incubated under processing-relevant conditions, this approach captures the transcriptional potential of the drain-associated microbial communities. This framework provides a reproducible and experimentally accessible platform for investigating gene expression dynamics in complex food-environment microbiomes, and establishes a foundation for future in situ and controlled in vitro studies. Collectively, these findings advance our understanding of drain microbiome ecology and may offer insights for designing intervention strategies to improve biofilm control in meat-processing environments.}, }
@article {pmid42215196, year = {2026}, author = {Ma, S and Liu, T and Wei, Y and Li, H and Li, Z}, title = {Comparative analysis of bacterial community dynamics in backslopped sourdoughs initiated with Maudiozyma humilis LB4 and Saccharomyces cerevisiae C1 using full-length 16S rRNA gene sequencing.}, journal = {Food microbiology}, volume = {139}, number = {}, pages = {105116}, doi = {10.1016/j.fm.2026.105116}, pmid = {42215196}, issn = {1095-9998}, mesh = {Fermentation ; *Saccharomyces cerevisiae/metabolism ; *Bread/microbiology/analysis ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Food Microbiology ; Triticum/microbiology ; }, abstract = {Using selected yeasts to prepare sourdough has become increasingly popular in recent years. However, the impact of various yeast species on the development of the autochthonous bacterial community during backslopped sourdough fermentation remains poorly characterised. This study investigated and compared the dynamics of the bacterial community in backslopped sourdough initiated with Maudiozyma humilis LB4 and Saccharomyces cerevisiae C1 using full-length 16S rRNA gene sequencing. During backslopping fermentation, the two types of sourdough exhibited significant variations in their dominant bacterial species. After 3 days of backslopping, Lactococcus lactis (26.87%) and Levilactobacillus brevis (25.54%) were identified as the dominant lactic acid bacteria (LAB) species in the LB4 initiated sourdough. For sourdough started with C1, however, Lactiplantibacillus plantarum (50.75%) and Enterococcus durans (30.51%) were found to dominate. Following 10 backslopping fermentation steps, both the sourdoughs initiated with LB4 and C1 harboured a core microbiome consisting of three species: Fructilactobacillus sanfranciscensis, Lacp. plantarum and Levl. brevis. However, the relative abundance of these species notably differed between the two types of sourdough. The reducing sugars (RDS), essential amino acids (EAA), non-essential amino acids (NEAA) and pH were biochemical factors significantly affecting the bacterial community (p < 0.05). EAA exhibited significant positive correlations with Frul. sanfranciscensis but negative correlations with Lacp.plantarum, while pH showed the opposite trend (p < 0.05). These findings contribute to an in-depth understanding of the influences of yeast species on the bacterial community in backslopped sourdough.}, }
@article {pmid42215197, year = {2026}, author = {Cazzaniga, M and Shen, P and Flegar, D and Bra, KK and Villoria Recio, M and Bahey-El-Din, M and Hueston, C and Claesson, MJ and Melgar, S and Gahan, CGM}, title = {Functional impact of dietary chitin upon Listeria monocytogenes pathogenesis.}, journal = {Food microbiology}, volume = {139}, number = {}, pages = {105117}, doi = {10.1016/j.fm.2026.105117}, pmid = {42215197}, issn = {1095-9998}, mesh = {*Chitin/administration &amp; dosage/metabolism ; Animals ; *Listeria monocytogenes/pathogenicity/genetics/drug effects ; Mice ; *Listeriosis/microbiology/immunology ; Virulence ; Macrophages/immunology/microbiology ; Humans ; Interleukin-6/immunology/genetics ; Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Female ; Dietary Supplements/analysis ; Diet ; }, abstract = {Chitin, the second most abundant polymer in nature, is recognized for biocompatibility and diverse effects on microbes and the host. However, the role of dietary chitin against foodborne pathogens such as Listeria monocytogenes remains underexplored. Here, we show that chitin functions as an environmental signal that attenuates L. monocytogenes virulence and mitigates infection outcomes. Consistent with previous studies, exposure of L. monocytogenes to chitin resulted in downregulation of key virulence genes and we demonstrate that this is accompanied by reduced pathogenesis in intestinal epithelial cells. While chitin can act as a pathogen-associated molecular pattern, stimulation of murine macrophages revealed no excessive induction of IL-6 or TNF-α after 24 h, indicating that it does not provoke detrimental inflammatory responses. In vivo, dietary supplementation with chitin significantly reduced bacterial burden in faeces and secondary organs within 24 h post-infection. These protective effects were further enhanced when mice were challenged with chitin-pretreated bacteria, highlighting the combined importance of host nutritional context and pathogen pre-exposure. Chitin also modulated host responses, promoting early IL-6 production and selectively shaping gut microbiota, with enrichment of potentially beneficial genera such as Alistipes, Eubacterium, and Duncaniella and suppression of pro-inflammatory Prevotella. Transcriptomic analyses revealed that L. monocytogenes responds to chitin by upregulating virR and dltD, indicative of an envelope stress response, though no direct link between VirR and virulence gene downregulation was observed. These findings establish chitin as a dietary molecule that simultaneously modulates pathogen virulence, host immunity, and microbial ecology, representing a potential strategy to mitigate gastrointestinal infection.}, }
@article {pmid42215210, year = {2026}, author = {Chen, L and Wang, G and Hu, Z and Teng, M and Cao, Q and Qin, X and Du, H and Yang, F and Tu, H and Wang, L}, title = {From diversity to stability: Acidification, antagonism, and resistance driven by Acetilactobacillus jinshanensis during jiang-flavor baijiu fermentation.}, journal = {Food microbiology}, volume = {139}, number = {}, pages = {105130}, doi = {10.1016/j.fm.2026.105130}, pmid = {42215210}, issn = {1095-9998}, mesh = {Fermentation ; Hydrogen-Ion Concentration ; Metagenomics ; *Wine/microbiology/analysis ; Microbiota ; Microbial Consortia ; Metabolomics ; }, abstract = {As a quintessential pillar of Chinese traditional industry, Baijiu relies on solid-state fermentation, a complex ecological succession process driven by highly diverse microbial consortia. While such systemic complexity often introduces stochasticity and uncertainty, baijiu solid-state fermentation is typically dominated by specific keystone species that exhibit remarkable resilience, maintaining high abundance while exerting top-down control over community structure and function. However, the mechanisms enabling these species to emerge from intensely competitive environments remain poorly understood. In this study, we employed Acetilactobacillus jinshanensis, a predominant species in the Moutai-flavor Baijiu microbiome, as a model to address these ecological questions. By integrating shotgun metagenomics, metatranscriptomics, and a pH-dependent generalized Lotka-Volterra model, we demonstrate that A. jinshanensis not only orchestrates environmental acidification but also reshapes the community landscape through active competitive inhibition. Leveraging comparative genomics and AlphaFold3-based structural predictions, we identified a unique GH25-LysM antibacterial module in A. jinshanensis predicted to target peptidoglycan with high specificity, potentially contributing to the suppression of acid-tolerant competitors. Furthermore, targeted metabolomics revealed a novel acid-resistance mechanism centered on an intra- and extracellular choline cycle, which significantly bolsters the organism's fitness under extreme acidic stress via metabolic modulation. Overall, we pinpoint a coupled mechanism set that explains the diversity-to-stability transition driven by A. jinshanensis in fermentation microbial community, offering process-relevant rules for improving reproducibility.}, }
@article {pmid42215271, year = {2026}, author = {Belasri, H and De Leye, H and Saerens, J and Vandermeersch, L and Badloe, FM and Vandeneynde, A and Lenie, S and De Vriese, S and Gies, I and Cools, F and Gucciardo, L and Kortekaas Krohn, I and Gutermuth, J}, title = {Development of IgE autoantibodies in newborns with atopic dermatitis (DIANA): protocol of a prospective, non-interventional, observational birth cohort.}, journal = {BMJ open}, volume = {16}, number = {5}, pages = {e114509}, doi = {10.1136/bmjopen-2025-114509}, pmid = {42215271}, issn = {2044-6055}, mesh = {Humans ; *Dermatitis, Atopic/immunology/blood ; *Autoantibodies/blood/immunology ; Prospective Studies ; *Immunoglobulin E/blood/immunology ; Infant, Newborn ; Infant ; Female ; Birth Cohort ; Male ; Research Design ; }, abstract = {INTRODUCTION: Atopic dermatitis (AD) is a chronic, pruritic inflammatory skin disorder that typically begins in early childhood and affects up to 20% of children. Infants with a family history of allergic diseases or with elevated total IgE levels are at increased risk of developing AD. Emerging evidence shows that a subgroup of AD patients produce IgE autoantibodies against skin self-peptides, which are suggested to play a role in disease pathophysiology and predict the development of allergic diseases later in life. Notably, such autoantibodies have been detected in up to 15% of infants with AD under 1 year of age, indicating that IgE autoantibodies can arise early in life. The 'Development of IgE Autoantibodies in Newborns with (high risk to develop) Atopic dermatitis' (DIANA) study is a prospective birth cohort designed to address these knowledge gaps by following a target of 500 newborns during their first 24 months of life.<br><br>METHODS AND DISSEMINATION: It aims to investigate the presence of IgE autoantibodies at birth (cord blood) and during early life (6, 12 and 24 months) using an immunoassay and their association with the development of AD in children from high-risk (n=400) and low-risk (n=100) families. Genetic and environmental influences are evaluated through questionnaires. Additional assessments will include skin and gut microbiome profiling using 16S rRNA sequencing (swabs), non-invasive evaluation of skin barrier function using electrical impedance spectrometry and analysis of the natural moisturising factor. We aim to decipher the underlying cause of IgE autoantibody development and allow preventive measures to counteract this.<br><br>ETHICS AND DISSEMINATION: This prospective, non-interventional observational study has been approved by the Ethics Committee of Universitair Ziekenhuis Brussel/VUB (07/06/2023; EC-2023-074) and will follow Good Clinical Practice, applicable regulations and the Declaration of Helsinki. Written informed consent will be obtained from parents or legal guardians. Participation is voluntary, and consent can be withdrawn at any time. All procedures comply with GDPR to ensure data confidentiality. Participant data will be pseudonymised, with the coding key accessible only to designated study members and securely stored on a restricted-access VUB server. Findings will be disseminated through peer-reviewed publications and conference presentations. Pseudonymised data will be made available upon reasonable request in accordance with institutional policies and data protection regulations TRIAL REGISTRATION NUMBER: NCT07316465.}, }
@article {pmid42215376, year = {2026}, author = {Kiguchi, Y and Suzuki, Y}, title = {Giants within: a new class of microbial mobile elements.}, journal = {Trends in genetics : TIG}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tig.2026.05.004}, pmid = {42215376}, issn = {0168-9525}, abstract = {Prokaryotes harbor a diverse spectrum of extrachromosomal elements (ECEs), which are intracellular replicons maintained independently of the primary chromosome. Historically, the ECE research field has focused on relatively small ECEs, such as plasmids. However, the advent of long-read sequencing has revealed that prokaryotes also harbor various types of giant ECEs, spanning hundreds of kilobases to over 1 Mb, that were not hitherto recognized. In this review, we describe how long-read sequencing has enabled the discovery of giant ECEs and compare the genetic architectures and functional repertoires of several recently characterized examples. The functions of most genes in these ECEs remain uncharacterized, and current computational tools frequently misclassify or overlook them. We further discuss how the discovery of these giant ECEs challenges existing classification frameworks that attempt to distinguish megaplasmids, chromids, and chromosomes. Together, these findings highlight giant ECEs as a largely unexplored layer of microbial genetics, whose characterization will have broad implications for our understanding of microbial adaptation and horizontal gene transfer.}, }
@article {pmid42215404, year = {2026}, author = {Lai, CT and Lee, WH and Chang, YY and Chiu, HM and Wu, CY and Chou, HC and Chen, MJ and Ei-Omar, EM}, title = {Concurrent evolution of infant oral and gut microbiota implies oral-to-gut transmission.}, journal = {Journal of the Formosan Medical Association = Taiwan yi zhi}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jfma.2026.05.060}, pmid = {42215404}, issn = {0929-6646}, abstract = {BACKGROUND/PURPOSE: Infant oral microbiome theoretically could serve as the seeding microorganisms in its own gut microbial construction from anatomical perspective. The purpose of this study was to investigate the relationship between oral and gut microbiota in early infantile life.<br><br>METHODS: This prospective longitudinal study included 15 healthy babies delivered in a single medical center during 2019&#x223c;2023. Stool samples were collected daily in the first 5 days after birth, while salivary and buccal mucosal samples were obtained once. All three samples continued acquisition at the end of 1st, 2nd, 4th and 6th month of age. The entire samples were 16S-rRNA sequenced. Investigation of the shared bacteria between oral and gut ecosystems was carried out.<br><br>RESULTS: Niche differentiation started very early in the infants' gut ecosystem since the 2nd day of life. Bifidobacterium appeared scarcely in the first 5 days after birth but gradually rose in abundance since the 1st month. The compositions of the infant salivary and buccal mucosal microbiome were similar. Most of the infant gut and oral microbiota evolved independently, whereas the oral Rothia, Prevotella and Veillonella correlated with the development of their gut counterparts. Coprococcus, Prevotella, Ruminococcaceae, Faecalibacterium and Megasphaera also showed associations between saliva and gut.<br><br>CONCLUSION: The optimal timing for examining and treating infant gut dysbiosis could be very early after birth. Together with the results from previous research, Ruminococcus and Veillonella deserve more investigation in the future to confirm their oral-to-gut transmission and potential effect in treating early-life intestinal dysbiosis.}, }
@article {pmid42215424, year = {2026}, author = {Liu, L and Tan, KR and Zhang, XH and Yuan, BJ and Li, YB and Jiang, ZY and Li, SX and Wang, YH and Tian, HD and Liu, HD and Wang, LP and Li, X and Li, Y and Zhang, XC and Johnston, RN and Liu, GR and Yang, XX and Liu, SL}, title = {Lignans Alleviate Depression by Modulating the Gut-Brain Axis: Effect and Mechanism Based on Multi-Omics Analyses.}, journal = {BioFactors (Oxford, England)}, volume = {52}, number = {3}, pages = {e70122}, doi = {10.1002/biof.70122}, pmid = {42215424}, issn = {1872-8081}, support = {82020108022//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Lignans/pharmacology ; Mice ; *Major Depressive Disorder/drug therapy/microbiology/metabolism/genetics ; *Gastrointestinal Microbiome/drug effects ; Humans ; Brain/drug effects/metabolism ; Disease Models, Animal ; Male ; Microglia/drug effects/metabolism ; Brain-Derived Neurotrophic Factor/metabolism/genetics ; *Brain-Gut Axis/drug effects ; Serotonin/metabolism ; Flax/chemistry ; *Antidepressive Agents/pharmacology ; gamma-Aminobutyric Acid/metabolism ; NF-kappa B/metabolism/genetics ; Mice, Inbred C57BL ; }, abstract = {Major depressive disorder (MDD) is a highly disabling psychiatric illness characterized by persistent low mood and psychomotor retardation, often leading to cognitive impairment or even suicidality. As the pathogenesis remains poorly understood, the currently available treatment regimens are mostly symptomatic therapies with little satisfactory curative effect. The emerging paradigm of gut-brain axis has highlighted gut dysbiosis as a key etiological factor to elicit neuro-inflammation and jeopardize the central nervous system homeostasis. In this study, we evaluated the ameliorating effects of flaxseed lignans on the gut microbiome to regain the gut micro-environmental functionality and alleviate MDD. The lignans significantly mitigated the severity of disease and markedly altered the gut microbiota structure in the participants. In the MDD mouse model, the lignans reversed the experimental depression-like behaviors, repaired neural and gut damage and restored barrier integrity. Of great significance, the lignans elevated the levels of 5-hydroxytryptamine (5-HT), brain-derived neurotrophic factor (BDNF) and γ-aminobutyric acid (GABA), and markedly attenuated microglial and systemic inflammation. Mechanistically, the lignans inhibited the IL-17/AP-1/NF-κB axis through direct interaction with the Fos protein. In the BV-2 cells, the lignan enterolactone reduced levels of nitric oxide and pro-inflammatory cytokines, further validating the anti-inflammatory mechanism of the lignans. Together, these findings demonstrate that lignans exert potent antidepressant effects by modulating the gut-brain axis and resolving neuro-inflammation, providing useful information for the development of novel therapeutic strategies for MDD prevention and treatment.}, }
@article {pmid42215593, year = {2026}, author = {Chen, Y and Han, X and Luo, M and Luo, L and Wang, T and Kong, C and Ye, L and Jin, J and Hou, D and Liao, H and Wang, Z and Xue, W and Lin, Z and Xu, S}, title = {Early detection of gastric cancer: a novel circulating microbiome DNA based liquid biopsy assay.}, journal = {NPJ precision oncology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41698-026-01532-9}, pmid = {42215593}, issn = {2397-768X}, support = {82302622//National Natural Science Foundation of China/ ; 2022KY675//Zhejiang Province Medical and Health Technology Project/ ; 2024KY862//Zhejiang Province Medical and Health Technology Project/ ; 2024C03050//"Pioneer" and "Leading Goose" R&amp;D Program of Zhejiang/ ; 2022C03002//"Pioneer" and "Leading Goose" R&amp;D Program of Zhejiang/ ; }, abstract = {Microorganisms play significant roles in gastric cancer (GC) progression. However, it is unknown whether circulating microbiome DNA (cmDNA) possesses GC specific features and could serve as diagnostic biomarker for GC detection. In this study, one cohort of 586 participants from Zhejiang Cancer Hospital were divided randomly into the training and testing datasets. Another cohort of 299 participants enrolled from three hospitals was used as an independent validation cohort. The cmDNA from plasma samples were analyzed by sequencing and various tools. The significant features of cmDNA were used as inputs to establish a machine learning diagnostic model (cmDNA-MLM). The cmDNA-MLM achieved the area under receiver operating characteristic curve (AUC) of 0.831 for GC across all stages in the testing cohort and 0.914 in the independent validation cohort. Notably, this model demonstrated strong performance in detecting early-stage GC, achieving an AUC of 0.792 for stage I GC in the validation cohort and exhibited favorable sensitivities across various molecular subtypes. The stage shift analysis showed a notable increase in the number of patients diagnosed at stage I. This cmDNA-MLM exhibited promising performance in early GC detection, which could be used as a clinical liquid biopsy methodology after more clinical validation studies.}, }
@article {pmid42215825, year = {2026}, author = {Lv, J and Wang, JH and Wang, YY and Huang, J and Chen, FR and Fang, S and Wang, XJ and Li, ZT and Shi, YP and Guo, L}, title = {Gut microbial alterations and functional shifts in patients with hypertriglyceridemia: insights from a northwestern Chinese metagenomic study.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {42215825}, issn = {1618-1905}, support = {2025JC-YBMS-916//Shaanxi Natural Science Foundation of China/ ; No. 81702067 and 82560411//National Natural Science Foundation of China/ ; }, abstract = {Although hypertriglyceridemia (HTG) is a significant contributor to lipid-associated pathologies such as atherosclerotic cardiovascular disease, its regulation by host‒microbiome interactions remain insufficiently characterized. While the gut microbiota (GM) is known to influence cholesterol metabolism, its specific role in systemic triglyceride (TG) homeostasis, particularly in non-Western populations, is poorly defined. This study aimed to identify preliminary robust GM signatures associated with HTG and to assess their translational potential using integrated multiomics and explainable machine learning approaches. In a cross-sectional investigation of 50 well-phenotyped adults from Northwest China, we combined 16S rRNA sequencing, shotgun metagenomics, and ensemble machine learning (LightGBM/XGBoost) to elucidate the associations between the GM and TGs. Microbial features were rigorously linked to serum lipid profiles through dual-algorithm validation and SHAP interpretability analysis, while functional potential was assessed via KEGG pathway mapping. Subjects with HTG exhibited a distinct gut microbial configuration, marked by consistent enrichment of Faecalibacterium and Bacteroides coprocola (positively correlated with serum TG levels) and depletion of Bifidobacterium pseudocatenulatum and Lactobacillus salivarius (inversely correlated). Machine learning converged on five exploratory consensus biomarker taxa, three of which were independently confirmed by LEfSe analysis (Faecalibacterium). Functional profiling further revealed the upregulation of microbial starch and sucrose metabolism pathways in the HTG cohort. Our findings establish a preliminary gut microbial signature for HTG patients and suggest context‑dependent associations of butyrate-producing taxa such as Faecalibacterium. By integrating multiomics with explainable artificial intelligence, this work addresses key challenges in reproducibility and mechanistic inference in microbiome research. These results pave the way for novel microbiota-targeted therapeutic strategies, including precision probiotics and dietary interventions, to modulate lipid metabolism, pending further validation in expanded cohorts and functional studies.}, }
@article {pmid42216036, year = {2026}, author = {Wang, T and Niu, B and Xia, S and Song, D and Yang, Y and Wei, H and Gao, M and Zhou, W}, title = {Distinct filtering processes shape bacterial and fungal communities and their co-occurrence patterns across garlic-associated compartments.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00870-2}, pmid = {42216036}, issn = {2524-6372}, support = {2022YFD1901300//National Key Research and Development Program of China/ ; 31870004//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Garlic (Allium sativum L.) is an important economic crop that is often subjected to continuous monoculture practices. Although the garlic rhizosphere is known to harbor growth‑promoting and disease‑suppressive potential, comprehensive investigations of microbial communities and interactions across the rhizosphere, roots, and leaves remain limited. In this study, bacterial and fungal communities in the rhizosphere soil, roots, and leaves of garlic plants grown under long-term monoculture in four major production regions of China were examined using amplicon sequencing, aiming to characterize the garlic‑associated microbiome and explore the potential pathogen‑antagonistic taxa under continuous monoculture.<br><br>RESULTS: Microbial communities and their predicted functions were more strongly influenced by the compartment niche than by the production area, with distinct bacterial and fungal community patterns in each compartment niche. Source-tracking analysis revealed distinct colonization routes for bacterial and fungal communities in the garlic leaf endosphere. Bacterial communities in leaves appeared to be predominantly derived from the root endosphere, while fungal communities in leaves showed a potential direct derivation from the rhizosphere soil rather than roots. Potential pathogenic fungi were more abundant in rhizosphere soil and leaves than in roots. In the bacterial co-occurrence network, two modules abundant in roots and characterized by Pseudomonas and Flavobacterium were negatively associated with pathogen relative abundance. In the cross-kingdom network, keystone taxa included potential pathogenic ASVs from Verticillium and Fusarium, and they were negatively associated with bacterial taxa such as Lysinimonas and Microbacterium.<br><br>CONCLUSIONS: These findings provide insights into the distinct colonization patterns of bacterial and fungal communities in garlic and their co-occurrence networks under long-term monoculture. The identification of bacterial taxa with antagonistic potential offers candidates for developing biocontrol agents to improve soil-borne disease management in garlic production.}, }
@article {pmid42216058, year = {2026}, author = {Liu, H and Han, S and Shi, K and Zhang, Y and Xu, Y and Song, S and Chen, Y}, title = {Biosynthesized selenium nanoparticles increase soybean resistance to root rot by recruiting beneficial microbes and reprogramming host metabolism.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02439-0}, pmid = {42216058}, issn = {2049-2618}, abstract = {BACKGROUND: Soybean root rot, primarily caused by Fusarium species, is a devastating soil-borne disease that severely threatens global soybean production. Conventional chemical controls are problematic due to their environmental impact and the risk of fostering pathogen resistance. There is therefore an urgent need to develop sustainable and eco-friendly alternative strategies.<br><br>RESULTS: This study demonstrated that selenium nanoparticles (SeNPs) biosynthesized by Bacillus subtilis ZY56 significantly increased soybean resistance to F. oxysporum. Characterization confirmed that the obtained SeNPs were spherical (approximately 147&#xa0;nm), consisting of amorphous-state elemental selenium (Se[0]) with a bioactive protein-polysaccharide coating. Treatment with 2.66&#xa0;mg/L SeNPs significantly promoted seed germination, seedling growth, and antioxidant enzyme activity, while markedly reducing the root rot disease index. Multiomics analyses revealed that SeNPs reprogrammed host metabolism by increasing the levels of key defense-related metabolites (camalexin and isoflavonoids) and upregulating associated biosynthetic pathways. Crucially, SeNPs reshaped the rhizosphere microbiome, enriching beneficial genera (e.g., Bradyrhizobium, Lysobacter, and Nocardioides). Moreover, the analysis predicted enhanced microbial tyrosine metabolism. Integrated correlation analysis identified tyrosine metabolism as a core hub linking microbiome restructuring to host defense, supporting a "microbe&#x2012;plant metabolic division of labor" model in which microbes supply precursors (e.g., L-tyrosine) for the synthesis of antifungal compounds in the host. This finding was functionally validated, as the accumulated metabolites (camalexin and isoflavonoids) directly inhibited F. oxysporum growth in vitro.<br><br>CONCLUSIONS: Our findings reveal a dual mechanism whereby SeNPs concurrently prime host defenses and modulate beneficial plant-microbe interactions, offering a sustainable nano-enabled strategy for managing soil-borne diseases. Video Abstract.}, }
@article {pmid42216074, year = {2026}, author = {Ding, D and Zhang, Y and Tian, H and Dong, B and Wu, X and Liu, S and Gao, T and Zhang, L and Fu, T}, title = {Dietary baicalin supplementation enhances growth performance in fattening Hu sheep via dual modulation of immunity and gastrointestinal microbiome-metabolic crosstalk.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42216074}, issn = {1674-9782}, support = {2024YFD1300204//National Key Research and Development Program of China/ ; }, abstract = {BACKGROUND: Baicalin is a bioactive flavonoid from Scutellaria baicalensis Georgi with antioxidant, anti‑inflammatory and antibacterial properties. However, its bitter taste and susceptibility to ruminal degradation limit its practical use in mammals. Enteric coating technology might overcome these limitations by enabling targeted intestinal release. This study investigated effects of dietary supplementation with baicalin and coated baicalin on rumen fermentation, gastrointestinal microbiota, immune function and growth performance in Hu sheep.<br><br>RESULTS: Thirty-six lambs with similar body weight (33.01&#x2009;&#xb1;&#x2009;2.68&#xa0;kg) were randomly assigned to three groups (4 replicates per group, 3 sheep per replicate). The control group was fed basal diet (CON) while treatment I (BAI) and treatment II (C-BAI) groups were fed a basal diet supplemented with 0.1% baicalin and coated baicalin, respectively. After a 60-d feeding trial, baicalin and coated baicalin supplementation improved total weight gain and average daily gain compared with CON group (P&#x2009;<&#x2009;0.05). In addition, BAI and C-BAI groups exhibited higher total antioxidant capacity (P&#x2009;<&#x2009;0.05) and catalase activity (P&#x2009;<&#x2009;0.05) with associated lower malondialdehyde levels (P&#x2009;<&#x2009;0.05). Immunoglobulin G and anti-inflammatory cytokines interleukin-4 (IL-4) were also increased (P&#x2009;<&#x2009;0.001). Notably, IgM, IL-10 and IL-4 in the C-BAI group exceeded those of the BAI group (P&#x2009;<&#x2009;0.001). Microbiome analysis revealed that baicalin supplementation enriched abundance of beneficial bacterial taxa including Firmicutes and Lachnoclostridium (P&#x2009;<&#x2009;0.05) and reduced potential pathogen abundance, e.g., Treponema and Ralstonia (P&#x2009;<&#x2009;0.05). The C-BAI group also showed increased abundance of the beneficial Bradyrhizobium compared with CON (P&#x2009;<&#x2009;0.05). Metabolomic analysis revealed that baicalin altered propionate and tyrosine metabolic pathways (P&#x2009;<&#x2009;0.05), while coated baicalin modulated penicillin metabolism and glyceride metabolism in jejunum (P&#x2009;<&#x2009;0.05) increasing ATP production. Overall, these results indicated enhanced nutrient metabolism and gut health in the presence of dietary baicalin.<br><br>CONCLUSIONS: Dietary supplementation with baicalin and coated baicalin improved growth performance, antioxidant status, immunity and beneficially modulated the microbiome-metabolome crosstalk in Hu sheep. Notably, uncoated baicalin exerted more pronounced effects on growth performance and supported a role for baicalin as a potential and functional feed additive.}, }
@article {pmid42216084, year = {2026}, author = {Zhang, Y and Ma, J and Zhang, L and Wang, R and Qu, X and Wei, T and Zhou, J and Liu, W and Wang, X}, title = {Longitudinal analysis of stowaway microorganisms aboard modules and cargo spacecraft of the Chinese Space Station.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02438-1}, pmid = {42216084}, issn = {2049-2618}, support = {32270119//National Natural Science Foundation of China/ ; KJZ-YY-NSM0518//Space Station Engineering Science Experiment Project/ ; }, abstract = {BACKGROUND: Although microbial contamination in crewed spacecraft is well studied, quantitative assessment of microorganisms from spacecraft structures and cargo remains overlooked. Here, we investigate 165 microbial samples collected from five critical environments of China Space Station (CSS) missions undertaken in 2016-2024: ground assembly, cargo loading, crewed simulation cabin, test cabin, and on-orbit. The investigation aims to elucidate the impact of cargo- and cabin-derived microorganisms on the CSS microbial community while characterizing the station's unique microbial profile.<br><br>RESULTS: The calculation results based on the microbial source tracking model revealed that the proportion of cabin-source microbes peaked during initial construction (14.02%) but declined after deployment, whereas cargo-source microbes reached 36.89%. The top three persistent microbial genera in orbit from both sources were Staphylococcus, Acinetobacter, and Corynebacterium. High-abundance CSS microorganisms in the orbital environment are commonly found in both humans and plants, and the few cabin- or cargo-derived microorganisms that entered the interior differed markedly from high-abundance microorganisms found in terrestrial environments. Cargo storage areas and controlled cleanrooms posed a high risk of microbial transfer into orbit, necessitating stricter sterilization measures.<br><br>CONCLUSIONS: These findings systematically characterize, for the first time, the dynamic patterns of structural/cargo-borne microbial contamination during CSS's early phases, providing critical data for biosecurity protocols of long-duration missions. Video Abstract.}, }
@article {pmid42216102, year = {2026}, author = {Atighetchi, S and Pilgrim, T and Bahtiyar, Y and Suc, G and Urena-Alcazar, M and Döring, Y and Chong-Nguyen, C}, title = {The potential role of sex related differences of the microbiome and its impact on calcific aortic stenosis: a narrative review.}, journal = {Biology of sex differences}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13293-026-00932-7}, pmid = {42216102}, issn = {2042-6410}, abstract = {Aortic stenosis (AS) presents with distinct sex-related differences in clinical manifestation, pathophysiology, and response to treatment. Women typically present at an older age, with greater frailty, more pronounced symptoms, and paradoxical low-flow AS, often associated with concentric left ventricular remodeling and fibrotic valve changes. In contrast, men show a predominance of calcific AS, eccentric remodeling, and more extensive aortic valve calcification. These differences are not solely anatomical or hemodynamic; they extend to molecular pathways and emerging contributors such as the gut microbiota.Recent evidence suggests that gut microbiota composition and its metabolites, particularly trimethylamine-N-oxide (TMAO) and indoxyl sulfate (IS), play a sex-specific role in AS pathogenesis. Women generally exhibit a more diverse and cardioprotective microbiota profile, shaped by estrogen and dietary habits, that might explain lower levels of pro-calcific metabolites and a fibrotic valve phenotype. Conversely, men tend to have higher TMAO and IS levels, driven by a Firmicutes-enriched microbiota and androgenic modulation, which might promote calcification and inflammatory signaling in the aortic valve.This review integrates current knowledge on sex-related differences in AS, spanning clinical patterns, valvular remodeling, cellular and molecular signaling, and gut-heart interactions, to propose a hypothesis-driven framework on how gut microbiota may contribute to sex-specific differences in AS.}, }
@article {pmid42216204, year = {2026}, author = {Zhang, W and Duan, C and Feng, X and He, L and Liu, H and Ke, H and Wang, Y and Zhao, J and Kong, L and Hu, Z}, title = {Integrative analysis of the meibum microbiome in dry eye disease: from dysbiosis and diagnostic biomarkers to immunomodulation by Bradyrhizobium-derived outer membrane vesicles.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-08327-3}, pmid = {42216204}, issn = {1479-5876}, support = {202501AY070001-209//Joint Project of Applied Basic Research of Kunming Medical University, Science and Technology Department of Yunnan Province of China/ ; ZKF2024055//National Key Clinical Specialty Open Research Project/ ; 2024YNLCYXZX0327//Yunnan Provincial Ophthalmology Disease Clinical Medicine Center Research Project/ ; }, abstract = {BACKGROUND: Dry eye disease (DED) is a multifactorial disorder involving tear film instability and inflammation. The ocular surface microbiome (OSM) modulates local immunity, but its functional role in DED remains elusive. We characterized OSM alterations in DED and investigated the immunomodulatory effects of bacterial outer membrane vesicles (OMVs).<br><br>METHODS: We enrolled 1,262 participants (520 DED, 742 controls). Clinical DED phenotypes were systematically identified using univariate, multivariate, and least absolute shrinkage and selection operator (LASSO) regression analyses. Meibum samples were subjected to 16S rRNA gene sequencing; amplicon sequence variants were generated using the divisive amplicon denoising algorithm 2 (DADA2) and taxonomically annotated against the SILVA database. Microbial diversity, community composition, and diagnostic biomarkers were evaluated, complemented by functional prediction (PICRUSt2) and co-occurrence network analyses. In vitro, OMVs isolated from Bradyrhizobium were applied to M1 macrophages to assess immunomodulatory effects through cytokine quantification, flow cytometric analysis of surface markers, and polarization-related gene expression profiling.<br><br>RESULTS: Clinical profiling identified eight independent risk factors associated with DED, including ocular surface disease index scores, tear break-up time, and meibomian gland dysfunction. DED patients exhibited markedly elevated alpha-diversity (P&#x2009;<&#x2009;0.001) and distinct microbial communities. Taxonomic shifts included reduced Alphaproteobacteria and Bradyrhizobium but enriched Gammaproteobacteria and Ralstonia. A six-genus panel distinguished DED from controls (AUC&#x2009;=&#x2009;0.793). Functional prediction highlighted upregulated pathways related to inflammation, tight junctions, and PI3K-Akt-mTOR signaling. In vitro, Bradyrhizobium OMVs attenuated pro-inflammatory cytokines (TNF-&#x3b1;, IL-6, IL-1&#x3b2;; P&#x2009;<&#x2009;0.001) while enhancing anti-inflammatory mediators (IL-10, TGF-&#x3b2;1). OMVs treatment decreased CD86&#x207a; and increased CD206&#x207a; macrophages (P&#x2009;<&#x2009;0.001), consistent with M2 polarization, supported by downregulated inducible nitric oxide synthase (iNOS) and upregulated arginase-1 (Arg-1) expression (P&#x2009;<&#x2009;0.001).<br><br>CONCLUSION: This study establishes DED as a multifactorial condition associated with sleep, systemic disease, meibomian gland blockage, and radiation. These clinical features coexist with ocular surface dysbiosis characterized by depletion of beneficial Bradyrhizobium and expansion of Ralstonia taxa. Notably, Bradyrhizobium-derived OMVs confer protective effects by driving M2 macrophage polarization and resolving inflammation. Collectively, these findings underscore the microbiome-immune axis as a critical node in DED pathogenesis and provide a mechanistic rationale for microbiome-targeted diagnostics and therapeutics. Given the low-biomass nature of meibum and the absence of sequenced negative controls, a contribution of reagent-associated taxa to the observed signal cannot be fully excluded and warrants confirmation in future studies with comprehensive contamination controls.}, }
@article {pmid42216221, year = {2026}, author = {Zhang, K and Duan, C and Chen, J and He, Q and Jin, Y and Liu, J and Lin, R and Han, C}, title = {Bone marrow mesenchymal stem cells synergize with fusobacterium nucleatum to drive colorectal tumorigenesis via gut microbiome dysbiosis.}, journal = {Gut pathogens}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13099-026-00839-z}, pmid = {42216221}, issn = {1757-4749}, support = {2024M761069//Postdoctoral Research Foundation of China/ ; 82470679//National Natural Science Foundation of China/ ; 2023YFC2307001//National Natural Science Foundation of China/ ; 82170570//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The oncogenic role of F. nucleatum (Fn) in colorectal cancer (CRC) is increasingly recognized, yet its interaction with host stromal components, such as bone marrow mesenchymal stem cells (BMSCs), remains poorly understood. Building on our previous discovery that BMSC-derived Wnt3a promotes Fn-driven tumorigenesis, this study aims to investigate the synergistic interplay between BMSCs and F. nucleatum in CRC pathogenesis via the gut microbiome.<br><br>METHODS: Based on the established Apc[Min/+] mouse model of CRC, animals were randomly assigned to four experimental groups: control, Fn-only, BMSCs-only, and Fn+BMSCs co-treatment group. Gut microbiota composition was continuously analyzed over 8 weeks by metagenomic sequencing. Metagenomic functions were predicted using PICRUSt2.<br><br>RESULTS: The Fn+BMSCs co-treatment group exhibited the highest enrichment of F. nucleatum and the greatest reduction in microbial diversity. Fn+BMSCs co-treatment induced a distinct pro-tumorigenic shift, marked by a decline in symbiont Lactobacillus and an increase in pathobiont Escherichia-Shigella. Metagenomic analysis revealed a unique enhancement of butanoate metabolism in the Fn+BMSC co-treatment group. Furthermore, a profoundly elevated LPS level was discovered in the Fn+BMSCs co-treatment group, indicating hyperactivation of the pro-inflammatory and proliferative TLR4/NF-&#x3ba;B pathway.<br><br>CONCLUSIONS: Our findings demonstrate that BMSCs synergize with F. nucleatum to create a tumorigenicmicroenvironment by driving microbial dysbiosis, reprogramming metabolic pathways, and amplifying pro-inflammatory signaling. Our findings reveal that BMSCs fuel CRC progression via multiple mechanisms: by altering the gut microbiome ecology and, as previously discovered, by providing oncogenic Wnt3a signals. Targeting the synergistic BMSC-Fn axis may thus offer a novel therapeutic strategy for CRC.}, }
@article {pmid42216230, year = {2026}, author = {He, Y}, title = {Re-Evaluating Probiotic Efficacy in Irritable Bowel Syndrome: A Call for Rigorous Statistics, Digital Therapeutics, and Microbiome-Driven Precision.}, journal = {Journal of gastroenterology and hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jgh.70459}, pmid = {42216230}, issn = {1440-1746}, }
@article {pmid42216535, year = {2026}, author = {Parolini, C and Amedei, A}, title = {The Microbiome Epoch: Cracking the Cardiovascular-Neurodegenerative Disorder Code.}, journal = {Frontiers in bioscience (Landmark edition)}, volume = {31}, number = {5}, pages = {47174}, doi = {10.31083/FBL47174}, pmid = {42216535}, issn = {2768-6698}, support = {B55F21007810001//Il bando si inserisce nelle iniziative finanziate dall'Unione Europea - Next Generation EU/ ; B83C22003920001//Project Tuscany Health Ecosystem (THE)/ ; }, mesh = {Humans ; *Cardiovascular Diseases/microbiology ; *Neurodegenerative Diseases/microbiology ; *Gastrointestinal Microbiome/physiology ; Dysbiosis/microbiology ; Animals ; Inflammation/microbiology ; Gastrointestinal Tract/microbiology ; Enteric Nervous System ; }, abstract = {Increasing evidence suggests that the gut microbiome (GM) may exert a seminal role in the maintenance of host health as well as in the pathogenesis of various illnesses, including cardiovascular disease (CVD) and neurodegenerative disorders (NDDs). GM influences host physiology by metabolizing dietary factors and host-derived substrates, thereby producing active molecules that trigger responses at local and systemic levels. The inflammatory process is characterized by a rapid "onset phase" followed by a "resolution phase", which is essential to curtail inflammation and restore tissue homeostasis. Unique individual and environmental conditions may alter the GM equilibrium as well as impair the "resolution phase" leading to GM dysbiosis and chronic low-grade inflammatory conditions, which eventually promote the development of common/widespread human pathologies, such as inflammatory bowel and autoimmune diseases, cancer, CVD, and NDDs. This review describes the different components of the gastrointestinal tract, namely the enteroendocrine and enteric nervous systems, and the GM. Secondly, it discusses the connections among unresolved and sterile inflammation, GM and human illnesses, namely CVD and NDDs. Finally, we emphasizes the limitations of current evidence and the need for further research to fill the gap in establishing the causal link between the GM and the pathogenesis of both CVD and NDDs.}, }
@article {pmid42216549, year = {2026}, author = {Ye, Z and Song, Z and Yang, D and Xiao, Y and Chen, J and Wang, G}, title = {The Gut-Bone Axis: Molecular Mechanisms and Therapeutic Perspectives in Skeletal Homeostasis.}, journal = {Frontiers in bioscience (Landmark edition)}, volume = {31}, number = {5}, pages = {46147}, doi = {10.31083/FBL46147}, pmid = {42216549}, issn = {2768-6698}, support = {2023ZYQJ02//The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Biomechanical research on cartilage transplantation based on the theory of "equal emphasis on muscle and bone"/ ; }, mesh = {Humans ; *Homeostasis ; *Bone and Bones/metabolism/physiology ; Animals ; *Gastrointestinal Microbiome/physiology ; *Bone Remodeling/physiology ; Signal Transduction ; Fatty Acids, Volatile/metabolism ; Bile Acids and Salts/metabolism ; *Gastrointestinal Tract/metabolism/microbiology ; }, abstract = {The gut-bone axis represents a paradigm shift in our understanding of skeletal biology, revealing how the gastrointestinal system and its microbial inhabitants profoundly influence bone homeostasis through complex bidirectional communication. This comprehensive review synthesizes recent high-impact research to elucidate the multifaceted mechanisms underlying gut-bone crosstalk, including microbial metabolite signaling, gut barrier integrity, immune modulation, and endocrine regulation. We examine how short-chain fatty acids (SCFAs), tryptophan metabolites, and bile acid derivatives modulate bone remodeling through epigenetic, immunologic, and hormonal pathways. The translational implications of these findings for the management of osteoporosis, osteoarthritis, and inflammatory bone disorders are critically evaluated, with particular emphasis on microbiome-targeted interventions, gut hormone-based therapies, and innovative approaches such as engineered microbial therapeutics. Furthermore, we explore the roles of farnesoid X receptor (FXR) signaling, G protein-coupled receptor activation, and mitochondrial function in bone cells as modulated by gut-derived factors. This review provides a framework for developing novel diagnostic and therapeutic strategies that target the gut-bone axis, highlighting the transition from traditional calcium-centric bone health paradigms toward integrated microbiome-targeted approaches that address the systemic nature of bone metabolism regulation.}, }
@article {pmid42216624, year = {2026}, author = {Taha, MME and Abdelwahab, SI and Sahli, KA and Jeraiby, M and Qadri, M and Alarifi, A and Farasani, A and Moshi, JM}, title = {A century of coffee and tea research in cognitive health and Alzheimer's disease: Structural, thematic, and translational insights (1911-2025).}, journal = {Journal of Alzheimer's disease : JAD}, volume = {}, number = {}, pages = {13872877261450996}, doi = {10.1177/13872877261450996}, pmid = {42216624}, issn = {1875-8908}, abstract = {BackgroundAlthough studies have explored tea and coffee in relation to Alzheimer's disease, no century-scale analysis has jointly examined both within a unified primary-evidence framework.ObjectiveThis study maps the structural, thematic, and temporal evolution of coffee and tea research in cognitive aging.MethodsScopus-indexed original English articles (1911-2025) were retrieved using a structured Boolean strategy under PRISMA guidance. Analyses were conducted using Bibliometrix and VOSviewer. Performance metrics, collaboration networks, co-citation mapping, Bradford's Law, co-word clustering, thematic evolution, and overlay visualization were applied to full-period and recent (2021-2025) datasets.ResultsA total of 2873 articles across 1285 sources demonstrated steady annual growth (4.96%) and substantial citation impact (mean 40.17 citations per document). Research productivity was concentrated in high-income countries, led by the United States, United Kingdom, and China, reflecting core-periphery stratification and citation asymmetry. Collaboration networks showed hub dominance with dense transatlantic-Eurasian linkages. Bradford analysis identified a limited core of highly productive journals. Thematic evolution revealed persistent anchoring in Alzheimer's disease, oxidative stress, and neuroprotection, with sustained prominence of coffee, caffeine, tea, and polyphenols. Recent years indicate translational expansion integrating microbiome science and computational methods. Overlay visualization demonstrated temporal stratification, highlighting emerging themes such as gut microbiota and deep learning alongside stable beverage-related cognitive frameworks.ConclusionsCoffee and tea research in cognitive aging has evolved into a mature, mechanistically grounded, and globally stratified field, increasingly integrating translational, microbiome, and computational approaches in dementia-related investigations.}, }
@article {pmid42217154, year = {2026}, author = {Parlindungan, E and Luah, JES and Wibowo, M}, title = {Bacillaceae in Probiotics and Postbiotics: Applications, Functional Traits, Mechanisms and Outlook.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {42217154}, issn = {1867-1314}, support = {I24D1AG061//Innovation &amp; Enterprise (I&amp;E), Agency for Science, Technology, and Research (A*STAR)/ ; I24D1AG061//Innovation &amp; Enterprise (I&amp;E), Agency for Science, Technology, and Research (A*STAR)/ ; }, abstract = {Despite the well-documented health benefits of non-spore-forming probiotics such as Lactobacillus and Bifidobacterium, their broader application can be constrained by limited stability and survivability during processing, storage and gastrointestinal transit. These limitations have driven growing interest in spore-forming bacteria belonging to Bacillaceae family for potential use as probiotics particularly for products that require heat processing or extended shelf-life. This review focuses on the genera Bacillus, Heyndrickxia and Priestia, which have established roles across biotechnology, food and industrial applications, with evidence demonstrating benefits in plants, animals and human nutrition. Key technological traits, carbohydrates and nitrogen metabolism capacities and bioactive outputs are highlighted in this review, including the production of enzymes, antimicrobial compounds such as bacteriocins and non-ribosomal synthesized peptides, as well as other metabolites relevant to host and microbiome modulation. The mechanistic basis underpinning reported functions, such as competitive exclusions, antimicrobial activity, and immunomodulatory effect are also discussed in the context of probiotic and postbiotic. Finally, translational considerations, challenges and outlook in spore-forming probiotic and postbiotic biosolutions are addressed, including strain specific efficacy, safety evaluation and long-term use, and the practical requirements for robust human validation. This review intends to provide a critical and comprehensive synthesis, to update and further encourage researchers and industry stakeholders in developing Bacillaceae-based probiotics and postbiotics that align with the market needs.}, }
@article {pmid42217184, year = {2026}, author = {Vandoren, R and Ha, M and Van Deuren, VML and De Roeck, N and Pu, T and Brand, EC and Kuznetsova, M and Besbassi, H and Bartholomeus, E and Affaticati, F and De Boeck, I and Gehrmann, T and Lebeer, S and Oldenburg, B and van Wijk, F and Delputte, P and Verbandt, S and Tejpar, S and Laukens, K and Ogunjimi, B and Meysman, P}, title = {AIRRWAS integrates TCR-microbiome data to reveal how the gut microbiome shapes the circulating and mucosal T cell repertoire.}, journal = {Cell reports}, volume = {45}, number = {6}, pages = {117479}, doi = {10.1016/j.celrep.2026.117479}, pmid = {42217184}, issn = {2211-1247}, abstract = {The gut microbiome modulates mucosal immunity and contributes to multiple diseases, but the extent to which it shapes circulating and mucosal T cell repertoires remains unclear. Here, we paired CD4[+] and CD8[+] T cell receptor (TCR) sequencing with fecal 16S rRNA microbiome profiling and developed adaptive immune receptor repertoire-wide association study (AIRRWAS), a framework integrating computational TCR-microbiome interaction analysis with targeted in vitro validation. Across three independent cohorts, AIRRWAS identified reproducible associations between convergent TCR clusters and 21 bacterial genera, including core commensals, probiotics, and taxa with immunomodulatory roles. Predicted clonotypes were enriched in genus-specific interaction networks and preferentially activated by matched bacterial stimuli. These findings reveal conserved microbiome-driven immune signatures across distinct repertoires and demonstrate that the gut microbiome shapes both local and circulating T cell populations, providing a resource for biomarker discovery, immune monitoring, and microbiome-targeted therapies.}, }
@article {pmid42217247, year = {2026}, author = {Gök, A and Arıkan, M}, title = {DDT exposure drives time-dependent restructuring of soil microbiomes in urban garden microcosms.}, journal = {Journal of environmental science and health. Part. B, Pesticides, food contaminants, and agricultural wastes}, volume = {}, number = {}, pages = {1-9}, doi = {10.1080/03601234.2026.2679866}, pmid = {42217247}, issn = {1532-4109}, abstract = {Dichlorodiphenyltrichloroethane (DDT) remains a pervasive legacy contaminant in urban soil matrices, yet the temporal dynamics of how it reshapes microbial community assembly remain poorly characterized. In this study, we investigated the successional response of an urban garden soil microbiome (Istanbul, Türkiye) to DDT exposure using a laboratory-scale microcosm framework. Soil samples were collected across a 15-day gradient (Days 0, 5, 10, and 15) and analyzed via 16S rRNA gene amplicon sequencing. DDT exposure was associated with time-dependent shifts in microbial diversity and community structure. Rather than showing evidence of broad diversity loss, Shannon diversity increased steadily in treated soils, suggesting niche expansion following the suppression of sensitive taxa. Differential abundance analysis identified a responder consortium; genera such as Rhodococcus, Kribbella, Nitrospira, Solirubacter, and Millisia significantly increased, whereas Pedomicrobium, Lysobacter, Pseudoarthrobacter, and Sedimentibacter declined. Inferred functional profiling revealed a marked metabolic restructuring in which pathways involved in aromatic amino acid and fatty acid metabolism decreased, while modules related to the degradation of chlorinated aromatic compounds, redox homeostasis, and stress responses were enriched. These findings suggest that DDT induces a specialized successional trajectory in soil microbiome, reflecting an adaptive transition toward a stress-resilient and potentially degradative community.}, }
@article {pmid42217285, year = {2026}, author = {Petersen, M and Walther, C and Borof, K and Heydecke, G and Beikler, T and Alawi, M and Müller, C and Nägele, FL and Zyriax, BC and Fiehler, J and Gallinat, J and Kühn, S and Twerenbold, R and Bang, C and Thomalla, G and Cheng, B and Aarabi, G}, title = {Subgingival microbiota composition is associated with brain health in the general population-the PAROMIND study.}, journal = {EBioMedicine}, volume = {128}, number = {}, pages = {106312}, doi = {10.1016/j.ebiom.2026.106312}, pmid = {42217285}, issn = {2352-3964}, abstract = {BACKGROUND: Periodontitis has gained attention as a key factor associated with cognitive decline and Alzheimer's dementia. However, the relationship between periodontitis-related oral microbiota shifts and brain health in the general population remains unclear.<br><br>METHODS: We investigated the oral microbiome-brain axis in 1026 participants from the population-based PAROMIND Study. Using 16S rRNA gene amplicon sequencing of subgingival crevicular fluid, we inferred via topological data analysis a microbiota similarity network. This network, which distills the complex high-dimensional data into an interpretable map of microbial similarity, revealed a continuous disease gradient mirroring the microbial pathogenicity spectrum, from taxa of low periodontal pathogenicity (e.g., Streptococcus) to periodontitis-associated taxa (e.g., Porphyromonas, Fusobacterium). Leveraging this network, we systematically examined associations between periodontal microbiota profiles and 40 brain health-related phenotypes, including cognition, brain structure, mental health, inflammatory biomarkers, diet, vascular risk factors, and demographics.<br><br>FINDINGS: Higher abundance of periodontitis-related bacterial taxa was associated with poorer cognitive performance, elevated leucocyte counts, and lower MIND diet adherence after covariate adjustment. Complementary forward model selection analysis supported the links to cognitive performance and inflammation, and additionally identified a significant association with brain structure (cortical thickness and subcortical volume). We identified associations with both established genera (Porphyromonas) and taxa not previously implicated in brain health (Fretibacterium, Tannerella, Dialister).<br><br>INTERPRETATION: These findings from a large cohort advance the understanding of the oral microbiome-brain axis, highlighting specific microbial profiles linked to subclinical cognitive, structural, and inflammatory brain health markers. By demonstrating these links in a non-demented population, our study suggests that monitoring the oral microbiome could inform early risk assessment for cognitive decline, positioning periodontal health as an accessible target for early intervention strategies.<br><br>FUNDING: Deutsche Forschungsgemeinschaft.}, }
@article {pmid42211118, year = {2026}, author = {Liu, J and Han, W and Wang, D and Aierken, Y and Liu, Z and Wang, J and Guo, J and Li, Y and Dai, X}, title = {Integrating gene-microbiome interactions and single-cell transcriptomics reveals therapeutic strategies for aortic aneurysm.}, journal = {iScience}, volume = {29}, number = {6}, pages = {115939}, pmid = {42211118}, issn = {2589-0042}, abstract = {Aortic aneurysm (AA) is a life-threatening vascular disorder lacking effective medical therapies. Gut microbiota contributes importantly to vascular homeostasis; yet, the underlying gene-microbiome interactions in AA remain unclear. Using two-sample Mendelian randomization, we identified and validated a protective causal effect of genus Intestinimonas abundance on AA risk. Genetic annotation pinpointed CCDC3 as a causal gene in the gut-aorta axis. Integration of bulk and single-cell RNA sequencing revealed that CCDC3 deficiency in vascular smooth muscle cells activates a pathogenic CXCL12-CXCR4 signaling axis, which recruits neutrophils and promotes neutrophil extracellular trap formation in aneurysmal tissue. These findings establish a mechanistic link between specific gut microbes, host genetics, and vascular inflammation at single-cell resolution, highlighting promising therapeutic targets for the treatment of aortic aneurysm.}, }
@article {pmid42211136, year = {2026}, author = {Rashidi, A and Minot, SS and Lee, SJ and Hill, GR and Podlesny, D}, title = {Cohesive modules of engraftment in fecal microbiota transplantation.}, journal = {iScience}, volume = {29}, number = {6}, pages = {116025}, pmid = {42211136}, issn = {2589-0042}, abstract = {While single-strain probiotics fail to address community-level microbiota injuries in dysbiosis-related conditions and fecal microbiota transplantation (FMT) produces unpredictable communities, a middle-ground approach has emerged. This approach involves using small consortia of species, combining the precision of single-strain probiotics and the holistic approach intrinsic to FMT. The species selection in this oligomicrobial strategy is typically proprietary or based on studies linking single species to disease or health. To advance this approach, we developed the concept of cohesive modules of engraftment (CME) and a workflow for their identification from FMT trials. CMEs represent small donor microbiota subsets that engraft as units (modularity), while maintaining their original composition (cohesiveness). In benchmarking, we identified >200 highly cohesive CMEs (2-5 species) in 5 FMT trials and found evidence for cross feeding as a mechanism for CME integrity. Due to their predictable post-treatment compositions, CMEs deserve investigation as potential ingredients of future therapeutic microbial consortia.}, }
@article {pmid42211226, year = {2026}, author = {Li, H and Gao, X and Jing, X}, title = {Characterization of the vaginal bacterial microbiota of sheep exhibiting abortion or repeat breeder syndrome.}, journal = {Veterinary and animal science}, volume = {33}, number = {}, pages = {100694}, pmid = {42211226}, issn = {2451-943X}, abstract = {Research on the microbiome's impact on abortion and repeat breeder syndrome (RBS) in sheep is lacking, despite the fact that the vaginal bacterial microbiota is related to their reproductive performance. To compare ewe vaginal bacterial microbial communities, vaginal swabs were randomly taken from aborted ewes (A), repeat breeder ewes (RB), and healthy ewes (H), and 16S rRNA gene Illumina MiSeq amplicon sequencing was performed after DNA was extracted. Six common pathogens associated with reproductive disease were detected by PCR. Differences existed in alpha diversity between group A and group H (p<0.05). Although there were no differences between group RB and group H or group RB and group A (p>0.05), the vagina of group H had a greater number of OTUs than group A and group RB, and there were also differences in the dominant genera within each group. Pathogenic bacteria (Campylobacter jejuni, Chlamydia abortus, Listeria monocytogenes, and Brucella melitensis) were detected in group A. Furthermore, changes in the relative abundance of bacterial genera such as Streptobacillus, unclassified Dysgonomonadaceae, Histophilus, unclassified Pasteurellaceae, and unclassified Leptotrichiaceae were observed in repeat breeder ewes; Pasteurellaceae was considered as the key factor to RBS. These findings suggest that the microbial diversity in the vagina of Hu sheep played a crucial role in reproductive regulation. Pathogens such as Brucella, Chlamydia are the main ones causing abortion in ewes, and the potential bacterial biomarkers could be discovered, and that would help prevent abortion or RBS.}, }
@article {pmid42211616, year = {2026}, author = {Carvajal Méndez, K and Álvarez Barrientos, AG and Gutiérrez Rivera, F and Aragón Leiva, D and Ulate Fuentes, D}, title = {Efficacy and Safety of Limosilactobacillus reuteri DSM 17938 in Infantile Colic: A Narrative Review From Pathogenesis to Clinical Practice.}, journal = {Cureus}, volume = {18}, number = {4}, pages = {e107824}, pmid = {42211616}, issn = {2168-8184}, abstract = {Infantile colic is one of the most common functional gastrointestinal disorders, affecting approximately 20% of infants worldwide. Characterized by paroxysmal episodes of inconsolable crying and fussing without an obvious cause, the condition imposes a significant psychosocial burden on the family unit, acting as a primary trigger for maternal postpartum depression, parental exhaustion, and premature cessation of breastfeeding. Despite its prevalence, traditional management in primary care remains heterogeneous and often ineffective, leaving a substantial therapeutic gap. Emerging research has identified gut dysbiosis as a cornerstone of its pathogenesis, where an imbalance in early microbial colonization, characterized by reduced diversity and a higher prevalence of gas-producing coliforms, triggers intestinal inflammation and visceral hypersensitivity through the gut-brain axis. This narrative review synthesizes the current clinical evidence regarding the efficacy and safety of Limosilactobacillus reuteri DSM 17938 in the management of infantile colic. This specific probiotic strain exerts its therapeutic effects through multifaceted mechanisms, including the production of the antimicrobial metabolite reuterin, the modulation of gastrointestinal motility via microvesicles, and the reduction of low-grade gut inflammation. Clinical evidence from large-scale meta-analyses confirms that L. reuteri DSM 17938 is significantly superior to placebo, particularly in breastfed infants, where it is twice as likely to achieve a 50% reduction in crying time within 14-21 days of treatment. However, its efficacy appears less predictable in formula-fed populations, potentially due to the absence of synergistic factors found in human milk. Clinical management in primary care should prioritize a rigorous diagnostic approach to rule out organic causes through a detailed physical examination and the application of the Rome IV criteria. The cornerstone of non-pharmacological management remains empathetic parental reassurance and education to mitigate the risk of infant abuse and support family well-being. When probiotic intervention is indicated, L. reuteri DSM 17938 represents a robust, evidence-based first-line therapy for healthy, full-term infants. Regarding safety, this strain maintains an excellent profile supported by its generally recognized as safe (GRAS) status, with no significant adverse effects reported in healthy populations. Nevertheless, recent clinical scrutiny emphasizes the need for caution and the use of pharmaceutical-grade products in vulnerable groups. Ultimately, L. reuteri DSM 17938 addresses both the biological triggers of colic and the psychosocial stability of the family unit.}, }
@article {pmid42211651, year = {2026}, author = {von Bargen, L and Patangia, D and von Ostau, N and Buer, J and Heß, J and Kehrmann, J}, title = {Microbial community structure and source contribution to the early neovaginal microbiota following penile inversion vaginoplasty.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1816814}, pmid = {42211651}, issn = {2235-2988}, mesh = {Female ; *Vagina/microbiology/surgery ; Humans ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Penis/microbiology/surgery ; *Bacteria/classification/genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Male ; DNA, Bacterial/genetics/chemistry ; DNA, Ribosomal/genetics/chemistry ; Gender-Affirming Surgery ; Urethra/microbiology ; Phylogeny ; }, abstract = {INTRODUCTION: The process of colonization of the neovagina in the first year after surgical creation is largely unknown. We characterized the microbiota of the donor tissue sites that formed the neovagina, of the gut and of the neovagina itself to evaluate the source of the neovaginal microbiota.<br><br>METHODS: Thirty transgender women assigned male at birth were included. Using 16S rRNA sequencing and aerobic culture, we analyzed the penile, scrotal, urethral and rectal microbiota before surgery, and the neovaginal microbiota in the period of 2 to 13 months after vaginoplasty.<br><br>RESULTS: Each of the sites was characterized by a specific microbiota. The neovagina was characterized by the second highest bacterial richness and diversity after the gut. The neovaginal microbiota was dominated by anaerobic bacteria of the phyla Firmicutes and Bacteroidota. The most abundant genera were Prevotella, Peptoniphilus, Anaerococcus and Porphyromonas. These genera, together with Dialister, Finegoldia and Actinomyces formed a neovaginal core microbiota, representing genera present in more than 50% of the samples, each with a minimum relative abundance of 1%. More than half of the neovaginal bacteria were not shared with the tissue sites that formed the neovagina. The site with the highest percentage of shared neovaginal Amplicon Sequence Variants (ASVs) was the gut, followed by the urethra. Complementary aerobic culturing showed that on average 38.7% of neovaginal bacterial species were shared with at least one other site.<br><br>DISCUSSION: The early neovaginal microbiota is highly diverse, dominated by anaerobic bacteria and is distinct from the microbiota of the tissue sites that form the neovagina. As most neovaginal ASVs are unshared, this indicates that bacteria from other environments may colonize the neovagina in this early period after creation of this new environment. These findings suggest implications for neovaginal health, potentially informing studies on probiotic therapies to support the colonization of the neovagina with beneficial bacteria.}, }
@article {pmid42211733, year = {2026}, author = {Najnine, F and Guo, X and Cai, J}, title = {Lactobacillus salivarius Probiotic Supplementation Modulates Gut Function, Improves Growth, and Meat Quality in Tropical Whiteleg Shrimp.}, journal = {Aquaculture nutrition}, volume = {2026}, number = {}, pages = {6285997}, pmid = {42211733}, issn = {1365-2095}, abstract = {Probiotics are increasingly incorporated into shrimp aquaculture, yet the comparative efficacy of single‑strain versus mixed‑strain formulations remains insufficiently defined, particularly in relation to gut microbiome remodeling, intestinal architecture, and proteomic determinants of meat quality. A 90‑day randomized grow‑out trial was conducted under semi‑intensive conditions using Litopenaeus vannamei fed three diets (triplicate ponds per treatment): basal diet (W), basal diet plus mixed‑strain EM probiotic (T), and basal diet plus Lactobacillus salivarius GZPH2 (H). Growth performance, survival, intestinal histology, microbiota composition and function (16S/18S rRNA sequencing), and meat quality (4D‑DIA proteomics) were evaluated. Both probiotics improved growth and feed utilization relative to controls, but H consistently outperformed T in survival (83.0% vs. 81.0%), meat yield (6.53% vs. 4.84%), lipid deposition (4.05% vs. 3.39%), and mineral enrichment (Fe, Se; Zn/Cu ratio: 2.27 vs. 1.97). H enhanced microbial α‑diversity and enriched metabolically versatile taxa (Achromobacter, Pedobacter, Photobacterium, and Labrenzia), whereas T produced Bacillus‑dominant communities (~85%) with reduced diversity. Intestinal morphology showed greater absorptive expansion in H (+14.10%) and higher goblet cell density in T (+51.21%). Functional profiling indicated that H activated KEGG pathways related to amino acid transport, nitrogen metabolism, fatty acid biosynthesis, and trace‑mineral transport, supporting enhanced protein turnover, lipid deposition, mineral assimilation, and redox‑homeostasis. In contrast, T favored carbohydrate metabolism and antimicrobial gene expression, promoting competitive exclusion but limiting metabolic versatility. Proteomic analysis identified 183 differentially expressed proteins (DEPs, 110 upregulated in H; 73 in T). H upregulated myofibrillar and antioxidant proteins, including myosin heavy chain type 2, hemocyanin, catalase, metallothionein, and selenium‑binding protein, while suppressing proteolytic and glycolytic enzymes, thereby improving texture, oxidative stability, and nutritional value of meat. Collectively, Lactobacillus salivarius GZPH2 demonstrated superior capacity for metabolic modulation, intestinal remodeling, and proteomic enhancement, highlighting its potential as a targeted probiotic for optimizing shrimp health and meat quality in aquaculture nutrition.}, }
@article {pmid42211787, year = {2026}, author = {Zhang, R and Chen, YK and Zhu, QY and Feng, RY and Liu, H and Ma, MM and Wang, XJ}, title = {Metagenomic profiling of ocular surface microbiome alterations in patients with progressive supranuclear palsy-Richardson's syndrome.}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100605}, pmid = {42211787}, issn = {2666-5174}, abstract = {This study employed shotgun metagenomic sequencing to characterize the ocular surface microbiome in 20 progressive supranuclear palsy-Richardson's syndrome (PSP-RS) patients, 17 Parkinson's disease (PD) patients, and 30 healthy controls (HC). Comparative analysis revealed that PSP-RS patients exhibited significantly altered microbial β-diversity compared to HC, while PD patients showed no such significant changes. Both patient groups demonstrated decreased abundance of g_Vibrio, with PSP-RS patients additionally showing marked increases in g_Acinetobacter and g_Anaerococcus. Importantly, correlation analyses identified that increased g_Acinetobacter abundance was positively associated with ocular motor impairment severity, while elevated g_Anaerococcus levels correlated with both freezing of gait severity and longer disease duration in PSP-RS patients. This is the first shotgun metagenomic investigation of the ocular surface microbiome in PSP-RS and these findings provide evidence that specific alterations in the ocular surface microbiome may contribute to PSP-RS pathogenesis and disease progression.}, }
@article {pmid42211834, year = {2026}, author = {Chang, L and Peng, F and Zuo, Y and Yang, S and Xie, K and Song, Z and He, X and Chen, Y}, title = {High-zinc diets accelerate molting and recovery by remodeling the cecal microbiome in laying hens.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1743943}, pmid = {42211834}, issn = {1664-302X}, abstract = {INTRODUCTION: Conventional fasting molting can restore laying performance but imposes substantial physiological stress and welfare concerns. High-zinc diets (2% ZnO) have been proposed as a less stressful alternative, but their mechanisms remain unclear.<br><br>METHODS: This study compared fasting-induced molting with zinc oxide supplementation in 384 Lohmann Pink hens (65 wk). Serum, cecal contents, and ovaries were sampled across six stages from pre-molt to post-molt recovery.<br><br>RESULTS: ZnO accelerated cessation of lay (5.75 vs. 8.87 d) and earlier recovery to 50% production (15.25 vs. 16.62 d) with lower weight loss (25% vs. 30%). Multi-omics revealed that high-zinc feeding enriched beneficial microbes (e.g., Coprenecus pullicola, Fournierella spp.) involved in amino acid and cofactor biosynthesis, consistent with activated glycine/serine/lysine metabolism. ZnO also reduced inflammatory and barrier-injury signals (IL-1&#x3b2;, LPS, DAO) and promoted earlier recovery of reproductive hormones (higher IGF-1, earlier increases in E2 and LH). Both treatments improved post-molt egg quality; zinc better preserved albumen height and Haugh unit, while fasting increased shell thickness and yolk color.<br><br>DISCUSSION/CONCLUSION: These findings support that a high-zinc-associated microbial-metabolic profile mitigates stress, accelerates ovarian reset, and shortens the time to restore production.}, }
@article {pmid42211835, year = {2026}, author = {Blanton, MB and Napier, EG and Keen, KE and Stuart, EV and Cinco, IR and Hemati, H and Bruntz, RC and Wilson, L and Barnes, S and Khadka, R and Grant, KA and Messaoudi, I}, title = {Chronic alcohol consumption disrupts the gut microbial and metabolic landscapes.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1794794}, pmid = {42211835}, issn = {1664-302X}, abstract = {INTRODUCTION: Alcohol use disorder (AUD) increases incidence of infections, organ damage, and cancers. Aberrant inflammation is likely a driver of these adverse outcomes. Indeed, chronic alcohol consumption (CAC) rewires macrophages/monocytes toward a hyper-inflammatory phenotype. Prior studies showed increased gut permeability and dysbiosis. Translocation of host- and microbial-derived metabolites could trigger the hyper-inflammatory responses generated by macrophages/monocytes. However, the exact changes in these metabolites remain poorly defined due to confounders that complicate clinical studies and the differences between human and rodent gut microbiomes.<br><br>METHODS: Here, we utilized a non-human primate model of ethanol self-administration to characterize alcohol-induced alterations in gut microbes and associated metabolomes. The microbiome was analyzed with 16s rRNA sequencing while a combination of GC-MS and LC-MS was used to assess changes in metabolites. Monocyte function was determined using flow cytometry.<br><br>RESULTS: Twelve months of alcohol use led to a decrease in SCFA-producing bacteria and disruption of fatty acid and amino acid metabolites. Moreover, fecal metabolites obtained after 12 months of CAC heightened monocytes' inflammatory responses.<br><br>DISCUSSION: These findings indicate that CAC-induced gut dysbiosis contributes to changes in fecal and circulating metabolites, which in turn can lead to monocyte dysregulation, possibly via innate immune training-like mechanisms.}, }
@article {pmid42211837, year = {2026}, author = {Singh, AP and Bulzu, PA and Lanta, V and Chaloupský, P and Salcher, MM and Shabarova, T}, title = {From soils to lake: interplay between hydrology and local environmental settings drives species selection across a karst landscape.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1813326}, pmid = {42211837}, issn = {1664-302X}, abstract = {Terrestrial and aquatic ecosystems are interconnected through runoff and hydrological networks that facilitate the transfer of microbial communities across landscapes. While microbial transport along surface waters is well documented, the role of subsurface hydrological paths in shaping microbial community composition remains poorly understood, particularly in complex karst systems. Here, we studied bacterial communities under stable hydrological conditions across a peri-alpine karst landscape, where mixed limestone-sandstone catchments drain via both surface and subsurface hydrological networks into Lake Thun (Switzerland). We profiled 16S rRNA gene sequences from soils, sediments, surface and subsurface waters, and distinct lake strata. All environments except the lake exhibited high microbial diversity. We observed a clear transitional gradient in bacterial communities along the terrestrial-aquatic interface, with environment type explaining 19% of total variation. Core microbiome analyses revealed both environment-specific and shared taxa, with the strongest overlap between surface and subsurface hydrological networks (63.8%-84.6% shared core taxa). Co-occurrence network analysis identified six major modules. Three of them represented distinct metabolic assemblages tightly associated with specific environment types: peat soils, lake strata, and the subsurface network, respectively. One recurrent module spanned multiple environments and was linked to redox-driven processes, including the oxidation of nitrogen compounds, metals, and methane. Two additional modules comprised aquatic copiotrophs associated with streams and soil heterotrophs prone to export and short-term persistence within the hydrological network. Overall, our results demonstrate that specific environmental settings and hydrological connectivity jointly contribute to selection of microbial species within the karst landscape.}, }
@article {pmid42211838, year = {2026}, author = {Drago, L and De La Motte, LR and Deflorio, L and Sansico, DF and Salvatici, M and Micaglio, E and Biazzo, M and Giarritiello, F}, title = {Correction: Systematic review of bidirectional interaction between gut microbiome, miRNAs, and human pathologies.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1872999}, doi = {10.3389/fmicb.2026.1872999}, pmid = {42211838}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2025.1540943.].}, }
@article {pmid42211841, year = {2026}, author = {Madhavan, K and Lanzel, E and Dabdoub, SM and Sidahmed, A and Hellstein, J and Drake, DR and Banas, JA and Ganesan, SM}, title = {Intralesional microbial community signatures across histopathologic categories of tongue lesions.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1775141}, pmid = {42211841}, issn = {1664-302X}, abstract = {BACKGROUND: The tissue-resident microbiome of oral epithelial lesions remains incompletely characterized, with most prior studies relying on saliva or surface sampling. This study aimed to characterize intralesional microbial communities across histopathologic categories of tongue lesions using formalin-fixed paraffin-embedded (FFPE) tissue.<br><br>METHODS: This cross-sectional study characterized the intralesional microbiome of 63 formalin-fixed, paraffin-embedded tongue tissues, including fibroma (n&#x202f;=&#x202f;15), low malignant potential dysplasia (LMP; n&#x202f;=&#x202f;24), high malignant potential dysplasia (HMP; n&#x202f;=&#x202f;24), and additional OSCC samples. Amplicon sequencing of the V3-V4 16S rRNA region was used to assess taxonomic composition, alpha and beta diversity, phylogenetic structure, predicted functional pathways (PICRUSt2), and machine-learning-based discrimination of lesion categories.<br><br>RESULTS: Microbial community profiles differed significantly across histopathologic groups. Non-dysplastic tissues exhibited higher richness and greater representation of commensal genera such as Streptococcus, Rothia, and Veillonella. Dysplastic tissues demonstrated reduced diversity and increased abundance of stress-adapted Proteobacteria including Bosea, Novosphingobium, Sphingomonas, and Pseudomonas. Beta diversity analyses revealed distinct community structures between fibroma, LMP, and HMP categories. Predicted functional profiles suggested differences in inferred metabolic potential, including pathways related to carbohydrate metabolism and xenobiotic degradation in dysplastic lesions. A supervised classifier demonstrated separation between groups (AUC 0.83-1.00), with several taxa contributing to classification; however, these findings should be interpreted cautiously given the sample size.<br><br>CONCLUSION: Intralesional microbial communities differ across fibroma, dysplasia, and OSCC of the tongue in both taxonomic composition and predicted functional profiles. These findings describe lesion-associated microbial signatures within tissue and provide a foundation for future studies incorporating longitudinal designs and multi-omics approaches to clarify their biological and clinical relevance.}, }
@article {pmid42211844, year = {2026}, author = {Valenzuela-Muñoz, V and Tapia, FJ and Gallardo-Escárate, C and Mestre, M and Navarrete, SA and Gutiérrez, MH and Morales-Rivera, MF and Jessen, GL}, title = {Microbiota responses to environmental stress in mobile and sessile marine invertebrates: evidence for the effect of dissolved oxygen variations.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1764313}, pmid = {42211844}, issn = {1664-302X}, abstract = {Microbiomes can modulate plant and animal responses to environmental fluctuations, revealing their central role in global biogeochemical cycles and the physiology of individual organisms, and in how these fluctuations are modulated. In marine ecosystems, Eastern Boundary Upwelling Systems (EBUS) allow us to examine host-microbiome dynamic interactions that respond to environmental variation, offering critical insights into the potential impacts of global environmental change. This study investigates the microbiota response of two marine invertebrates that co-occur at sites with strong synoptic and seasonal fluctuations in temperature and dissolved oxygen concentration between winter and summer. Specimens of the sessile marine tunicate Pyura chilensis ("Piure") and the porcelain crab Allopetrolisthes punctatus ("Changai") were collected at about 10 m depth under contrasting oxygen regimes in summer and winter at Chome, central Chile. Microbiota from gills and digestive glands were assessed via 16S rRNA Nanopore sequencing, which showed clear differences in bacterial community structure and composition between species and across summer and winter surveys. Functional predictions suggest that shifts in the microbiota are primarily associated with variations in exposure to hypoxic waters induced by intensified upwelling. This suggests that the microbiomes may positively influence host performance under environmental stress, enhancing resistance to low dissolved oxygen conditions.}, }
@article {pmid42211846, year = {2026}, author = {Nidhin, IK and Chattopadhyay, I}, title = {Integrated study of rhizosphere microbiome and metabolome profiles across tropical plantations in the Western Ghat regions of Kerala and Tamil Nadu, India.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1840024}, pmid = {42211846}, issn = {1664-302X}, abstract = {BACKGROUND: Soil physicochemical properties, plantation types, plant taxa, and geographical locations are the major factors influencing the microbial composition and diversity of the rhizosphere soils.<br><br>METHODS AND RESULTS: The present study aimed to investigate the variations in microbiome and metabolome composition across rhizosphere soils of plantations in the Western Ghats, based on 'plantation types' (mixed-species and mono-species), 'sampling locations' (Kerala and Coonoor), 'plant types' (shrubs and trees) and 'plant genera' (Eucalyptus, Pine, Silver oak, Tea, Rubber and Coffee); using 16S rRNA sequencing and GC-MS analysis. The mono-species samples had higher concentrations of K and heavy metals, such as Pb, Cr, Ni, and Cu than the mixed-species samples. The soil dehydrogenase activity (DHA) was highest in the mono-species tea and coffee samples from Kerala. However, the mixed-species pine and eucalyptus had comparatively higher DHA values than the mono-species pine and eucalyptus. Paludisphaera borealis, Candidatus Solibacterusitatus, Candidatus Xiphinematobacter sp. Idaho Grape, Gemmatimonas phototrophica, and Conexibacter woesei had significantly higher abundance in mixed-species samples based on the LEfSe analysis (LDA score>3 and FDR-adjusted p-value&#x202f;<&#x202f;0.05). Whereas, Chthoniobacter flavus, Tepidisphaera mucosa, Acidibacter ferrireducens, Paludibaculum fermentans, and Gaiella occulta had significantly higher abundance in mono-species samples. The strong positive correlations (r values >0.9 and <-0.9, with p-value < 0.05) of bacterial taxa with plant metabolites such as phytane, Friedelan-3-one, gamma-gurjunene, eucalyptol, (-)-globulol and epiglobulol, indicate that these plant metabolites may play crucial roles in the differential bacteriome compositions of these rhizospheres.<br><br>CONCLUSION: This study provides new insights into the alterations in the rhizosphere bacteriome across various plantations in the Western Ghats region based on plantation type, plant genera, metabolites, and other soil physiochemical properties.<br><br>IMPACT STATEMENT: Plantation type and sampling location were the factors that significantly influenced the rhizosphere metabolome and microbiome profiles, followed by plant genera and plant type.}, }
@article {pmid42211848, year = {2026}, author = {Tahir, N and Pusztahelyi, T}, title = {Editorial: Microbial degradation of agricultural waste.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1856978}, doi = {10.3389/fmicb.2026.1856978}, pmid = {42211848}, issn = {1664-302X}, }
@article {pmid42211862, year = {2026}, author = {Tran, HT and Mercado, AJ and Lahoti, MM and Murali, RR and Davis, E and Crowder, S and de Rodas, B}, title = {Effects of a novel feed additive on clinical symptoms and the nasal and cecal microbiome in nursery pigs challenged with PRRSV and Streptococcus suis.}, journal = {Translational animal science}, volume = {10}, number = {}, pages = {txag060}, pmid = {42211862}, issn = {2573-2102}, abstract = {Porcine reproductive and respiratory syndrome virus (PRRSV) is a major endemic disease in swine, causing significant economic losses to the pork industry. PRRSV infection predisposes pigs to secondary infections, leading to a costly and challenging respiratory disease complex. Effective mitigation strategies are needed to reduce negative impacts of PRRSV on swine health and productivity. This study evaluated the efficacy of a novel feed additive (EP) containing a blend of activated medium-chain fatty acids, phytogenic compounds, and probiotics in PRRSV viral load, clinical symptoms, lung lesions, and nasal and cecal microbiome in nursery pigs experimentally co-challenged with PRRSV and Streptococcus suis. Twenty-six weaned pigs were randomly assigned to three groups: 1) non-challenged fed a control diet (Unchallenged), 2) PRRSV and S. suis co-challenged fed a control diet (Challenged), and 3) PRRSV and S. suis co-challenged fed control diet supplemented with 0.4% EP (Challenged + EP). Pigs were fed their respective diets for 29 days and were monitored for respiratory distress symptoms. On days 10 and 21, subsets of pigs were euthanized and necropsied to evaluate lung lesions, quantify viral load in the lung and serum, and characterize the nasal and cecal microbiome. Challenged pigs showed increased viral loads at days 10 and 21, respiratory distress score, and lung lesion score at day 21, and reduced overall weight gain (P < 0.05) compared to the Unchallenged pigs. The Challenged pigs supplemented with EP had lower PRRS viral load in both serum and lung (day 21; P < 0.05) and tended to have a reduced percentage of lungs affected by pneumonia lesions (day 21; P < 0.10) compared to the Challenged group. The Challenged pigs were enriched with nasal opportunistic bacteria, including Streptococcus, Trueperella, Mycoplasma, Actinobacillus, and Pasteurella (LDA score > 3; P < 0.05). However, EP supplementation reduced the abundance of these bacteria and Klebsiella (LDA score > 3; P < 0.05). Both Unchallenged and Challenged + EP pigs were dominated with cecal Prevotella and Blautia (LDA score > 4; P < 0.05). The Challenged + EP group also demonstrated an enrichment in Blautia and Negativibacillus in both nasal and cecal microbiome. In conclusion, dietary supplementation with EP reduced PRRSV infection severity and decreased enrichment of opportunistic bacteria during co-infection.}, }
@article {pmid42211983, year = {2024}, author = {Eleutério, J and Cavalcante, DIM and Maia, GH and Eleutério, RMN}, title = {Cancer of the uterine cervix: a narrative review.}, journal = {Gynecology and pelvic medicine}, volume = {7}, number = {}, pages = {33}, pmid = {42211983}, issn = {2617-4499}, abstract = {BACKGROUND AND OBJECTIVE: Uterine cervical cancer remains a major global public health challenge. This narrative review aims to provide a comprehensive overview of the epidemiology, pathogenesis, histological classification, screening, diagnostic approaches, treatment, and prevention of cervical cancer.<br><br>METHODS: We searched MEDLINE, Google Scholar, and Scopus for publications in English without date limits and using the search terms "cervical cancer" AND "human papillomavirus" AND "screening" OR "staging" OR "diagnosis" OR "microbiome" OR "treatment" OR "HPV DNA test". We also used references from the texts retrieved via our literature searches.<br><br>KEY CONTENT AND FINDINGS: Cervical cancer has several histological types, with squamous cell carcinoma being the most common, followed by adenocarcinoma. Human papillomavirus (HPV) is considered the main, but not exclusive, player in oncogenesis. The mechanisms of cancer development are well understood, especially the roles of E6 and E7. The vaginal microbiome is an essential cofactor in this process. Prevention can be via either primary (vaccination) or secondary (screening) intervention. The Papanicolaou test and HPV DNA test are the primary screening tools. Index screening cases must undergo colposcopy and biopsy to identify high-grade squamous intraepithelial lesions (true precancerous lesions), and such cases must be treated according to guidelines. However, if an invasive cancer occurs, it must be staged to define the treatment.<br><br>CONCLUSIONS: The pathogenesis of cervical cancer has been studied extensively, and various well-defined forms of prevention have been devised. However, it is still prevalent, especially in developing countries. The present review is vital for updating knowledge and helping in the fight against this disease that kills so many women.}, }
@article {pmid42211993, year = {2026}, author = {Wilkinson, SW and Wright, HC and Cotton, TEA and Pascual-Pardo, D and Campbell, SA and Wickramaarachchi, U and Cameron, DD and Gulyas, BZ and Ho, P and Mackie, AR and Caton, SJ and Ton, J and Rolfe, SA}, title = {Synthetic microbial communities for sustainable hydroponic tomato production.}, journal = {NPJ sustainable agriculture}, volume = {4}, number = {1}, pages = {42}, pmid = {42211993}, issn = {2731-9202}, abstract = {Hydroponic horticulture will play a key role in future food production as the growing global population becomes increasingly urbanised. Tomato (Solanum lycopersicum) is a widely grown and consumed crop that is already cultivated hydroponically in glasshouses in areas of the world with cooler climates, such as Northern Europe. Hydroponic growing systems enable high yields but can enhance disease susceptibility which increases the risk of devastating yield losses. Manipulation of the hydroponic microbiome has been proposed as a strategy to protect plants against disease. However, this hypothesis remains largely untested. We examined whether introducing synthetic communities of plant-beneficial microbes (SynComs) could offer a sustainable disease protection solution for hydroponic tomato production. We identified individual microbes and in turn two SynComs that induce systemic disease resistance during the vulnerable early stages of development. The two SynComs were evaluated further in a commercial-scale greenhouse trial. Although both SynComs reduced early growth, they had no adverse effects on yield or fruit quality. Strikingly, while only one SynCom strain consistently persisted in the hydroponic stone wool substrate throughout the six-month trial, the introduction of disease-suppressive SynComs at sowing had significant and similar impacts on bacterial community structure six months later. Our findings demonstrate that microbial SynComs can reduce disease susceptibility of hydroponically grown tomato without compromising yield, offering a viable and sustainable approach for crop protection in controlled environment agriculture.}, }
@article {pmid42212103, year = {2026}, author = {Nair, B and Kamath, AJ and Devan, AR and Gopalakrishna, R and Unni, AR and Nath, LR}, title = {Gut microbiota and pediatric metabolic dysfunction-associated steatotic liver disease: clinical evidence and therapeutic implications.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1773294}, pmid = {42212103}, issn = {2296-2360}, abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD), previously referred to as Non-alcoholic fatty liver disease (NAFLD), is among the most common chronic liver conditions globally. The incidence of MASLD has been rising, primarily due to lifestyle changes, excessive calorie intake, and other metabolic conditions like obesity and Type 2 diabetes mellitus in both adults and children. An inclusive understanding of risk factors of childhood MASLD is still unknown. Based on the limited case studies published, familial clustering is prominent in MASLD suggesting role of genetic factors. Moreover, children with MASLD are at higher risk of obesity, diabetes and hypertension. Studies associating the colonic microbiome with MASLD have been limited and complicated by inconsistencies in study design and approach but mostly indicate a role in the pediatric population. The present review provides a comprehensive understanding of the most recent clinical studies (2013-2026) on the role of gut microbiome in the development of pediatric MASLD.}, }
@article {pmid42212131, year = {2026}, author = {Vecellio, M}, title = {Editorial: Understanding eQTLs and their Association with Spondyloarthropathies.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1868391}, doi = {10.3389/fimmu.2026.1868391}, pmid = {42212131}, issn = {1664-3224}, }
@article {pmid42212158, year = {2026}, author = {Yong, B and Luo, Z and Luo, B and Liu, J and Zeng, Z and Zheng, X}, title = {The role of the complement system in gastrointestinal-related diseases.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1801628}, pmid = {42212158}, issn = {1664-3224}, mesh = {Humans ; *Complement System Proteins/immunology/genetics/metabolism ; *Gastrointestinal Diseases/immunology/metabolism/etiology ; Animals ; Immunity, Innate ; Complement Activation/immunology ; Gastrointestinal Microbiome/immunology ; Adaptive Immunity ; Tumor Microenvironment/immunology ; Inflammatory Bowel Diseases/immunology ; }, abstract = {The complement system bridges innate and adaptive immunity, orchestrating immune surveillance and maintaining tissue homeostasis. This review summarizes the role of the complement system in gastrointestinal-related diseases, including its function in innate immunity, impact on adaptive immunity, and regulatory role under physiological and pathological conditions in the gut. The activation pathways, regulatory mechanisms, and interactions of the complement system with the gut microbiome are crucial for maintaining intestinal homeostasis. Genetic deficiencies or excessive activation of the complement system are closely associated with the development of various intestinal diseases, including infections, inflammatory bowel disease (IBD), and tumors. This review also explores the role of the complement system in the tumor microenvironment (TME) of the gut and its potential as a therapeutic target. By deepening our understanding of the mechanisms by which the complement system operates in gastrointestinal diseases, we can provide a theoretical foundation for the development of novel treatment strategies.}, }
@article {pmid42212334, year = {2026}, author = {Liu, L and Hu, W and Spaink, HP}, title = {The function of TLR2 and the microbiome in macrophage-dependent dissemination of nontuberculous mycobacterial gut infection.}, journal = {International journal of biological sciences}, volume = {22}, number = {10}, pages = {5359-5384}, pmid = {42212334}, issn = {1449-2288}, mesh = {Animals ; *Toll-Like Receptor 2/metabolism/genetics ; Zebrafish/microbiology ; *Macrophages/metabolism/microbiology ; *Mycobacterium Infections, Nontuberculous/metabolism/microbiology ; *Microbiota/physiology ; }, abstract = {BACKGROUND: Nontuberculous mycobacteria (NTM) infections are increasing in incidence and mortality worldwide, yet the in vivo determinants of early intestinal colonization and subsequent dissemination remain poorly defined. Using a zebrafish larval model, we studied dissemination of two NTM strains, Mycobacterium avium subspecies hominissuis Chester (strain MAC 101) and M. marinum (strain Mma20) through the gastrointestinal (GI) tract. We performed bacterial immersion experiments and gut microinjection with these pathogens using tlr2 mutant and wild-type zebrafish larvae in both germ-free (GF) and microbiome-colonized conditions. This study for the first time shows the roles of Toll-like receptor 2 (TLR2) and the microbiome in orchestrating immune responses in NTM gut infection and dissemination.<br><br>RESULTS: In wild-type microbiome-colonized larvae, MAC 101 predominantly localizes in the posterior gut, in contrast to an anterior-biased distribution for Mma20 after 2.5 days of immersion infection. Both MAC 101 and Mma20 disseminate to posterior body region after 2.5 days of immersion infection. Robotic gut microinjection confirms the protective roles of TLR2 and the microbiome against proliferation of MAC 101 and Mma20. Expression analysis of downstream genes indicate that patterns of TLR2-dependent gene regulation differ between the two NTM species and show that the presence or absence of the microbiome differentially influences specific transcriptional responses to infection. Macrophage ablation studies show that macrophages facilitate dissemination of gut bacteria to the posterior body region. Quantification of macrophages containing bacteria throughout the body show that the dissemination of bacteria by macrophages depends on TLR2, but not on the microbiome. Using the same approach, TLR2 chemical antagonist treatment confirms the results observed in tlr2 mutant larvae. Live imaging of macrophage trajectories after bacterial gut microinjection show that macrophage motility after infection is impaired in tlr2 mutant larvae compared to the wild type. Notably, the effect of TLR2 on macrophage motility differs between GF and microbiome-colonized conditions.<br><br>CONCLUSIONS: TLR2 and the microbiome play critical roles in modulating host responses to MAC 101 and Mma20 gut infection. Our findings provide new insights into the coordinated roles of TLR2 signaling and the microbiome in controlling infection of mycobacteria via the gut and underscore the importance of TLR2 in macrophage function during mycobacterial gut infection and dissemination.}, }
@article {pmid42212501, year = {2026}, author = {Sugimoto, H and Toyoda, A and Furuta, Y and Iwase, T and Yaokawa, R and Kitagawa-Yogo, R and Ito, M and Katahira, S}, title = {Adaxial-abaxial leaf surface asymmetry is a key ecological driver of the phyllosphere microbiome.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/erag255}, pmid = {42212501}, issn = {1460-2431}, abstract = {Microorganism-driven ecosystems on leaf surfaces play pivotal roles in regulating plant health and fitness. While individual leaves provide distinct microhabitats on their adaxial (upper) and abaxial (lower) surfaces, most studies have assessed phyllosphere microbial community assembly and function using whole leaves, thereby overlooking their inherent spatial heterogeneity. Here, we independently analyzed bacterial and fungal communities on adaxial and abaxial leaf surfaces across seven temperate tree species over a 6-month period. We further assessed their metabolic and ecological profiles to understand how leaf surface compartmentalization shapes microbial communities. Our results revealed that compositionally distinct microbial communities were consistently established on each leaf surface. Co-occurrence network analyses showed that the abaxial communities exhibited differences in interaction structure compared to the adaxial communities, characterized by a higher proportion of negative correlations. Predicted functional profiles indicated that adaxial communities were enriched in degradation pathways, potentially reflecting nutrient-poor, high-stress conditions, whereas abaxial communities were enriched in biosynthetic and energy-generating functions, consistent with resource-rich environments. Collectively, our results highlight adaxial-abaxial leaf surface asymmetry as a key ecological driver shaping the structure, function, and interaction dynamics of the phyllosphere microbiome.}, }
@article {pmid42212551, year = {2026}, author = {Jiang, Q and Chen, S and Li, Y and Zhou, Z and Zhang, M and Sun, Y and Zhang, L and Li, Y and Zhang, X and Qu, Y and Lv, Z}, title = {Dietary inclusion of black soldier fly larvae as a partial protein source: effects on growth performance, carcass traits and meat quality of broilers.}, journal = {British poultry science}, volume = {}, number = {}, pages = {1-12}, doi = {10.1080/00071668.2026.2620609}, pmid = {42212551}, issn = {1466-1799}, abstract = {1. Black soldier fly larvae (BSF) can convert kitchen waste (KW) into usable organic resources. This study evaluated the effects of BSF derived from kitchen waste on the growth performance, carcass traits, meat quality and caecal microbiota in broilers.2. A total of 180 broilers were randomly assigned to three groups: a control group (CON), LBF or HBF group (containing 3% and 6% of BSF respectively). Performance was measured as feed intake (FI), Average daily weight gain (ADG), allowing feed conversion ratios (FCR) to be calculated. Carcass and muscle yields and characteristics were recorded. Caecal samples were taken for analysis of populations.3. The results showed that the 3% BSF group had better performance, including significant reductions in FI and abdominal fat and increased breast meat yield and muscle fibre diameter (p < 0.05). The mRNA levels of myostatin (MSTN), muscle RING finger protein 1 (MuRF1) and muscle atrophy F-box (MAFbx) were significantly downregulated (p < 0.05). The LBF group showed significantly elevated levels of specific fatty acids in breast meat, such as lauric acid and myristoleic acid (p < 0.05). However, replacing soybean meal with BSF in diet reduced meat quality and increased cooking loss and toughness (p < 0.05).4. The 16S rRNA microbiome sequencing showed that the LBF birds had significant increases in beneficial bacteria, including Butyricicoccus pullicaecorum and Akkermansia muciniphila and reduced Alistipes finegoldii abundance (p < 0.05). Spearman correlation analysis showed that Butyricicoccus pullicaecorum was positively associated with breast meat yield, muscle fibre size and cooking loss and negatively associated with the expression of MSTN, MuRF1 and MAFbx. Alistipes finegoldii showed opposite correlated trends to these indicators.5. In conclusion, dietary inclusion of BSF can regulate gut microbial composition and the expression of genes related to muscle development, thereby improving meat production, but affecting meat quality. Additionally, BSF alter the fatty acid profile of breast meat.}, }
@article {pmid41998538, year = {2026}, author = {Opbroek, J and Koch, S and Soto, SM and Borràs, S and Pozdniakova, S and Gonzalez, &#xd3; and Khan, AH and Eliasson, K and Papamanolis, A and Karatzas, S and Fytili, D and Vantarakis, A and Garcia-Aymerich, J and Mueller, N}, title = {TwinAIR health study: protocol for a European multi-centred, longitudinal study on indoor environmental quality (IEQ) related health and well-being.}, journal = {BMC public health}, volume = {26}, number = {1}, pages = {}, pmid = {41998538}, issn = {1471-2458}, support = {101057779//TwinAIR project funded by EU Horizon Europe Program/ ; }, abstract = {BACKGROUND: The term indoor environmental quality (IEQ) encompasses indoor air quality (IAQ), temperature, humidity, noise, and light. As people spend approximately 90% of their time indoors, at work, school, home, or during travel, understanding the relationship between IEQ and health is essential for health promotion, disease prevention, and sustainable building design and management. As part of the EU-funded TwinAIR project, the TwinAIR health study is a multi-centered, longitudinal investigation of how IEQ factors influence health and well-being across diverse European indoor spaces. This protocol describes a holistic study design integrating subjective and objective IEQ and health assessments and evaluating potential IEQ intervention effects.<br><br>METHODS: The TwinAIR health study will recruit and longitudinally follow 900 participants across 45 indoor spaces in five European countries (Germany, Greece, Spain, Sweden, and the United Kingdom), spanning work, study, leisure, and transport settings. Continuously measured IEQ parameters, including light, noise, temperature, humidity, nitrogen dioxide (NO[2]), ozone (O[3]), carbon dioxide (CO[2]), particulate matter (PM), particle number (PN), typical particle size (TPS), total volatile organic compounds (TVOC), and formaldehyde (HCHO), are assessed using advanced sensors with one-minute resolution. Sensor data are integrated with software-based digital twins and a data management platform. Health and well-being data include questionnaires assessing IEQ perceptions, respiratory and allergic symptoms, general health, mental health, somatization, well-being, and productivity, alongside objective measures including spirometry and skin and nasal samples for microbiome and resistome analyses. Air purification interventions are implemented in selected indoor spaces. The longitudinal design enables evaluation of intervention effects on IEQ and occupant health and well-being.<br><br>DISCUSSION: The TwinAIR health study addresses the growing impact of indoor environments on health and well-being and aims to elucidate the interactions between IEQ parameters, occupant behaviours, building management practices, and health outcomes, an area that remains comparatively understudied relative to outdoor environmental research. The study will generate actionable insights for creating and managing healthier indoor spaces using innovative sensing technologies and comprehensive health assessments. Findings will inform evidence-based strategies to guide healthier indoor space design and management in Europe and beyond.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12889-026-27371-8.}, }
@article {pmid41998606, year = {2026}, author = {Danaf, D and Karam, L and Sleem, R and Naamani, AER and Eldawra, E and Ibrahim, JN}, title = {Exploring the anti-cancer potential of gut microbiota-derived short-chain fatty acids in ovarian cancer: a comparative analysis of sodium butyrate and sodium propionate on proliferation, cell cycle, and apoptosis.}, journal = {Cancer cell international}, volume = {26}, number = {1}, pages = {}, pmid = {41998606}, issn = {1475-2867}, support = {PIRF # I0047//The Lebanese American University President's Intramural Research Fund/ ; }, abstract = {BACKGROUND: Short-chain fatty acids (SCFAs) are microbial metabolites produced by the gut microbiome through the fermentation of dietary fibers and non-digestible carbohydrates. SCFAs have received considerable interest as potential regulators of various cancers, including colorectal cancer and breast cancer. However, their roles and underlying mechanisms in ovarian cancer remain elusive. This study aimed to investigate and compare the anti-cancer effects of sodium butyrate (NaB) and sodium propionate (NaP) in two distinct ovarian cancer cell lines, SKOV-3 and PA-1.<br><br>RESULTS: Both NaB and NaP significantly reduced proliferation and colony formation, and impaired spheroid formation of SKOV-3 and PA-1 cells in a dose- and time-dependent manner. Notably, NaB exhibited greater anti-cancer potency than NaP, as evidenced by its lower IC&#x2085;&#x2080; values&#x2014;being 4.8-fold and 3.2-fold lower at 72&#xa0;h and 96&#xa0;h, respectively, in SKOV-3 cells, and 4.4-fold and 1.7-fold lower at 72&#xa0;h and 96&#xa0;h, respectively, in PA-1 cells. Additionally, treatment with NaB for 24&#xa0;h and with NaP for 24&#x2013;48&#xa0;h induced cell cycle arrest at the G2/M phase in both cell lines, accompanied by an upregulation of p21 and a decrease in the expression of cyclins A2, B1, and B2. Moreover, 48&#xa0;h post-treatment, both compounds induced apoptosis, with NaB demonstrating more pronounced effects. NaB increased the percentage of late apoptotic cells to 21.85% at 10 mM in SKOV-3 cells and to 69.9% at 5 mM in PA-1 cells, while 15 mM NaP resulted in 4.3% and 16.8% late apoptotic cells in SKOV-3 and PA-1, respectively. This was accompanied by modulation of apoptosis-regulatory proteins, including PARP-1 cleavage and an increased BAX/BCL2 ratio in the treated cells, suggesting the involvement of the intrinsic apoptotic pathway.<br><br>CONCLUSION: Our study demonstrated that NaB and NaP inhibited the growth and survival of two different ovarian cancer subtypes through cell cycle arrest and apoptosis. While NaB exhibited greater potency, our findings highlight the promising therapeutic potential of both compounds in ovarian cancer and lay the groundwork for further mechanistic and clinical studies.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12935-026-04284-5.}, }
@article {pmid42210596, year = {2026}, author = {Li, X and Wang, F and Shi, F and Wei, Y and Zhou, M and Wu, F and Su, H and Liu, X}, title = {Multiomics Reveals the Mechanisms of Rhizosphere Symbiotic Fungi in Mitigating Micro(nano)plastics Transfer and Toxicity in Food Chains.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c16131}, pmid = {42210596}, issn = {1520-5851}, abstract = {Soil micro(nano)plastics (MNPs) pollution is becoming increasingly prominent, posing a serious threat to ecological security. However, few studies have examined the remediation of soil MNPs pollution. This study constructed a multidimensional coupled system of soil-microbe interface plants-animals, in order to investigate the pathways and key mechanisms underlying rhizosphere microbiome-mediated inhibition of trophic transfer and toxicity of MNPs. The findings demonstrated that the common root-associated soil microorganisms, arbuscular mycorrhizal fungi (AMF), exhibit a mitigation effect on the food chain ecological stress of various MNPs in the environment. The mitigation was primarily manifested as a 45.57-56.52% reduction of MNPs concentration in animals and plants (due to changes in the rhizosphere environment and MNPs aging, which inhibit MNPs migration) and a decrease in MNPs binding ability to organisms. Additionally, analysis of molecular regulatory mechanisms showed that AMF mediation improved the substance synthesis and defensive pathways of plants under MNPs stress, and their palatability as food, leading to increased immune regulation and energy metabolism functions in snails consuming AMF-mediated leaves. These findings provide a theoretical basis and technical support for the development of green and efficient biological control technologies for soil MNPs pollution.}, }
@article {pmid42210811, year = {2026}, author = {Egidi, E and Nielsen, UN}, title = {Predator-Microbe Dynamics Inform Strategies for Robust Synthetic Community Assembly.}, journal = {Environmental microbiology}, volume = {28}, number = {6}, pages = {e70336}, doi = {10.1111/1462-2920.70336}, pmid = {42210811}, issn = {1462-2920}, mesh = {Rhizosphere ; Animals ; *Microbiota ; Soil Microbiology ; Nematoda/physiology ; Bacteria ; Food Chain ; }, abstract = {Synthetic microbial communities (SynComs) hold great promise for enhancing plant health and productivity, yet their field performance is often inconsistent due to challenges in establishing stable populations within complex rhizosphere environments. Predation by microbial grazers, including protists, nematodes, and bacterial predators, plays a significant role in regulating SynCom engraftment, population dynamics, and functional outcomes, but remains largely overlooked in SynCom design. Here we review the ecological processes governing predator-prey interactions in the rhizosphere, microbial traits conferring resistance to predation, and suggest strategies to incorporate these defences into SynCom assembly. By integrating predator resistance as a design criterion, we argue that SynComs can achieve greater resilience and persistence under natural biotic pressures, reducing variability in SynCom performance and improving their functional reliability in agricultural applications.}, }
@article {pmid42211112, year = {2026}, author = {Liu, Y and Li, M and Pan, M}, title = {Effect of kombucha soymilk on high fat diet mice: integrated insights from gut microbiome and metabolome analyses.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1815305}, pmid = {42211112}, issn = {2296-861X}, abstract = {INTRODUCTION: Kombucha, soymilk, and tea-derived bioactive compounds have individually been associated with metabolic benefits, while the effects of kombucha soymilk on diet-induced hyperlipidemia and its associated gut microbiome-metabolome changes remain unclear.<br><br>METHODS: In this study, we established a high-fat diet (HFD)-induced obese mouse model and administered kombucha soymilk as a dietary intervention. We systematically investigated the effects on body weight gain, lipid levels, and hepatic antioxidant capacity, and further explored the associated changes in gut microbiota composition and key metabolites underlying its lipid-lowering effects.<br><br>RESULTS AND DISCUSSION: Biochemical and histological analyses revealed that kombucha soymilk consumption significantly attenuated body weight gain in mice (p< 0.05), reduced serum and hepatic triglyceride (TG) and total cholesterol (TC) levels (p < 0.01), enhanced hepatic antioxidant capacity, and ameliorated hepatic steatosis. Microbiome analysis revealed that kombucha soymilk consumption altered the gut microbial community structure in mice, increasing the relative abundances of Enterococcus, Bifidobacterium, and Turicibacter. Untargeted metabolomics further suggested altered enrichment of pathways related to pyruvate metabolism, linoleic acid metabolism, bile secretion, and cAMP signaling. In conclusion, kombucha-fermented soymilk improved hyperlipidemia-related phenotypes in HFD-fed mice and was associated with selective gut microbial and metabolic alterations. These findings support its potential as a functional dietary intervention, although the mechanistic interpretation remains exploratory and requires further validation.}, }
@article {pmid42200732, year = {2026}, author = {Narain, S and Gupta, P and Pyare, R and Shroff, D and Rath, PD}, title = {Recent updates in human leukocyte antigen B27-associated uveitis.}, journal = {Indian journal of ophthalmology}, volume = {74}, number = {6}, pages = {817-820}, doi = {10.4103/IJO.IJO_64_26}, pmid = {42200732}, issn = {1998-3689}, mesh = {Humans ; *HLA-B27 Antigen/immunology ; *Uveitis, Anterior/immunology/diagnosis ; }, abstract = {There has been progressive understanding in etiopathogenesis, clinical presentation, and effective treatment of anterior uveitis (AU) over the years. Sudden onset, symptomatic acute anterior uveitis (AAU) in a young adult, often male, classically arouses suspicion for human leukocyte antigen (HLA) B27-related uveitis. While the ocular presentation is frequently the earliest manifestation, its systemic counterparts within the spectrum, viz., spondyloarthropathies (SpA), including ankylosing spondylitis (AS), reactive arthritis (RA), psoriatic arthritis (PA), and inflammatory bowel disease-associated inflammation, pose greater diagnostic and therapeutic challenges for rheumatologists and internists. This places the ophthalmologist in a uniquely advantageous yet responsible position in initiating etiologic evaluation and facilitating early systemic recognition. Rapid advances in immunology and molecular medicine have significantly expanded the diagnostic and therapeutic landscape of HLA B27-related disease. Emerging insights implicating the gut microbiome, autoinflammatory mechanisms, and innate immune dysregulation have reshaped traditional concepts of pathogenesis. Concurrently, an improved understanding of cytokine networks and immune signaling pathways has led to the development of targeted biologic and synthetic disease-modifying therapies. Given the dynamic, multisystem nature of HLA B27-associated disease and its variable organ involvement, optimal management necessitates close multidisciplinary collaboration among ophthalmologists, rheumatologists, gastroenterologists, and internists. This article briefly explores the evolving concepts of the complex enigma of the HLA B27 molecule and the basis for recent trends in its understanding at the cellular, molecular, biochemical, and clinical levels.}, }
@article {pmid42200819, year = {2026}, author = {Pan, Y and Dunleavy, KA and Ananthakrishnan, AN}, title = {Impact of advanced therapy initiation on antibiotic dependence in chronic pouchitis.}, journal = {Inflammatory bowel diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/ibd/izag086}, pmid = {42200819}, issn = {1536-4844}, support = {R38AG070229/NH/NIH HHS/United States ; /NH/NIH HHS/United States ; }, abstract = {BACKGROUND: A quarter of patients with ulcerative colitis who undergo total proctocolectomy with ileal pouch-anal anastomosis experience chronic pouchitis. While advanced therapies (ATs) are effective in some patients, their impact on antibiotic dependence is unclear.<br><br>METHODS: In a multicenter, retrospective study, we identified adults with chronic pouchitis during treatment with AT. Those with complete pre-AT antibiotic data formed the "incident AT user" cohort. Those with only post-AT data formed the "prevalent AT user" cohort. Antibiotic prescription was modeled as percentage of time, calculated as the number of weeks of antibiotic prescription during the weeks of observed time. The pooled prevalence of antibiotic use during AT was calculated in a systematic review and meta-analysis,.<br><br>RESULTS: Of the 67 incident AT users, 24 (36%) initiated treatment with tumor necrosis factor-&#x3b1; antagonist, 17 (25%) with anti-integrin, 23 (34%), with interleukin (IL) inhibitors (anti-IL), and 3 (5%) with Janus kinase inhibitors. The mean time on antibiotics was unchanged from 38% to 33% after AT initiation, and 61% of patients (n&#x2009;=&#x2009;44) had a reduction in antibiotic use. Compared to the patients without reduction, the reduction group had a higher proportion of patients on anti-IL (46% vs 15%, adjusted odds ratio [OR] 11.1; 95% CI, 2.12-57.62). There were no differences in disease-related parameters. Seventy-nine percent (22/28) of prevalent AT users required antibiotics. On meta-analysis, pooled prevalence of antibiotic use was 0.46 (95% CI, 0.35-0.57).<br><br>CONCLUSIONS: Just over half of patients on AT for chronic pouchitis saw reduced antibiotic use; however, further studies are needed to identify impact of AT on antibiotic use and define which patients benefit from immune-mediated vs microbiome-directed therapy.}, }
@article {pmid42201013, year = {2026}, author = {Duarte, SAC and Pinto-Leite, R and Queiroga, FL}, title = {A One Health Perspective on Cancer: A Narrative Review.}, journal = {Medical sciences (Basel, Switzerland)}, volume = {14}, number = {2}, pages = {}, pmid = {42201013}, issn = {2076-3271}, support = {UID/00772/2025//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; }, mesh = {Humans ; *Neoplasms/prevention &amp; control/epidemiology/etiology ; Animals ; *One Health ; Risk Factors ; Public Health ; }, abstract = {Cancer is a major public health challenge worldwide, with increasing incidence and a growing economic and societal burden. Despite therapeutic advances, prevention remains the most effective strategy to reduce its impact. The One Health approach, which recognizes the interconnection between human, animal, and environmental health, provides a valuable framework to address cancer risk factors in a more integrated and sustainable way. This narrative review addresses cancer through a One Health lens. Human health aspects include the global burden, major lifestyle and infectious risk factors, and key prevention strategies. Environmental determinants of cancer are summarized with emphasis on climate change, air pollution, occupational exposures, microplastics, ultraviolet radiation, and nutrition/food safety. Animal health contributions include insights from comparative oncology, which offer translational opportunities for prevention, diagnosis, and treatment, and from microbiome research revealing promising biomarkers for early detection and treatment response. Integrating cancer prevention into the One Health framework is essential for addressing the complex interplay between environmental, animal, and human health. A multidisciplinary approach can enhance public health policies, promote sustainable prevention measures, and improve early detection and treatment strategies, ultimately reducing healthcare costs and advancing global health outcomes.}, }
@article {pmid42201256, year = {2026}, author = {Saberian, E and Petrášová, A and Jenča, A and Jenčová, J and Shirali, K and Jenča, A and Więckiewicz, MA and Zare-Zardini, H and Ebrahimi Far, M}, title = {Oral microbiota diversity and composition in patients with oral lichen planus: An observational molecular analysis study.}, journal = {Dental and medical problems}, volume = {}, number = {}, pages = {}, doi = {10.17219/dmp/210087}, pmid = {42201256}, issn = {2300-9020}, abstract = {BACKGROUND: Oral lichen planus (OLP) is a chronic inflammatory condition affecting the oral mucosa. The oral microbiome has been identified as a potential contributing factor to OLP.<br><br>OBJECTIVES: The aim of the study was to evaluate the prevalence and diversity of the oral microbiota in patients with OLP.<br><br>MATERIAL AND METHODS: This observational study included 78 patients with clinically and histopathologically confirmed OLP, recruited in accordance with the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) guidelines. Buccal mucosa samples were collected using standardized protocols. DNA was extracted from 12 high-quality samples and subjected to 16S rRNA gene amplification and sequencing. Alpha and beta diversity indices were calculated using the Quantitative Insights Into Microbial Ecology (QIIME) platform. Statistical analyses were performed using the IBM SPSS Statistics for Windows software, v. 26.0 (IBM Corp., Armonk, USA) (p < 0.05).<br><br>RESULTS: Intratissue bacterial communities exhibited decreased alpha diversity and increased beta diversity compared with those present on the mucosal surface. Streptococcus, a genus within the Firmicutes phylum, was found to be the most abundant, with 5 Streptococcus strains identified in the OLP samples. Following Streptococci, Bacilli and Clostridia displayed considerable diversity. Other frequently detected species included Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa, Eikenella corrodens, Actinobacillus, as well as members of the Proteobacteria phylum, which are commonly found in high quantities in the oral cavity. Prevotella and Capnocytophaga, belonging to the Bacteroidetes phylum, were also frequently observed. Alpha diversity analysis revealed significant differences in the colony numbers of the investigated species across studied samples.<br><br>CONCLUSIONS: The findings indicate an association between the composition of the oral microbiota and OLP. The microbial populations obtained from affected individuals exhibited distinct bacterial compositions. Modulation of the oral microbiome may represent a potential strategy for improving the management of OLP.}, }
@article {pmid42201339, year = {2026}, author = {Sekhon, S and Tompkins-Rhoades, C and Uzoekwe, M and Rajaii, R and Trinh, M and Sheff, S and Hansen, SL}, title = {Shorter Wound-healing Times Associated With Select Perioperative Medical Therapies in Hidradenitis Suppurativa Surgery, and a Limited Clinical Role of Intraoperative Cultures: A 194-Case Retrospective Review.}, journal = {Annals of plastic surgery}, volume = {}, number = {}, pages = {}, doi = {10.1097/SAP.0000000000004777}, pmid = {42201339}, issn = {1536-3708}, abstract = {BACKGROUND: Hidradenitis suppurativa (HS) is a chronic inflammatory disease of apocrine gland-bearing areas characterized by abscesses, tunneling, scarring, and recurrent flares. Surgical excision is central in refractory disease, but perioperative protocols are variable. We evaluated whether specific perioperative medical therapies are associated with shorter time to documented postoperative wound-healing progress after HS surgery, and whether intraoperative cultures meaningfully guide antibiotic management.<br><br>METHODS: We conducted a retrospective cohort study of 194 HS surgeries performed at a quaternary care center between January 1, 2013, and July 1, 2021. We abstracted perioperative medical therapies (including antibiotics and spironolactone), intraoperative culture results, postoperative antibiotics, and healing times from the medical record. Healing was defined as days from surgery to the first follow-up note documenting substantial wound-healing progress. Time to healing was analyzed with Kaplan-Meier survival curves and Cox proportional hazards models. We also examined whether intraoperative cultures were associated with postoperative antibiotic selection.<br><br>RESULTS: Perioperative trimethoprim-sulfamethoxazole was associated with shorter time to documented healing [hazard ratio (HR) 2.55, 95% CI: 1.46-4.46, P=0.00099]. Preoperative cephalexin was also associated with shorter time to heal (HR: 4.17, 95% CI: 1.40-12.44, P=0.01), whereas postoperative cephalexin was not (HR: 0.89, 95% CI: 0.44-1.79, P=0.74). Perioperative spironolactone was associated with faster healing (HR: 5.72, 95% CI: 2.08-15.74, P=0.00073). Intraoperative cultures were collected in 28% of surgeries, yielded gram-positive, gram-negative, and anaerobic organisms, showed only weak, nonsignificant associations with preoperative antibiotic exposure, and were not significantly associated with postoperative antibiotic choice.<br><br>CONCLUSIONS: Perioperative trimethoprim-sulfamethoxazole, cephalexin, and spironolactone were each associated with shorter time to documented wound-healing progress after HS surgery in this retrospective cohort. Routine intraoperative cultures demonstrated limited observed clinical utility in guiding immediate postsurgical antibiotics. These findings support efforts to streamline perioperative care while de-emphasizing routine intraoperative culture collection in HS surgery.}, }
@article {pmid42201411, year = {2026}, author = {Marzanni, A and Landolfi, M and Tiziani, R and Bombardelli, S and Celi, D and Pittertschatscher, M and Buttarelli, A and Bruni, S and Pecchioni, E and Perito, B and Cnudde, V and Cappitelli, F and Mimmo, T and Villa, F and Borruso, L}, title = {Rosy Discolouration in an Alpine Chapel: Beyond Salt Dependence.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02795-2}, pmid = {42201411}, issn = {1432-184X}, abstract = {Stone heritage is central to cultural identity, yet alpine monuments remain understudied and vulnerable to deterioration. In mountain environments, moisture and temperature fluctuations promote salt crystallisation in porous geomaterials, frequently associated with rosy discolouration attributed to pink biofilms, a phenomenon still poorly explored at higher elevations. Here, we investigated rosy discolouration at about 1000 m altitude on the walls of St. Cyprian Chapel (South Tyrol) using metabarcoding and chemical analyses. We compared two cases of rosy discolouration: one on the north wall, where salt efflorescence is present, and one on the south wall, where it is absent. The aim was to characterise how salt efflorescence modulates rosy discolouration by comparing the two walls and linking substrate chemistry and mineralogy to biofilm pigments, structure, and microbial community composition. Despite similar mineralogy, the north wall exhibited distinct surface chemistry consistent with salt efflorescence. Biofilm biomass was comparable between walls, and no photosynthetic organisms were detected in either biofilm, yet microbial communities differed markedly. The south wall hosted carotenoid-producing biomarkers, including Rubrobacter and Pontibacter, although Raman did not detect carotenoid signals, indicating low pigment expression. In contrast, the north wall showed stronger discolouration and clear detection of bacterioruberin. Notably, the north-wall biomarker Chryseobacterium may also contribute to the rosy discolouration through flexirubin-type pigments. Overall, salt efflorescence is not required for pink biofilm establishment, but salt-rich microhabitats appear to enhance pigment production. This study provides new insights into the drivers of rosy discolouration and contributes to the still-limited research on alpine cultural heritage.}, }
@article {pmid42201500, year = {2026}, author = {Repanovici, A and Vîlcu, ME and Pantea, I}, title = {Mapping the research landscape on diabetes mellitus and periodontal disease: a scientometric study.}, journal = {The Saudi dental journal}, volume = {38}, number = {6}, pages = {}, pmid = {42201500}, issn = {1013-9052}, abstract = {To map the scientific landscape linking diabetes mellitus and periodontal disease using bibliometric methods, identify major thematic clusters, and examine how research supports clinical and educational perspectives relevant to integrated diabetes-oral health research. The central research question was: What are the dominant knowledge structures and interdisciplinary connections in the literature on diabetes mellitus and oral health? A bibliometric analysis was conducted using the Web of Science Core Collection (1995-2024). The search strategy combined diabetes related and oral health-related terms. After applying the eligibility criteria, 1,058 publications were included. Keyword preprocessing involved synonym unification, abbreviation harmonization, and manual validation. VOSviewer v1.6.18 was used for keyword co occurrence mapping. Potential sources of bias related to database selection and keyword variability were acknowledged. Eight thematic clusters were identified, covering periodontal disease, prevention, epidemiology, systemic comorbidities, microbiome research, quality of life, clinical interventions, and biomarkers. Cluster structure remained stable across sensitivity thresholds. The literature on diabetes and oral health exhibits recurring thematic patterns and interconnected research domains. While bibliometric clustering reflects co occurrence structures rather than conceptual maturity, the findings provide an analytical overview of how research areas relate to one another. The findings indicate recurring thematic patterns and interconnected research domains. The identified clusters outline priority domains relevant to risk assessment, prevention, and interdisciplinary care. Although bibliometric findings do not directly inform clinical decision making, they highlight areas where integrated diabetes-oral health strategies may be strengthened.}, }
@article {pmid42201625, year = {2026}, author = {Akram, F and Zainab, S and Shabbir, I and Haq, IU}, title = {Gut microbiota and cancer immunotherapy: from dysbiosis to personalized immune checkpoint blockade optimization.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {42201625}, issn = {1874-9356}, abstract = {Cancer has become one of the most prominent causes of death worldwide due to its increasing mortality rate. Immune checkpoint blockade therapy is an effective regimen for tumor control. Still, it faces challenges, including primary resistance and interindividual variations, thereby directing the field towards a new era of immunotherapy adjuncts. Recent studies have shown that the microbiota of cancer patients influences the outcomes of ICB (immune checkpoint blockade) therapy through microbiome-immune system crosstalk. Homeostatic commensal microbial consortia aid in combating tumors by enhancing immunity, whereas dysbiotic microbes facilitate cancer development by mediating immunosuppression. Microbiota modulation via microbiome-targeted interventions, including fecal microbiota transplantation or washed microbiota transplantation from responders, biotic supplements, and dietary modifications, can convert primary resistance to durable responses and thus augment immunotherapy responsiveness in cancer treatment. This review discusses the dual nature of microbiota in mediating the development and treatment of cancer, its crucial role in shaping ICB therapy responsiveness, and the identification of microbial biomarkers into a refined Discovery-Validation-Clinical (DVC) pipeline linked to multi-omics profiling and personalized microbiome-modulation interventions for ICB therapy optimization. In addition, it presents the translational clinical decision framework that highlights patient stratification, intervention timing, and implementation barriers to support clinical translation. Ultimately, the gut microbiome emerges as a "force multiplier" of cancer ICB therapy, thereby enabling microbiome-guided precision oncology and strengthening a roadmap toward personalized cancer care.}, }
@article {pmid42201651, year = {2026}, author = {He, J and Bao, J and Deng, S and Zang, W and Yan, H and Zhao, Z and Zhang, G and Liu, R and Chen, J and Hu, Y and Xue, W}, title = {β-Elemene Rescues Radiation-Induced Enteritis by Orchestrating a Host-Microbiome Circuit That Fuels Epigenetic DNA Repair.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e21445}, doi = {10.1002/advs.202521445}, pmid = {42201651}, issn = {2198-3844}, support = {82473448//National Natural Science Foundation of China/ ; 82102720//National Natural Science Foundation of China/ ; 82203096//National Natural Science Foundation of China/ ; BK20221272//Natural Science Foundation of the Jiangsu Province, China/ ; YJXYY202204-2-YSC16 YJXYY202204-ZD18//Jiangsu Provincial Research Hospital/ ; YJXYY202204-2-YSB23//Jiangsu Provincial Research Hospital/ ; }, abstract = {Radiation-induced enteritis (RIE) is a severe, dose-limiting toxicity of cancer radiotherapy lacking mechanism-based therapies. While the gut microbiome regulates radiation injury, harnessing it therapeutically remains challenging. Here, we show that the natural product β-elemene protects against RIE through a synergistic mechanism coordinating host and microbial responses. β-elemene directly rescues the radiation-disrupted interaction between the lactate transporter MCT1 and its chaperone CD147 in intestinal epithelial cells, priming them for enhanced lactate uptake. Concurrently, β-elemene selectively enriches for Lactobacillus gasseri, increasing intestinal lactate production. The convergence of host priming and elevated lactate availability triggers a metabo-epigenetic cascade. Specifically, lactate drives the lactylation of the chromatin-associated protein RBBP4, which in turn recruits EP300 to activate the transcription of essential DNA damage repair genes. We further identify EP300 as a lactyl-transferase, establishing a self-amplifying positive feedback loop that robustly enhances the repair signal. Our findings delineate a complete drug-microbe-metabolite-epigenome axis, establishing a 'prime-and-fuel' therapeutic strategy where a single agent orchestrates inter-kingdom communication to promote tissue regeneration.}, }
@article {pmid42201863, year = {2026}, author = {Kaptan, D and Flemming Elvers, AC and Kjær Knudsen, A and Schroeder, H and Hollund, HI}, title = {Histological and metagenomic analysis of microbial communities in archaeological human bones.}, journal = {PloS one}, volume = {21}, number = {5}, pages = {e0340244}, pmid = {42201863}, issn = {1932-6203}, mesh = {Humans ; *Bone and Bones/microbiology/pathology ; *Metagenomics/methods ; *Archaeology ; *Microbiota/genetics ; Bacteria/genetics/classification ; Fungi/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Norway ; Phylogeny ; }, abstract = {Buried archaeological bones tend to be heavily degraded by microorganisms. This type of biodegradation was already identified in the 19th century and remains a subject of continuous investigation. However, the underlying processes are still not fully understood, and the organisms responsible for the decay have not been clearly identified. Technological advances in genetic sequencing now allow detailed study of the bone microbiome. And yet, identifying the species causing the observed bioerosion has proven challenging. Relatively few studies have combined the investigation of bone degradation by microscopy, so-called histotaphonomy, with metagenomic analyses. This study aims to bridge this gap. We utilize a large set of human bone samples from medieval cemeteries in south-western Norway. Detailed microscopic analyses have been carried out, showing diverse levels of preservation. The extent of bioerosion is correlated with the results from metagenomic analyses as well as environmental factors. Microbiome diversity is greater and more evenly distributed in well-preserved bones with limited bioerosion, particularly those recovered from burials beneath church floors, contrasting with outdoor cemeteries. Fungal taxa were detected in only a single sample in the metagenomic data despite histological evidence of fungal structures, and their role in bone bioerosion remains unclear. Our findings show that preservation state is strongly associated with microbiome composition. The most prevalent genus found was Streptomyces, supporting previous research suggesting that bacteria within this group could be involved in bone bioerosion.}, }
@article {pmid42201874, year = {2026}, author = {Davis, TL and Dirks, B and Carnero, EA and Corbin, KD and Smith, SR and Marcus, A and Krajmalnik-Brown, R and Rittmann, BE}, title = {Modeling the microbial contribution to human energy balance using the Digestion, Absorption, and Microbial Metabolism (DAMM) model.}, journal = {PloS one}, volume = {21}, number = {5}, pages = {e0347668}, pmid = {42201874}, issn = {1932-6203}, mesh = {Humans ; *Energy Metabolism/physiology ; *Models, Biological ; *Digestion/physiology ; *Gastrointestinal Microbiome/physiology ; Colon/microbiology/metabolism ; Fatty Acids, Volatile/metabolism ; Intestinal Absorption ; Diet ; }, abstract = {Colonic microorganisms have been linked to human health and disease, specifically metabolic disease states such as obesity, but causal relationships remain to be established. Previous work demonstrated that interactions between the host's diet and intestinal microbiome were associated with human energy balance by affecting the human's energy absorption, quantified by metabolizable energy. We developed the Digestion, Absorption and Microbial Metabolism (DAMM) model, which explicitly accounts for the energy contributions of the colonic microbial community in five steps. 1) The DAMM model breaks down the diet composition into the gross energy of the individual macronutrients. 2) It calculates direct absorption in the upper gastrointestinal tract. 3) It uses microbial stoichiometry to estimate the consumption of the remaining unabsorbed nutrients by microbes in the large intestine. 4) It quantitatively predicts microbial production of short-chain fatty acids (SCFA) and methane in the colon. 5) The DAMM model estimates absorption from the colonic tract to the host, including SCFAs. When used to predict the results from a clinical study that compared two distinctly different diets, the DAMM model captured the directionality and magnitude of change in measured metabolizable chemical oxygen demand (which can be converted to metabolizable energy), estimated substrate availability within the colon, and predicted rate of production of microbially derived short-chain fatty acids. It improved on the accuracy of metabolizable chemical oxygen demand predictions compared to the Atwater factors, increasing the fit from R2 = 88% (Atwater) to R2 = 96% (DAMM). The model reduced systematic bias on one of the diets and decreased the mean difference between measurement and predictions from -22.3 gCOD d-1 to -2.5 gCOD d-1. The DAMM model now can be linked to existing human models that predict changes in body energy stores to extend our understanding of how microbial metabolic processes affect macronutrient absorption and metabolizable energy.}, }
@article {pmid42202371, year = {2026}, author = {Afzal, A}, title = {Biological responses to heat stress in livestock: From thermoregulation to cellular and epigenetic adaptation.}, journal = {Journal of thermal biology}, volume = {139}, number = {}, pages = {104473}, doi = {10.1016/j.jtherbio.2026.104473}, pmid = {42202371}, issn = {0306-4565}, abstract = {Climate change driven increases in ambient temperature have positioned heat stress (HS) as a major biological constraint on livestock productivity and welfare. Excessive thermal load disrupts thermoregulatory balance, reduces feed intake and digestive efficiency, and perturbs immune and endocrine function, culminating in impaired energy metabolism and systemic dysfunction. Reproductive processes show pronounced thermal sensitivity, as HS alters hypothalamic-pituitary-gonadal axis signaling, compromises gametogenesis, reduces embryo viability, and suppresses fertility. Productive traits, including milk yield, growth rate, egg production, and carcass quality, decline as cumulative heat load exceeds adaptive capacity. Emerging evidence identifies the gut-brain axis as a critical mediator of HS pathology, where heat-induced vascular redistribution, epithelial hypoxia, and microbiome dysbiosis amplify inflammatory and metabolic stress. At the cellular level, HS triggers mitochondrial dysfunction, oxidative imbalance, activation of heat shock responses, immune dysregulation, and epigenetic remodeling with potential long-term consequences. Current mitigation strategies encompass nutritional and phytogenic modulation of stress pathways, genetic selection for thermo-tolerance, microclimate control, and precision livestock farming (PLF) technologies for real-time detection of thermal strain. However, partial understanding of molecular thresholds, epigenetic plasticity, and integrative system responses limits effective translation. Addressing these gaps through mechanistically driven and interdisciplinary research is essential for enhancing thermal resilience and sustaining livestock production under ongoing climate warming.}, }
@article {pmid42202591, year = {2026}, author = {Baba, IA and Mustapha, LS and Obayomi, OV and Obayomi, KS and Zhang, J}, title = {From contaminated waters to living ecosystems: Heavy-metal remediation as a driver of aquatic habitat and biodiversity restoration.}, journal = {Marine pollution bulletin}, volume = {231}, number = {}, pages = {119919}, doi = {10.1016/j.marpolbul.2026.119919}, pmid = {42202591}, issn = {1879-3363}, abstract = {Contaminations of soils by hydrocarbons are significant threats to both ecosystems and human health as a result of their persistent nature and potential to cause adverse toxicological effects along with bioaccumulation. This review will discuss the state-of-the-art nanotechnologies used for remediation of soils contaminated with hydrocarbons and their role in processes of adsorption, catalytic oxidation, photocatalysis, electron transfer, redox cycling, and stimulation of microorganisms. While most studies on this topic only highlight the efficiency of biodegradation, this work is going to integrate all aspects of physicochemical transformations of the contaminants, ecology, and sustainability of nanomaterials into one comprehensive overview. Metal nanoparticles, metal oxide nanoparticles, carbon-based nanomaterials, nanoscale zero-valent iron, magnetic nanocomposites, nanoscale zeolites, and hybrid nanomaterials will be analyzed in relation to their impact on the process of hydrocarbon mineralization and degradation rate. The importance of new technologies that involve green synthesis of nanomaterials, their surface modification, and their coupling with microorganisms will be discussed about the improvement of catalytic properties, selectivity, and safety of nanomaterials. Potential ecotoxicological risks such as nanoparticle aggregation, disturbance of the microbiome, bioaccumulation, and changes to the structure of the soil will be also considered.}, }
@article {pmid42202778, year = {2026}, author = {Nogal, A and Wang, K and Thompson, KN and Kim, H and Bhosle, A and Piccinno, G and Maharjan, S and Upreti, C and Nguyen, LH and Segata, N and Rimm, EB and Garrett, WS and Chan, AT and Huttenhower, C and Song, M}, title = {Long-lasting gut microbiome and fecal metabolome alterations after colorectal adenoma removal and their relationship to colorectal cancer.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.05.001}, pmid = {42202778}, issn = {1934-6069}, abstract = {Although the gut microbiome is implicated in colorectal cancer (CRC), microbiome and metabolome alterations along the adenoma-carcinoma sequence remain unclear. Here, we profile stool metagenomes obtained from 354 women 12.1 ± 4.8 years following adenoma resection and from their 1:1-matched controls, as well as stool metabolomes from 184 pairs. Metagenomic profiles are compared with those from 14 independent CRC case-control studies. Microbial composition differs between adenoma cases and controls and agrees with CRC-associated alterations (Pearson's rho = 0.26, p < 0.0001). Thirty-one microbes, including Faecalibacterium prausnitzii and Flavonifractor plautii, are altered in both conditions and correlate with lifestyle factors. Thirty metabolites and 7 sub-pathways, particularly sphingolipids, are associated with adenomas. Adenomas also exhibit disease-specific microbe-metabolite associations, including those between Bilophila wadsworthia and alanine-containing dipeptides. These findings reveal gut microbial and metabolomic alterations detectable years after adenoma resection, supporting the presence of an altered microbiome along the adenoma-CRC continuum.}, }
@article {pmid42202790, year = {2026}, author = {Toubon, G and Boulund, F and Escobedo, CM and Brunius, C and Engstrand, L and Larsson, SC and Nordin, E and Schuppe-Koistinen, I and Wolk, A and Wittenbecher, C and Landberg, R}, title = {Gut microbiome composition and functional potential associate with incident type 2 diabetes in 4,685 adults from a Swedish prospective cohort.}, journal = {Cell reports. Medicine}, volume = {}, number = {}, pages = {102835}, doi = {10.1016/j.xcrm.2026.102835}, pmid = {42202790}, issn = {2666-3791}, abstract = {Cross-sectional studies link gut microbiome alterations to type 2 diabetes (T2D), but prospective evidence remains limited. We aim to identify taxonomic and functional features associated with future T2D risk. We analyze shotgun metagenomic data from 4,685 participants (mean age, 73.9 years; 49.0% women) in the Swedish SIMPLER cohort, followed for a median 5.3 years, during which 383 developed T2D. Six species are associated with increased T2D risk: Desulfovibrio piger, Alistipes communis, Alistipes finegoldii, Akkermansia muciniphila, Ruminococcus gnavus, and GGB3614_SGB4886 (Lachnospiraceae), while three are protective: Erysipelotrichaceae bacterium, Coprococcus catus, and Clostridia unclassified SGB6317. We observe context-specific associations, including a dietary fiber-modified effect for A. muciniphila indicative of diet-dependent patterns. Three gut metabolic modules are associated with incident T2D: asparagine degradation (higher risk), mannose degradation, and the non-oxidative pentose phosphate pathway (lower risk). These prospective findings offer insights into T2D etiology and may support microbiome-informed strategies for risk prediction and prevention.}, }
@article {pmid42203014, year = {2026}, author = {Wang, S and Cheng, H and Shao, J and Wang, Y and Feng, C and Yan, S and Zhang, X}, title = {Air purification modulates PM-associated nasal microbiota and exhaled metabolome to enhance cardiopulmonary health in children: A randomized crossover trial.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {403}, number = {}, pages = {128441}, doi = {10.1016/j.envpol.2026.128441}, pmid = {42203014}, issn = {1873-6424}, abstract = {Recent studies have identified the association between exposure to environmental particulate matter (PM) and upper respiratory tract microbiota or lower respiratory tract metabolites; however, direct evidence linking the respiratory microbiome to metabolomic responses remains limited. This study examines how short-term air purification influences PM-related health outcomes, nasal microbiota, and exhaled breath condensate (EBC) metabolites in children. In a randomized crossover trial involving 67 children living near a coking plant, the linear mixed-effects model analyses showed that PM exposure was associated with changes in vital capacity and heart rate. Moreover, PM exposure reduced the abundance of nasal Rothia, which was closely connected to changes in EBC metabolites, including hexylresorcinol and β-carotene. Network and mediation analyses revealed that the PM-Rothia-metabolite axis may exert a significant impact on cardiopulmonary function, among which β-carotene is likely to mediate the effect of PM on vital capacity. Our findings indicate that short-term air purification can reduce PM-associated cardiopulmonary risks in children by modulating Rothia-dependent metabolic pathways.}, }
@article {pmid42203025, year = {2026}, author = {Magosso, N and Fioretto, MN and Fávaro, I and de Souza, PV and Moreira, MF and Rocha, VA and Barbosa, FC and Rodrigues, J and Scarano, WR}, title = {Early-life exposure to phthalates and nanoplastics alters gut microbiota and intestinal morphophysiology in rat dams and male offspring.}, journal = {Toxicology}, volume = {525}, number = {}, pages = {154510}, doi = {10.1016/j.tox.2026.154510}, pmid = {42203025}, issn = {1879-3185}, abstract = {Phthalates and nanoplastics, common contaminants in everyday products and a result of their degradation, respectively, are linked to environmental degradation and human exposure. Research suggests that these substances can affect the gut microbiota and morphology, especially during pregnancy and lactation. Changes in the maternal microbiota can have lasting immunological and inflammatory effects on the offspring. This study investigated the effects of gestational (design 1) and gestational and lactational (design 2) exposure to a mixture of phthalates (PM) and nanoplastics (NPs), isolated or in combination, on colon histology and gut microbiota composition of directly exposed mothers (1), and of the male pups of these mothers (2). Pregnant Sprague Dawley rats were randomly divided into 4 groups: CTR (control; vehicle), PM (20 μg/kg/day of phthalate mixture), NPs (1 mg/kg/day nanoplastics NPs-100nm), PM+NPs (20 μg/kg/day PM + 1 mg/kg/day NPs-100nm). Treatment was administered orally from gestational day 5 (GD5) to GD20 for maternal fecal collection (design 1), or from GD10 to postnatal day 22 (PND22) for fecal collection from male pups (design 2). At the end of the treatment period, pregnant rats (GD20) and post-weaning male rats (PND22), 5-6 rats from each group, were euthanized. Colon samples and feces were collected for morphological and microbiome composition analysis, respectively. PM exposure increased goblet cells and reduced class and order Erysipelothichia/Erysipelotrichales at GD20, and reduced class and order Clostridia/Clostridiales at PND22. In addition, PM+NPs exposure increased goblet cells and class and order Bacilli/Lactobacillales and Gammaproteobacteria/Enterobacteriales at GD20. These findings provide evidence that exposure to PM+NPs during gestation affects the maternal microbiota and goblet cells; while this exposure during gestation and lactation causes alterations in the gut microbiota of the offspring, without histological changes. This may also provide information about the mechanistic effects of co-exposure in humans.}, }
@article {pmid42203116, year = {2026}, author = {Yun, YR and Kim, S and Lee, DY and Yu, S and Kim, KH and Yun, EJ}, title = {Valorizing renewable biomass into potential prebiotic oligosaccharides: Enzymatic, microbial, and synthetic biology strategies.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134974}, doi = {10.1016/j.biortech.2026.134974}, pmid = {42203116}, issn = {1873-2976}, abstract = {Biomass valorization has become a central strategy in the transition toward a circular bioeconomy, enabling the conversion of underutilized terrestrial and marine resources into value-added functional ingredients. The production of prebiotic oligosaccharides (POs) has garnered increasing attention owing to their demonstrated health benefits, scalability, and compatibility with existing food systems. This review summarizes recent advances in enzymatic and microbial technologies for producing potential POs-including neoand agarooligosaccharides, cello-oligosaccharides, xylo-oligosaccharides, and pectin oligosaccharides-from renewable biomass, such as marine macroalgae, lignocellulosic residues, and pectin-rich crops. These oligosaccharides act as prebiotics that modulate the gut microbiota and promote the formation of bioactive metabolites, which include short-chain fatty acids, indole-3-lactic acid, and spermidine. With advances in metabolic engineering and synthetic biology, progress has also enabled the microbial biosynthesis of lacto-N-neotetraose and 2'-fucosyllactose, which are human milk oligosaccharides, from biomass-derived sugars using GRAS-designated microbial hosts. These biotechnologies offer sustainable and scalable alternatives to conventional extraction or chemical synthesis. We also discuss recent developments in enzyme engineering, bioprocess optimization, and microbial co-culture systems aimed at enhancing product yield and specificity. This review highlights the industrial applications and beneficial health effects of biomass-derived oligosaccharides, emphasizing their role as next-generation functional ingredients in personalized nutrition and microbiome-targeted therapies.}, }
@article {pmid42203119, year = {2026}, author = {Shen, X and Lei, X and Zhang, H and Guo, E and Chen, L and Sun, C and Muhammad, A and Shao, Y}, title = {From multi-omics insights to single-strain proof: How traditional agricultural system enhances fish flavor via the microbiome-gut-muscle axis.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134992}, doi = {10.1016/j.biortech.2026.134992}, pmid = {42203119}, issn = {1873-2976}, abstract = {Intensive aquaculture has significantly boosted aquatic product yields, but it often compromises sensory quality and remains constrained by reliance on unsustainable fishmeal. The Mulberry-dyke and Fish-pond system, used in China for millennia, suggests a circular approach, yet the underlying mechanism remains poorly understood. In this study, silkworm excrement (SE) from traditional sericulture (TSE) and modern insect factories (ISE) was evaluated as a functional aquafeed. Body weight, gut histology, and immunohistochemistry were employed to assess host health. Gut microbiome, electronic tongue analysis, and muscle metabolomics were conducted to assess fish flavor and identify flavor-related microorganisms. A single-strain feeding experiment further validated the microbiome-gut-muscle axis using electronic tongue analysis, gut transcriptomics, and determination of free amino acids and nucleotides. SE supplementation maintained fish yield while improving intestinal structure. Compared with commercial feed (CF), both SE treatments increased gut microbial diversity and community stability, and more than half of the significantly different ASVs were shared between the TSE and ISE groups, mainly involving immune regulation, nutrient metabolism, and flavor formation. SE, particularly TSE, enhanced antioxidant capacity and reduced lipid peroxidation, possibly through microbial regulation of lysophosphatidylcholines. As consistently indicated by electronic tongue and muscle metabolomics analyses, SE significantly improved fish flavor, with increased umami and reduced bitterness. Network analysis and single-strain feeding further suggested that Methylorubrum populi, Gemmobacter aquatilis, and Rhodobacter sphaeroides contributed to flavor improvement by regulating host amino acid and nucleotide metabolism along the microbiome-gut-muscle axis. These findings highlight SE as a promising sustainable bioresource for aquaculture.}, }
@article {pmid42203202, year = {2026}, author = {Shao, Y and Yu, S and Zhang, M and Huang, Y and Dou, Z and Tian, B and Lu, J}, title = {Beyond Suppression: The Plasticity, Dysfunction, and Therapeutic Reprogramming of Regulatory T Cells in Inflammatory Bowel Disease.}, journal = {Journal of leukocyte biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jleuko/qiag067}, pmid = {42203202}, issn = {1938-3673}, abstract = {Inflammatory bowel disease (IBD) is a chronic relapsing inflammatory disorder of the gut, whose pathogenesis is closely related to immune dysregulation. Regulatory T cells (Tregs), as a key cell population maintaining intestinal immune tolerance, exhibit not only reduced frequency but, more critically, profound functional deficiencies, including the generation of pro-inflammatory ex-Tregs, and loss of lineage stability in the inflamed gut microenvironment of IBD. This review systematically delineates the sophisticated biological characteristics of Tregs, with a particular focus on the epigenetic and metabolic checkpoints that govern their stability. We critically summarize the aberrant changes of Tregs in IBD, emphasizing mechanisms such as inflammatory cytokine-induced Treg plasticity (e.g., Th1-like or Th17-like conversion) and microbiota-metabolite axis-mediated functional modulation. Furthermore, we provide an in-depth analysis of emerging therapeutic strategies aimed at restoring Treg suppressive capacity, including selective cytokine therapy (e.g., low-dose/engineered IL-2), adoptive transfer of engineered antigen-specific Tregs (including CAR-Tregs), microbiome/dietary interventions, and pharmacological modulation of Treg differentiation. We also discuss the disrupted crosstalk between Tregs and other innate and adaptive immune cells within the IBD milieu. Finally, this review highlights how cutting-edge technologies like single-cell multi-omics and spatial transcriptomics are delineating the heterogeneous landscape and uncovering novel, disease-specific Treg subpopulations, thereby paving the way for precise Treg-targeting therapies. Unlike previous reviews that broadly catalog Treg abnormalities, this review offers a refined conceptual framework centered on the critical distinction between lineage-defective ex-Tregs and exhausted effector Tregs (eTregs), and integrates recent multi-omics insights to redefine Treg functional failure in IBD.}, }
@article {pmid42203230, year = {2026}, author = {Acevedo-Whitehouse, K and Domínguez-Sánchez, CA and Nieves-Martínez, DP}, title = {Profiling of the Guadalupe Fur Seal (Arctocephalus philippii townsendii) Fecal Bacteriome in Relation to Alopecic Syndrome.}, journal = {Journal of wildlife diseases}, volume = {}, number = {}, pages = {}, doi = {10.7589/JWD-D-25-00154}, pmid = {42203230}, issn = {1943-3700}, abstract = {Alopecic syndrome in Guadalupe fur seals, Arctocephalus philippii townsendii (GFSs), was first observed a decade ago, coinciding with an anomalous warm sea surface temperature event and shifts in foraging behaviors of otariid pinnipeds from Mexican North Pacific colonies. With no evidence of dermatophytes or ectoparasites commonly associated with alopecia, it has been proposed that nutritional or metabolic changes, secondary to altered foraging, may increase the risk of alopecia. We employed 16S rRNA gene deep sequencing to investigate changes in the fecal bacteriome of GFS with and without alopecia. We found no significant differences in species richness nor Simpson's diversity index, and alopecia accounted for less than 6% of the variation in bacteriome structure. However, five bacterial phyla (Bacteroidota, Firmicutes, Fusobacteriota, Proteobacteria, and Spirochaetota) were overrepresented, and two (Actinobacteriota and Campylobacterota) were underrepresented, in GFSs with alopecia. At the genus level, animals with alopecia had a higher abundance of various bacteria, including Parabacteroides, Bacteroides, Lachnospiraceae, Roseburia, and genera within Erysipelotrichaceae, which have been linked to alopecia in humans. The GFS fecal bacteriome revealed 322 distinct bacterial functional pathways, of which 163 varied significantly between cases and controls. The most prominent differences found in GFSs with alopecia were overrepresentation of critical precursors for bacterial cell wall components, aromatic amino acid biosynthesis and pantothenate and CoA biosynthesis, and underrepresentation of glucosyltransferases and bacterial surface antigens, nitrogen and sulfur metabolism, and bacterial secretion systems. Our study provides preliminary evidence that changes in enteric microbiota may contribute to the pathogenesis of alopecia in GFSs via three main mechanisms: dysregulation of immune modulation and sustained inflammation, altered metabolism, and reduced redox balance and detoxification in the gut. While future studies need to explore these possibilities, our findings offer insight into the role of the microbiome in emerging pathologies of wildlife.}, }
@article {pmid42203331, year = {2026}, author = {Rafique, A and Koh, YS}, title = {Unveiling the Anti-tumor Actions and Therapeutic Potential of Calcitriol in Colorectal Cancer.}, journal = {Anticancer research}, volume = {46}, number = {6}, pages = {2985-3004}, doi = {10.21873/anticanres.18175}, pmid = {42203331}, issn = {1791-7530}, mesh = {Humans ; *Calcitriol/therapeutic use/pharmacology ; *Colorectal Neoplasms/drug therapy/metabolism/pathology ; Receptors, Calcitriol/metabolism ; Animals ; Signal Transduction/drug effects ; Tumor Microenvironment/drug effects ; *Antineoplastic Agents/therapeutic use/pharmacology ; }, abstract = {Calcitriol (1,25-dihydroxyvitamin D3), the active form of vitamin D, signals through the vitamin D receptor (VDR) and has been linked to colorectal cancer (CRC) risk and progression. This review summarizes current evidence on calcitriol/VDR actions relevant to CRC prevention and therapy. A structured literature search of PubMed, Scopus, and Web of Science was conducted through December 2025 for studies on calcitriol, VDR, and CRC, including mechanistic, preclinical, epidemiological, and clinical trial reports. Evidence was synthesized narratively with an emphasis on pathways connecting epithelial biology, inflammation, and the tumor microenvironment. Across model systems and patient studies, calcitriol/VDR signaling is associated with reduced proliferation, enhanced differentiation and apoptosis, and repression of oncogenic programs including Wnt/beta catenin and MYC-driven transcription. Calcitriol can also shape the tumor immune milieu by limiting pro-inflammatory signaling (for example, NF-κB, COX 2, IL-6 and IL-8), supporting epithelial tight junctions, and modulating the microbiome and bile acid metabolism, which together may enhance immune surveillance and reduce tumor-permissive inflammation. Evidence from supplementation trials is mixed, suggesting heterogeneity in baseline vitamin D status, tumor stage and VDR pathway context. Calcitriol engages convergent epithelial and immune mechanisms that plausibly limit CRC initiation and progression, but optimal patient selection and dosing strategies remain unresolved. Future trials integrating molecular biomarkers and VDR-responsive gene signatures are needed to define when vitamin D-based interventions can provide meaningful benefit in CRC.}, }
@article {pmid42203372, year = {2026}, author = {McCann, P and Megaw, J and Gobert, GN}, title = {Parasite-associated microbiomes: An unseen microenvironment.}, journal = {Advances in parasitology}, volume = {131}, number = {}, pages = {31-70}, doi = {10.1016/bs.apar.2026.03.001}, pmid = {42203372}, issn = {2163-6079}, mesh = {Animals ; Humans ; *Microbiota ; *Host-Parasite Interactions ; *Parasites/microbiology/physiology ; Symbiosis ; }, abstract = {Parasites harbor diverse microbial ecosystems that include not only bacteria but also archaea, fungi, viruses and microbial eukaryotes. These parasite-associated microbiomes, long overlooked, are now recognized as important determinants of parasite development, fitness, virulence and interactions with hosts across medical, veterinary, agricultural and ecological systems. However, current understanding of parasite-associated microbiomes remains fragmented, with most studies focusing on a narrow set of human parasites, relying heavily on bacterial surveys and rarely capturing the full multi-kingdom diversity of microbial partners. Important challenges include expanding research to encompass neglected parasite groups and their non-bacterial associates, establishing causal links between microbiome members and parasite phenotypes, and overcoming the technical barriers posed by low-biomass, host-contaminated and/or experimentally intractable systems. Progress will also depend on developing robust reference genomes and analytical tools that can resolve multi-kingdom communities and integrate parasite and symbiont biology. This chapter synthesizes current knowledge across helminths, protozoa, ectoparasites and plant-infecting parasites. We consider how microbiome manipulation may contribute to parasite control while recognizing the evolutionary and ecological complexities involved in altering host-parasite-microbiome interactions. Embracing an explicitly multi-kingdom, holobiont-focused perspective promises to illuminate fundamental aspects of parasitism. Such knowledge may contribute to new avenues for mitigating the impact of parasitic diseases on human and animal health, food security and ecosystems.}, }
@article {pmid42203413, year = {2026}, author = {Baker, JM and Dickson, RP}, title = {The Role of the Respiratory Microbiome in Pneumonia.}, journal = {Clinics in chest medicine}, volume = {47}, number = {2}, pages = {199-213}, doi = {10.1016/j.ccm.2025.12.004}, pmid = {42203413}, issn = {1557-8216}, mesh = {Humans ; *Microbiota ; COVID-19 ; *Lung/microbiology ; SARS-CoV-2 ; *Pneumonia, Viral/microbiology ; Pandemics ; *Pneumonia/microbiology ; Betacoronavirus ; }, abstract = {The lung microbiome field has matured into a promising area of translational research. Emerging evidence from the past decade, including studies of COVID pneumonia, indicates a role for respiratory microbiota in pneumonia pathogenesis. Here, the authors discuss areas of investigation that will be essential to refine an ecology-based conceptual framework of pneumonia pathogenesis, which will ultimately guide the development of microbiome-targeted diagnostics and therapeutics for pneumonia management.}, }
@article {pmid42203422, year = {2026}, author = {Van Besien, RF and Vazquez Guillamet, MC}, title = {The Evolving Etiology of Hospital-Acquired and Ventilator-Associated Pneumonia.}, journal = {Clinics in chest medicine}, volume = {47}, number = {2}, pages = {321-329}, doi = {10.1016/j.ccm.2025.12.013}, pmid = {42203422}, issn = {1557-8216}, mesh = {Humans ; *Pneumonia, Ventilator-Associated/microbiology/epidemiology/etiology/diagnosis/drug therapy ; *Healthcare-Associated Pneumonia/microbiology/epidemiology/diagnosis/etiology/drug therapy ; *Cross Infection/microbiology/epidemiology ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {Nosocomial pneumonia (NP), including hospital-acquired and ventilator-associated pneumonia, remains a major threat to hospitalized patients. NP arises from aspiration of pathogens in the setting of alterations in the pulmonary microbiome and weakened host defenses. Pseudomonas aeruginosa and Staphylococcus aureus predominate, though there has been a rise in carbapenem-resistant gram negatives, complicating treatment and increasing mortality. Viral and fungal pathogens further contribute to the NP burden. Diagnostic challenges persist due to nonspecific clinical features, though multiplex polymerase chain reaction testing is improving pathogen identification. This article highlights emerging trends in NP epidemiology, antibiotic resistance, and novel diagnostics.}, }
@article {pmid42203427, year = {2026}, author = {Pantaleón García, J and Chung, CJ and Flowers, RC and Evans, SE and Wu, BG}, title = {Non-antibiotic Treatments for Pneumonia: Host-Directed Therapies, Next-Steps and Future Directions.}, journal = {Clinics in chest medicine}, volume = {47}, number = {2}, pages = {383-397}, doi = {10.1016/j.ccm.2025.12.018}, pmid = {42203427}, issn = {1557-8216}, mesh = {Humans ; *Host-Directed Therapy ; *Pneumonia/therapy/microbiology/drug therapy ; }, abstract = {Pneumonia is one of the deadliest and most common infections worldwide. Traditional management has focused on pathogen-directed therapy with antimicrobial drugs. However, continued increase of antimicrobial resistance represents a growing health care crisis and heightens the urgency of shifting the treatment focus outside of the traditional paradigm. Adjunctive and host-directed therapies (HDT) target the response to infection by either enhancing the host immune response or mitigating immunopathology. They encompass a broad range of treatments, repurposed medications, and interventions that alter how the host responds to infections. This review summarizes adjunctive and HDTs for bacterial, tuberculous, fungal, and viral pneumonia.}, }
@article {pmid42203454, year = {2026}, author = {Sawangpanyangkura, T and Suparan, K and Wechwithayakhlung, C and Kunasol, C and Chattipakorn, N and Chattipakorn, SC}, title = {Stage-Associated Subgingival Dysbiosis Across the Periodontal Disease Spectrum in a Thai Cohort.}, journal = {Journal of clinical periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jcpe.70147}, pmid = {42203454}, issn = {1600-051X}, support = {N42A660301//National Research Council of Thailand/ ; N42A670125//National Research Council of Thailand/ ; N42A690147//National Research Council of Thailand/ ; //Chiang Mai University Excellent Center award/ ; JRCMU2566R_023//CMU Junior Research Fellowship Program/ ; }, abstract = {AIMS: This cross-sectional study aimed to investigate the subgingival microbiota and predict functional profiles across the 2018 EFP/AAP periodontal disease spectrum in a Thai clinical cohort.<br><br>MATERIALS AND METHODS: Subgingival plaque from 100 participants (gingivitis, n&#x2009;=&#x2009;30; Stage II-IV periodontitis, n&#x2009;=&#x2009;70) was analysed by 16S rRNA gene sequencing with taxonomic assignment using the Human Oral Microbiome Database.<br><br>RESULTS: Peptostreptococcaceae-related taxa, Dialister pneumosintes, Shuttleworthia satelles, Prevotella sp. HMT-304, and Bacteroidetes [G-3] bacterium HMT-280 were recurrently identified across differential abundance and penalised regression analyses. Penalised regression models showed limited stage-discriminative performance (multinomial AUC 0.68-0.78), with gingivitis achieving the highest classification accuracy (63%) and Stage IV the lowest, consistent with overlapping microbial profiles across stages. Nonetheless, some stage-enriched taxa included Campylobacter species in Stage III and Porphyromonas gingivalis with Odoribacter bacterium HMT-516 in Stage IV. Stage-enriched taxa correlated with anaerobic fermentation pathways, while co-occurrence networks became less dense but broader across stages.<br><br>CONCLUSION: Stage-associated microbiome shifts were detectable using a gingivitis reference group, with a disease-associated&#xa0;core and accompanying anaerobic functional enrichment. The findings suggest that subgingival dysbiosis across periodontitis stages does not follow a simple linear trajectory and that clinical stage is not determined by microbiome composition&#xa0;alone.}, }
@article {pmid42203551, year = {2026}, author = {Kamrad, S and Gagliani, N and Lawley, TD and Patil, KR and Tintelnot, J}, title = {Gut microbial metabolites for potentiating cancer therapy.}, journal = {Trends in cancer}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.trecan.2026.04.005}, pmid = {42203551}, issn = {2405-8025}, abstract = {The gut microbiome exerts distant and local effects on tumours, healthy epithelial cells, and the immune system through the production of bioactive metabolites. This influences cancer therapy responses across treatment modalities and cancer types. In this review, we discuss promising approaches to boost beneficial microbiota-derived metabolites to enhance existing cancer therapies, including prebiotics, probiotics, postbiotics, and live biotherapeutic products. Each approach faces challenges in achieving physiological concentrations and tissue distribution, as well as different regulatory regimes and commercial landscapes. With promising early clinical trials and significant scientific and commercial activity in these areas, there is hope that targeted, metabolite-focused interventions will soon benefit cancer patients.}, }
@article {pmid42203770, year = {2026}, author = {So, Y and Pichler, MJ and Kappel, SS and Jin, C and Eriksen, C and Chatzigiannidou, I and Andersen, MHB and Tsiamis, V and Lukassen, MV and Skytthe, LE and Teneberg, S and Kristiansen, K and Brix, S and Aunsholt, L and Abou Hachem, M}, title = {Dual human milk oligosaccharide-fibre utilisation is a selection cue for the weaning gut microbiome.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73297-5}, pmid = {42203770}, issn = {2041-1723}, support = {1026-00386B//Natur og Univers, Det Frie Forskningsr&#xe5;d (Natural Sciences, Danish Council for Independent Research)/ ; }, abstract = {Gut microbiome (GM) maturation in early life follows organised taxonomic successions, yet how the weaning diet impacts these trajectories remains underexplored. Here, we collected faecal samples at pre-, early and late weaning from seven mother-infant dyads forming the Milkome cohort, designed to evaluate the contribution of human milk oligosaccharides (HMOs) to GM maturation during weaning (NCT07026526). Surprisingly, all preweaning infant faecal consortia grew on multiple dietary fibres, consistent with the prevalence of fibre-degradation genes in their metagenomes. Utilisation of both HMOs and dietary fibres was discovered as a metabolic hallmark of the weaning GM, as supported by metagenomics and the growth of faecal consortia on HMOs, following their enrichment on fibres. The growth of a defined consortium on weaning-mimic substrates, further showed that distinct Clostridia simultaneously deploy HMO and fibre utilisation pathways, which confers competitive growth against HMO- or fibre-utilising bifidobacteria. Metagenomics, culturomics and HMO-utilisation profiles of 137 maternal isolates were concordant with retention of the HMO-utilisation capacity by the adult GM. Our findings highlight dual HMO-fibre utilisation as an unrecognised selection cue of core adult GM species during weaning, which outlines a plausible mechanism of GM maturation in early life and extends the importance of HMOs to the weaning transition.}, }
@article {pmid42203795, year = {2026}, author = {Wang, M and Zhang, L and Li, S and Cha, E and Guo, A and Sun, B and Li, X and Wu, S and Yu, T}, title = {Heritable gut microbiota decreases fat accumulation in pregnant sows and optimizes gestational outcomes.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00998-6}, pmid = {42203795}, issn = {2055-5008}, support = {HAAS2023RCOD01//the Research and Development of Key Technology for Precise and Efficient Breeding of Local Pigs in Hainan Province/ ; YSPTZX202304//Academician Workstation/ ; 2021YFD1301205//the Breeding and Promotion of New Varieties of Qinling Black Pigs/ ; 2022GD-TSLD-46//the Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 2023-YBNY-106//the Key Research and Development Plan of Shaanxi Province/ ; }, abstract = {This study investigates the interplay between host genetics and gut microbiota in regulating fat deposition and reproductive outcomes in sows. Integrating multiomics data from 348 Yorkshire sows-including whole-genome sequencing, 16S rRNA sequencing, and metabolomic profiling-we identified 37 microbial taxa significantly associated with thick backfat (TBP) through microbiome-wide association studies (MWAS). Microbial genome-wide association analysis (mGWAS) revealed heritable genera, including Ezakiella and Corynebacterium, and implicated host genes such as MED17 and VSTM5 in microbial modulation. Concurrently, genome-wide association studies (GWAS) identified MC4R and MEDAG as candidate genes directly influencing TBP. Metabolomic analysis highlighted acetate, a short-chain fatty acid, as a key mediator in host adipogenesis. Functional validation in experimental models demonstrated that exogenous acetate supplementation alters lipid metabolism and enhances reproductive performance. These findings elucidate a mechanistic axis wherein host genetics shape gut microbial composition, which in turn modulates fat metabolism via acetate production, ultimately affecting pregnancy outcomes. This integrated approach provides insights into host-microbe co-regulation of metabolic traits and highlights potential targets for improving reproductive efficiency in livestock.}, }
@article {pmid42203854, year = {2026}, author = {Bostanci, N and Antony, AT and Silbereisen, A and Esmaili, T and Krog, MC and Sterpu, I and Bashir, Z and Engstrand, L and Wiberg-Itzel, E and Nielsen, HS and Hugerth, LW and Schuppe-Koistinen, I}, title = {Shotgun metagenomic mapping of saliva reveals insights into diversity and function of the oral microbiome in pregnancy.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42203854}, issn = {2045-2322}, mesh = {Humans ; Female ; Pregnancy ; *Saliva/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; Adult ; *Mouth/microbiology ; Shotgun Sequencing ; Cross-Sectional Studies ; Metagenome ; Bacteria/genetics/classification ; }, abstract = {The oral microbiome is a complex and dynamic microecosystem that fluctuates continually throughout the lifespan of a woman. Nevertheless, the function of the oral microbiome in reproductive health is not yet fully understood. Monitoring oral health and providing necessary dental care before and during pregnancy could help maintain a balanced oral microecology and support healthier microbial transfer to newborns. Here, we aimed to compare the salivary microbiome of pregnant and non-pregnant women using shotgun metagenomics to describe their taxonomic and functional composition and assess whether the resulting data is better explained by the reproductive stage. We conducted a comparative cross-sectional study involving pregnant women (n = 71; gestational age 37-42 weeks) and non-pregnant women (n = 143 with regular menstrual cycles; 3 saliva samples per participant across different menstrual phases). Shallow shotgun metagenomic sequencing was used to characterize both taxonomic and functional profiles of the oral microbiome. Socransky's color complex analysis was performed to assess group differences in key microbial complexes. Quantitative PCR was used to validate the abundance of selected oral bacteria. Participant data, including demographic, behavioral, clinical, and oral health variables (such as dentist visits), were collected and incorporated as covariates to adjust for potential confounding effects. Additionally, a sensitivity analysis was performed by excluding participants with identified behavioral or clinical risk factors. Ten phyla including Actinomycetota, Bacteroidota, Chloroflexota Bacillota, Fusobacteriota, Pseudomonadota, Spirochaetota, Synergistota Candidatus Saccharimonadota and Mycoplasmatota, 102 genera, and 410 species were identified. Pregnant women had lower saliva microbiome diversity, driven by reduced richness but unchanged evenness. The microbial composition varied between the groups, even after adjusting for confounding factors. Differential abundance analysis, adjusted for potential confounders, identified 25 species that significantly differed between groups (q < 0.05), with 13 taxa more than three-fold higher in pregnant women. Notably, red complex species were more abundant in pregnant women (p < 0.05). Functional pathway analysis identified 40 modules that differed by pregnancy status. These results further suggest a connection between pregnancy and changes to the oral microbiome in women. As many of these changes are in a pro-inflammatory direction, further research is warranted to assess its potential impact on pregnant women and their newborns.}, }
@article {pmid42203970, year = {2026}, author = {Ning, K and Chen, Y and Yang, X and Dou, X and Liu, S and Wang, DE and Niu, Y and Xu, H}, title = {Gut microbiota alteration contributes to bone marrow mesenchymal stem cells connexin43 response to high-fat diet induced obesity in mice.}, journal = {International journal of obesity (2005)}, volume = {}, number = {}, pages = {}, pmid = {42203970}, issn = {1476-5497}, abstract = {BACKGROUND/ OBJECTIVE: Bone marrow mesenchymal stem cells (BMSCs) contribute to controlling adipose tissue homeostasis and may be a potential target for obesity therapy. Since lack of connexin43(Cx43) in mesenchymal stem cells (MSCs) is known to combat high-fat diet (HFD)-induced adiposity. Also, HFD is a well-known risk factor for gut microbiota dysbiosis. Here we attempt to address the interaction between HFD, gut microbiota, and Cx43 deficiency in BMSCs during the development of obesity.<br><br>METHODS: BMSC-specific Cx43 knockout (Prrx1-Cre;Cx43[flox/flox](cKO)) and control littermate (Cx43[flox/flox](flox))mice were fed a regular chow diet or a HFD for 8 weeks. Cecal microbiome composition was assessed by 16S ribosomal RNA (rRNA) sequencing, and further analyzing correlation between gut microbiota and obesogenic parameters. Moreover, transplantation fecal microbiota was used to probe the salutary effect of BMSC Cx43.<br><br>RESULTS: HFD fed cKO mice notably altered cecal microbiome composition as proved by a distinctively clustered separation from flox mice. Concomitantly, Allobaculum induced by HFD was strongly correlated positively with body weight, glucose intolerance, and adipose mass. The recipients with gut microbiota from cKO mice displayed anti-obesity phenotype as the donors.<br><br>CONCLUSIONS: Gut microbiota alteration may be one main reason for the salutary effect of BMSC Cx43 knockout on body adiposity.}, }
@article {pmid42203993, year = {2026}, author = {Saka, WA and Oyedokun, PA and Alade, TA and Oyeleke, BT and Oyelaran, AO and Oyedokun, MD and Irozuoke, CA and Olayemi, OM and Oladepo, S and Ndako, JA}, title = {Intervening at the microbial crossroads: targeting inflammation across the oral-gut-reproductive microbiome crosstalk in atherosclerosis.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {7}, pages = {}, pmid = {42203993}, issn = {1572-9699}, mesh = {Humans ; *Atherosclerosis/microbiology ; *Gastrointestinal Microbiome ; *Inflammation/microbiology ; Animals ; Dysbiosis/microbiology ; *Mouth/microbiology ; }, abstract = {Despite the increasing burden of mortality due to cardiovascular disease, the traditional risk factors fail to explain the complexity of the pathology of cardiovascular disease, especially in the context of chronic inflammation. Emerging scientific evidence indicates that dysbiosis of the oral, gut, and reproductive microbiome is associated with systemic vascular dysfunction. This review comprehensively discusses the available scientific data on the interactions between the mucosal colonizing microbiota and their modulation of whole-body inflammation and cardiovascular disease pathogenesis. It underlines the roles of microbial metabolites, including trimethylamine N-oxide and lipopolysaccharides, in immune activation, epithelial barrier cell injury, and their effects in endothelial activation, vascular remodeling and dysfunction, oxidative stress, and inflammation. This review describes the mechanistic interplay that drives atherosclerosis and vascular dysfunction, mediated by immune activation and cytokine-driven inflammatory cascades. Sex hormones influence the composition of the microbiota and the host immune responses, thereby influencing vascular disease manifestations and responses to therapy. These mechanisms present the potential of intervening at the microbial crossroads through microbiome-targeted approaches as an effective treatment strategy for cardiovascular disease.}, }
@article {pmid42204344, year = {2026}, author = {Olubayo, L and Hazelhurst, S}, title = {Advocating for return-of-results to participants in microbiome research.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {42204344}, issn = {2058-5276}, support = {TW 012077//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; }, }
@article {pmid42204477, year = {2026}, author = {Wu, Q and Zhang, A and Ning, Z and Figeys, D}, title = {MetaTree: an interactive web platform for aligned hierarchical data visualization and multi-group comparison.}, journal = {BMC bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12859-026-06475-3}, pmid = {42204477}, issn = {1471-2105}, support = {RGPIN-03905-2018//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {BACKGROUND: Hierarchical quantitative profiles are widely used in microbiome studies and other domains. However, comparing multiple samples and experimental groups while preserving hierarchical structure remains challenging. Many existing workflows require extensive manual figure assembly or do not support aligned comparisons across conditions on a shared hierarchy.<br><br>RESULTS: We developed MetaTree, an open-source platform that runs in a web browser for interactive visualization and comparative analysis of hierarchical quantitative data. MetaTree anchors samples, groups, and contrasts between groups to a shared reference hierarchy, preserving one-to-one node correspondence so that the same clade is compared in the same position across views. In addition to visualization, MetaTree integrates statistical testing for comparisons between two groups with false discovery rate (FDR) control, enabling users to identify clades with consistent differences between conditions and interpret them in hierarchical context. MetaTree also provides user configurable controls for visual encoding, filtering thresholds, label density, and layout, allowing figures to be adapted to different datasets and reporting needs. The interface remains usable for large hierarchies through interactive navigation, adaptive label handling, and branch collapsing.<br><br>CONCLUSIONS: MetaTree is an installation-free web platform (https://byemaxx.github.io/MetaTree) for topology-consistent visualization and comparison of hierarchical profiles, supporting coordinated multi-panel exploration and automated comparison matrices to enable rapid generation of publication-ready figures for microbiome and other hierarchical datasets.}, }
@article {pmid42204538, year = {2026}, author = {Cheng, CH and Wong, CC}, title = {The mycobiome, virome and archaeome in gastrointestinal cancers: molecular pathogenesis and therapeutic intervention.}, journal = {Molecular cancer}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12943-026-02698-3}, pmid = {42204538}, issn = {1476-4598}, support = {2023ZD0501400; 2023ZD0500200//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 14101725; 14107924; 14101322//Research Grants Council-General Research Fund/ ; C4008-23WF, C4042-24GF//RGC-Collaborative Research Fund/ ; }, abstract = {Gastrointestinal (GI) cancers remain a significant global health challenge. For decades, research has concentrated on the bacterial microbiome's role in tumour development, largely neglecting the important roles of the non-bacterial kingdoms, including mycobiome (fungi), the virome (viruses), and archaeome (archaea). These elements represent an underexplored and crucial "dark matter" of the microbiome. This review aims to systematically summarize current evidence on the compositional alterations of viruses, fungi, and archaea across the major types of GI cancer, including colorectal, hepatocellular, gastric, pancreatic and esophageal/oral cancers. We critically examine how viruses, fungi, and archaea directly affect host cellular processes and indirectly influence cancer risk through complex cross-kingdom interactions with the bacterial microbiota and the host immune system. Additionally, we explore the significant translational potential of this knowledge, emphasizing opportunities to use these non-bacterial communities in developing new diagnostic biomarkers and therapeutic strategies. Finally, we highlight the importance of future multi-kingdom integrative analyses to fully understand the microbial ecosystem involved in GI oncogenesis and to translate these insights into clinical practice.}, }
@article {pmid42204557, year = {2026}, author = {Preetam, S and Bora, J and Porna Dutta, S and Talukdar, N and Rustagi, S and Thapliyal, S and Malik, S and Choudhary, N and Kumar, D and Kondaveeti, SB}, title = {Role of gut microbiota in cancer modulation: molecular mechanisms and emerging therapeutic strategies.}, journal = {Infectious agents and cancer}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13027-026-00767-2}, pmid = {42204557}, issn = {1750-9378}, abstract = {The gut microbiota exerts profound effects on host physiology, immunity, and disease susceptibility, with growing evidence implicating its role in cancer initiation, progression, and therapy response. Dysbiosis and microbial-derived metabolites contribute to oncogenesis by modulating epithelial signalling, immune regulation, and systemic inflammation. This review synthesises current knowledge on the crosstalk between the gut microbiome and cancer, spanning molecular mechanisms, site-specific malignancies, and treatment outcomes. We discuss how microbial pathways, including NF-κB, STAT3, Wnt/β-catenin, and inflammasome activation, shape tumour biology, and how microbiota profiles correlate with cancer risk and progression in colorectal, gastric, liver, breast, gynaecological, and pulmonary cancers. Furthermore, we highlight the microbiome's impact on responses to chemotherapy, radiotherapy, and immunotherapy. Finally, we evaluate therapeutic strategies targeting the microbiota, from conventional dietary and probiotic interventions to cutting-edge approaches such as faecal microbiota transplantation, engineered bacterial strains, and microbiome-based biomarkers. Understanding these complex interactions offers novel opportunities to integrate microbiome science into precision oncology.}, }
@article {pmid42204605, year = {2026}, author = {Zhang, C and Lv, P and Hou, Y and Yao, Z and Jiang, S and Chen, K and Liu, Z and Liu, L}, title = {The formation and function of tertiary lymphoid structures.}, journal = {Biomarker research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40364-026-00939-7}, pmid = {42204605}, issn = {2050-7771}, abstract = {Tertiary lymphoid structures (TLSs) are immune cell aggregates that emerge in nonlymphoid tissues during various disease states, including chronic inflammation, autoimmunity, and cancer. TLSs are structurally and functionally analogous to secondary lymphoid organs, and exhibit a maturation continuum (progressing from initial aggregation to mature structures with germinal centers). TLS formation is synergistically regulated by local chemokine networks (e.g. CXCL13, CCL19, and CCL21), lymphotoxin signaling axes, stromal cells, metabolic reprogramming, and the microbiome. This review comprehensively elucidates the biological foundations of TLSs, including their cellular composition, spatial architecture, and developmental dynamics of maturation. We explore the crucial roles of TLSs as favorable prognostic factors and predictors of the immunotherapy response in various solid tumors, including melanoma, breast cancer, lung cancer, hepatocellular carcinoma, and colorectal cancer. Additionally, we analyze their "pathogenic" role in causing tissue damage and disease progression in autoimmune disorders such as rheumatoid arthritis and Sjögren's syndrome, as well as chronic inflammatory diseases such as COPD, IgA nephropathy, and atherosclerosis. In addition, we thoroughly examine TLS research methodologies, covering a wide range of approaches from conventional hematoxylin and eosin (H&amp;E) and immunohistochemical staining to advanced multiplex fluorescence staining, imaging mass spectrometry, and spatial transcriptomic techniques. We summarize multiple gene expression signatures (e.g. the 12-chemokine signature and TLS score) for TLS identification and quantification. Finally, we highlight multiple strategies for artificially inducing TLS formation, including cytokine delivery, immunotherapy, engineered scaffolds, microbiome modulation, and organoid technologies, designed to enhance antitumor immunity or reverse immunopathology. This review provides a comprehensive framework for understanding the complex functions of TLSs in human disease and explores their clinical translation potential as biomarkers and therapeutic targets.}, }
@article {pmid42204631, year = {2026}, author = {Fu, YT and Deng, YP and Duan, DY and Peng, YY and Liu, YL and Zhang, Y and Xu, ZK and Elsheikha, HM and Liu, GH}, title = {Insights into the microbiota profile of Pediculus humanus capitis using metagenomic next-generation sequencing and molecular detection of unexpected pathogen DNA in Hunan Province, China.}, journal = {Parasites &amp; vectors}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13071-026-07471-5}, pmid = {42204631}, issn = {1756-3305}, support = {2024JJ6548//the Hunan Natural Science Foundation Youth Fund Project/ ; 32473057//the National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The head louse, Pediculus humanus capitis, remains a significant public health concern affecting millions of people worldwide and has been implicated as a potential vector for multiple human pathogens. Characterization of the microbiota of head lice could improve our understanding of their public health significance and potential role in pathogen transmission. Here, we characterize the microbiota of head lice and investigate microbiota differences among different clades of head lice.<br><br>METHODS: Head lice were collected from Hunan Province, China, and classified into clade A and clade B (CACB) using polymerase chain reaction (PCR)-based genotyping. The microbiota of pooled CACB of head lice samples&#xa0;(n&#x2009;=&#x2009;46) was investigated by metagenomic shotgun sequencing&#xa0;and comparatively analysed at the&#xa0;phylum,&#xa0;genus, and&#xa0;species levels. In addition, the prevalence of potential pathogen DNA in head lice samples&#xa0;(n&#x2009;=&#x2009;204) was assessed&#xa0;using real-time PCR with stringent negative controls.<br><br>RESULTS: We obtained non-redundant CACB microbial gene catalog comprising 79,232 genes, of which 4.70% (3,722&#xa0;genes) were taxonomically assigned. The relative abundance of bacteria (2.52%) was higher than that of eukaryotes (2.04%), viruses (0.11%), and archaea (0.02%). Comparative analysis identified 655 and 750 unique genes in CACB, respectively. The dominant phyla in the CACB of head lice were Proteobacteria. At the genus level,&#xa0;DNA sequences corresponding to Anaplasma (25.98%; 53/204), Mycobacterium (24.02%; 49/204), Chlamydia (23.53%; 48/204), Ehrlichia (10.29%; 21/204), and Vibrio (0.49%; 1/204) were detected, suggesting the presence of bacterial&#xa0;DNA&#xa0;from these taxa.<br><br>CONCLUSIONS: Our results provide a preliminary characterization of the annotated fraction of the CACB&#xa0;microbiome in head lice. The high proportion of unannotated genes (>95%)&#xa0;underscores the limited representation of louse-associated microbial genomes in public databases and suggests &#xa0;substantial, yet unexplored, microbial diversity. The detection of pathogen DNA does not confirm organism viability or vector competence,however it may&#xa0;suggest prior&#xa0;exposure, mechanical carriage, or residual DNA from&#xa0;blood meals. These exploratory findings contribute new&#xa0;insights into the microbiota associated with human lice.}, }
@article {pmid42204645, year = {2026}, author = {Zhao, N and Wu, L and Peng, S and Yang, H and Song, Y and Zhang, Y and Ding, L}, title = {Decoding the microbiome-immune crosstalk in cancer: from mechanisms to therapeutic translation.}, journal = {Biomarker research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40364-026-00930-2}, pmid = {42204645}, issn = {2050-7771}, support = {82303235//National Natural Science Foundation of China/ ; 2025SF-YBXM-358//Key Research and Development Projects of Shaanxi Province/ ; 2025JC-YBQN-1236//Natural Science Basic Research Program of Shaanxi Province/ ; NUHSRO/2023/005/Startup/3//NUS STARTUP grant/ ; MOH-OFIRG24jan-0001, MOH-OFIRG23jul-0007 and MOH-OFIRG21nov-0007//NUS-NJU Research Collaboration Fund 2025, OF-IRG grant from National Medical Research Council/ ; NRF, CRP28-2022RS-0001//CRP grant from National Research Foundation/ ; }, abstract = {The gut microbiome plays a critical role in shaping host immunity and profoundly affects the efficacy of cancer immunotherapy. Accumulating evidence suggests that interventions designed to alter the microbial community, including fecal microbiota transplantation, probiotics, and engineered bacteria, can reprogram the tumor-immune microenvironment and enhance clinical efficacy. This Review provides a comprehensive overview of the molecular and cellular mechanisms through which the gut microbiota influences antitumor immunity, and it highlights recent clinical studies evaluating these interventions. We further examine inherent challenges, including inter-individual variability in microbial composition, difficulties in achieving stable and durable colonization, technical barriers in delivery, and potential safety concerns associated with immune activation or off-target effects. Finally, we discuss future directions for translating microbiome-targeted therapies into oncology, emphasizing the need for mechanistic insight, standardized protocols, rigorous evaluation, and integration with precision immunotherapy strategies to optimize therapeutic outcomes.}, }
@article {pmid42204817, year = {2026}, author = {Han, B and Rawat, A and Parween, S and Alzayed, W and Zhang, H and Alkhateeb, RS and Schmidt, T and Wu, Y and Rodriguez, CP and Saad, MM and Hirt, H}, title = {Plant immune dysregulation disrupts microbe-induced growth promotion and microbiome compatibility.}, journal = {Plant communications}, volume = {}, number = {}, pages = {101927}, doi = {10.1016/j.xplc.2026.101927}, pmid = {42204817}, issn = {2590-3462}, abstract = {Plants associate with diverse microbial communities that influence growth and health. Although the plant immune regulatory network balances defense activation and microbial accommodation during pathogen attack, how it coordinates beneficial plant-microbe interactions across complex microbial contexts remains unclear. Here, we performed a systematic screen of 39 immune-pathway mutants using individual plant growth-promoting bacteria (PGPBs), binary combinations, synthetic and natural communities. We identified the bik1-1 mutant as exhibiting a broad defect in growth promotion across multiple beneficial microbial systems. Extensive genetic analyses using independent BIK1 CRISPR and T-DNA insertion alleles, as well as overexpression lines, demonstrated that the growth promotion defect observed in the bik1-1 line is not caused by loss of BIK1 function but instead correlates with a chromosomal fragment duplication. Although ISR and beneficial bacteria-mediated pathogen protection remain intact in bik1-1, immune activation is elevated during beneficial interactions. Microbiome profiling revealed reduced diversity and altered community structure, and microbiome transfer experiments indicate that host immune status influences the selection of microbial taxa associated with growth promotion. These findings indicate that immune signaling balance is a key determinant of plant-microbiome compatibility across diverse microbial contexts.}, }
@article {pmid42204951, year = {2026}, author = {Tomar, K and Khodlan, P and Malik, T and Rana, P and Tariq, M and Mishra, R and Mohan, A and Fatima, S and Gautam, H and Kumar, S and Abdin, MZ and Kumar, A}, title = {Microbiota-derived indole derivatives as anticancer agents: mechanistic insights and major perspectives.}, journal = {Future microbiology}, volume = {}, number = {}, pages = {1-10}, doi = {10.1080/17460913.2026.2677452}, pmid = {42204951}, issn = {1746-0921}, abstract = {Cancer remains a major global health challenge, and emerging research highlights the role of the gut microbiota in cancer development. This complex microbial community supports digestion, immunity, and even mental well-being, adapting to lifestyle factors like diet and exercise. One key function is the breakdown of tryptophan (Trp) into indole. Studies have linked these compounds to cancer, inflammatory conditions, and brain disorders. This review compiles evidence showing that indole derivatives produced by gut bacteria could serve as potential anticancer agents by targeting specific biochemical pathways. Mechanistically, these metabolites inhibit IDO1, lower kynurenine levels, decrease regulatory T cells, and increase CD8+ T cell responses. They also activate tumor-suppressive signaling pathways such as the aryl hydrocarbon receptor (AhR), pregnane X receptor (PXR), and nuclear factor erythroid 2-related factor 2 (NRF2), while regulating reactive oxygen species (ROS). In addition, some indole derivatives trigger interleukin-12 (IL-12)-mediated T cell activation, leading to metabolic stress in cancer cells by downregulating UHRF1 and activating AMP-activated protein kinase (AMPK), thereby depleting ATP and causing cell death. Relevant literature was identified from PubMed, Google Scholar, and Scopus up to January 2026. Collectively, understanding this link could support development of personalized diets and microbiota-based cancer therapies.}, }
@article {pmid42205017, year = {2026}, author = {Zhang, ZN and Wang, Q and Dong, XY and Li, X and Lu, B and Xu, DQ}, title = {Microbial Diversity in Airport Terminal Environments and Potential Aerosol Transmission Risks.}, journal = {Biomedical and environmental sciences : BES}, volume = {39}, number = {5}, pages = {512-528}, doi = {10.3967/bes2026.018}, pmid = {42205017}, issn = {2214-0190}, mesh = {Aerosols/analysis ; *Air Microbiology ; *Bacteria/isolation &amp; purification/classification ; *Airports ; Environmental Monitoring ; Humans ; *Fungi/isolation &amp; purification/classification ; *Microbiota ; *Air Pollution, Indoor/analysis ; }, abstract = {OBJECTIVE: To characterize the distribution of bacterial and fungal pathogens in airport terminal environments, compare airborne aerosol sampling methods, identify high-abundance pathogenic species based on the WHO priority pathogens list, and provide a scientific basis for optimizing microbiological monitoring and control measures.<br><br>METHODS: Sampling was conducted in the transit transfer area (A1), domestic arrivals area (A2), and domestic departures area (A3). Airborne aerosols were collected using cyclonic and filtration samplers, and surface samples were collected using sterile swabs. DNA analysis was performed using 2bRAD sequencing for microbiome profiling (2bRAD-M). Microbial community diversity and compositional differences were assessed using &#x3b1;-diversity indices (Chao1, Shannon, and Simpson) and &#x3b2;-diversity metrics.<br><br>RESULTS: Bacteria dominated the indoor air microbiota of the airport terminal (98.4%), with Pseudomonadota (39.4%-62.9%) and Actinomycetota (18.9%-32.9%) as the predominant phyla. Microbial diversity was significantly higher in surface samples than in airborne aerosols. High-frequency contact surfaces (e.g., handrails) were enriched with human commensal bacteria, including Cutibacterium acnes (9.71%-19.4%). Multiple WHO-prioritized pathogens were detected, including Acinetobacter baumannii (0.3%-1.4%) and Pseudomonas aeruginosa (0.01%-1.24%). The transit transfer area (A1), characterized by poorer ventilation, showed higher microbial richness. Filtration samplers captured more microorganisms per unit volume than cyclonic samplers, with significant differences in detection profiles.<br><br>CONCLUSION: Sampling methods, sample types, and environmental conditions influence microbial distribution patterns across terminals. Detection of WHO Critical and High priority pathogens indicates potential risks of aerosol and contact transmission. Enhanced ventilation and disinfection of high-frequency contact surfaces can mitigate public health risks.<br><br>GRAPHICAL ABSTRACT: available in www.besjournal.com.}, }
@article {pmid42205261, year = {2026}, author = {Gradisteanu Pircalabioru, G and Ionescu, MI and Bernstein, R}, title = {Editorial: Maternal nutrition, gut microbiota, and endocrine programming in early life.}, journal = {Frontiers in endocrinology}, volume = {17}, number = {}, pages = {1859900}, doi = {10.3389/fendo.2026.1859900}, pmid = {42205261}, issn = {1664-2392}, }
@article {pmid42205289, year = {2026}, author = {Honour, JW}, title = {Problems in the use of chemical and functional nomenclatures for steroids in human physiology, biology and pharmacology.}, journal = {RSC advances}, volume = {16}, number = {30}, pages = {27678-27691}, pmid = {42205289}, issn = {2046-2069}, abstract = {Steroid compounds are important messengers in the human body that can be described using multiple nomenclature systems, each reflecting a different perspective on structure or function. Chemical nomenclature, based on IUPAC conventions, classifies steroids according to their ring structure and functional groups, whereas functional nomenclature reflects a compound's source, biological action, regulatory pathways, metabolism, or clinical application. These parallel systems are often applied inconsistently across disciplines, leading to ambiguity in interpretation and communication. This review outlines the foundations of chemical and functional naming, highlights circumstances in which nomenclature becomes inconsistent, and illustrates how physiology, molecular biology, receptor diversification, genetics, oncology, and the microbiome complicate terminology. Because clinicians, biochemists, pharmacologists, and researchers often apply different naming logics, coherent definitions and consistent usage are necessary for clear scientific discourse. This review proposes considerations to support more precise application of steroid nomenclature in academic publications.}, }
@article {pmid42205323, year = {2026}, author = {Sun, X and Yi, X and Zhang, J}, title = {Ecology-microbiome engineering in Sauce-flavor Baijiu via Single-Cell Raman Spectroscopy.}, journal = {Biodesign research}, volume = {8}, number = {2}, pages = {100089}, pmid = {42205323}, issn = {2693-1257}, abstract = {Sauce-flavor Baijiu owes its layered aroma to a diverse microbial consortium fermenting under extreme, open, solid-state conditions. High-throughput sequencing has revealed marked spatiotemporal heterogeneity in community composition, yet a fundamental composition-function disconnect persists: bulk omics average signals across heterogeneous micro-niches and cultivation recovers only a minor fraction of total diversity, leaving "who is doing what" unresolved. Closing this disconnect is a prerequisite for rational design of fermentation microbiomes and demands cell-resolved functional tools within an iterative engineering framework. This review proposes that Single-Cell Raman Spectroscopy (SCRS) and its derivatives, including D2O-Raman activity mapping, scRACS-Seq phenotype-to-genome linkage, scRACS-Culture recovery of rare functional strains, and Intra-Ramanome Correlation Analysis (IRCA) predictive metabolic phenotyping, collectively provide a label-free, culture-independent toolkit suited to this role in solid-state matrices. We delineate how these single-cell insights feed each stage of a Design-Build-Test-Learn (DBTL) cycle, from phenotype-informed strain selection through consortium assembly and functional validation to data-driven iterative optimization. This convergence of cell-resolved functional dissection, synthetic ecology, and process analytical technologies establishes the foundation for advancing Sauce-flavor Baijiu from experience-dependent craftsmanship toward intelligent brewing.}, }
@article {pmid42205326, year = {2026}, author = {Jenkins Hall, W and Garvey, I}, title = {Selling Clean Vaginas: An Examination of Feminine Hygiene Products' Health and Cultural Messaging and Its Implications for Black Women's Sexual Health.}, journal = {International journal of sexual health : official journal of the World Association for Sexual Health}, volume = {38}, number = {2}, pages = {390-403}, pmid = {42205326}, issn = {1931-762X}, abstract = {BACKGROUND: Feminine hygiene products (FHPs), including washes, deodorants, suppositories, and wipes, are widely marketed in the United States as essential to vaginal cleanliness, pH balance, and odor control. However, these products may contribute to adverse outcomes such as microbiome disruption, irritation, and infection. Black women disproportionately use FHPs and experience higher rates of reproductive health issues, yet the content and marketing of these products remain underexamined. This study investigates the health claims, ingredients, and marketing strategies of FHPs, with a focus on products explicitly marketed to Black women in the US.<br><br>METHODS: A conventional content analysis was conducted on 83 FHPs identified through US-based retail and e-commerce platforms between July 2022 and November 2024. Products were categorized by name, brand, claims, ingredients, point-of-sale (retail vs. e-commerce), and Black-owned. Products were also labeled "Black consumer focused" if they were produced by self-identified Black-owned brands and (1) marketed using culturally specific terms, language, or practices (e.g., "yoni", vaginal steaming), and/or (2) marketed claims related to health concerns disproportionately affecting Black women (e.g., fibroids, endometriosis).<br><br>RESULTS: Of the products analyzed, 63.8% claimed to balance vaginal pH, 33.7% targeted odor elimination, and 15.6% claimed to treat BV or yeast infections. Products often contained acidic ingredients (56.6%) and fragrances (28%), despite limited safety data. Products marketed to Black women disproportionately used spiritual or empowerment language such as "yoni," promoted herbal or botanical formulations (90%), and made unsubstantiated claims to treat reproductive conditions such as fibroids, infertility, and menstrual irregularities.<br><br>CONCLUSION: Marketing of FHPs reinforces myths about vaginal cleanliness and targets Black women with racially coded and scientifically unsupported claims. These practices may contribute to reproductive health disparities and warrant increased regulatory oversight, provider education, and culturally grounded health communication.}, }
@article {pmid42205570, year = {2026}, author = {Semlali, A and Al-Zharani, M and Al-Ansari, J}, title = {The role of extracellular vesicles in intercellular communication within the oral cavity.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2673760}, pmid = {42205570}, issn = {2000-2297}, abstract = {BACKGROUND: Extracellular vesicles (EVs), including exosomes, microvesicles, and apoptotic bodies, are nanoscale membrane-bound structures that mediate intercellular communication through the transfer of proteins, lipids, and nucleic acids. In the oral cavity, EVs are present in saliva and gingival crevicular fluid, where they contribute to immune regulation, epithelial barrier integrity, and host-microbiome interactions.<br><br>OBJECTIVE: This review aimed to critically summarize current knowledge regarding EV biogenesis, molecular composition, cellular and microbial sources, and their roles in oral homeostasis and disease pathogenesis.<br><br>RESULTS: Current evidence demonstrates that EVs derived from host cells and oral microorganisms actively regulate inflammatory responses, biofilm dynamics, tissue regeneration, and microbial colonization. Dysregulation of EV-mediated communication has been implicated in the development and progression of periodontal disease, oral candidiasis, and oral squamous cell carcinoma (OSCC). In addition, salivary EVs have emerged as promising non-invasive biomarkers and potential therapeutic tools in oral medicine. However, important methodological limitations remain, particularly regarding EV isolation, characterization, and standardization.<br><br>CONCLUSIONS: EVs represent central mediators of communication within the oral microenvironment and play dual roles in maintaining oral homeostasis and promoting disease progression. Further standardized and clinically relevant studies are required to better define EV biology and facilitate the translation of EV-based diagnostic and therapeutic strategies into clinical oral medicine.}, }
@article {pmid42205571, year = {2026}, author = {DeClercq, V and Murphy, RE and Zinck, N and Langille, MGI and Wallace, A}, title = {Association between the oral microbiome and clinical indicators of resectable non-small cell lung cancer (NSCLC).}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2675065}, pmid = {42205571}, issn = {2000-2297}, abstract = {BACKGROUND: Oral microbial implications for lung cancer outcomes and association with clinical markers are largely unknown.<br><br>OBJECTIVE: This work aimed to characterize the oral microbiome in relation to clinical indicators and identify oral microbial biomarkers associated with lung cancer outcomes in patients with non-small cell lung cancer (NSCLC).<br><br>DESIGN: This is an observational prospective study of saliva samples from patients undergoing curative surgery for NSCLC. Taxonomic and composition profiles were generated using full-length 16S rRNA gene sequencing (n=64). Differences in bacterial diversity and composition with cancer stage, histological subtype, overall survival (OS), and event-free survival (EFS) were examined.<br><br>RESULTS: Most alpha diversity measures were lower with stage III cancer compared to stage I. All other clinical features were not statistically associated with alpha diversity (P>0.05). The relative abundance of Haemophilus and Solobacterium was detected as significantly differentially abundant in participants with stage III NSCLC by at least 2 differentially abundant tools and an FDR-corrected p-value<0.1.<br><br>CONCLUSION: This study shows a significant association between cancer stage with oral bacterial diversity and the relative abundance of specific genera in relation to OS in participants with resectable NSCLC. This study is limited by sample size and needs to be confirmed in larger studies.}, }
@article {pmid42205580, year = {2026}, author = {Sami, A and Mao, W and Wang, Q and Rui, G and Xu, Q and Wang, J and Wu, K and Li, J and Jiang, L}, title = {Interaction ecology and functional stability: a mechanistic framework for managing plant microbiomes in drylands.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1816170}, pmid = {42205580}, issn = {1664-302X}, abstract = {Drylands are critical ecosystems that support grazing and agriculture, but they are increasingly constrained by environmental stresses such as altered precipitation, warming, salinity/alkalinity, soil pH variability and desertification, which limit plant performance and ecosystem stability. In these conditions, sustaining development through severe, pulse-driven stress is more important for plant "success" than optimizing growth. In addition, soil pH acts as a chemical regulator that modulates microbial activity and resource availability under arid conditions. Through an ecological perspective, this study summarizes how plant-associated microbiomes, particularly bacteria and fungus found in the root and rhizosphere, improve plant performance under arid conditions. Under this filters, microbial communities with functional redundancy, robust interaction networks, and microhabitat-forming characteristics are preferred over single-strain inoculants, which frequently fail under desiccation, UV exposure, temperature extremes, and competition. Key microbial traits, including biofilm formation and extracellular polymeric substances (EPS), contribute to plant resilience under dry conditions. The study further highlights landscape microbial infrastructures-biocrusts and fertility islands-as upstream drivers of microbial source pools and patch-scale resource maps. Finally, it outlines translational priorities for development of stress-adapted consortia and management plans aligned with dryland assembly rules and climate-driven variability.}, }
@article {pmid42205583, year = {2026}, author = {Herrera, H and Sinha, A and Sarkar, S and Cambronero-Heinrichs, JC}, title = {Editorial: Microbial-fungal symbioses: ecological implications, environmental impact, and biotechnological applications in natural and agricultural systems.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1861156}, pmid = {42205583}, issn = {1664-302X}, }
@article {pmid42205706, year = {2026}, author = {Lehr, K and Vilchez-Vargas, R and Skieceviciene, J and Hipler, NM and Gedgaudienė, G and Gustaityte, I and Kucinskas, L and Urba, M and Thon, C and Schanze, D and Zenker, M and Kupcinskas, J and Link, A}, title = {The gut mycobiome is shaped by interactions with the bacterial community in twins.}, journal = {iScience}, volume = {29}, number = {6}, pages = {115786}, pmid = {42205706}, issn = {2589-0042}, abstract = {The human gut microbiome comprises bacteria, viruses, and fungi, yet the fungal component (mycobiome) remains poorly characterized. Here, we investigated gut fungal composition and fungal-bacterial interactions in healthy monozygotic and dizygotic twins. Fungal communities showed substantially higher inter-individual variability than bacterial communities. Zygosity, age, and shared environment had no major influence on fungal abundance, similarity, or dominant genera. Candida was the most abundant genus (mean 5.2% in 161 individuals), followed by Geotrichum (3.7% in 132), whereas Saccharomyces was detected less frequently (0.8% in 92). Most bacterial genera were negatively correlated with Candida and Geotrichum, with stronger negative associations observed at higher bacterial abundances (up to rho = -0.6 for Alistipes). Network analysis revealed complex negative correlations among Bacteroides, Prevotella, and Candida. Overall, our findings reveal a highly variable gut mycobiome independent of host zygosity, pointing to a competitive bacterial-fungal interplay as a key regulator of fungal homeostasis in humans.}, }
@article {pmid42205797, year = {2026}, author = {Wang, Y and Chen, Z and Hua, C and Mao, J and Geng, W and Feng, X and Ye, S and Song, S and Wang, H and Wang, X and Lin, L}, title = {Cross-sectional analysis of feline gut microbiota reveals differences across age-defined groups under varying environments.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1775401}, pmid = {42205797}, issn = {2297-1769}, abstract = {The gut microbiome plays a critical role in host health; however, its variation across age groups in domestic cats (Felis catus) remains unclear. This study characterized differences in the feline gut microbiota using 16S rRNA gene sequencing in 83 cats across five age-defined groups under varying environments: Pre-weaning (1.5 months, n = 16), Early kitten (3 months, n = 16), Late kitten (6-10 months, n = 15), Young adult (2 years, n = 20), and Mature adult (7-10 years, n = 16). Significant differences in microbial diversity and composition were observed across groups. Alpha-diversity was lowest in Pre-weaning kittens, peaking in Young adults, and declining in Mature adults. Beta-diversity revealed distinct clustering among groups (PERMANOVA, R [2] = 0.33, p = 0.001). Sensitivity analysis excluding the heterogeneous Mature adult group showed consistent patterns and increased the explanatory power of age (R [2] = 0.48). At the taxonomic level, Pre-weaning microbiota were enriched in Proteobacteria, particularly Escherichia-Shigella. Following weaning, the relative abundance of Negativibacillus increased, whereas Lactobacillus decreased. Bifidobacterium was more abundant in kitten stages, while Faecalibacterium exhibited higher abundance in Young adults. These patterns were generally consistent in sensitivity analyses. In contrast, the Mature adult group exhibited reduced Prevotella and increased Escherichia-Shigella relative to Young adults. Overall, this cross-sectional study identified compositional differences in the feline gut microbiota across age-defined groups under varying environments. These findings should be interpreted as group-level associations rather than independent age effects. Further controlled and longitudinal studies are needed to disentangle these effects.}, }
@article {pmid42205829, year = {2026}, author = {Zhou, XJ and Chen, JL and Hu, CF and Li, ZK and Zheng, HB and Ding, TN and Chen, Y and Zhu, Y and Li, JN and Fu, Q and Fu, Y}, title = {Associations between prevalent unhealthy lifestyles and the gut microbiota: a comprehensive multi-database bibliometric analysis of pathogenic mechanisms and clinical trajectories.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1834916}, pmid = {42205829}, issn = {2296-858X}, abstract = {BACKGROUND: Unhealthy lifestyles are associated with gut microbiota dysbiosis through complex inflammatory and immune-related pathways. Despite extensive primary research, comprehensive big-data syntheses mapping this field remain limited. This study systematically analyzes the research landscape, related pathophysiological processes, and emerging trends in the field of lifestyle-microbiome interactions using a multi-database bibliometric framework.<br><br>METHODS: A dual-database retrieval strategy utilized the Web of Science Core Collection (WoSCC) and PubMed. The analysis targeted five predominant unhealthy lifestyles: smoking, alcohol consumption, sleep disorders, sedentary behavior, and high-sugar diets. A primary dataset of 5,380 records published between January 1, 2001, and March 13, 2026, was extracted from WoSCC. A parallel clinical analysis incorporated 172 targeted studies from PubMed. Bibliometric analyses, encompassing publication trends, network topologies, citation bursts, keyword evolution, and clinical trajectories, were performed and visualized using Microsoft Excel 2024, VOSviewer, CiteSpace, SCImago, and R.<br><br>RESULTS: Publication output exhibited exponential growth from 2001 to 2026. China and the United States emerged as the dominant academic contributors. Thematic analyses identified inflammation, oxidative stress, obesity, metabolic dysfunction, and microbiome-associated metabolomics as core pathophysiological nodes. The literature frequently describes these elements as mediating the association between behavioral exposures and microbial dysbiosis. Clinical research trajectories demonstrated an evolution toward high-rigor methodological designs, systemic blood biomarker integration, and demographic stratification. The bibliometric data highlight targeted lifestyle intervention as a heavily researched non-pharmacological strategy for gut microbiota preservation.<br><br>CONCLUSION: This multi-database bibliometric study delineates the structural landscape of research on the association between unhealthy lifestyles and the gut microbiota. Inflammation, oxidative stress, and metabolic dysfunction emerge as central themes within the existing literature. These findings provide a systematic framework for understanding microenvironmental interactions and offer valuable insights to inform future research and the development of precise, lifestyle-oriented strategies for gastrointestinal health.}, }
@article {pmid42205836, year = {2026}, author = {Abuova, A and Meiramova, A and Zueva, Y and Kunz, J and Chulenbayeva, L and Issilbayeva, A and Jarmukhanov, Z and Vinogradova, E and Ainabekova, B and Kozhakhmetov, S and Kushugulova, A}, title = {Oral microbiota alterations in radiographic axial spondyloarthritis.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1815404}, pmid = {42205836}, issn = {2296-858X}, abstract = {OBJECTIVE: To investigate alterations in the oral microbiome of patients with radiographic axial spondyloarthritis (r-axSpA), to identify microbial taxa associated with disease status and structural progression, and to explore potential links between oral microbiota composition and systemic immunological profiles.<br><br>METHODS: An observational cross-sectional study was conducted including 57 radiographic axial spondyloarthritis patients and 41 healthy controls. Oral samples were analyzed using 16S rRNA gene sequencing; amplicon sequence variants (ASVs) were generated using LotuS2/DADA2 and taxonomically annotated with SILVA, Greengenes, and HITdb. Alpha and beta diversity were assessed using ACE, Pielou indexes, and UniFrac distances with PERMANOVA and ANOSIM. Differential abundance was determined via LEfSe (LDA&#x202f;>&#x202f;2, p&#x202f;<&#x202f;0.05). Associations between microbial taxa, disease activity, structural damage, and immunological markers were evaluated using linear modeling and Spearman correlation analysis.<br><br>RESULTS: R-axSpA patients showed alterations in oral microbiome composition compared with controls, although alpha diversity remained largely comparable. Actinobacteria, Spirochaetes, and Synergistetes tended to be enriched in r-axSpA patients, mainly driven by an increased abundance of Actinomyces and Selenomonas. Several key periodontal pathogens, including Porphyromonas gingivalis and Actinomyces species, were more abundant in the r-axSpA group. Within the r-axSpA group, the abundance of Porphyromonas and Saccharimonadaceae showed associations with the severity of sacroiliitis and ankylosis. These taxa also exhibited positive correlations with systemic pro-inflammatory cytokines (such as IL-17), which may suggest a possible link between oral dysbiosis and enhanced Th17-driven inflammation in r-axSpA.<br><br>CONCLUSION: Patients may exhibit a distinct proinflammatory oral microbiome profile, with increased representation of Actinomyces and Porphyromonas species. Certain microbial taxa, including members of Porphyromonadaceae and Patescibacteria, have been reported to correlate with cytokines implicated in the immunopathogenesis of radiographic axial spondyloarthritis. These observations suggest that oral dysbiosis could play a role in the maintenance or modulation of systemic inflammation in r-axSpA, and that the oral microbiome might serve as a potential source of biomarkers or a target for future therapeutic strategies.}, }
@article {pmid42205899, year = {2026}, author = {Patil, BL and Shanmugaraj, C and Madhusudan, M}, title = {Metagenomic profiling of endophytic microbiomes associated with fruit pulp and seed kernels of different mango varieties reveals conservation of bacterial communities in seed kernels.}, journal = {3 Biotech}, volume = {16}, number = {6}, pages = {222}, pmid = {42205899}, issn = {2190-572X}, abstract = {UNLABELLED: Bacterial and fungal communities associated with mango pulp and seed kernels from eight Indian mango varieties were profiled using 16 S rRNA and ITS amplicon sequencing. Bacterial diversity was consistently higher in seed kernels (647 ± 238 OTUs) than in pulp tissues (196 ± 112 OTUs). Seed kernel-associated bacterial communities were dominated by Firmicutes (35.8-44.0%) and Bacteroidota (16.8-35.8%) and showed high compositional consistency across varieties, with core genera including Prevotella, Ruminiclostridium, and Lachnoclostridium. In contrast, pulp-associated bacterial communities were enriched in Proteobacteria (6.5-88.5%) and Actinobacteria (4.4-34.6%) and exhibited pronounced inter-varietal variability, particularly in the relative abundance of Bacteroidota (0.8-53.8%). Fungal communities displayed lower richness (14-72 OTUs) and higher variability, with Candida kruisii (15-67%) and Hanseniaspora uvarum (up to 86%) as dominant taxa. Non-metric multidimensional scaling and hierarchical clustering revealed clear tissue-driven segregation of bacterial communities, whereas fungal assemblages showed weaker tissue-associated structuring. Seed kernels harbored approximately 3.3-fold more unique bacterial OTUs than pulp tissues, with the Amrapali seedkernel exhibiting the highest richness (789 OTUs). Across varieties, 82% of kernel-associated bacterial OTUs were shared, compared with 31% in pulp, indicating a conserved kernel microbiome and a more variable, cultivar-specific pulp microbiome. These results highlight strong tissue-level compartmentalization of mango-associated bacterial communities across cultivars.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04848-2.}, }
@article {pmid42205903, year = {2026}, author = {Hameed, A and Ghate, SD and Shastry, RP}, title = {Fecal functional metagenomics reveals increased gut Bacillota/Pseudomonadota (Firmicutes/Proteobacteria) ratio and altered bacterial CAZyme profile in human colorectal cancer.}, journal = {3 Biotech}, volume = {16}, number = {6}, pages = {230}, pmid = {42205903}, issn = {2190-572X}, abstract = {UNLABELLED: Gut microbial dysbiosis has been implicated in the onset and/or progression of colorectal cancer (CC). We recently identified the emergence of low-abundance bacterial taxa affiliated with the phylum Bacillota in the gut microbiome of CC patients, as revealed by 16S rRNA gene amplicon sequencing. Here, we subjected the fecal samples from CC (n = 4) and healthy control (HC, n = 4) participants to functional metagenomics using the Illumina Novaseq 6000 platform. Metagenome-assembled genomes (MAGs) showed compositional differences among bacterial phylotypes in CC and HC. Species observed, richness (Chao1), and diversity (Shannon's) were high in CC, whereas species abundance peaked in HC. The Bacillota to Pseudomonadota ratio was high (> 3-fold) in CC (2.45) as compared to HC (0.70). MAGs revealed a decline in the distribution frequency of COGs involved in carbohydrate transport and metabolism (G), inorganic ion transport and metabolism (P), and unknown function (S) in CC. However, CC and HC samples exhibited marginal variations in terms of G/P (1.29 and 1.18, respectively) and G/S (0.35 and 0.40, respectively) ratios. Analysis further revealed a significant increment in glycosyltransferases GT1, GT2 and GT4, particularly in CC. In contrast, the glycoside hydrolases GH5 and GH9 declined in CC. GT/GH ratios were found to increase > 2-fold in CC (3.94) compared with HC (1.37). The present pilot-scale dataset-specific work reflects perseverance of Bacillota, significant decline in Pseudomonadota, a stable G/P and G/S ratios and enrichment of glycosyltransfererases in CC. Further transcriptomic-based studies in larger cohorts are warranted to gain insights into the implications of dysbiosis and its pathophysiological relevance.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04882-0.}, }
@article {pmid42206016, year = {2026}, author = {Watz, H and Korn, S and Kornmann, O and Singh, D and Wilkinson, T and Hanrott, K and Staples, KJ and Ackland, J and Norris, V}, title = {A randomised controlled trial of EP395, a novel anti-inflammatory macrolide, in stable COPD patients.}, journal = {ERJ open research}, volume = {12}, number = {3}, pages = {}, pmid = {42206016}, issn = {2312-0541}, abstract = {BACKGROUND: Macrolide antibiotics have immunomodulatory activity and when taken chronically reduce exacerbations of COPD. However, chronic use can cause bacterial resistance. EP395 (glasmacinal), a novel macrolide, is being developed as a treatment to reduce exacerbations of COPD without inducing antimicrobial resistance.<br><br>METHODS: In this double-blind, placebo-controlled, phase 2a trial (NCT05572333), patients (&#x2265;45&#x2005;years old, diagnosed with COPD for &#x2265;2&#x2005;years and stable on at least one maintenance inhaled therapy) were randomised (2:1) to EP395 or placebo daily for 12&#x2005;weeks. The primary objective was safety, with key secondary objectives assessing pharmacodynamic effects of EP395.<br><br>RESULTS: A total of 61 patients were randomised (42 EP395, 19 placebo). A 12-week course of EP395 was well tolerated: no serious adverse events were considered related to EP395, and adverse events occurred in similar proportions in both groups (64.3% EP395, 63.2% placebo). Four patients were withdrawn due to adverse events (three EP395, one placebo). Sputum neutrophil elastase and myeloperoxidase, mediators of neutrophil activation, were reduced with EP395 (treatment difference (log scale): neutrophil elastase -0.415&#x2005;ng&#xb7;mL[-1], 95% CI -0.787 to -0.043&#x2005;ng&#xb7;mL[-1], p=0.030; myeloperoxidase -0.282&#x2005;ng&#xb7;mL[-1], 95% CI -0.640 to 0.076&#x2005;ng&#xb7;mL[-1], p=0.119). Relative changes in neutrophil elastase and myeloperoxidase from baseline with EP395 were 66% and 75%, respectively, of those observed with placebo. Exploratory 16S rRNA sequencing of sputum showed EP395 had no detectable effect on the lung microbiome, including the proportion of pathogenic Proteobacteria species.<br><br>CONCLUSION: In patients with stable COPD, EP395 for 12&#x2005;weeks was well tolerated, demonstrated selective anti-inflammatory activity and had no detectable effect on the lung microbiome.}, }
@article {pmid42206046, year = {2026}, author = {Zhang, W and Yi, J and Li, Z}, title = {Correction: Microbiome-innate immune crosstalk in acute exacerbation of idiopathic pulmonary fibrosis: an amplification framework.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1874174}, doi = {10.3389/fimmu.2026.1874174}, pmid = {42206046}, issn = {1664-3224}, mesh = {Humans ; *Microbiota/immunology ; *Idiopathic Pulmonary Fibrosis/immunology/microbiology ; *Immunity, Innate ; Animals ; Inflammasomes/metabolism/immunology ; NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; Disease Progression ; Biofilms ; }, abstract = {[This corrects the article DOI: 10.3389/fimmu.2026.1847027.].}, }
@article {pmid42206055, year = {2026}, author = {Zhang, W and Yi, J and Li, Z}, title = {Microbiome-innate immune crosstalk in acute exacerbation of idiopathic pulmonary fibrosis: an amplification framework.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1847027}, pmid = {42206055}, issn = {1664-3224}, mesh = {Humans ; *Idiopathic Pulmonary Fibrosis/immunology/microbiology/pathology/metabolism ; *Microbiota/immunology ; *Immunity, Innate ; Animals ; Disease Progression ; Neutrophils/immunology ; Lung/immunology/microbiology/pathology ; Macrophages/immunology ; Dysbiosis/immunology ; }, abstract = {Acute exacerbation of idiopathic pulmonary fibrosis (AE-IPF) remains a major cause of short-term mortality, yet its biological drivers are incompletely understood. Increasing evidence indicates that the distal lung is not sterile and that microbial burden, ecological disruption, and host immune responses may interact within the fibrotic niche. Here, we summarize current evidence and propose a focused, hypothesis-generating framework for microbiome-immune crosstalk in AE-IPF. In this model, pulmonary dysbiosis and persistent microbial stimulation may converge with epithelial injury-derived danger signals to amplify pattern-recognition receptor signaling, reshape macrophage states, and promote injurious neutrophil responses, including excessive neutrophil extracellular trap formation. Emerging data from fibrotic lung disease also raise the possibility that SPP1-associated macrophage programs may contribute to both impaired host defense and maladaptive repair. These observations also support the view that immune-cell state transitions, rather than microbial burden alone, may shape how acute injury is translated into persistent fibroinflammatory remodeling. We also discuss how antimicrobial exposure and resistance-associated persistence traits, including biofilm formation, could contribute to impaired microbial clearance and sustained innate immune activation, while emphasizing that direct in situ evidence in AE-IPF remains limited. Rather than proposing a universal mechanism, this mini review highlights a testable amplification framework that may help refine pathogen-aware stratification, antimicrobial stewardship, and biomarker-guided host-directed strategies in future studies.}, }
@article {pmid42206057, year = {2026}, author = {Hu, Z and Yue, P and Yuan, M and Zhang, Z and Li, Q and Yang, T and Li, Y and Ding, BS and Fan, Z and Yang, B and Cao, Z}, title = {Stress accelerates hepatocellular carcinoma progression via a gut microbial-metabolite axis.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1790214}, pmid = {42206057}, issn = {1664-3224}, mesh = {*Liver Neoplasms/pathology/metabolism/microbiology/etiology ; Animals ; *Carcinoma, Hepatocellular/pathology/metabolism/microbiology/etiology ; Humans ; *Gastrointestinal Microbiome ; Indoles/metabolism/pharmacology ; Disease Progression ; Tumor Microenvironment ; *Stress, Physiological ; Mice ; Male ; Cell Line, Tumor ; }, abstract = {BACKGROUND: Hepatocellular carcinoma ranks among the most prevalent malignancies worldwide. While stress can modulate tumor initiation, progression, metastasis, and therapeutic response through diverse mechanisms, its specific role in hepatocellular carcinoma pathobiology remains elusive. This study aimed to elucidate the role of the gut microbiota in stress-promoted hepatocellular carcinoma progression and to uncover the pathways associated with disease progression.<br><br>METHODS: Integrating clinical and preclinical models, we delineated stress-induced restructuring of the gut microbiota and functionally restored specific microbial constituents. Mechanistic insights into the microbial metabolite indole-3-propionic acid were derived through in vitro and in vivo interrogations of the hepatocellular carcinoma tumor microenvironment.<br><br>RESULTS: Stress profoundly remodels the gut microbiota, with Phocaeicola vulgatus being significantly reduced. Restoration of Phocaeicola vulgatus or administration of its tryptophan-derived metabolite indole-3-propionic acid significantly attenuated hepatocellular carcinoma progression in vivo. Indole-3-propionic acid treatment reduced endothelial JAM2 expression and was associated with reduced JAM2-F11R-mediated endothelial-macrophage crosstalk in hepatocellular carcinoma, which may contribute to suppression of tumor progression.<br><br>CONCLUSIONS: These findings support a role for the stress-gut microbiota-metabolite-tumor microenvironment axis in hepatocellular carcinoma progression and suggest potential translational targets for microbiome-based therapeutic strategies.}, }
@article {pmid42206066, year = {2026}, author = {Zhang, Q and Li, S and Wang, X and Sun, Y and Liu, J and Gao, J and Deng, C and Zhao, W and Ma, Y and Quan, J and Yin, Q and Jian, D and Zhang, R and Qi, R}, title = {Multi-metal contamination shapes abundance, co-occurrence, and mobility potential of resistance and virulence genes in mining-impacted soils.}, journal = {Infectious medicine}, volume = {5}, number = {2}, pages = {100260}, pmid = {42206066}, issn = {2772-431X}, abstract = {BACKGROUND: Antimicrobial resistance is a growing global public health concern, posing a serious threat to human health. This study aimed to characterize the composition and distribution of microbial communities, metal resistance genes (MRGs), antibiotic resistance genes (ARGs), and virulence factor genes (VFGs) under multi-metal stress and assess the impacts of metal and soil properties on the diversity, abundance, carrying rate (proportion of gene carriers), co-occurrence rate (proportion of microorganisms co-carrying multiple gene types), and mobility potential (MP, likelihood of horizontal gene transfer) of these genes.<br><br>METHODS: Soil samples were collected from eight sampling sites within a metal mining area (metal-contaminated soil group, MS) and four sites located more than 3 km away from the mining area (control group). Metal concentrations and physicochemical properties of the soils were measured using standard methods. Metagenomic sequencing was performed to characterize the composition and distribution of the microbiome, resistome, and virulome. Statistical modeling was applied to examine the effects of heavy metal content and soil properties on the relative abundance, co-occurrence, and mobilome potential of the three gene types.<br><br>RESULTS: Fe, V, Cr, and Cu primarily promoted the diversity, carrying rate, and co-occurrence rate of microbial communities, MRGs, ARGs, and VFGs. In contrast, Ni and Zn exhibited overall inhibitory effects. For every unit increase in Fe and V, the MP of MRGs and VFGs was associated with an increase of 3.0 &#xd7; 10&#x207b;&#x2075; and 1.2 &#xd7; 10&#x207b;&#x2075;, respectively. A per 1 mg/kg increase in Cr and Cu was correlated with a decrease of 4.3 &#xd7; 10&#x207b;&#x2075; and 1.1 &#xd7; 10&#x207b;&#x2074; in the MP of ARGs and of MRGs, respectively. Positive correlations were found between the MP of plasmid&#x2011;mediated ARGs and Cr, and between transposon&#x2011;mediated ARGs and Cr/V. The MP of transposon&#x2011;mediated MRGs correlated positively with Fe, while Cu correlated negatively with plasmid&#x2011;mediated ARGs but positively with insertion sequence&#x2011;mediated ARGs. Ni concentration was positively associated with the MP of IS&#x2011;mediated VFGs.<br><br>CONCLUSIONS: Metals alter the composition and distribution of microbial communities, MRGs, ARGs, and VFGs. A key mechanism underlying this regulation is the modulation of their mobile potential, which either facilitates or restricts horizontal gene transfer.}, }
@article {pmid42206103, year = {2026}, author = {Xu, J and Cai, L and Lu, S and Chen, L and Zhang, T and Wang, J}, title = {Relationship between gestational diabetes mellitus and anxiety symptoms and gut microbiome composition in pregnant women.}, journal = {Open life sciences}, volume = {21}, number = {1}, pages = {20251317}, pmid = {42206103}, issn = {2391-5412}, abstract = {Gestational diabetes mellitus (GDM) is a common metabolic complication of pregnancy associated with poor outcomes for both mother and baby. An expanding body of research highlights the gut microbiota's influence on host metabolism and neurobehavioral processes, yet how gestational diabetes mellitus, anxiety symptoms, and microbial communities interact is still unclear. To address this gap, we profiled gut-microbiome changes in pregnant women presenting with both GDM and clinically significant anxiety. A total of 120 participants were categorized into four groups: GDM with anxiety (G + A), GDM without anxiety (G + NAF), non-GDM with anxiety (NG + A), and non-GDM without anxiety (NG + NA). Stool specimens were obtained and subjected to 16S rRNA gene profiling of the V3-V4 hypervariable region using Illumina MiSeq sequencing. Results showed significant differences in fasting blood glucose between GDM and non-GDM groups. GDM groups exhibited enrichment of Enterobacteriaceae and reduction of Faecalibacterium, while anxiety groups showed increased Lactococcus and Streptococcus. The dual-exposure group (G + A) demonstrated unique enrichment of oral-derived genera (e.g., Fusobacterium and Actinomyces). Among 963 OTUs identified, 681 were core OTUs shared across groups. GDM and anxiety groups possessed 42 and 32 unique OTUs, respectively, with 26 OTUs specific to the G + A group. LEfSe analysis revealed 16 phylogenetically conserved taxa distinguishing GDM and non-GDM groups, while anxiety-positive groups were characterized by Bacilli and Negativicutes. These findings suggest that GDM and anxiety are associated with distinct gut microbiota profiles, highlighting potential microbial biomarkers for early diagnosis and intervention.}, }
@article {pmid42206189, year = {2026}, author = {De Jaegher, S and Pinzauti, D and D'Aguanno, M and Parkinson, E and Schofield, J and Strazzeri, F and Skipp, P and Penrice-Randal, R and Kunicki, A and McCausland, B and Kipps, C and Amin, J and Biazzo, M}, title = {Identifying microbial biomarkers of neurodegeneration: a comparative study in Alzheimer's and Parkinson's disease.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1831956}, pmid = {42206189}, issn = {2813-4338}, abstract = {INTRODUCTION: Neurodegenerative disorders such as Alzheimer's disease (AD) and Parkinson's disease (PD) have been increasingly linked to alterations of the gut microbiota, although reported microbial signatures remain heterogeneous and often lack taxonomic resolution.<br><br>METHODS: In the present study, we applied full-length 16S rRNA gene sequencing to characterize gut microbiota composition in 152 individuals, including patients with AD (n = 37), PD (n = 65), and age-matched healthy controls (n = 50), using a unified bioinformatic and statistical framework with adjustment for relevant demographic covariates.<br><br>RESULTS: Alzheimer's disease was associated with a modest but significant reduction in microbial richness and Shannon diversity compared with controls, whereas no alpha diversity differences were observed in PD. Beta diversity analyses revealed significant compositional differences across diagnostic groups, driven primarily by PD and modulated by sex but not age. Species-level differential abundance analysis identified a PD-associated microbial signature characterized by reduced abundances of short-chain fatty acid-producing bacteria, including Faecalibacterium prausnitzii, Agathobacter rectalis, Roseburia intestinalis, and Faecalicatena fissicatena, together with increased abundance of Ruminococcus sp. JE7A12. In contrast, AD exhibited minimal species-level changes, with only Bacteroidales bacterium CF showing reduced abundance compared with controls.<br><br>DISCUSSION: Overall, these findings indicate that Parkinson's disease is characterized by a targeted disruption of beneficial butyrate-producing bacteria, whereas Alzheimer's disease exhibits subtler and less consistent microbiome alterations. Our results underscore the importance of species-level resolution for identifying disease-associated microbial signatures.}, }
@article {pmid42206330, year = {2026}, author = {Flores-Núñez, VM and Dal'Sasso, TCS and Hansen, M and Reinhardt, G and Braun, S and Stukenbrock, EH}, title = {Host-specific fungal plant pathogens exhibit distinct interactions with the leaf microbiota of wild grasses.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {381}, number = {1951}, pages = {}, doi = {10.1098/rstb.2025.0112}, pmid = {42206330}, issn = {1471-2970}, support = {//ERC consolidator grant FungalSecrets/ ; }, mesh = {*Ascomycota/physiology/pathogenicity ; *Plant Leaves/microbiology ; *Microbiota ; *Host-Pathogen Interactions ; *Plant Diseases/microbiology ; *Aegilops/microbiology ; *Hordeum/microbiology ; }, abstract = {The plant's microbiome is influenced by the plant species and biotic factors such as infection by pathogens. Pathogen-microbiome interactions are relevant for disease progression since both can compete within the host. We hypothesize that pathogens specialized to different hosts have distinct, direct and indirect influence on the host microbiome. We focused on the host-specific leaf pathogens Zymoseptoria tritici and Zymoseptoria passerinii. By using microbiome metabarcoding and coculture interactions, we evaluated the influence of virulent (wild host-infecting pathogen) and avirulent (domesticated host-infecting pathogen) Zymoseptoria isolates on the leaf microbiome of the wild grasses Aegilops cylindrica and Hordeum murinum, which are hosts to virulent lineages of Z. tritici and Z. passerinii, respectively. Our microbiome analysis showed that the fungal communities were affected by virulent lineages, while the avirulent lineages had the most negative correlations with bacteria. Both virulent and avirulent pathogens had a similar spectrum of interactions when experimentally cocultured with bacteria. The intensity of pathogen-induced growth enhancement on bacteria differed between Z. tritici isolates. We demonstrated that the pathogen-secreted invertases can be a determinant of bacterial growth enhancement. Our study illustrates the extent of specificity in pathogen-microbe coexistence and suggests an interaction mechanism that may influence in planta interactions. This article is part of the theme issue 'Wild plant pathosystems'.}, }
@article {pmid42206333, year = {2026}, author = {Tanford, P and Vargas, RC and Bugay, MJ and Dantas, G and Stein, C and Penczykowski, RM and Mangan, SA}, title = {Foliar pathogens and drought drive plant-soil feedback between two co-occurring herbaceous plant species.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {381}, number = {1951}, pages = {}, doi = {10.1098/rstb.2025.0115}, pmid = {42206333}, issn = {1471-2970}, support = {//Washington University in St. Louis InCEES/ ; //Directorate for Biological Sciences/ ; }, mesh = {*Soil Microbiology ; *Droughts ; *Plantago/microbiology/physiology ; *Ascomycota/physiology ; *Plant Diseases/microbiology ; Soil/chemistry ; *Microbiota ; Plant Leaves/microbiology ; *Host-Pathogen Interactions ; }, abstract = {Plants alter soil biotic and abiotic properties with consequences for plant community dynamics at local and global scales, but how plant-soil interactions are affected by other environmental and biotic interactions remains poorly understood. We performed a fully reciprocal plant-soil feedback (PSF) experiment between two herbaceous plants, Monarda fistulosa and Plantago lanceolata, and tested how PSFs were influenced by drought and foliar powdery mildew pathogen infection. We observed significant negative feedbacks between the two plant species, but only when plants were grown with live soil biota and infected with powdery mildew. The strongest feedback was observed under both foliar infection and drought. High-throughput sequencing of soil fungi and bacteria from the treatment groups with foliar infection and drought revealed that both fungal and bacterial community composition were influenced by soil condition (live versus sterile) and soil training (Monarda versus Plantago). Together, our results indicate that the observed negative PSF was driven by foliar pathogens and plant species-specific soil microbial communities and intensified by drought. Our study suggests that PSF can be sensitive to both aboveground plant-pathogen interactions and climatic factors, improving our understanding of microbial impacts on plant community dynamics. This article is part of the theme issue 'Wild plant pathosystems'.}, }
@article {pmid42206334, year = {2026}, author = {Henry, L and Rat, A and Laderman, E and Lion, R and Mayjonade, B and Team Pathocom,  and Roux, F and Weigel, D and Bergelson, J}, title = {Seasonality, land use and plant community diversity shape microbiome-pathogen interactions in wild populations of Arabidopsis thaliana.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {381}, number = {1951}, pages = {}, doi = {10.1098/rstb.2025.0116}, pmid = {42206334}, issn = {1471-2970}, support = {//Simons Foundation/ ; /ERC_/European Research Council/International ; //Charles H. Revson Foundation/ ; }, mesh = {*Arabidopsis/microbiology/physiology ; *Microbiota ; Seasons ; *Plant Diseases/microbiology ; *Biodiversity ; *Host-Pathogen Interactions ; }, abstract = {The microbiome often protects plants against pathogens, but most findings are limited to controlled experiments in the lab. In the context of wild populations, one key challenge is to understand sources of variation that impact the commensal microbiome, which in turn shapes the degree of protection. Here, we surveyed both disease symptoms and microbiomes from wild populations of Arabidopsis thaliana over four consecutive seasons (Autumn/Spring) across three different land use types. Land use types varied in the extent of anthropogenic influences and included forest meadows, human-impacted fields adjacent to agriculture or municipal parks and highly disturbed habitats near railroad tracks. By building an integrative map of abiotic and biotic variables, we find that a key predictor of disease was biodiversity across ecological scales. Plant communities with higher diversity were associated with increased microbial diversity and reduced disease burden in A. thaliana populations, particularly in the Spring. However, the diversity-microbiome-disease relationships were all sensitive to season and further modulated by land use. Taken together, our work highlights the importance of anthropogenic change reshaping species interactions across ecological scales to impact disease risk in wild plant populations. This article is part of the theme issue 'Wild plant pathosystems'.}, }
@article {pmid42206338, year = {2026}, author = {Romero-Jiménez, MJ and Pérez-Pazos, E and Leopold, DR and Lebeis, SL and Busby, PE}, title = {Yeast species interactions and composition modulate leaf rust severity in Populus trichocarpa.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {381}, number = {1951}, pages = {}, doi = {10.1098/rstb.2025.0121}, pmid = {42206338}, issn = {1471-2970}, support = {//Division of Integrative Organismal Systems/ ; //National Institute of Food and Agriculture/ ; //Agricultural Research Service/ ; }, mesh = {*Populus/microbiology ; *Plant Diseases/microbiology ; *Basidiomycota/physiology ; *Yeasts/physiology ; Plant Leaves/microbiology ; *Microbiota ; *Microbial Interactions ; }, abstract = {Plant microbiomes are recognized for increasing defence against pathogens. Yet, identifying the role of beneficial microbes beyond their individual effects remains poorly explored. In a series of in planta greenhouse experiments, we tested the effects of individual foliar yeasts, yeast interactions and the combination of yeast richness and diversity on disease severity caused by the leaf rust pathogen Melampsora × columbiana in the model tree, Populus trichocarpa. We found that single yeasts can either antagonize or facilitate the rust; nevertheless, most yeasts did not modify disease severity. For some individual disease-modifying yeasts, interactions with additional yeasts changed the outcome of disease severity. In one case, a rust facilitator was neutralized by other interacting yeasts; in another, increasing richness in communities containing a rust antagonist was associated with increasing disease severity. However, we did not find evidence for a positive or negative relationship between yeast richness or diversity and disease severity overall. A follow-up in vitro experiment showed strong interspecific competition between yeasts, which might explain changes in disease severity with varying community membership. Our results highlight the role of microbial interactions and composition for plant disease severity, yet caution against interpreting plant microbiome richness or diversity as inherently disease protective. This article is part of the theme issue 'Wild plant pathosystems'.}, }
@article {pmid42206504, year = {2026}, author = {Brandt, E and Koivisto, A and Pereira, P and Mustanoja, E and Auvinen, P and Saari, T and Rusanen, M and Leinonen, V and Scheperjans, F and Kärkkäinen, V}, title = {Gut Microbiome Differences Between Early Alzheimer Disease and Idiopathic Normal Pressure Hydrocephalus.}, journal = {Alzheimer disease and associated disorders}, volume = {}, number = {}, pages = {}, doi = {10.1097/WAD.0000000000000726}, pmid = {42206504}, issn = {1546-4156}, abstract = {BACKGROUND: Alzheimer disease (AD) and idiopathic normal pressure hydrocephalus (iNPH) are neurodegenerative diseases causing memory decline. Previous studies have demonstrated an altered gut microbiome (GM) in both conditions. In this study, we compared the GM composition between the groups to find out how if the GM composition differed between the cognitively healthy individuals (CO) and AD groups, as well as between the AD and iNPH groups.<br><br>METHODS: Thirty-seven CO participants, 21 mild AD patients and 10 participants with shunted iNPH gave fecal samples, which were subjected to 16S amplicon sequencing. Then, genus-level differences were analyzed. Information about comorbidities and diet was collected, and cognitive function was evaluated.<br><br>RESULTS: Compared with the CO group, Anaerovorax and an unknown genus of the Comamonadaceae family increased, whereas Enterobacter, Absicoccus, Buttiauxella, Raoultella, and Lacticaseibacillus decreased in the AD group. Compared with the iNPH group, Paramuribaculum, an unknown genus of the Desulfovibrionaceae family, Ruficoccus and Mitsuokella increased, whereas Anaeromassilibacillus and Desulfovibrio decreased in the AD group.<br><br>CONCLUSIONS: We demonstrated differences in the GM composition between the AD and CO groups, as well as between the AD and iNPH groups. To our knowledge, this is the first report to compare the 2 neurodegenerative diseases and demonstrate GM differences.}, }
@article {pmid42206586, year = {2026}, author = {Yeo, S and Park, H}, title = {Dereplication-assisted culturomics enables strain-level ecological analysis of the human gut microbiome.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2681840}, doi = {10.1080/19490976.2026.2681840}, pmid = {42206586}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Enterococcus faecium/isolation &amp; purification/classification/genetics ; Metagenomics/methods ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; *Bifidobacterium/isolation &amp; purification/classification/genetics ; }, abstract = {Recent advances in culturomics have enabled large-scale recovery of microbial isolates from the human gut, generating extensive culture collections that bridge metagenomic predictions and experimental validation. However, these isolate resources remain largely underutilized, as conventional culturomics prioritizes the discovery of novel species while massive collections of commensal isolates persist as unexplored biological datasets. Dereplication, particularly based on MALDI-TOF MS spectral features, has been largely regarded as a logistical tool for managing redundancy rather than an analytical asset. Here, we reposition dereplication as an analytical framework for interpreting large-scale culturomics datasets and resolving strain-level ecological patterns. We applied the SPeDE pipeline to a comprehensive collection of 2,231 isolates, including Bifidobacterium spp. and Enterococcus faecium, recovered from healthy donor feces. Spectrum-derived operational isolation units (OIUs) revealed host-associated strain-level repertoires and lineage-like clustering within species. Notably, distinct spectral clusters observed in E. faecium corresponded to clade-level patterns identified through shotgun metagenomic analysis. These findings demonstrate that dereplication-assisted culturomics can extend beyond redundancy control to enable high-resolution ecological interpretation of cultured microbiome datasets. By reframing dereplication as a bridge between large-scale isolate generation and strain-level microbiome ecology, this study outlines a conceptual and practical direction for the next phase of human microbiome research in the post-culturomics era.}, }
@article {pmid42206818, year = {2026}, author = {Shatta, A and Chavarria, X and Choi, JH and Oh, S and Kim, M and Kang, D and Cho, YH and Choi, DY and Yi, MH and Kim, JY}, title = {High-throughput microbiome profiling and co-occurrence with antibiotic resistance genes in Lucilia sericata.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnag063}, pmid = {42206818}, issn = {1574-6968}, abstract = {Blow flies such as Lucilia sericata (Diptera: Calliphoridae) serve important ecological functions as decomposers. However, due to their close association with decaying organic matter, they also play potential roles as reservoirs of pathogenic bacteria and antimicrobial resistance genes (ARGs). In this study, we characterized the bacterial communities and targeted key antibacterial resistance markers of L. sericata specimens using 16S rRNA gene metabarcoding and targeted PCR screening. The microbiome was dominated by Dysgonomonas, Vagococcus, Pseudomonas, Ignatzschineria, and Providencia with geographic variation in community structure. Flies from Chungnam exhibited the lowest microbial diversity, while samples from Jeonnam and Gyeonggi showed greater richness and evenness. Beta diversity analyses confirmed geographic structuring of bacterial communities, with semi-urban and rural locations harboring more diverse taxa. Notably, opportunistic pathogens such as Proteus mirabilis and Providencia were detected alongside a range of ARGs (blaTEM, ermB, sul1, aac(6')-Ib-cr, cat and mecA) and integron elements (intI and intII), suggesting that L. sericata may act as a reservoir of clinically important microbes and resistance genes.}, }
@article {pmid42206849, year = {2026}, author = {Ahrens, AP and Dias, R and Hyötyläinen, T and White, PA and Orešič, M and Triplett, EW and Ludvigsson, J}, title = {Early-life proteomic and microbiome features signal obesity risk across 26 years of follow-up.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0142425}, doi = {10.1128/msystems.01424-25}, pmid = {42206849}, issn = {2379-5077}, abstract = {UNLABELLED: Childhood obesity is rising globally. Yet, few studies have examined the microbiome and proteome in early childhood in relation to this outcome, and most are cross-sectional by design. Early-life factors in the ABIS birth cohort (n = 16,683) were associated with obesity up to age 26 (mean follow-up 25.3 years, range 23.7-26.5 years): psychosocial stressors, smoking, infections, and diet in the first year. We assessed biomarkers, including cord blood metabolome (n = 290) and proteome (n = 358), by liquid chromatography, mass spectrometry, and Olink. Gut microbial composition at age one (n = 1,743) was assessed using stool samples and 16S rRNA sequencing. In this prospective longitudinal cohort study, significant differences were found in infants with future obesity, including elevated angiopoietin-like 4 (ANGPTL4), follistatin, and hepatocyte growth factor (independently of maternal weight) and reduced isocaproic acid, tryptophan, and oleic acid, with prenatal mediation. Akkermansia, asaccharolytic bacteria (Phascolarctobacterium and Senegalimassiliensia), and equol-producers (Adlercreutzia and Slackia) were depleted. Machine learning models selecting 40 most predictive features showed long-term prediction from birth proteomics and bacterial taxa at age one (area under the curve [AUC] = 0.83 ± .05, n = 1,877) and additional metrics, for example, parental and child body mass index in the first 8 years (AUC = 0.89 ± .02, n = 1,877), suggesting durable biological encoding. Proteomic markers across folds included fibroblast growth factor 19, ANGPTL4, sulfotransferase family 2A member 1, and interleukin 20. These findings suggest clinically relevant biomarkers indicating early-life regulation of bile acid metabolism, lipid storage vs. oxidation, and immune-metabolic signaling and pathways to prospectively prevent childhood- and adult-onset obesity across a 26-year predictive gap.<br><br>IMPORTANCE: Understanding the origins of obesity is critical for developing preventive strategies, and early life represents a particularly sensitive window. This study leverages a large, general-population cohort with prospectively collected data, including parental body mass index (BMI), cord blood proteomics, and the gut microbiome at age one, linked to obesity outcomes over 26 years. Using integrated machine learning models, we show that in addition to parental BMI, specific proteomic and microbial markers present in infancy can predict long-term obesity risk, highlighting the role of early metabolic programming. Several key markers point to bile acid signaling as a mechanism connecting early microbiome development with fat accumulation and insulin regulation. By identifying these early-life predictors long before obesity manifests, these results provide new insights into intergenerational risk and suggest measurable targets for preventing obesity and related metabolic disorders from the earliest stages of life.}, }
@article {pmid42207032, year = {2026}, author = {Giani, N and John, J and Campbell, B}, title = {Shotgun metagenomics and metatranscriptomics of soil microbial communities under monoculture and polyculture cover crops.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0030926}, doi = {10.1128/mra.00309-26}, pmid = {42207032}, issn = {2576-098X}, abstract = {Here, we present 30 metagenomes, 21 metatranscriptomes, and 334 metagenome-assembled genomes collected from soils under different cover crop species. This data set will be useful for studying microbial interactions, especially functional redundancy, with relevance to agricultural management and sustainability.}, }
@article {pmid42207174, year = {2026}, author = {Liao, Y and Zhang, Q and Zheng, J and Zhang, J and Dai, T and Zhu, F and Carrión, VJ and Delgado-Baquerizo, M and Sonne, C and Cao, F and Li, X}, title = {CHD-18g-modulated Pseudomonas taxa support poplar salt tolerance.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag138}, pmid = {42207174}, issn = {1751-7370}, abstract = {Against the background of global climate change, soil salinization has emerged as a major abiotic stressor constraining agroforestry productivity worldwide. Root-recruited microbes enhance plant stress resilience, and host-microbe interactions depend on plant root metabolism. Stress-tolerant plant genotypes exhibit a marked capacity to enrich beneficial root-associated microbes through specialized metabolic responses, thereby facilitating phenotypic plasticity. However, the molecular mechanisms underlying these plant-microbe interactions remain unclear. In this study, we compared salt tolerance among three poplar varieties under aseptic and non-aseptic conditions, and analyzed their rhizosphere bacterial community responses to salt stress. We found that microbial inoculation modulated poplar salt tolerance, and poplar shaped rhizosphere bacterial communities in a genotype-dependent manner. Transcriptome sequencing and targeted metabolomic analysis indicated that salt-tolerant poplar plants preferentially activate the phenylpropanoid biosynthesis pathway, accompanied by the enhanced root secretion of benzoic acid (BA) and salicylic acid (SA) and up-regulation of CHD-18g encoding cinnamoyl-CoA hydratase/dehydrogenase. Overexpression of CHD-18g increased rhizosphere Pseudomonas abundance by enhancing BA and SA biosynthesis. Binary interaction assays further showed that the BA-induced Pseudomonas taxa mitigated salt stress and promoted poplar growth under salt stress. Our findings propose a framework linking host gene expression, root metabolism, and key microbial taxa in conferring salt tolerance. This work uncovers a metabolic signaling mechanism by which trees shape their root microbiome to enhance stress adaptation, offering actionable genetic and ecological strategies for improving tree resilience in sustainable agroforestry systems.}, }
@article {pmid42207344, year = {2026}, author = {Cagirgan, OY and Korkmaz, S and Diker, KS}, title = {Intestinal microbiome in necrotic enteritis infection of broiler and comparison of treatment alternatives.}, journal = {Tropical animal health and production}, volume = {58}, number = {5}, pages = {}, pmid = {42207344}, issn = {1573-7438}, support = {VTF-190002//Bilimsel Ara&#x15f;t&#x131;rma Projeleri Birimi, Ayd&#x131;n Adnan Menderes &#xdc;niversitesi/ ; }, mesh = {Animals ; *Chickens/microbiology ; *Clostridium Infections/veterinary/microbiology/drug therapy ; *Poultry Diseases/microbiology/drug therapy ; *Enteritis/veterinary/microbiology/drug therapy ; Clostridium perfringens/physiology ; Anti-Bacterial Agents/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; *Bacillus/physiology ; *Probiotics/administration &amp; dosage ; Amoxicillin/therapeutic use/administration &amp; dosage ; Necrosis/veterinary/microbiology ; Male ; }, abstract = {Clostridium perfringens is the primary causative agent of necrotic enteritis (NE), a gastrointestinal disease that leads to substantial economic losses in poultry. This study aims to characterize the intestinal microbiome of chickens and assess the effects of Bacillus velezensis on gut microbiota and recovery from necrotic enteritis, comparing its efficacy to antibiotic treatment. The experiment involved five groups, each consisting of 16 chickens. The first group, the start-of-challenge (DB) group, included day-old chicks. The second group, the post-challenge control (DS) group, was reared until the end of the trial. The third group was infected with C. perfringens (NE group). The fourth group received both C. perfringens and B. velezensis (BV group), while the fifth group was treated with C. perfringens and amoxicillin (AB group). All chickens were euthanized via cervical dislocation following the experimental infection. Fecal samples collected from the cecum underwent 16 S rRNA gene-based metagenomic analysis, and the resulting data were statistically evaluated. Macroscopic examination after euthanasia revealed pathological changes in the intestines of chickens in the NE group, which had received only C. perfringens. Their intestines appeared swollen, with slight mild mucosal hemorrhage. In contrast, no macroscopic lesions were observed in the DB, DS, BV, or AB groups. Microbiome analysis showed a decline in microbial diversity within the NE group. The BV group exhibited a microbial composition most similar to that of healthy animals, followed by the AB group. The study concludes that B. velezensis could serve as an alternative to prophylactic antibiotics in mitigating the adverse effects of necrotic enteritis on the gut microbiome.}, }
@article {pmid42207404, year = {2026}, author = {Alanazi, M and Al-Kuraishy, HM and Mohamed, AA and Abass, SA and Shokr, MM and Alruwaili, M and Batiha, GE}, title = {Targeting Gut Microbiota by DPP-4 Inhibitors in Obesity: Mechanistic Insights and Therapeutic Implications.}, journal = {Current nutrition reports}, volume = {15}, number = {1}, pages = {}, pmid = {42207404}, issn = {2161-3311}, mesh = {Humans ; *Obesity/drug therapy/microbiology ; *Dipeptidyl-Peptidase IV Inhibitors/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; Animals ; Dysbiosis/drug therapy ; *Dipeptidyl Peptidase 4/metabolism ; Energy Metabolism/drug effects ; Insulin Resistance ; }, abstract = {PURPOSE OF REVIEW: Obesity is a complex metabolic disorder driven by factors such as chronic inflammation, insulin resistance, and significant alterations in the gut microbiota. Dipeptidyl peptidase-4 (DPP-4), an enzyme primarily known for inactivating incretin hormones like glucagon-like peptide-1 (GLP-1), is now recognized as a critical link between metabolic dysfunction and gut microbiome dysbiosis. This review aims to examine the mechanistic role of DPP-4 and its inhibitors in obesity, specifically focusing on how they modulate the gut microbiome to influence host energy balance and metabolic health.<br><br>RECENT FINDINGS: Recent experimental and clinical evidence indicates that DPP-4 activity contributes to obesity by influencing microbial composition, diversity, and function. Studies demonstrate that DPP-4 inhibitors can reshape the gut microbiota by reducing dysbiosis, decreasing the Firmicutes-to-Bacteroidetes ratio, and enhancing the production of short-chain fatty acids (SCFAs). Furthermore, these inhibitors improve gut barrier integrity and regulate bile acid metabolism, which helps attenuate systemic inflammation and restore insulin sensitivity. While DPP-4 inhibitors are often weight-neutral in clinical settings, they appear to assist in maintaining metabolic stability by enhancing central satiety signaling and reducing neuroinflammation. The gut microbiome acts as a key intermediary in the metabolic regulation managed by DPP-4. By restoring microbial balance and promoting beneficial metabolites, DPP-4 inhibitors offer therapeutic advantages that extend beyond traditional glycemic control to include improved energy equilibrium and reduced adiposity. Targeting the interactions between DPP-4 and the microbiota represents a promising future therapeutic strategy for managing obesity and its associated metabolic complications.}, }
@article {pmid42207427, year = {2026}, author = {Li, Q and Zhang, L and Qin, Y and Mei, W}, title = {Response of microbial community in the soil plastisphere of polypropylene microplastics to the stress of phenanthrene pollution: Microbial composition, function, and network.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {6}, pages = {}, pmid = {42207427}, issn = {1573-0972}, support = {32560012//National Natural Science Foundation of China/ ; 2023GXNSFBA026331//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; }, mesh = {*Phenanthrenes/metabolism/analysis ; *Soil Microbiology ; *Soil Pollutants/metabolism ; Bacteria/classification/metabolism/genetics/drug effects/isolation &amp; purification ; *Microplastics/metabolism ; *Polypropylenes ; Biodegradation, Environmental ; Soil/chemistry ; *Microbiota/drug effects ; RNA, Ribosomal, 16S/genetics ; Carbon/metabolism ; }, abstract = {Microplastics (MPs) accumulate in soils, forming microbial habitats termed the "plastisphere", which can concentrate hydrophobic pollutants like phenanthrene (PHE). This study investigated how PHE stress influences the microbial community in the polypropylene-amended soil plastisphere compared to bulk soil, revealing its "microbial refuge" function. Significant differences in microbial composition were observed. Under PHE stress, the number of unique genera in the plastisphere increased from 4 (without PHE) to 9, and the composition of significantly enriched genera changed substantially, with only 1 out of 6 enriched genera shared between PHE-stressed and non-stressed conditions. In contrast, the depleted genera remained largely consistent. Functional prediction indicated that PHE stress was associated with reduced health risks in the plastisphere relative to bulk soil. Carbon and methane metabolism pathways were significantly enriched in the plastisphere regardless of PHE stress. In contrast, nitrogen metabolism, aromatic compound degradation, and PAH degradation pathways did not differ significantly between the plastisphere and soil. Although several pathways reached statistical significance, fewer than 8.33% exhibited an absolute log2FC > 1. This discrepancy indicates that microplastics exert a limited biological impact on the overall metabolic potential of the soil microbiome, irrespective of PHE contamination. Microbial co-occurrence networks initially showed similar complexity between plastisphere and soil. However, PHE stress markedly reduced network complexity (degree) in the plastisphere and increased the proportion of negative correlations (indicating competition/antagonism) from ~ 60% to ~ 50% in both habitats. This study advances the mechanistic understanding of pollutant-driven microbial responses in soil plastispheres, with a focus on how this unique plastic-associated microbial niche mediates microbial composition, function, and network under PAH stress, thereby informing targeted bioremediation and ecological risk models for microplastic-organic co-contaminated environments.}, }
@article {pmid42207498, year = {2026}, author = {Ding, JB and Lin, MX and Zang, D and Chen, J}, title = {The impact of gut microbiota and metabolite-driven immune cell spatiotemporal dynamics on tumors.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2681842}, doi = {10.1080/19490976.2026.2681842}, pmid = {42207498}, issn = {1949-0984}, mesh = {Humans ; *Tumor Microenvironment/immunology ; *Gastrointestinal Microbiome/immunology ; *Neoplasms/immunology/microbiology ; Animals ; }, abstract = {Cancer poses a significant threat to human health. The immune response plays a pivotal role in tumor cell elimination, with increasing attention given to the spatiotemporal dynamics of immune cells across temporal, spatial, and functional dimensions. The gut microbiota, which constitutes the majority of the human microbiome, contributes to tumor initiation and progression. The tumor microenvironment (TME) serves as the primary site for immune cell-mediated anti-tumor responses, with the gut microbiota and its metabolites driving immune cell activation and spatiotemporal remodeling. This review explores the mechanisms by which the gut microbiota and its metabolites influence anti-tumor immunity, alongside the impact of immune cell dynamics on tumors. Furthermore, it proposes novel research strategies, including the "gut microbiota-immune cell dynamic monitoring model" and the "organoid-microbe co-culture platform." This work lays a theoretical foundation for advancing our understanding of the underlying mechanisms and developing innovative therapeutic approaches.}, }
@article {pmid42207652, year = {2026}, author = {Brodin, P}, title = {Immune System Development-Pro Tips for Paediatricians.}, journal = {Acta paediatrica (Oslo, Norway : 1992)}, volume = {}, number = {}, pages = {}, doi = {10.1111/apa.70627}, pmid = {42207652}, issn = {1651-2227}, abstract = {There are many misconceptions about the immune system in children, its impact on infectious disease susceptibility and its role in the rapidly increasing rates of immune mediated diseases in industrialized societies. In this mini review, I will discuss common believes and the data supporting or countering such believes, with a focus on clinically relevant topics of relevance to trainees and practicing paediatricians. I will emphasize data from studies performed in humans rather than reductionist mouse models. I discuss open questions requiring further investigation and end with a discussion on clinical observations of particular concern which paediatricians should consider when caring for children in their practices. Immune development is increasingly recognized as an important determinant of health, not just early in life, but also long term and all of us caring for children should know more about it.}, }
@article {pmid42207845, year = {2026}, author = {Shen, C and Wedell, E and Pop, M and Warnow, T}, title = {TIPP-SD: A new method for species detection in microbiomes.}, journal = {PLoS computational biology}, volume = {22}, number = {5}, pages = {e1014347}, doi = {10.1371/journal.pcbi.1014347}, pmid = {42207845}, issn = {1553-7358}, abstract = {In this study, we present TIPP-SD (i.e., TIPP for Species Detection), a new technique for species detection in a microbiome sample. TIPP-SD uses a substantially modified version of TIPP3, which is a recently developed abundance profiling tool based on maximum likelihood phylogenetic placement into marker gene taxonomies. TIPP-SD depends on a parameter (i.e., "threshold") for the required support for species detection, thus allowing us to compute a precision-recall curve as we vary this parameter. In comparing the precision-recall curves for TIPP-SD, TIPP3, Kraken2, Bracken, Metabuli, and Metapresence, we find that TIPP-SD improves on the other methods with respect to accuracy under conditions where there is a highly variable distribution of species abundance or where there is sequencing error. Under other conditions, TIPP-SD is close to the best of these methods. Finally, although TIPP-SD is slower than the other methods, it is still fast enough to be used on large datasets. TIPP-SD is available in github as part of the TIPP3 software package.}, }
@article {pmid42208156, year = {2026}, author = {Asif, M and Chen, Y and Bian, BR and Huang, J and Ahmad, K and Dong, L and Li, WJ}, title = {Plant-driven assembly and maintenance of disease-suppressive soil microbiomes in a changing climate.}, journal = {Microbiological research}, volume = {310}, number = {}, pages = {128557}, doi = {10.1016/j.micres.2026.128557}, pmid = {42208156}, issn = {1618-0623}, abstract = {Disease-suppressive soils are a fundamental aspect of sustainable agriculture, where native microbiomes help control soilborne pathogens through antagonistic interactions, protecting plant health even in favorable environmental conditions. This review synthesizes the current understanding of how plants actively assemble and maintain protective root microbiomes, a process that initiates and sustains this suppressiveness. The mechanistic depth of this synthesis is anchored primarily in annual cereal and vegetable crop systems, where the genetic, chemical, and ecological bases of plant-driven suppression have been most extensively characterized. While illustrative examples from perennial and woody systems are included to highlight specific principles, a comprehensive treatment of their distinct assembly dynamics, shaped by root persistence and long-term legacy accumulation, lies beyond the scope of this review. We detail how plants recruit beneficial microbes through a dynamic dialogue involving root exudates and immune system modulation, creating rhizosphere hotspots that enrich for protective consortia. This assembly is governed by host genetics, which shapes microbial recruitment and the plant's responsiveness to beneficial feedback. Critically, these interactions foster self-reinforcing legacies, where pathogen-induced stress reprograms exudate profiles to recruit suppressors, establishing durable microbiome shifts that confer intergenerational protection. However, escalating climate change threatens this equilibrium by perturbing microbial community structure, reducing beneficial diversity, favoring opportunistic pathogens, and eroding suppression efficacy. By integrating plant-microbe communication with soil-borne disease ecology, this perspective illuminates strategies for breeding crops and engineering soils to harness protective feedbacks for sustainable, microbiome-mediated disease management.}, }
@article {pmid42208158, year = {2026}, author = {Kumar, V and Sahoo, S and Kumar, P}, title = {Alopecia areata: Mechanisms, targeted therapies, and translational challenges.}, journal = {Current opinion in pharmacology}, volume = {89}, number = {}, pages = {102635}, doi = {10.1016/j.coph.2026.102635}, pmid = {42208158}, issn = {1471-4973}, abstract = {Alopecia areata (AA) is an immune-mediated disorder characterized by non-scarring hair loss and substantial psychosocial burden. Although recent advances have clarified key pathogenic mechanisms and expanded therapeutic options, important uncertainties persist regarding disease heterogeneity, treatment durability, and long-term safety. Central to AA pathogenesis is the collapse of hair follicle immune privilege, driven primarily by cytotoxic CD8[+] NKG2D[+] T-cells and sustained by interferon-γ-dependent Janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling. However, emerging evidence indicates immunological variability across patient subsets, including inconsistent contributions from T helper cell pathways and regulatory immune dysfunction. The clinical approval of JAK inhibitors-baricitinib, ritlecitinib, and deuruxolitinib-represents a major therapeutic milestone, validating targeted immune modulation as an effective strategy for moderate-to-severe AA. Nevertheless, relapse following treatment discontinuation, interindividual variability in response, and unresolved long-term safety considerations highlight the limitations of current approaches. In parallel, regenerative therapies, microbiome-based interventions, gene-targeted strategies, and device-assisted technologies are under investigation, yet most face substantial translational, regulatory, and scalability challenges. This review critically synthesizes current evidence on AA pathogenesis and therapy, with particular emphasis on unresolved controversies, translational barriers, and clinical implications. By integrating mechanistic insights with emerging clinical data, the article highlights priorities for future research, including biomarker development, precision medicine approaches, and strategies aimed at achieving durable disease control rather than transient immune suppression.}, }
@article {pmid42208188, year = {2026}, author = {Gilevska, T and Rotaru, AE and Anestis, K and Fonseca, A and Kümmel, S and Krauss, M and Inostroza, PA and Bonaglia, S}, title = {Wastewater-impacted Skagerrak Sea microbiomes anaerobically demethylate micropollutants.}, journal = {Water research}, volume = {302}, number = {}, pages = {126138}, doi = {10.1016/j.watres.2026.126138}, pmid = {42208188}, issn = {1879-2448}, abstract = {Methylated micropollutants such as naproxen and caffeine persist in wastewater effluents and accumulate in coastal sediments, including Hakefjorden, Skagerrak Sea, yet their anaerobic fate and role in methane emissions remain unresolved. In particular, it is unclear whether pollutant-derived methyl groups are routed mainly to CO2 or can be transformed into CH4 in sulfate-rich coastal sediments. Our primary objective was to resolve this routing by tracing the fate and microbiome responses to [13]C-labeled naproxen and caffeine in sediment microcosms. We show that naproxen underwent rapid O-demethylation to desmethylnaproxen, with 90% ± 15.5% removed within 25 days, producing primarily [13]CO2 and some [13]CH4. Naproxen enriched methylotrophic and hydrogenotrophic Methanomicrobia, alongside Lokiarchaeia, Bathyarchaeia, and bacterial taxa like Eubacterium (Alkalibaculum A sporogenes) and Syntrophomonadaceae. Metagenomics revealed O-demethylation genes in enriched bacterial MAGs affiliated with uncultured Thermoanaerobaculia, indicating a bacterial demethylation potential. In contrast, caffeine was largely recalcitrant to degradation (∼85% ± 5% remaining), yet its [13]C-labeled N-methyl groups fueled trace [13]CH4 production. These results show that methylated micropollutants can activate both bacterial and archaeal demethylation pathways in coastal sediment microbiomes.}, }
@article {pmid42208332, year = {2026}, author = {Yao, B and Song, C and Li, S and Ran, Z and Wang, C and Wu, M and Yuan, Q}, title = {Th17/Treg imbalance: a key driver of neutrophilic inflammation in severe asthma.}, journal = {International immunopharmacology}, volume = {184}, number = {}, pages = {116920}, doi = {10.1016/j.intimp.2026.116920}, pmid = {42208332}, issn = {1878-1705}, abstract = {Severe asthma, characterized by neutrophilic airway inflammation, poses a significant clinical obstacle, primarily due to its frequent association with glucocorticoid resistance. This review provides a systematic analysis of how the imbalance between T helper 17 (Th17) cells and regulatory T (Treg) cells contributes to this glucocorticoid-resistant phenotype. We emphasize three interconnected mechanisms that transcend traditional cytokine networks: immunometabolic reprogramming, which promotes glycolytic adaptation in Th17 cells while simultaneously impairing oxidative metabolism in Tregs; microbiome dysregulation, acting via the "gut-lung axis", which disrupts local and systemic immune tolerance; and Treg plasticity, wherein inflammatory signals transform suppressive Tregs into pro-inflammatory Th17-like cells, thereby exacerbating immune imbalance. Consequently, these processes establish a self-perpetuating inflammatory environment that sustains neutrophilic infiltration and impairs glucocorticoid sensitivity. On this basis, we evaluate emerging therapeutic strategies targeting the Th17/Treg axis, including Interleukin-17/Interleukin-23 (IL-17/IL-23) blockade, Janus kinase inhibitors, and Treg-enhancing approaches. We conclude that biomarker-guided patient stratification, rather than a "one-size-fits-all" strategy, will be essential to translate these mechanistic insights into effective precision immunotherapy for severe neutrophilic asthma.}, }
@article {pmid42208345, year = {2026}, author = {Lauriola, M and Dejongh, S and Steigert, S and Zadora, W and Valkenburg, S and Augustijns, P and Glorieux, G and Oswald, S and Farré, R and Meijers, B}, title = {Kidney dysfunction regulates gut transporters.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {200}, number = {}, pages = {119581}, doi = {10.1016/j.biopha.2026.119581}, pmid = {42208345}, issn = {1950-6007}, abstract = {BACKGROUND: The gut-kidney axis is crucial in chronic kidney disease (CKD). As kidney function declines, uremic toxins accumulate in plasma, and gut dysbiosis, oxidative stress, and inflammation arise, potentially affecting the expression of proteins involved in absorption, distribution, metabolism, and excretion (ADME). We aimed to determine the colonic expression of ADME proteins in CKD and explore modulatory mechanisms.<br><br>METHODS: RNA and protein expression of key gut transporters, enzymes and receptors were determined in colon biopsies from 17 patients with CKD and 12 healthy volunteers using RNA sequencing and targeted mass spectrometry. In parallel, we induced CKD in rats by 5/6th nephrectomy, and we administered an antibiotic cocktail to assess differences when depleting the gut microbiome. Caco-2 cells exposed to human serum or fecal water derived from CKD patients were used to elucidate modulatory mechanisms.<br><br>RESULTS: CKD downregulated the colon efflux transporter proteins P-gp (apical), MRP3 (basolateral) and BCRP (apical) (BCRP only in patients not undergoing hemodialysis). P-gp downregulation was mediated by aromatic gut microbiome-derived uremic toxins in patients, consistently with in vitro observation that P-gp was downregulated in Caco-2 cells exposed to CKD serum. In CKD rats' colon, Mdr1a was downregulated, and Bcrp was upregulated only when antibiotics were administered, indicating the gut microbiome influences P-gp and BCRP in CKD.<br><br>CONCLUSIONS: We confirmed kidney-gut crosstalk, highlighting how uremic environment and gut dysbiosis consequent to CKD impact gut transport physiology. P-gp and BCRP can be downregulated via gut microbiome metabolites, thus shedding light on the importance of therapies targeting microbial activity.}, }
@article {pmid42208480, year = {2026}, author = {Pecourt, A and Bertrand, A and Catterou, M and Rochex, A and Arnauld, S and Lacoux, J and Sarazin, V and Leclère, V and Dubois, F and Duclercq, J}, title = {Reduced nitrogen fertilization combined with microbial bio-inputs restores soil bacterial functional profiles and sustains wheat performance.}, journal = {The Science of the total environment}, volume = {1040}, number = {}, pages = {181886}, doi = {10.1016/j.scitotenv.2026.181886}, pmid = {42208480}, issn = {1879-1026}, abstract = {Nitrogen (N) fertilization is a major driver of wheat productivity but also entails significant environmental costs, underscoring the need for strategies that reduce N inputs without compromising yield. Microbial bio-inputs are increasingly proposed as complementary tools to improve N use efficiency, yet their effects on soil microbial communities and functions under reduced N fertilization remain poorly documented in wheat agrosystems. In this study, we investigated the effects of two microbial bio-inputs, Sphingomonas sediminicola Dae20 and the cell-free supernatant of Bacillus velezensis GA1, applied alone or in combination under reduced N fertilization, on wheat performance, soil microbial functioning and bacterial community structure. A field experiment was conducted with five management treatments, including conventional or reduced N fertilization and reduced N combined with each bio-input or their combination. Grain yield and quality were measured, alongside soil microbial metabolic activity, functional richness, and bacterial community structure at tillering, stem elongation and ripening. Reducing N fertilization resulted in a yield decrease of approximately 20%, while grain quality remained unaffected. Both bio-inputs partially compensated for yield losses, and their combined application restored yields obtained under conventional fertilization, without increasing grain N and protein concentrations. Bio-input effects were mainly functional, as bacterial diversity remained stable across treatments. In contrast, microbial metabolic activity and functional richness declined sharply at the end of the crop cycle in untreated soils but were maintained in bio-input-treated soils. These late-season effects coincided with wheat senescence, suggesting that bio-inputs stabilize microbial functioning when rhizosphere resources become limiting. Together, our results indicate that microbial bio-inputs do not reshape soil bacterial diversity but act as functional buffers of the soil microbiome, contributing to improved crop performance under reduced N fertilization and highlighting the importance of integrating functional and temporal indicators when evaluating bio-input strategies for sustainable agroecosystems.}, }
@article {pmid42208489, year = {2026}, author = {Mösenlechner, M and Ignatius, A and Haffner-Luntzer, M and Halbgebauer, R and Huber-Lang, MS}, title = {Beyond survival: What drives senescence in trauma, shock and sepsis?.}, journal = {Injury}, volume = {57}, number = {7}, pages = {113395}, doi = {10.1016/j.injury.2026.113395}, pmid = {42208489}, issn = {1879-0267}, abstract = {Cellular senescence is a conserved stress response characterized by stable growth arrest, resistance to apoptosis, and a pro-inflammatory secretome that shapes tissue repair, tumor suppression, and aging. In this review, senescence is framed in the context of trauma, hemorrhagic shock, and sepsis. Severe injuries to brain, lung, abdomen, and bone, as well as ischemia-reperfusion and hemorrhagic shock, rapidly induce p21- and p16-governed senescence-like programs that modulate neurodegeneration, fibrosis, fracture healing, and organ dysfunction. In sepsis, senescence extends beyond immunosenescence to endothelial, epithelial, and stromal compartments, intersecting with ferroptosis, mitochondrial failure, and microbiome dysbiosis, and contributing to post-sepsis syndrome. Integrating mechanistic data with high-dimensional profiling and early interventional studies, this review proposes a context- and time-dependent model in which acute "pseudosenescence" may be organ-protective, whereas persistent senescent reservoirs fuel inflammaging and chronic pathology. Future translational studies are required to define the clinical rationale for phase-specific senotherapeutic interventions in trauma, shock, and sepsis, particularly with respect to long-term outcomes beyond survival.}, }
@article {pmid42208527, year = {2026}, author = {Zhou, Y and Ding, J and Ning, L and Xu, X and Dou, L and Shen, J and Xuan, B and Wang, Z and Jiang, Y and Zhao, Y and Zhang, Y and Huang, X and Hu, M and Shao, Y and Li, L and Chen, C and Li, M and Fang, JY and Shen, N and Liu, NN and Chen, H and Sheng, C and Hong, J}, title = {Cross-kingdom metabolic interactions govern Candida albicans overgrowth and colitis progression.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.04.020}, pmid = {42208527}, issn = {1934-6069}, abstract = {Inflammatory bowel disease is shaped by complex microbial communities, yet the contribution of fungal-bacterial interactions to disease progression remains poorly defined. Here, we identify Cladosporium tenuissimum (C. tenuissimum) as a gut fungus with potent colitis-alleviating activity. Mechanistically, C. tenuissimum restrains Candida albicans (C. albicans) overgrowth through nutrient competition, particularly via the utilization and subsequent limitation of the amino acid ornithine. C. albicans can evade this suppression and potentiate intestinal inflammation through nutrient escape by preferentially exploiting specific amino acids, such as threonine. We further reveal a bacterial-fungal metabolic axis in which threonine-producing Bacteroides fragilis facilitates C. albicans escape from gut microbiome-mediated fungal control, thereby exacerbating colitis. Notably, dietary threonine restriction markedly attenuates C. albicans-driven colitis in mice. Together, our findings uncover a cross-kingdom metabolic network that determines C. albicans homeostasis and, in turn, governs intestinal inflammatory outcomes, offering new conceptual and therapeutic avenues for IBD.}, }
@article {pmid42208622, year = {2026}, author = {Geng, BJ and Wei, GX and Niu, XL and Tang, MR and Zhang, YJ}, title = {Distinct Cutaneous Microbial Community Signatures Across Keloids, Surgical Scars, and Healthy Skin.}, journal = {Journal of the American Academy of Dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jaad.2026.05.069}, pmid = {42208622}, issn = {1097-6787}, }
@article {pmid42208757, year = {2026}, author = {Fawzy, MN and Abdelaziz, AM and Shokr, MM and Fathy, MK}, title = {Targeting the Microbiome-NLRP3-Ferroptosis Axis in Multiple Sclerosis: Neuropharmacological Implications for Microglial Dysfunction and Demyelination.}, journal = {Neuropharmacology}, volume = {}, number = {}, pages = {111042}, doi = {10.1016/j.neuropharm.2026.111042}, pmid = {42208757}, issn = {1873-7064}, abstract = {Multiple sclerosis (MS) is a chronic autoimmune disorder of the central nervous system (CNS) characterized by neuroinflammation, demyelination, and neurodegeneration. Recent evidence has established a mechanistic connection between gut microbial dysbiosis, the activation of the NOD-like receptor protein 3 (NLRP3) inflammasome, and ferroptosis, an iron-dependent regulated cell death marked by lipid peroxidation. This review synthesizes current understanding of how alterations in the gut microbiome disrupt the gut-brain axis and compromise the blood-brain barrier (BBB), thereby promoting the activation of the microglial NLRP3 inflammasome in the central nervous system. The resulting neuroinflammatory milieu, marked by oxidative stress and iron dysregulation, renders oligodendrocytes and neurons susceptible to ferroptosis via essential enzymes like ACSL4 and ALOX15. We examine the reciprocal relationship between NLRP3-induced inflammation and ferroptotic cell death, emphasizing microglia as crucial mediators of this detrimental cycle. We explore innovative neuropharmacological strategies targeting the gut microbiota, NLRP3 inhibition, and ferroptosis pathways (e.g., ACSL4/ALOX15 inhibitors) to achieve neuroprotection and reduce disease progression. This extensive perspective enhances understanding of MS pathophysiology and identifies actionable therapeutic targets within the microbiome-inflammasome-ferroptosis axis for the development of mechanism-based therapies.}, }
@article {pmid42208782, year = {2026}, author = {Leibovitzh, H and Neustaeter, A and Lee, SH and Xue, M and Espin-Garcia, O and Olivera, PA and Huynh, HQ and Griffiths, AM and Turner, D and Madsen, KL and Silverberg, MS and Steinhart, AH and Mack, DR and Jacobson, K and Moayyedi, P and Aumais, G and Bernstein, CN and Marshall, JK and Panaccione, R and Xu, W and ,  and Turpin, W and Croitoru, K}, title = {IL23R genetic variants associate with Crohn's disease risk and microbiome changes in healthy first-degree relatives.}, journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cgh.2026.05.011}, pmid = {42208782}, issn = {1542-7714}, abstract = {BACKGROUND AND AIMS: Single nucleotide polymorphisms (SNPs) in the Interleukin-23 receptor (IL23-R) gene are associated with Crohn's disease (CD), suggesting a role in pathogenesis and several biologic agents targeting this pathway are now established therapies. IL-23 has been suggested to be involved in regulation of intestinal barrier function and may impact gut microbial composition. We investigated whether IL23-R genetic variants predict CD risk and influence gut barrier function and microbiome composition in healthy first-degree relatives (FDRs).<br><br>METHODS: 3,055 healthy FDRs with genotypic data from the Genetic Environmental Microbial (CCC-GEM) cohort were included. A weighted IL23R genetic risk score (IL23R-GRS) was generated from seven CD-associated IL23R SNPs and dichotomized as High (top quintile) vs. Low IL23R-GRS. A subset of this cohort was assessed for intestinal permeability (n=1,698) and microbiome profiling (n=2,523). Cox proportional-hazards models evaluated CD onset risk.<br><br>RESULTS: High IL23R-GRS was associated with increased CD risk (hazard ratio 1.67, 95% confidence interval 1.01-2.75, p=0.044). This association remained significant after adjusting for fecal calprotectin, indicating genetic risk independent of subclinical inflammation. High IL23R-GRS was not associated with intestinal permeability (p=0.84) but was associated with differences in 15 genera, including decreased Faecalibacterium and increased Akkermansia (q<0.1).<br><br>CONCLUSION: High IL23R-GRS was associated with increased CD risk in healthy FDRs and was associated with microbial differences, but not with intestinal permeability. These findings suggest potential clinical applications for IL23R-GRS in identifying high-risk individuals who may benefit from closer monitoring or future IL-23 pathway-targeted preventive interventions.}, }
@article {pmid42208810, year = {2026}, author = {Vasil, E and Papanicolas, LE and Miller, SJ and Shoubridge, AP and Taylor, SL and Rogers, GB}, title = {Exposure to antibiotics with anaerobe coverage in later life is associated with higher enteric pathobiont carriage.}, journal = {The Journal of infection}, volume = {}, number = {}, pages = {106774}, doi = {10.1016/j.jinf.2026.106774}, pmid = {42208810}, issn = {1532-2742}, abstract = {OBJECTIVES: Infections involving enteric bacteria commonly cause hospitalisation and death in long-term residential aged care (LTC) populations. The risk of such infections has been linked with antibiotic-associated depletion of gut anaerobic commensals and the resulting increase in asymptomatic carriage of gut pathobionts. We sought to determine how antibiotic characteristics, particularly activity against anaerobes, influence pathobiont prevalence in LTC residents.<br><br>METHODS: Stool samples from 164 LTC residents (median age: 87.9 years, interquartile range: 81.3-93.0 years) underwent metagenomic analysis. Associations between prior antibiotic exposures (categorised according to anaerobe coverage and type) and gut microbiome characteristics were explored using multivariable models.<br><br>RESULTS: Of the 164 participants, 138 (84.1%) carried at least one enteric pathobiont. Compared to those with no prior antibiotic exposure, treatment with anaerobe covering (EAC) antibiotics was associated with higher rates of pathobiont carriage (&#x3b2;=1.36, P=0.010) and higher overall pathobiont relative abundance (&#x3b2;=3.53, P=0.013). In contrast, exposure to antibiotics with limited anaerobe coverage (LAC) showed no such associations. Investigation of commonly prescribed EAC and LAC antibiotics (amoxicillin-clavulanate and cefalexin, respectively) were consistent with these findings, with higher detection (&#x3b2;=1.60, P=0.007) and relative abundance (&#x3b2;=3.32, P=0.039) of pathobiont species in amoxicillin-clavulanate recipients. Pathobionts with greater representation included both species with inherent resistance (i.e. Enterococcus faecium) and sensitivity (i.e. Klebsiella pneumoniae) to amoxicillin-clavulanate.<br><br>CONCLUSIONS: Antibiotics that deplete commensal anaerobes are associated with pathobiont prevalence in the gut, even where pathobiont species are sensitive to the administered antibiotic. Off-target disruption of commensal anaerobes should be considered when selecting antibiotic treatments, particularly for LTC individuals.}, }
@article {pmid42208893, year = {2026}, author = {Singh, J and Grant, TD and Gulick, AM}, title = {Structure of a Stand-Alone Homodimeric Nonribosomal Peptide Synthetase Condensation Domain Reveals Occlusion of the Canonical Carrier-Protein Interface.}, journal = {The Journal of biological chemistry}, volume = {}, number = {}, pages = {113208}, doi = {10.1016/j.jbc.2026.113208}, pmid = {42208893}, issn = {1083-351X}, abstract = {Fatty acid amides (FAAs) produced by gut-resident bacteria act as potent modulators of host G-protein coupled receptor signaling, yet the enzymatic mechanisms underlying their biosynthesis remain poorly understood. In many bacteria from the gut microbiome, including Coprococcus eutactus, FAA production is mediated by a nonribosomal peptide synthetase (NRPS)-like pathway that includes OaaC, a free-standing condensation domain that catalyzes amide bond formation between acyl carrier protein (ACP) tethered fatty acids and small-molecule amine acceptors. Here, we combine structural, biophysical, biochemical, and evolutionary analyses to interrogate the molecular basis of OaaC function. Solution scattering and X-ray crystallography reveal that OaaC adopts an atypical homodimeric architecture that occludes the canonical ACP-binding surface and donor access pathways. Mass photometry demonstrates that this homodimer is stable in the absence of substrates and is insensitive to free fatty acids, free amines, and apo-ACP. In contrast, holo or acyl-loaded OaaACP selectively destabilizes the homodimer forming the OaaC-OaaACP complex population. LC-MS reconstitution assays confirm that OaaC catalyzes fatty acid amide formation in vitro and can utilize acyl donors spanning multiple chain lengths and saturation states. Phylogenetic and sequence analyses place FAA-associated condensation domains in a distinct clade most closely related to starter condensation domains and reveal a conserved noncanonical active site motif that differentiates them from PCP-dependent NRPS condensation domains. Together, these findings support a model in which OaaC activity is regulated through substrate-dependent modulation of oligomeric state, providing a model framework for understanding FAA biosynthesis in gut microbes and expanding the known functional diversity of NRPS condensation domains.}, }
@article {pmid42208955, year = {2026}, author = {Yu, W and Qu, H and Wang, S and Shi, M and Lu, Y and Xia, S and Stanton, C and Zhang, C and Wang, Y and Zhu, T and Zhu, D and Zhou, X and Ross, RP and Zhou, Z and Huang, Y}, title = {From microbiomes to predictive ecosystems: challenges and opportunities in artificial intelligence-based approaches.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {101428}, doi = {10.1016/j.lanmic.2026.101428}, pmid = {42208955}, issn = {2666-5247}, abstract = {Microbiome systems encompass diverse ecological niches and host associations, with their scale and complexity challenging traditional analytical frameworks. Advances in artificial intelligence are transforming microbiome research by enabling improved integrative analyses of microbial genomes, community structure, and functional potential. In this Review, we outline how these developments create opportunities for microbiome research to move beyond descriptive analyses towards predictive modelling and hypothesis generation, including emerging insights into microbial function, host-microbe interactions, and ecosystem-level organisation. As the field grapples with challenges in model interpretability, generalisability, and causal inference, emerging strategies, such as multiomics and multicohort integration, provide promising avenues to deepen biological understanding. Addressing ethical considerations, including data privacy, algorithmic bias, and equitable access, will be crucial for translating artificial intelligence-driven microbiome discoveries into robust and inclusive clinical applications.}, }
@article {pmid42209192, year = {2026}, author = {Leggio, M and Schramm, S and Dietz, L and Ocón, B and Wirtz, S and Puertolas Balint, F and Yilmaz, B and Petzold, J and Liu, LJ and Dedden, M and Ekici, A and ,  and Meng, X and Bingham, D and Ullrich, KA and Heltmann-Meyer, S and Günther, C and Hildner, K and Atreya, R and Atreya, I and Müller, TM and Gerlach, RG and Schroeder, BO and Macpherson, A and Butcher, EC and Neurath, MF and Zundler, S and , }, title = {The endogenous peptide GPR15L shapes the intestinal microbiota to counteract colitis.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-337619}, pmid = {42209192}, issn = {1468-3288}, abstract = {BACKGROUND: The peptide GPR15L is produced by colonic epithelial cells and has been implicated in T cell recruitment to the large intestine. However, its role in chronic colitis has been unclear so far.<br><br>OBJECTIVE: To explore the role of GPR15L in the pathogenesis of experimental colitis and IBD.<br><br>DESIGN: We studied how genetic deletion or overexpression of Gpr15l as well as rectal application of recombinant GPR15L alters the course of acute dextran sodium sulfate colitis and T cell transfer colitis. The impact of GPR15L on microbiota was explored with co-housing, littermate and faecal microbiota transfer studies, by 16S rRNA sequencing as well as anti-microbial assays and shotgun metagenomics. The expression of GPR15L was evaluated across three independent cohorts of patients with IBD and correlated to microbial diversity and flare-free survival.<br><br>RESULTS: GPR15L clearly mitigated experimental colitis, but this was independent of T cell recruitment and GPR15. Instead, we observed that the effects of GPR15L were mediated by altered microbiomes in the large intestine and, consistently, showed that GPR15L acts as an antimicrobial peptide under anaerobic conditions and shapes microbial communities towards a homeostatic phenotype. Rectal supplementation of GPR15L counteracted experimental colitis. In patients with IBD, GPR15L expression was decreased in active inflammation, correlated with microbial diversity and was associated with flare-free survival.<br><br>CONCLUSIONS: GPR15L is a host-defence peptide that plays a beneficial role in the pathogenesis of intestinal inflammation. It seems promising to further evaluate its potential as a future therapeutic approach in IBD.}, }
@article {pmid42209465, year = {2026}, author = {Ghiotto, G and Zampieri, G and Orellana, E and Chatzis, A and Kougias, PG and Camargo, A and Roux, S and Campanaro, S and Kyrpides, NC and Treu, L}, title = {Single nucleotide variants drive evolutionary phage-host arms race in anaerobic carbon dioxide-converting microbiome.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73084-2}, pmid = {42209465}, issn = {2041-1723}, abstract = {Microbial bioconversions are shaped by environmental perturbations and the adaptation of resident microbiomes. Prokaryotes coexist with bacteriophages, yet their coevolutionary trajectories remain underexplored. Here, we investigate the effects of a cultivation vessel leak on an anaerobic consortium performing carbon dioxide reduction. Using time-series shotgun metagenomic sequencing, we reconstruct microbial and viral genomes to track community shifts. We further apply single-nucleotide variant profiling and CRISPR array analysis to monitor viral microdiversity and host defense mechanisms. After bioaugmentation restores bioconversion efficiency, the consortium undergoes pronounced restructuring, with new dominant taxa emerging from the rare biosphere. We identify patterns consistent with phage predation selectively removing certain species, while others exhibit resilience to infection. This shift aligns with a widespread viral outbreak and a transient increased frequency of single nucleotide variants in bacterial CRISPR-Cas defense genes. Expansion of CRISPR spacers further supports that CRISPR-mediated processes influence microbial resilience. Concurrently, phages infecting resilient hosts exhibited adaptive evolution, marked by high genetic heterogeneity. Selective pressure varies across their genomes, targeting infectivity genes and protospacer-adjacent motifs. These findings highlight a dynamic evolutionary arms race driven by the selection of beneficial genetic variants, providing a mechanistic framework for multi-omics investigations, and informing biotechnological applications, including phage-based microbiome manipulation.}, }
@article {pmid42209510, year = {2026}, author = {Dommann, J and Sprecher, VP and Beisel, C and Ballmer, D and Hürlimann, E and Coulibaly, JT and Keiser, J and Schneeberger, PHH}, title = {Combined high-quality metagenomics reveals off-target effects of albendazole, ivermectin-albendazole and moxidectin-albendazole on the human gut bacteria.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01018-3}, pmid = {42209510}, issn = {2055-5008}, support = {101019223/ERC_/European Research Council/International ; 101019223/ERC_/European Research Council/International ; }, abstract = {Human whipworm infections caused by Trichuris trichiura and Trichuris incognita remain a major public health problem, affecting over 400 million people globally and responding poorly to standard benzimidazole chemotherapy. Ivermectin-albendazole and moxidectin-albendazole have emerged as promising combination therapies, but recent in vitro evidence suggests that ivermectin and moxidectin may also affect gut bacteria. We therefore characterized their off-target effects on the gut microbiome in a randomized controlled trial including 204 Trichuris spp.-infected individuals in Côte d'Ivoire treated with albendazole (400 mg), ivermectin-albendazole (200 µg/kg/400 mg), or moxidectin-albendazole (8 mg/400 mg). By combining Illumina short reads and Nanopore long reads, we recovered over 800 high-quality metagenome-assembled genomes. Albendazole and moxidectin-albendazole induced taxonomic shifts with only mild functional consequences. In contrast, individuals receiving higher absolute ivermectin doses based on their bodyweight (≥ 15 mg) showed pronounced changes in taxonomic composition and microbial function, whereas the resistome remained largely stable. These findings confirm that ivermectin can exert antibacterial off-target effects in the human gut beyond those previously observed in vitro. Given its central role in parasite control, its broader microbiome effects warrant careful evaluation in future treatment strategies.}, }
@article {pmid42209531, year = {2026}, author = {Song, T and Hou, Z and Zhang, C and Luo, T and Wen, P and Mei, L and Yuan, D and Shen, X and Dong, H and Zhao, K and Chu, Y and Wang, X and Chen, F and Sun, W and Lin, J and Jiang, W}, title = {The gut commensal Bacteroides thetaiotaomicron harbors prevalent class A and D β-lactamases with cross-taxa dissemination potential.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01024-5}, pmid = {42209531}, issn = {2055-5008}, support = {No. HZ(2025)108//Zunyi Municipal Bureau of Industry and Science and Technology/ ; No. MTXYJCY(2025)008//Special Project of the Liquor Industry Research Center of Moutai Institute/ ; }, abstract = {The abundant gut commensal Bacteroides thetaiotaomicron is repeatedly challenged by β-lactam exposure in the human intestine, yet its β-lactamase repertoire and dissemination potential remain incompletely characterized. Here, we screened 626 publicly available B. thetaiotaomicron genomes and identified 1059 putative β-lactamase homologs, all belonging to class A or class D families. Four highly prevalent representatives-BTA-1 and CfxA-3 (class A) and OXA-347 and OXA-1327 (class D)-were prioritized for experimental validation. Heterologous expression in Escherichia coli revealed heterogeneous resistance phenotypes, with ones conferring only modest MIC increases (e.g., OXA-347, ~2-fold for amoxicillin) and others producing strong resistance to penicillins (e.g., BTA-1caused a 256-fold increase in amoxicillin MIC). Purified BTA-1 and OXA-347 were active under gut-relevant conditions, with pH optima at 7 and 8 and temperature optima at 40 °C and 30 °C, respectively. Notably, OXA-347 hydrolyzed representatives of penicillins, cephalosporins, carbapenems, and monobactams, and mass spectrometry confirmed β-lactam ring opening. Beyond B. thetaiotaomicron, these β-lactamase alleles were detected across multiple gut commensal genera as well as taxa annotated as opportunistic pathogens. Genomic context analyses showed similar gene-cluster patterns in B. thetaiotaomicron, across gut commensal genera, and in opportunistic-pathogen-associated taxa. Collectively, our findings clarify the diversity, activity, and distribution of B. thetaiotaomicron-associated β-lactamases across the gut microbiome and clinically relevant taxa.}, }
@article {pmid42209548, year = {2026}, author = {Bakari, C and Holzschuh, A and Seth, MD and Madebe, RA and Pereus, D and Mandara, CI and Schneeberger, P and Juliano, JJ and Bailey, JA and Ishengoma, DS and Nsanzabana, C}, title = {Development of an Oxford nanopore sequencing technology-based whole genome sequencing method for Plasmodium falciparum to support malaria molecular surveillance.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-46451-8}, pmid = {42209548}, issn = {2045-2322}, support = {INV. 002202 &amp; INV. 067322//Gates Foundation, United States/ ; INV. 002202 &amp; INV. 067322//Gates Foundation, United States/ ; INV. 002202 &amp; INV. 067322//Gates Foundation, United States/ ; INV. 002202 &amp; INV. 067322//Gates Foundation, United States/ ; INV. 002202 &amp; INV. 067322//Gates Foundation, United States/ ; INV. 002202 &amp; INV. 067322//Gates Foundation, United States/ ; }, abstract = {Whole genome sequencing (WGS) is critical for malaria molecular surveillance (MMS). While short-read platforms have been widely used for Plasmodium falciparum genomics; they have limitations in resolving repetitive regions and structural variation in this highly complex genome. Long-read technologies, such as those developed by Oxford nanopore technologies (ONT), offer complementary capabilities and may be particularly suitable for low-resource settings. We optimized an ONT-based WGS protocol for P. falciparum from DBS and whole blood samples. Laboratory strains (3D7, HB3, and Dd2) were mixed with whole blood to create mock infections and dried blood spots (DBS). DNA was extracted using Qiagen or Tween-Chelex 100, and parasite DNA was enriched using McrBC/MspJI digestion, NEBNext microbiome DNA enrichment Kit (NMDEK), and selective whole genome amplification (sWGA). Parasite and human DNA levels were quantified by multiplex qPCR. Sequencing was performed on ONT (R10.4.1 flow cell). The protocol was validated with? clinical samples from a therapeutic efficacy study. Tween-Chelex 100 had a higher DNA yield compared to Qiagen kit (2-4 Ct value difference), though Qiagen extractions gave longer reads (median 2791 vs. 2252 bp). NMDEK effectively depleted human DNA by increasing the Ct value of β-tubulin human gene by ~ 10 cycles, while sWGA increased parasite DNA. Combined enrichment yielded > 75% parasite DNA at 100 p/µl and > 90% genome coverage. WGS of mock and clinical samples achieved median read lengths > 2 kb, > 30× depth, and 99.8% accuracy. Whole blood outperformed DBS in depth and coverage. ONT WGS showed high concordance with Sanger sequencing and detected additional mutations and structural variants, including pfmdr1 and pfgch1 copy number variations. The optimized ONT-WGS protocol enabled accurate, high-coverage sequencing from whole blood and DBS. It provides a practical option for generating long-read data with relatively rapid turnaround and modest infrastructure requirements, supporting its application for MMS in malaria-endemic settings.}, }
@article {pmid42209780, year = {2026}, author = {}, title = {Gut microbiome screens could identify risk of Parkinson's disease years before symptoms appear.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, pmid = {42209780}, issn = {1546-170X}, }
@article {pmid42209868, year = {2026}, author = {Ajeh, IJ and Ikukpla'si, OSI}, title = {The non-bacterial oncobiome: the role of the mycobiome and virome in tumor plasticity.}, journal = {Journal of the Egyptian National Cancer Institute}, volume = {38}, number = {1}, pages = {}, pmid = {42209868}, issn = {2589-0409}, mesh = {Humans ; Tumor Microenvironment ; *Neoplasms/pathology/microbiology/virology ; *Mycobiome ; *Virome ; Epithelial-Mesenchymal Transition ; Cell Plasticity ; }, abstract = {Tumor plasticity, the capacity of malignant cells to undergo reversible phenotypic switching, is a fundamental driver of lineage diversion and therapeutic resistance. While the bacterial microbiome is a recognized modulator of the tumor microenvironment (TME), the non-bacterial oncobiome, comprising the mycobiome (fungi) and virome (viruses), represents a critical but under-explored frontier in cellular adaptability. This review synthesizes current evidence regarding the mechanistic contributions of fungal and viral constituents to tumor plasticity and characterizes the molecular cross-talk that facilitates host cell reprogramming. We conducted a structured narrative synthesis of literature indexed in PubMed, Scopus, and Web of Science (2020-2026), focusing on high-throughput studies such as ITS sequencing, metagenomics NGS (mNGS), and single-cell network analyses. We specifically evaluated evidence concerning the activation of host pattern recognition receptors and the subsequent transcriptional rewiring of lineage-defining markers. Emerging data indicate that fungal dysbiosis, particularly involving Candida and Malassezia species, triggers the Dectin-1/STAT3 signaling axis, a known inducer of epithelial-mesenchymal transition (EMT). Concurrently, the virome, ranging from integrated oncoviruses to reactivated endogenous retroviruses (ERVs), is shown to hijack the Wnt/ β-catenin pathway, enforcing a progenitor-like stemness state. This inter-kingdom synergy promotes an immune-excluded niche, effectively shielding plastic sub-populations from cytotoxic stress and targeted therapies. The non-bacterial oncobiome provides genomic momentum and inflammatory cues necessary to lower the threshold for phenotypic switching. This review highlights that stabilizing the TME ecosystem through ecologically targeted therapy may be a prerequisite for overcoming drug resistance and improving clinical outcomes in refractory cancers.}, }
@article {pmid42210016, year = {2026}, author = {Hatlestad, S and Wagoner, BE and Kim, H and Xia, JS and Shim, C and Wang, Y and Lua, A and Yang, J and Flaws, JA and Mei, W}, title = {Iodoacetic acid causes developmental toxicity in zebrafish.}, journal = {Toxicological sciences : an official journal of the Society of Toxicology}, volume = {}, number = {}, pages = {}, doi = {10.1093/toxsci/kfag062}, pmid = {42210016}, issn = {1096-0929}, abstract = {Water disinfection can generate disinfection byproducts (DBPs) such as iodoacetic acid (IAA) by reacting with organic matter in water supplies. In vitro studies have shown that IAA is a cytotoxic and genotoxic DBP. In vivo studies using animal models further indicate that IAA has toxic effects on reproductive function and the endocrine system. Yet, its developmental toxicity remains unknown. In this study, we show that exposure to IAA at concentrations ranging from 1 to 100 µM induces dose-dependent embryonic mortality, with the greatest sensitivity observed during the first 24 hours of development. Sublethal concentrations cause delayed or failed hatching and disrupt the development of multiple vital organs. Notably, IAA exposure impairs swim bladder inflation, reduces otolith size, and decreases heart rate. Moreover, IAA reduces intestinal mucus production by suppressing genes essential for mucin production. Given the crucial role of intestinal mucus in defending against pathogens and maintaining host and gut microbiota homeostasis, the deleterious effect of IAA on mucus production highlights its potential pathogenic role in driving disorders linked to epithelial barrier dysfunction and microbiome dysfunction. Together, these findings demonstrate that IAA induces pronounced developmental toxicity affecting multiple organ systems in zebrafish. This study provides the first in vivo evidence that IAA disrupts embryonic development and intestinal function.}, }
@article {pmid42210027, year = {2026}, author = {Juenke, A and Longoria, CR and Patel, A and Subrahmanian, A and Blaser, MJ and Rivera-Nunez, Z and Barrett, ES}, title = {Zearalenone exposure and the mammalian gut microbiome: A systematic review of the literature.}, journal = {Toxicological sciences : an official journal of the Society of Toxicology}, volume = {}, number = {}, pages = {}, doi = {10.1093/toxsci/kfag064}, pmid = {42210027}, issn = {1096-0929}, abstract = {Mycotoxins are fungal derived metabolites found in the global food supply, particularly in cereal grains and processed foods. Zearalenone (ZEN), one of the more common mycotoxins, widely contaminates human food supplies at concentrations above established maximum contamination levels. However, the effects of ZEN exposure on human health have only begun to be explored, with most studies on this topic focusing on its endocrine-disrupting effects in the reproductive system. ZEN is readily absorbed following oral administration, making the gastrointestinal (GI) tract and its microbiota primary targets for toxicity. The gut microbiome plays a critical role in nutrient processing and immune function and can be heavily influenced by dietary and chemical exposures. Given widespread human dietary exposure to ZEN, we conducted a comprehensive literature review of ZEN and its metabolites in relation to the mammalian gut microbiome. We identified 19 studies, all conducted in animal models, and each reported alterations in gut microbiome composition in ZEN-treated groups compared to control animals. Several papers reported modified metabolism in ZEN-treated groups, particularly related to short chain fatty acids. In light of this small but compelling literature and the expected increase in mycotoxin contamination due to the industrialization of the food supply and warmer weather conditions, we identified several priority areas for future study. These include better understanding the mechanisms by which ZEN and its metabolites affect the microbiome and ultimate translation to human health.}, }
@article {pmid42210032, year = {2026}, author = {Pu, R and Wang, Z and Chen, Y and Zhou, D and Yang, G and Jiang, Z}, title = {Association between oral microbial diversity and periodontitis in a nationally representative U.S. population: A cross-sectional study.}, journal = {Journal of periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1002/jper.70101}, pmid = {42210032}, issn = {1943-3670}, support = {82370991//National Natural Science Foundation of China/ ; 82571129//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: To investigate the association between salivary oral microbiome diversity and periodontitis in a nationally representative U.S.<br><br>METHODS: A total of 5323 participants with both periodontal examination and oral microbiome data from NHANES 2009-2012 were included. Periodontitis was defined using 2012 CDC/AAP criteria. Four alpha diversity indices (operational taxonomic unit [OTU] richness, Faith's phylogenetic diversity [FPD], the Shannon-Weiner index [SWI], and the inverse Simpson index [ISI]) were calculated. Beta diversity metrics (Bray-Curtis, weighted and unweighted UniFrac) were assessed using PERMANOVA for group comparisons and hierarchical clustering to identify subgroups. Ordered logistic regression was employed to examine the associations between periodontitis severity and microbial alpha diversity, beta diversity clusters, and bacterial genus abundances.<br><br>RESULTS: Higher alpha diversity was positively associated with greater periodontitis severity (OTU richness: OR&#xa0;=&#xa0;1.01, 95%CI: 1.01-1.02; FPD: OR&#xa0;=&#xa0;1.21, 95%CI: 1.19-1.24; SWI: OR&#xa0;=&#xa0;2.03, 95%CI: 1.81-2.30; ISI: OR&#xa0;=&#xa0;16.61, 95%CI: 1.75-157.59). Beta diversity analyses revealed significant community compositional differences across periodontitis severity levels (PERMANOVA, all p&#xa0;=&#xa0;0.001). Hierarchical clustering identified distinct microbial subgroups with varying odds of belonging to more severe periodontitis levels. Eighty-two bacterial genera were significantly associated with periodontitis, including taxa showing strong positive associations consistent with the red and orange complexes (e.g., Porphyromonas, Tannerella, Treponema) and taxa exhibiting negative associations involving health-associated genera (e.g., Rothia, Veillonella).<br><br>CONCLUSIONS: Salivary microbiome diversity, particularly higher alpha diversity and specific beta diversity clusters, was associated with periodontitis severity, supporting its potential relevance as a non-invasive indicator of periodontal health status.<br><br>PLAIN LANGUAGE SUMMARY: This national study examined the relationship between the types and quantities of microbes present in saliva and the severity of periodontitis in more than 5,300 U.S. adults. We found that the more diverse the microbial community in a person's saliva-meaning a greater variety and number of different types-the more severe their periodontitis tended to be. We also found that the composition of these microbes differed depending on the severity of the periodontitis. Specifically, certain clusters of microbes, including well-known disease-causing bacteria such as Porphyromonas and Treponema (often called the red and orange complexes), were strongly associated with more severe periodontitis. Conversely, other common, generally healthy bacteria were less abundant. These findings suggest that analyzing the diversity and composition of microbes in saliva could be a valuable, noninvasive way to check for and potentially monitor the severity of periodontitis.}, }
@article {pmid42210074, year = {2026}, author = {Ku, D and Yang, SB and Kwack, KH and Jang, EY and Jun, SK and Moon, JH and Lee, JH}, title = {Complete genome sequence of Streptococcus sp. strain KHUD_013 isolated from the human buccal mucosa.}, journal = {BMC genomic data}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12863-026-01438-2}, pmid = {42210074}, issn = {2730-6844}, support = {RS-2024-00404660//Korea Basic Science Institute/ ; RS-2021-NR061563//National Research Foundation of Korea/ ; RS-2025-16066503//National Research Foundation of Korea/ ; RS-2025-20512973//National Research Foundation of Korea/ ; }, abstract = {OBJECTIVE: The genus Streptococcus constitutes a major component of the human oral microbiome and exhibits substantial genomic diversity at the species level. However, complete and high-quality reference genomes remain limited for many closely related oral streptococci, constraining accurate comparative and taxonomic analyses. The objective of this Data Note was to generate and report a complete genome sequence of Streptococcus sp. strain KHUD_013, isolated from the human buccal mucosa, and to provide a genomic context for comparison with closely related species.<br><br>DATA DESCRIPTION: Long-read sequencing using the PacBio Revio platform generated 89,500 high-fidelity (HiFi) reads with a mean read length of 6,960&#xa0;bp. Genome assembly produced a single circular chromosome of 1,988,919&#xa0;bp with a G&#x2009;+&#x2009;C content of 42.5%. Genome annotation identified 1,827 protein-coding genes, four ribosomal RNA operons (5&#xa0;S, 16&#xa0;S, and 23&#xa0;S), and 62 transfer RNA genes, with an estimated completeness of 98.8%. Average Nucleotide Identity (ANI) analysis indicated that strain KHUD_013 is most closely related to the Streptococcus ilei type strain (GCA_000479335.1), with a value of 94.39% and an alignment coverage of 86.55%, consistent with genomic divergence at the species boundary. Comparative genomic analysis with four publicly available S. ilei genomes identified 179 gene clusters unique to KHUD_013, predominantly associated with replication, recombination, and repair, as well as cell wall and membrane biogenesis and transcription. This genome sequence provides a valuable resource for strain-level comparative and taxonomic studies of oral streptococci.}, }
@article {pmid42210082, year = {2026}, author = {Childs, H and Frankenfeld, CL and Dailey, A and Couch, R and Slavin, M}, title = {Cardiovascular disease risk factors in women with O-desmethylangolensin producing and non-producing gut microbial metabotypes: an observational study.}, journal = {BMC cardiovascular disorders}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12872-026-06007-0}, pmid = {42210082}, issn = {1471-2261}, abstract = {BACKGROUND: Daidzein, an isoflavone in soy, is metabolized to O-desmethylangolensin (ODMA) by select gut bacteria. Not all individuals have gut microbiomes capable of producing ODMA, resulting in ODMA producer and non-producer metabotypes. A limited body of research suggests that ODMA producers have lower systolic blood pressure, percent body fat and total cholesterol, compared to non-producers. More work is needed to confirm this relationship in other populations.<br><br>METHODS: Data from the Study of Women's Health Across the Nation (SWAN), a study of women in their middle years, was used. A subset of women who reported consumption of isoflavones in diet or supplements was included for this analysis. Urinary ODMA and daidzein of 148 participants were measured via HPLC-MS-MS to classify metabotypes: ODMA (nmol/L)/daidzein (nmol/L)&#x2009;=&#x2009;0, non-producers (n&#x2009;=&#x2009;23); ODMA (nmol/L)/daidzein (nmol/L)&#x2009;>&#x2009;0 but less than 0.5, low-producers (n&#x2009;=&#x2009;90); and ODMA (nmol/L)/daidzein (nmol/L)&#x2009;>&#x2009;0.5, high-producers (n&#x2009;=&#x2009;35). Multivariable linear regression models were used to compare cardiovascular disease (CVD) risk markers among groups. Models were adjusted for age, race, self-reported health, blood pressure medication, smoking, menopausal status and anthropometry.<br><br>RESULTS: ODMA non-producers had higher systolic blood pressure (adj. mean difference&#x2009;=&#x2009;7.6 mmHg, 95% CI: 1.1, 14.1, p&#x2009;=&#x2009;0.02) compared to high producers. Another trend but not statistically significant difference observed included higher fasting serum glucose (adj. mean difference&#x2009;=&#x2009;6.1&#xa0;mg/dl, CI: -0.9, 13.2, p&#x2009;=&#x2009;0.09) in ODMA non-producers when compared to ODMA producers.<br><br>CONCLUSIONS: In this diverse sample of U.S. women, this study observed higher blood pressure in ODMA non-producers than ODMA producers. This aligns with prior work associating ODMA producers with a more favorable CVD risk profile compared to non-producers, and provides additional evidence that this gut microbial metabotype may be related to cardiovascular health.}, }
@article {pmid42210085, year = {2026}, author = {Mermans, F and Poelman, B and Saghi, M and Teughels, W and Boon, N}, title = {Interindividual differences in acidogenic potential of the salivary microbiome after mouthwash exposure.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05207-0}, pmid = {42210085}, issn = {1471-2180}, support = {G0B2719N//Fonds Wetenschappelijk Onderzoek/ ; G0B2719N//Fonds Wetenschappelijk Onderzoek/ ; G0B2719N//Fonds Wetenschappelijk Onderzoek/ ; }, abstract = {BACKGROUND: Fluoride mouthwashes are commonly used for prevention of dental caries. The most common forms of fluoride are stannous fluoride (SnF2), amine fluoride (AmF) and sodium fluoride (NaF), each with differing activities against oral bacteria. Since the microbiome has been linked to interindividual differences in responses to treatment, the phenotype of the microbiome may provide information on potential treatment responses. Flow cytometry successfully tracks microbial phenotypic heterogeneity and may prove useful for capturing interindividual treatment responses.<br><br>METHODS: We compared the effect of fluoride-containing mouthwashes, Elmex Anti Caries (AmF/NaF), Listerine Anti Caries (NaF) and Meridol (AmF/SnF2) on the salivary microbiome in vitro. We determined the effect on the microbial community structure using 16&#xa0;S rRNA gene amplicon sequencing, assessed the acidogenic potential by measuring organic acids after incubation, and constructed flow cytometric fingerprints of the microbial community to evaluate if it could be used to capture the response to treatment and to assess if it has potential for precision medicine.<br><br>RESULTS: We observed mouthwash- and donor-dependent changes in the salivary microbiome composition and acidogenic potential. Meridol affected more bacterial taxa and showed the strongest reduction in organic acids, followed by Elmex. The response to treatment could be captured in the flow cytometric fingerprint of the initial intact salivary microbiota and a random forest classifier predicting the optimal mouthwash for each donor was successfully trained (MCC&#x2009;=&#x2009;0.95).<br><br>CONCLUSIONS: Treatment with fluoride mouthwashes induces a shift in the salivary microbiome in vitro and alter its potential to produce organic acids, contributing to the prevention of dental caries. Moreover, flow cytometry shows promise for tailoring treatments to patients.}, }
@article {pmid42210241, year = {2026}, author = {Sun, W and Jin, X and Li, Y and Zhou, M and Liu, X and Wang, H and Geng, H and Li, L and Hu, J and Zhou, X and Liu, Y and Zhu, X}, title = {Gut microbiota dysbiosis and host metabolite-immune crosstalk drives the pathogenesis of neonatal lupus erythematosus: a multi-omics analysis.}, journal = {BMC medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12916-026-04963-0}, pmid = {42210241}, issn = {1741-7015}, support = {825B2049//National Natural Science Foundation of China/ ; 82571973; 82271741//National Natural Science Foundation of China/ ; ZD2021013//Jiangsu Provincial Health and Family Planning Commission Medical Research Project/ ; GSWS2022055//SuZhou Health Leaders Program/ ; }, abstract = {BACKGROUND: Neonatal lupus erythematosus (NLE) is a rare autoimmune condition triggered by the transplacental transfer of maternal antibodies. Despite its recognized clinical manifestations, the underlying pathogenesis remains incompletely understood. This study seeks to explore the disruption of the gut microbiota-host metabolism-immune axis in anti-Ro/La-positive neonates, and to assess its potential role in the development of NLE.<br><br>METHODS: This multicenter, cross-sectional study included 90 neonates, divided into three groups: 30 with neonatal lupus erythematosus (NLE), 30 with positive antibodies but without clinical manifestations (No-NLE), and 30 healthy controls. We performed 16&#xa0;S rRNA sequencing to analyze gut microbiota composition, untargeted plasma metabolomic profiling, and proteomic analysis to identify alterations associated with the pathogenesis of NLE.<br><br>RESULTS: We identified significant alterations in the gut microbiota, plasma metabolome, and proteome profiles of anti-Ro/La-positive neonates. NLE infants exhibited marked enrichment of Enterobacteriaceae and depletion of Bifidobacterium and Clostridium butyricum. Metabolomic analysis revealed hyperactivation of &#x3b2;-alanine and purine metabolism, along with impaired &#x3b1;-linolenic acid metabolism and endocannabinoid signaling. Proteomic profiling indicated aberrant protein expression that modulated IFN signaling, particularly within the C-type lectin receptor pathway. Dysregulation of the spleen tyrosine kinase (SYK) and high-affinity immunoglobulin epsilon receptor subunit gamma (FCER1G) decoupling was observed, correlating with elevated IFN-&#x3b1; and NF-&#x3ba;B p65 levels. Integrated correlation analysis revealed significant associations among differential microbial taxa, plasma metabolites, and proteins. Notably, E. coli-associated metabolites and proteins displayed inverse relationships with those associated with C. butyricum.<br><br>CONCLUSIONS: These findings represent comprehensive evidence of dysregulation along the "gut microbiota-host metabolism-immune" axis in neonatal lupus erythematosus (NLE), providing novel insights into the disease's underlying heterogeneity.}, }
@article {pmid42210268, year = {2026}, author = {Liang, Y and Zhang, M and Guan, M and Liu, S and Chen, J and Yang, R and Zhang, Y}, title = {Microplastics reshape rhizosphere microbial communities and nutrient cycling in tomato agroecosystems.}, journal = {BMC biology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12915-026-02633-4}, pmid = {42210268}, issn = {1741-7007}, abstract = {BACKGROUND: Microplastics (MPs) are emerging soil contaminants increasingly recognized for their capacity to alter agroecosystem functioning; however, their impacts on horticultural crops and rhizosphere microbial processes remain insufficiently understood.<br><br>RESULTS: We examined the impacts of MPs, polyethylene (PE), polypropylene (PP), and polyvinyl chloride (PVC), on rhizosphere soil physicochemical properties, bacterial community structure, and functional genes associated with carbon (C), nitrogen (N), and phosphorus (P) cycling in tomato (Solanum lycopersicum L.), a major horticultural crop cultivated worldwide. Both PVC-MPs and PE-MPs significantly reduced soil ammonium nitrogen and available phosphorus contents, modifying rhizosphere elemental composition. In contrast, PP-MPs had no significant effects on these nutrients but significantly increased soil pH by 0.76% compared with the control (p&#x2009;<&#x2009;0.05). PE-MPs exposure markedly reduced bacterial &#x3b1;-diversity and selectively enriching bacterial taxa involved in recalcitrant organic matter degradation and nitrogen cycling. High-throughput quantitative PCR (qPCR) revealed that MPs suppressed the degradation of labile carbon substrates, including starch, cellulose, and hemicellulose (as evidenced by downregulation of apu, manB, and xylA), as well as methane metabolism, while promoting carbon fixation and phosphorus cycling.<br><br>CONCLUSIONS: Our results indicate selective reprogramming of bacterial carbon metabolism, enhancing recalcitrant carbon turnover while constraining labile carbon mineralization, thereby disrupting C-P metabolic coupling and promoting soil organic carbon accumulation. Additionally, MPs stimulated nitrogen fixation and nitrification while inhibiting denitrification, particularly under PE- and PVC-MPs treatments. These findings provide bacterial ecological insights into MPs-induced reshape rhizosphere processes and nutrient cycling dynamics in horticultural systems.}, }
@article {pmid42210279, year = {2026}, author = {Turunen, J and Kyrö, K and Virta, J and Suokas, M and Hekkala, J and Karikka, S and Kaisanlahti, A and Reunanen, J and Paalanne, N and Tejesvi, MV and Ruuska-Loewald, T}, title = {Maternal factors associate with microbiota-derived extracellular vesicle profiles in pregnancy: a clinical cohort study.}, journal = {BMC medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12916-026-04960-3}, pmid = {42210279}, issn = {1741-7015}, abstract = {BACKGROUND: While most clinical microbiome research has investigated gut microbiota, less is known about extracellular vesicles (EVs) produced by microbiota. Microbiota-derived EVs form a distinct taxonomic entity from the gut microbiota. Recently, microbiota-derived EVs from maternal microbiota have been shown to reach the fetus, which could be an important mechanism of microbiota-host interaction during the fetal period. We hypothesized that maternal factors could change the composition of microbiota-derived EVs during pregnancy.<br><br>METHODS: We compared the influence of antibiotics and maternal weight on microbiota-derived EVs secreted by maternal microbiota during pregnancy. We collected fecal samples from 60 pregnant women and 18 amniotic fluid samples from those undergoing C-section. Microbiota-derived EVs were isolated from the samples using size-exclusion chromatography and density-gradient ultracentrifugation and characterized using transmission electron microscopy (TEM) and nanoparticle tracking analysis (NTA). RNA was isolated from the microbiota-derived EVs and converted to complementary DNA (cDNA), and 16&#xa0;S rRNA gene sequencing was performed.<br><br>RESULTS: Altogether, 18 (30%) women had received antibiotics during pregnancy and 37 (62%) during delivery. Twenty (33%) women were lean, 27 (45%) had overweight and 13 had obesity (22%) during the first trimester. Taxonomic diversity of microbiota-secreted microbiota-derived EVs was lower in women exposed to antibiotics during pregnancy. When women exposed to antibiotics during delivery were excluded, the differences were not statistically significant. The microbiota-derived EVs differed in the amniotic fluid and maternal feces in women with overweight and obesity, gestational diabetes (GDM), and those who gained&#x2009;>&#x2009;15&#xa0;kg during pregnancy, as many bacterial origins of microbiota-derived EVs were depleted in these women. A beta diversity analysis of microbiota-derived EVs from fecal samples showed significant differences between the overweight and obesity groups. Diversity analysis showed no differences in various health factors during pregnancy, including asthma, allergies, or smoking.<br><br>CONCLUSIONS: Maternal factors influence the composition of microbiota-derived extracellular vesicles in feces and amniotic fluid of pregnant women, which may change host-microbiota interaction in the fetal period.}, }
@article {pmid42210382, year = {2026}, author = {Huang, Q and He, L and Wu, J and Yue, S}, title = {Regulatory mechanisms of high-polyphenol dietary intervention on exercise-induced immunosuppression during high-intensity training periods in adolescent athletes: a systems biology analysis based on immune-metabolic pathways.}, journal = {Nutrition &amp; metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12986-026-01132-1}, pmid = {42210382}, issn = {1743-7075}, abstract = {BACKGROUND: Exercise-induced immunosuppression poses significant health risks for adolescent athletes during intensive training. This study investigated whether high-polyphenol dietary intervention could maintain immune homeostasis through immunometabolic reprogramming.<br><br>METHODS: Eighty adolescent athletes (aged 15-17) were randomized to receive either high-polyphenol supplementation (1200&#xa0;mg/day: quercetin, EGCG, resveratrol, curcumin) or placebo during a 12-week high-intensity training period. Multi-omics profiling (transcriptomics, proteomics, metabolomics, microbiomics) was performed at baseline, weeks 4, 8, and 12.<br><br>RESULTS: The high-polyphenol group maintained CD4&#x2009;+&#x2009;/CD8&#x2009;+&#x2009;ratios above clinical thresholds (1.65&#x2009;&#xb1;&#x2009;0.29 vs. 1.38&#x2009;&#xb1;&#x2009;0.42, p&#x2009;<&#x2009;0.001) at peak training. Regulatory T cells increased 17.2% while Th17 cells remained stable, yielding favorable Treg/Th17 ratios (3.09&#x2009;&#xb1;&#x2009;0.82 vs. 1.58&#x2009;&#xb1;&#x2009;0.54, p&#x2009;<&#x2009;0.001). Multi-omics integration revealed 1,847 differentially expressed genes converging on NF-&#x3ba;B suppression, AMPK-mTOR activation, and Nrf2-mediated antioxidant responses. Gut microbiome analysis showed doubled butyrate-producing bacteria and twofold increased short-chain fatty acid production. Salivary IgA declined only 6.5% versus 29.3% in placebo (p&#x2009;<&#x2009;0.001).<br><br>CONCLUSIONS: High-polyphenol dietary intervention effectively prevents exercise-induced immunosuppression through coordinated immunometabolic reprogramming, establishing a practical strategy for maintaining immune resilience in adolescent athletes.}, }
@article {pmid42210393, year = {2026}, author = {Lopez Leyva, L and Gonzalez, E and Maurice, CF and Koski, KG}, title = {Distinct associations among human milk microbiota and minerals in relation to early infant growth: a longitudinal study.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-08315-7}, pmid = {42210393}, issn = {1479-5876}, abstract = {BACKGROUND: Currently there is a knowledge gap in relation to the interaction of milk components and their association with infant growth. Our aim was to analyze the associations between minerals and the milk microbiome and how they associate with infant growth in the Mam-Mayan indigenous population of Guatemala.<br><br>METHODS: In this longitudinal study, a total of 114 milk samples were collected from 57 mothers during early (5-46&#x2009;days) and established (4-6&#x2009;months) lactation. Concentrations of 12 milk minerals were analyzed. Infant growth was assessed according to the infant growth parameters [weight-for-age (WAZ) and head circumference-for-age (HCAZ) into &#x2265;-1 SD and <-1 SD and length-for-age (LAZ) into &#x2265;-2 SD and <-2 SD]. The milk microbiome diversity was obtained by 16S rRNA gene amplicon sequencing of the V5-V6 region.<br><br>RESULTS: The milk microbiome diversity differed between infants with normal and impaired growth in weight and length during early lactation, but not in established lactation. In established lactation, milk microbiome diversity only differed between infants with normal and impaired head circumference. Some bacteria could be associated with normal growth, such as Luteococcus peritonei (for all growth parameters measured, that is WAZ, LAZ and HCAZ), Bifidobacterium longum, Lancefieldella parvula, Phascolarctobacterium, Rothia mucilaginosa, Streptococcus agalactiae and Streptococcus pneumoniae (only for the LAZ and HCAZ), Janthinobacterium lividum (only WAZ) and Lactobacillus johnsonii (only HCAZ parameter). Similarly, C. acnes could be associated with impaired growth as it was identified in infants with impaired WAZ and LAZ. Manganese and magnesium emerged as key minerals due to their high number of correlations with the milk microbiome in both normal and impaired growth. Namely, Cutibacterium acnes was differentially abundant (DA) in the mildly underweight and stunted infants and was negatively associated with manganese. On the other hand, in non-stunted and normal head circumference infants Phascolarctobacterium and Streptococcus agalactiae were positively associated with magnesium, and Streptococcus pneumoniae was positively associated with manganese.<br><br>CONCLUSION: Milk microbial composition was associated with milk mineral concentrations, and both were associated with infant growth status.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov ID NCT02755012 (http://Clinicaltrials.gov/study/NCT02755012). Retrospectively Registered 2016-04-26.}, }
@article {pmid42210496, year = {2026}, author = {Gourabi, MJR and Kargar, M and Kamali, A and Sharahi, JY}, title = {Fungal-Bacterial Interactions in Polymicrobial Infections: Hidden Threats.}, journal = {MicrobiologyOpen}, volume = {15}, number = {3}, pages = {e70320}, doi = {10.1002/mbo3.70320}, pmid = {42210496}, issn = {2045-8827}, mesh = {Humans ; *Coinfection/microbiology/drug therapy ; Biofilms/growth &amp; development ; *Microbial Interactions ; Anti-Bacterial Agents/therapeutic use/pharmacology ; Candida albicans/physiology ; *Bacteria/drug effects ; *Fungi/physiology/drug effects ; *Mycoses/microbiology ; *Bacterial Infections/microbiology ; }, abstract = {Polymicrobial infections involving fungi and bacteria represent a major and increasingly recognized clinical challenge, in which interkingdom interactions significantly amplify disease severity, antimicrobial resistance, and treatment failure. Rather than passive co-existence, fungal-bacterial communities form highly coordinated systems driven by physical adhesion, quorum sensing, metabolic interdependence, and biofilm-mediated structural reinforcement. These cooperative interactions, exemplified by pairs such as Candida albicans-Staphylococcus aureus and Pseudomonas aeruginosa-Aspergillus fumigatus, promote the development of treatment-recalcitrant biofilms with enhanced immune evasion and multidrug tolerance. The global rise of multidrug-resistant (MDR) and extensively drug-resistant (XDR) pathogens has further intensified this burden, with polymicrobial biofilms now representing a post-antibiotic clinical scenario in which therapeutic failure is driven not by individual resistant organisms but by emergent, cooperative resistance architectures. Conventional diagnostic approaches remain insufficient, as culture-based methods frequently fail to capture the complexity of mixed microbial communities. Emerging technologies such as MALDI-TOF mass spectrometry, metagenomic sequencing, and fluorescence in situ hybridization offer improved resolution but are not yet fully integrated into routine clinical practice. Therapeutically, increasing evidence indicates that monotherapy is inherently inadequate in polymicrobial infections due to the emergent nature of microbial cooperation. Effective management therefore requires combination strategies that simultaneously target multiple pathogens and their shared biofilm infrastructure. These include antibiotic-antifungal combinations, phage therapy, enzymatic and nanoparticle-mediated biofilm disruption, metabolic interference, and host-directed immunomodulation. Importantly, recent advances also highlight the role of biophysical properties such as biofilm viscoelasticity and matrix stiffness as critical and previously underappreciated therapeutic targets. This review uniquely integrates biochemical, biophysical, and therapeutic dimensions of polymicrobial infections into a unified systems-level framework in which microbial cooperation is the central driver of pathogenesis, resistance, and treatment failure. Fungal-bacterial interactions are thereby positioned along a dynamic continuum from commensalism to pathogenesis, shaped by host susceptibility and environmental perturbations. Future progress will depend on interdisciplinary strategies combining multi-omics technologies, precision diagnostics, and microbiome-informed therapeutic design to effectively disrupt these complex microbial networks.}, }
@article {pmid42197533, year = {2026}, author = {Badhan, A and Li, C and Guan, LL and McAllister, TA}, title = {Rumen-Derived Consortia Shaped by Substrate-Specific Enrichment Show Specialized Lignocellulose Utilization, Diversified Hydrogen Metabolism, and Cryopreservation Stability.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, pmid = {42197533}, issn = {2076-2607}, support = {BCRC FDE.02.24//Beef Cattle Research Council/ ; 2025F3700R//Results Driven Agriculture Research , RDAR/ ; ALLRP 588541 - 23)0//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Efficient utilization of lignocellulosic biomass by the rumen microbiome is critical for improving feed efficiency in ruminants, yet the development of stable, functionally specialized microbial consortia remains limited. This study aimed to assemble substrate-adapted rumen microbial consortia using an ecology-guided enrichment approach. Rumen fluid collected from cannulated Angus × Hereford heifers was sequentially enriched over 10 generations on four substrates with distinct cell wall characteristics: alfalfa, barley straw, carboxymethyl cellulose (CMC), and xylan. Fermentation parameters, including gas production and volatile fatty acids (VFAs), and bacterial community dynamics were analyzed, and selected consortia (alfalfa and xylan) were evaluated for stability following one month of cryopreservation. Across enrichments, total VFA concentrations declined (e.g., xylan: 109.8 mM (G0) to 56.37 mM (G10)), accompanied by reduced gas production and decreased alpha diversity, indicating substrate-driven selection. Distinct functional profiles emerged, including increased propionate in alfalfa consortia, higher acetate in barley straw, lactate-propionate cross-feeding with CMC, and caproate production (6.3 mM at G10) in xylan enrichments associated with Caproiciproducens and Megasphaera. Cryopreserved consortia retained core community structure and fermentation characteristics upon revival. These results demonstrate that substrate-driven enrichment can generate stable, functionally specialized rumen consortia and provide a framework for developing ecologically compatible microbial communities with potential applications in improving rumen fermentation efficiency.}, }
@article {pmid42197547, year = {2026}, author = {Zhao, M and Zhao, H and Li, P and Peng, S and Lin, F and Wu, Q and Tashi, P and Li, Z}, title = {Multi-Omics Analysis Reveals Age-Related Enhancements in Gut Morphology, Microbiome, and Metabolism of Tibetan Pigs.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, pmid = {42197547}, issn = {2076-2607}, support = {CDKJ-2025QY001.//This research was funded by Changdu City Science and Technology Bureau 2025 District-City Science and Technology Collaborative Innovation Special Project, grant number/ ; }, abstract = {Age-related changes in the gut significantly impact host health, yet the multi-omics dynamics during the maturation of Tibetan pigs remain unclear. This study aimed to investigate the morphological, microbial, metabolic, and transcriptomic transformations in the intestines of aging Tibetan pigs. We analyzed the ileum and colon of 1-year-old and 3-year-old Tibetan pigs using histological evaluation, 16S rRNA sequencing, metabolomics, and transcriptomics. Aging to 3 years significantly improved ileal architecture, notably increasing the villus height to crypt depth ratio. Older pigs exhibited higher colonic microbial diversity, a decreased Firmicutes to Bacteroidota ratio, and enrichment of homeostasis-associated taxa, including Lactobacillus, Prevotellaceae, and Ruminococcaceae. Metabolomics revealed higher abundance of certain metabolites, including docosahexaenoic and arachidonic acids, enriching lipid metabolism and bile secretion pathways. Transcriptomics identified 2363 differentially expressed genes in the ileum, primarily involved in immune regulation and nutrient digestion. Integrated analysis showed strong positive correlations between enriched microbes (Lactobacillus porci) and up-regulated host genes (UGT2B31, CCL28) governing intestinal homeostasis. The transition from 1 to 3 years of age in Tibetan pigs fosters a synergistic host-microbiome environment, enhancing intestinal barrier function, immune capacity, and metabolic efficiency.}, }
@article {pmid42197563, year = {2026}, author = {Ma, Y}, title = {Microbe-Induced Abiotic Stress Alleviation in Plants: From Hidden Partners to Central Drivers of Resilience.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {10}, pages = {}, pmid = {42197563}, issn = {2223-7747}, abstract = {Our understanding of plant stress biology has shifted with debate toward a more integrative, microbiome-centered perspective [...].}, }
@article {pmid42197619, year = {2026}, author = {Zhang, J and Zhang, X and Chen, Q}, title = {Biomass Seedling Trays Drive Rhizosphere Microbiome Restructuring and PGPR Enrichment in Tomato.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {10}, pages = {}, pmid = {42197619}, issn = {2223-7747}, support = {2023YFD1901205//National Key Research and Development Program of China, project titled "Technology Model and Application of Soil Ecological Restoration and Green Capacity Enhancement in the Dry-Hot Valley of Southwest China"./ ; }, abstract = {Tomato (Solanum lycopersicum) is a globally important high-value cash crop. However, long-term continuous cropping causes frequent soil-borne diseases and soil microecological imbalance, while overreliance on chemical pesticides leads to pesticide residues and water eutrophication. Plant growth-promoting rhizobacteria (PGPR) are key resources for addressing tomato cultivation challenges, with their functions partly depending on the rhizosphere microenvironment inherently shaped by seedling tray materials. Using rhizosphere soil and substrates of tomato at different growth stages under biomass (BM) and plastic (PM) seedling tray treatments, this study combined culture-independent and culture-dependent techniques to analyze microbial community characteristics and screen high-efficiency PGPR. Results showed that pH and available nitrogen drove microbial community assembly. BM significantly enriched beneficial taxa (e.g., Trichoderma and Bacillus) and enhanced culturable microbial abundance and genetic diversity, while PM enriched potential pathogens (e.g., Fusarium and Pyrenochaeta). The multifunctional strain S25095 from BM, with phosphate-solubilizing, potassium-solubilizing, and indole-3-acetic acid (IAA)-producing abilities, significantly promoted tomato shoot and root growth, outperforming single-functional strains and synthetic consortia. This study reveals the effects of growth stages and seedling tray treatments on tomato rhizosphere microorganisms, providing valuable PGPR resources for tomato cultivation.}, }
@article {pmid42197679, year = {2026}, author = {Gao, C and Wan, G and Cheng, R and Li, Q and Fan, Q and Cui, J and Wu, L}, title = {Gradient Potassium Application Differentially Regulates Rhizosphere Bacterial and Fungal Communities in Cherry Tomato (Solanum lycopersicum var. cerasiforme).}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {10}, pages = {}, pmid = {42197679}, issn = {2223-7747}, support = {NYHXGG, 2023AA302//Xinjiang Production and Construction Corps/ ; }, abstract = {Potassium (K) is an essential macronutrient for plants and plays a critical role in soil microbial processes. However, its systemic effects on rhizosphere microorganisms in high-value crops like cherry tomato remain poorly understood. This study established a potassium gradient (K0 represents the no-potassium application, K1 represents low-potassium application, K2 represents a moderate-potassium application, K3 represents the conventional-potassium application, and K4 represents excessive-potassium application) to investigate responses in growth and rhizosphere bacterial and fungal communities of cherry tomato. Moderate potassium (K2) significantly enhanced dry matter accumulation in cherry tomato. Bacterial and fungal communities displayed distinct patterns: bacterial structure shifted continuously along the gradient, with specific enrichment of functional genera (nitrogen-fixing Ensifer, biocontrol-related Lysobacter), increased unique OTUs, and gradual co-occurrence network optimization at K2. In contrast, fungal community composition and network structure showed threshold responses to potassium. Low K (K1) suppressed dominant Ascomycota and increased unclassified fungi, while high potassium (K4) enriched parasitic/pathogenic fungi (Alternaria, Curvularia), increased network modularity, and reduced stability. This microbial ecological perspective highlights that optimized potassium application regulates functional microorganisms and differentially shapes rhizosphere communities, providing a theoretical basis for precision potassium management in cherry tomato.}, }
@article {pmid42198214, year = {2026}, author = {Alkan, Y and Yalçıntaş, YM and Bechelany, M and Karav, S}, title = {Edible Plant-Derived Exosome-like Nanoparticles as Prebiotic Nanocarriers: Gut Microbiota Modulation and Functional Food Potential.}, journal = {Pharmaceutics}, volume = {18}, number = {5}, pages = {}, pmid = {42198214}, issn = {1999-4923}, abstract = {The gut microbiota takes charge in a pivotal role in metabolic equilibrium, immune response, and modulating gut lining stability and has become the main focus of nutrition and functional food research. In this regard, the definition of prebiotics has progressed past the traditional approach limited to indigestible dietary fibers, embracing more targeted, biologically active, and functional delivery systems. In recent years, plant-derived exosomes (PDEs), a subclass of exosomes defined as extracellular vesicles (EVs) in the 30-150 nm size range, have emerged as an innovative class of nanostructures supporting this transformation. Plant-derived exosome-like nanoparticles (PELNs) have been taken into account as natural nanocarriers which are suitable for the gastrointestinal system with the help of their high biocompatibility, low immunogenicity profiles and rich bioactive cargo contents. This review discusses structural features of PELNs, molecular cargo content, and biological roles comprehensively and focuses especially on gut microbiota interactions. MicroRNAs, proteins, lipids, polyphenols, and glycans which PELNs contain are discussed with regard to shaping the microbial composition, regulating microbial metabolic activity, and modulating host-microbe communication. Findings derived from in vitro, in vivo, and limited translational studies indicate that PELNs can modulate specific microbial taxa, increase short-chain fatty acid (SCFA) yield, strengthen mucosal immune homeostasis, and induce source-dependent responses in the gut microbiota. In their traditional definition, prebiotics are taken into account as food components which selectively support proliferation and metabolism of helpful microbes, especially Bifidobacteria and Lactobacilli. Within this framework, PELNs are not only passive carriers of functional components but also evaluated as active systems which can directly affect microbiota composition and metabolic functions. Thus, they are repositioned as "prebiotic nanocarriers." Also this review evaluates the potential of functional food and integration of major edible PELNs into synbiotic formulations by discussing their isolation and characterization methods and stabilities in the gastrointestinal environment. Limitations of clinical applications and lack of research from a prebiotic nanocarrier perspective of PELNs show that this field still contains important research gaps. The novelty of the study lies in its integration of PELN research with nutrition-based approaches to microbiota modulation and innovative functional food strategies under a single multidisciplinary conceptual framework.}, }
@article {pmid42198228, year = {2026}, author = {Tang, R and Zeng, F and Lyu, C and Tuerheng, J and Guo, Z and He, K and Wu, D}, title = {Advances of Cell Membrane-Coated Nanotechnology and Membrane Vesicles in Intestinal Targeted Drug Delivery Systems.}, journal = {Pharmaceutics}, volume = {18}, number = {5}, pages = {}, pmid = {42198228}, issn = {1999-4923}, support = {Grant No. BRWEP2024W034010103//Beijing Research Ward Excellence Program/ ; Grant No. 3332025015//Fundamental Research Funds for the Central Universities, Peking Union Medical College/ ; Grant No. L232016//Beijing Natural Science Foundation/ ; }, abstract = {Although nanomedicine has enabled significant advances in drug delivery, the clinical translation of conventional synthetic nanocarriers is limited by immune clearance, non-specific biodistribution, and gastrointestinal instability. This poses major challenges for therapy targeting the intestines. Cell membrane-coated nanotechnology (CMCT) and membrane vesicle-based systems have emerged as biomimetic platforms integrating synthetic nanomaterials with naturally derived biological interfaces. These biohybrid systems inherit biological functions originating from cells, including immune evasion, prolonged circulation, lesion homing, and microenvironment-responsive interactions, through the direct transfer of intact membrane components. This review summarizes recent advances in CMCT and membrane vesicle-based strategies for intestinal drug delivery. It covers fabrication methodologies, programmable manufacturing approaches, and functional regulation enabled by diverse membrane sources and hybrid engineering designs. Applications in inflammatory bowel disease, colorectal cancer, and intestinal infections are highlighted, emphasizing key therapeutic mechanisms, such as targeting inflammation, neutralizing toxins, modulating the immune system, and regulating the microbiome. We also discuss the major challenges of translation, such as preserving membrane and coating integrity, ensuring oral stability, achieving batch reproducibility, and ensuring biosafety. Overall, this review establishes a conceptual and engineering framework to guide the transition of membrane-based nanocarriers from passive biomimicry to adaptive, clinically translatable intestinal delivery systems.}, }
@article {pmid42198371, year = {2026}, author = {Rocha, M and Fierro-Arias, L and Layton, A and Bettoli, V and Dlova, N and Merika, E and Dirschka, T and Rerknimitr, P and Newaj, R}, title = {A Global Delphi Consensus on Acne and the Microbiome: Integrating International Expertise for Innovative Prevention and Therapeutic Strategies.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {19}, number = {5}, pages = {}, pmid = {42198371}, issn = {1424-8247}, abstract = {Acne is a prevalent dermatological condition occurring globally and influenced by a variety of endogenous and exogenous factors. The microbiome and its contribution to skin disease have been increasingly explored, along with the influence of the exposome and host immune responses on this complex microbial system. Nine experts from different countries in Africa, America, Asia, and Europe gathered to harmonise definitions, identify key pathogenic and protective microbial strains, and prioritise the factors that most significantly impact the skin's microbiome in the context of acne. Opportunity areas on the role of the microbiome in the prevention, treatment, recurrence, and sequelae avoidance in acne were identified. The relationships between current treatments and the diversity of the microbiome were described. Current microbiome-targeted strategies were assessed, including practical considerations of innovative future perspectives. The panel discussions emphasise the urgent need for universally adaptable guidelines encompassing alternatives to oral antibiotic therapies, in light of increasing antimicrobial resistance and the significant burden of treatment-related adverse events.}, }
@article {pmid42198430, year = {2026}, author = {Nagy, C and Miere Groza, F and Ganea, M and Vicaș, LG and Mureșan, ME and Antonescu, A and Vicas, SI and Dobjanschi, L}, title = {The Role of Phytocompounds and the Physiological Response of the Skin in Common Dermatological Conditions: A Narrative Review and Bibliometric Analysis of Trends.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {19}, number = {5}, pages = {}, pmid = {42198430}, issn = {1424-8247}, support = {not applicable//University of Oradea/ ; }, abstract = {Background: The skin, as the largest organ of the human body, plays a crucial role in protection, immunity and homeostasis. Its exposure to environmental and internal factors contributes to the development of various dermatological conditions. Conventional treatments are often associated with adverse effects and increased resistance. This review aims to explore the growing role of phytotherapeutic approaches in dermatology, along with mapping recent research trends in the field. Methods: The paper presents three parts: the first part highlights the mapping of interest in the addressed topic through a systematic selection of the specialized literature using the Web of Science database. A bibliometric analysis was conducted using the Web of Science Core Collection, with data visualized in VOSviewer to identify publication trends, keyword clusters, and collaboration networks across European countries. Subsequently, in the second part of the review, the main topical topics regarding the skin were addressed (the immune and non-immune response system, microbiome composition and physiological responses in different situations). The third part of the paper addresses phytotherapy targeted at the dermatological sphere and controlled release therapeutic systems. Results: The analysis identified a total of 267 publications, with a significant increase in recent years. Key research clusters included phytochemical-based therapies, nanocarrier systems, and inflammatory skin conditions. Keyword co-occurrence analysis revealed emerging trends in nanoformulations and targeted delivery systems. The main research groups focused on polyphenols, antioxidant activity, anti-inflammatory effects and advanced delivery systems, such as nanoparticles and liposomes. In addition, innovative formulations have improved bioavailability and targeted administration. Conclusions: Phytotherapeutic approaches represent a promising alternative to conventional dermatological treatments, offering effective, safer and more sustainable solutions. The integration of natural compounds with modern delivery systems improves therapeutic outcomes and minimizes side effects, supporting their increasing relevance in clinical and pharmaceutical research.}, }
@article {pmid42198436, year = {2026}, author = {Zou, Y and Hu, RT and Yu, Q and Rao, PL and Cui, HY and Wei, WJ and Cai, X and Li, HK and Shen, YH}, title = {Liuweidihuang Pill Attenuates Early Bleomycin-Induced Pulmonary Fibrosis in Mice and Is Associated with Gut Microbiome.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {19}, number = {5}, pages = {}, pmid = {42198436}, issn = {1424-8247}, support = {ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; }, abstract = {Background: Pulmonary fibrosis (PF) is a chronic, progressive lung disease with limited treatment options. Liuweidihuang pill (LDP), a classical formula for kidney-yin deficiency, has been reported to have anti-inflammatory and anti-oxidative activities, suggesting potential relevance to PF. Purpose: This study evaluated whether LDP attenuates bleomycin-induced PF in mice and whether gut microbiota remodeling may contribute to its protective effects. Methods: Mice received intratracheal bleomycin followed by LDP gavage. Lung pathology was assessed by hematoxylin-eosin (HE) and Masson staining. Inflammatory cytokines, hydroxyproline (HYP), and α-SMA were measured. LDP and LDP-containing serum were profiled by UPLC-MS. The gut microbiota was analyzed using 16S rDNA sequencing. To further explore whether microbiota-related changes were associated with the protective phenotype, fecal microbiota transplantation (FMT) and probiotic VSL#3 intervention were performed. In addition, LDP-containing serum was tested in a TGF-β1-induced EMT model in A549 cells. Results: LDP reduced lung index, inflammatory infiltration, interstitial fibrosis, α-SMA expression, HYP content, and pro-inflammatory cytokine levels in bleomycin-treated mice. These effects were accompanied by gut microbiota remodeling and transcriptomic changes related to inflammation, metabolism, and fibrosis. VSL#3 partially reproduced the protective phenotype, whereas FMT showed limited efficacy. LDP-containing serum had a limited inhibitory effect on EMT inhibited EMT in vitro, suggesting that systemic host responses may contribute to the in vivo effect. Conclusions: LDP attenuated early bleomycin-induced PF and was associated with reduced inflammation and gut microbiota remodeling. These findings suggest a possible role for microbiota-host interactions in LDP-associated protection; however, causal directionality, key active effectors, and protein-level pathway validation remain unresolved.}, }
@article {pmid42198457, year = {2026}, author = {Pastras, P and Aggeletopoulou, I and Psalti, V and Triantos, C}, title = {Gut Microbiota in Irritable Bowel Syndrome and Inflammatory Bowel Disease: Differences in Pathophysiology, Biomarkers, and Treatment Implications.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {19}, number = {5}, pages = {}, pmid = {42198457}, issn = {1424-8247}, abstract = {Alterations in the intestinal microbiota have been implicated in both irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD). However, their biological significance and therapeutic implications differ substantially between the two conditions. Although dysbiosis is a common feature, the mechanisms by which alterations in the microbiota contribute to disease pathophysiology and clinical expression are distinct. Some pathways are more prominent in IBS (e.g., the gut-brain axis), whereas others are more prominent in IBD (e.g., reduced microbial diversity). Equally important are pathways that appear to play a role exclusively in IBD [e.g., Adherent-invasive Escherichia coli (AIEC) and Paneth cells], as well as others that seem to be specific to IBS (e.g., mast cell activation). In IBD, microbiota changes are primarily linked to immune dysregulation, mucosal barrier impairment, and inflammation-driven pathways, whereas in IBS, they are mainly associated with functional disturbances mediated by neuroimmune signaling and microbial metabolites. Furthermore, several microbiome-associated biomarkers differ between these two diseases, and some are already assessed by international guidelines. Although the microbiota plays a key role in IBS and IBD pathophysiology, microbiome-based treatments remain limited, especially in IBD. There are clinically available treatments in IBS (e.g., rifaximin, low-FODMAP diet), but in IBD, only the probiotic VSL#3 is guideline-approved in ulcerative colitis pouchitis prophylaxis. Nevertheless, the dynamic nature of the microbiota continues to support the investigation of already studied (e.g., probiotics, fecal microbiota transplantation) and potential novel therapeutic approaches at the research level. The aim of this review is to compare the gut-microbiota-related pathophysiological pathways and biomarkers between IBS and IBD, to summarize the microbiome-related medications that have already been studied in both diseases, and to suggest new potential therapeutic options based on the gut microbiota.}, }
@article {pmid42198530, year = {2026}, author = {Wu, J and Chen, C and Geng, H and Zhao, B and Gao, J}, title = {Source, Monitoring Techniques and Prospects of Bioaerosols: A Review.}, journal = {Toxics}, volume = {14}, number = {5}, pages = {}, pmid = {42198530}, issn = {2305-6304}, support = {42075182//National Natural Science Foundation of China/ ; 202304041101011//the International Scientific and Technological Cooperation Projects of Shanxi (China) for Designated Countries/ ; }, abstract = {Bioaerosols play significant roles in ecological interactions, climate change, and public health. Their diverse origins contribute to a dynamic atmospheric microbiome with considerable spatiotemporal variability, which are generally categorized as natural and anthropogenic sources. Accurate monitoring and source apportionment are critical for assessing environmental impacts and health risks. This review systematically summarizes the characteristics of bioaerosol sources and emphasizes emission risks from intensive human activities. This study also elucidates source apportionment strategies of bioaerosols and analyzes the technological evolution from traditional culture-based methods to advanced molecular and real-time physicochemical systems. In addition, the shift of bioaerosol monitoring technologies towards high-sensitivity, culture-independent, and online monitoring is emphasized in this review. An outlook on future research priorities is provided in the end. We emphasize the pressing need to establish localized characteristic databases, develop integrated real-time monitoring systems coupling rapid screening with deep biological analysis, and optimize the application of machine learning and AI algorithms to enhance the precision of multi-source contribution modeling in complex environments.}, }
@article {pmid42198631, year = {2026}, author = {Kim, TJ and Schneider, S and Defreitas, A and Walker, LP and Shenker, BJ and Boesze-Battaglia, K}, title = {Cellugyrin (Synaptogyrin-2) Regulates Macrophage Phagocytosis of Aggregatibacter actinomycetemcomitans (Aa).}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, pmid = {42198631}, issn = {2076-0817}, support = {1K08DE032119-01/DE/NIDCR NIH HHS/United States ; 5R01DE023071-09/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; *Phagocytosis ; *Aggregatibacter actinomycetemcomitans/immunology ; *Macrophages/immunology/microbiology/metabolism ; *Host-Pathogen Interactions/immunology ; }, abstract = {Grade C molar-incisor pattern periodontitis (C-MIP) is a rapidly progressive form of periodontal disease affecting young individuals that is often linked to a highly virulent genotype of Aggregatibacter actinomycetemcomitans (Aa). Although Aa is present in the healthy oral microbiome, its transition into subgingival tissue correlates with the conversion from healthy to diseased status within the periodontal pocket. These changes may be due to immune evasion strategies attributed to Aa exotoxins. We previously demonstrated that a host cell protein, cellugyrin, plays a critical role in exotoxin internalization and subsequent cytotoxicity. Herein, we assess the contribution of cellugyrin to Aa phagocytosis and intracellular trafficking in human macrophages. Confocal imaging demonstrated that Aa co-localizes with cellugyrin. Importantly, cellugyrin-deficient macrophages exhibited a significant reduction in phagocytosed Aa. Furthermore, we analyzed the role of retrograde trafficking in Aa survival. Retro-2-mediated inhibition of this trafficking pathway resulted in increased intracellular Aa, likely due to increased survival. Collectively, our findings suggest that cellugyrin is involved in Aa phagocytosis and that retrograde trafficking may play a role in subsequent host cell clearance of Aa.}, }
@article {pmid42198714, year = {2026}, author = {Bako, RS and Kelley, CF}, title = {Unraveling the Rectal Virome: Microbial Crosstalk, Immune Modulation, and Clinical Outcomes in People with and Vulnerable to HIV.}, journal = {Viruses}, volume = {18}, number = {5}, pages = {}, pmid = {42198714}, issn = {1999-4915}, mesh = {Humans ; *HIV Infections/immunology/virology ; *Virome/immunology ; *Rectum/virology/microbiology/immunology ; *Gastrointestinal Microbiome/immunology ; Male ; Homosexuality, Male ; }, abstract = {The rectal mucosa houses a large number of viruses with important roles in shaping the local microbial communities and modulating immune responses, which could influence host susceptibility to infection and other diseases. Unique composition of the gut microbiome, including the predominance of clinically significant eukaryotic viruses like herpesviruses, cytomegalovirus, and human papillomavirus, has been described in both people with HIV (PWH) and men who have sex with men (MSM) vulnerable to HIV. Despite these insights, the rectal virome and the clinical implications of virome-bacteriome-immune interactions in the rectal mucosa remain poorly understood. In this review, we synthesize existing data on the composition of the rectal virome, its interactions with the bacteriome and the immune system, and implications on clinical outcomes in people living with or vulnerable to HIV. We also highlight the gaps and research needed to further explore and unravel these relationships.}, }
@article {pmid42198756, year = {2026}, author = {Guan, F and Zhang, J and Tian, Y and Fu, B and Liu, J and Song, Y and Yan, A and Zhang, B and Chen, L and Zhang, M and Du, P and Wang, L and Yang, X and Guo, S and Yang, C and Zhang, H and Zhang, Q}, title = {Gut Microbiota and Probiotics in Influenza: A Narrative Review of Mechanisms and Emerging Evidence.}, journal = {Viruses}, volume = {18}, number = {5}, pages = {}, pmid = {42198756}, issn = {1999-4915}, support = {2024YFD1800303//Ministry of Science and Technology of China/ ; }, mesh = {Humans ; *Probiotics/therapeutic use ; *Influenza, Human/immunology/virology/microbiology ; Animals ; *Gastrointestinal Microbiome ; Lung/immunology/virology ; Orthomyxoviridae ; }, abstract = {The gut microbiota, often referred to as the "forgotten organ", plays an indispensable role in maintaining host physiological metabolism, immune function, and nutrient absorption. Moreover, the gut microbiome serves as a critical biological barrier against viral infections and is increasingly recognized as a potential target to augment antiviral therapies. Recent studies have revealed that microbial ligands and metabolites derived from the gut microbiota are pivotal in modulating respiratory immune responses, providing compelling evidence of the complex interaction network between microorganisms and the host, particularly the signaling pathways linking the gut to distal organs such as the lungs. This review examines the communication and regulatory mechanisms between the gut microbiota and pulmonary mucosal surfaces during influenza virus infection, emphasizing how gut microbial communities and probiotics influence host immune responses, promote the production of immune-related molecules, and enhance antiviral defenses. The aim is to provide comprehensive insights into the gut-lung axis and its implications for respiratory health.}, }
@article {pmid42198807, year = {2026}, author = {Korth, N and Borrero, I and Rumley, K and Woodley, AL and Choudoir, MJ and Gage, JL}, title = {Investigating GERMs: how genotype, environment, and rhizosphere microbiome interactions underlie heat response in maize and sorghum.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71297}, pmid = {42198807}, issn = {1469-8137}, support = {R35GM151048/NH/NIH HHS/United States ; 2024-38420-41520//National Institute of Food and Agriculture/ ; 2025-67012-44807//National Institute of Food and Agriculture/ ; 7002327//National Institute of Food and Agriculture/ ; 7004439//National Institute of Food and Agriculture/ ; }, abstract = {Plant responses to heat stress emerge from interactions among host genotype, environment, and the rhizosphere microbiome, yet most studies examine these components in isolation. We applied the Genotype × Environment × Rhizosphere Microbiomes (GERMs) framework to test how host-microbe coordination contributes to heat tolerance in cereal crops Zea mays and Sorghum bicolor. We analyzed maize and sorghum grown under optimal and heat-stressed conditions across contrasting soil treatments using integrated plant-microbial metatranscriptomics. Host and microbial gene expression profiles were jointly analyzed alongside microbiome composition and plant phenotypes and compared with amplicon-based profiling. Metatranscriptomics captured microbial community structure comparable to amplicon sequencing while providing enhanced functional and taxonomic resolution. Host genotype and temperature jointly shaped microbial functional profiles. Conserved plant orthologs across maize and sorghum were linked to microbial pathways, specifically microbial d-amino acid metabolism was associated with plant heat tolerance. These findings indicate the rhizosphere microbiome actively participates in plant heat stress responses through coordinated transcriptional interactions with the host. Integrating host and microbial transcriptomes reveals mechanistic insights into plant adaptation and establishes a framework for dissecting plant-microbiome interactions under environmental stress.}, }
@article {pmid42198875, year = {2026}, author = {Wong, SH and Kwong, TNY and Zhang, R and Lam, TYT and Ho, AMY and Leung, WW and Kang, X and Lau, HCH and Chu, ESH and Wong, MTL and Lau, LHS and Lui, RNS and Tang, RSY and Lau, JYW and Ng, SSM and Yu, J and Sung, JJY}, title = {Comprehensive microbiome profiling reveals mucosal microbiome heterogeneity in patients with left- and right-sided colorectal neoplasia.}, journal = {Cancer biology &amp; medicine}, volume = {}, number = {}, pages = {}, doi = {10.20892/j.issn.2095-3941.2025.0846}, pmid = {42198875}, issn = {2095-3941}, support = {CIRG23jan-0004//Singapore National Medical Research Council Clinician Scientist Individual Research Grant/ ; OFLCG22may-0009//Large Collaborative Grant/ ; OFLCG23may-0031//Large Collaborative Grant/ ; OFLCG24may-0025//Large Collaborative Grant/ ; }, abstract = {OBJECTIVE: Left- and right-sided colorectal cancer (CRC) exhibit distinct molecular and clinicopathologic features. However, little is known about the spatial heterogeneity of microbial signatures. In this study the profiles and ecologic patterns of disease-associated intestinal microbiome were investigated in patients with an adenoma(s) or CRC at different anatomic locations.<br><br>METHODS: A total of 690 stool, colonic aspirate, and mucosal biopsy samples were prospectively collected from 32 healthy, 30 adenoma, and 31 CRC patients.<br><br>RESULTS: CRC was associated with alterations in fecal and mucosal microbiomes. Furthermore, the overall composition of the mucosal microbiome, stratified by metacommunities, differed between the patients with left- and right-sided neoplastic lesions. Patients with right-sided CRC had an elevated inter-phylum ecologic network, while patients with left-sided CRC had an enriched abundance of Fusobacterium. Interestingly, rectal neoplasia harbored a tumor microbiome that was distinctly different from the tumor microbiome at other anatomic sites.<br><br>CONCLUSIONS: The mucosal microbiome of right-sided CRC was distinctly different from the mucosal microbiome of left-sided CRC patients, suggesting distinct microbial ecology and heterogeneous host-microbial ecologic relationships that may contribute to differences in the tumor microenvironment between left- and right-sided CRC.}, }
@article {pmid42198884, year = {2026}, author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW}, title = {Rhizosphere microbes are partners in plant stress adaptation.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/erag254}, pmid = {42198884}, issn = {1460-2431}, }
@article {pmid42198941, year = {2026}, author = {Briers, Y}, title = {Disruptive innovation in antibiotic development: a vision for lysins.}, journal = {Expert review of anti-infective therapy}, volume = {}, number = {}, pages = {1-14}, doi = {10.1080/14787210.2026.2680018}, pmid = {42198941}, issn = {1744-8336}, abstract = {INTRODUCTION: Antimicrobial resistance is escalating globally, while the development of new antibiotic classes has stagnated. This trend is reminiscent of the late-stage dynamics of S-curve innovation, where incremental advances no longer meet clinical needs. To overcome this impasse, disruptive innovation is required. As protein-based antibacterials, lysins represent a fundamentally different modality from traditional small-molecule antibiotics and offer new opportunities for disruptive innovation in terms of resistance development and microbiome preservation.<br><br>AREAS COVERED: Sourced from a vast natural reservoir, lysins exhibit rapid, targeted bactericidal activity with low resistance potential and high specificity. Their narrow-spectrum nature supports a potential for microbiome preservation and the conceptual development of theranostic platforms for precision infectious disease management, combining ultra-fast pathogen detection with targeted therapeutic activity.<br><br>EXPERT OPINION: To initiate new innovation cycles, disruptive modalities such as protein-based lysins will be needed, offering a paradigm shift in antimicrobial therapy. Their modular architecture and amenability to protein engineering enable a hit-to-lead development strategy akin to small-molecule pipelines. Their synergistic interactions with standard-of-care antibiotics and booster-like activity could facilitate incremental clinical integration into existing treatment protocols. This positioning supports regulatory acceptance and paves the way for lysins to become transformational components of precision antimicrobial therapy.}, }
@article {pmid42198987, year = {2026}, author = {Keigler, JI and Leite Nobrega de Moura Bell, JM and Marco, ML}, title = {Myco-foods and the gut microbiome: impacts of mycelial extracts, biomass, and mold-fermented foods.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2677948}, doi = {10.1080/19490976.2026.2677948}, pmid = {42198987}, issn = {1949-0984}, mesh = {Humans ; *Fungi/chemistry/metabolism ; Animals ; *Mycelium/chemistry/metabolism ; *Gastrointestinal Microbiome ; *Fermented Foods/microbiology/analysis ; Bacteria/classification/isolation &amp; purification/metabolism/genetics ; Biomass ; Fermentation ; }, abstract = {Edible filamentous fungi include mushrooms and molds, which are consumed as extracts, mycelial biomass, and fermented foods. These fungal foods are often high in protein and fiber and are generally regarded as nutritious. This narrative review examines current knowledge on how mycelia from molds, including edible strains of Aspergillus, Rhizopus, Neurospora, Fusarium, Mucor, and Paecilomyces, affect the gut microbiome. Allfour human trials on these foods (two extracts, one biomass, and one fermented food) reported a measurable effect on the gut microbiome. These studies, plus the additional eight animal and eight in vitro studies performed, frequently found increases in the proportions of intestinal Akkermansia, Bifidobacterium, and lactobacilli. Bacteroides, Roseburia, and Eubacterium, which are recognized for their roles in fiber metabolism, were also frequently enriched, and numerous studies reported increases in fecal short-chain fatty acids. Notably, effects on the gut microbiome may be fungal species and food format-dependent. Although β-glucans and chitin are likely key determinants of gut microbiome responses to dietary mycelium, future studies should investigate how these and other potentially bioactive components of mycelia and fungal metabolites are metabolized by intestinal microorganisms. Such studies will result in an improved understanding of how myco-foods could support human health.}, }
@article {pmid42199000, year = {2026}, author = {Shamsuzzaman, M and Dahal, RH and Kim, J}, title = {Bifidobacterium intestinale sp. nov., and Blautia caeci sp. nov., from the Human Gut Microbiome with Candidate Probiotic Potential.}, journal = {Journal of microbiology and biotechnology}, volume = {36}, number = {}, pages = {e2603013}, doi = {10.4014/jmb.2603.03013}, pmid = {42199000}, issn = {1738-8872}, mesh = {Humans ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Base Composition ; Feces/microbiology ; DNA, Bacterial/genetics ; *Bifidobacterium/classification/isolation &amp; purification/genetics ; *Probiotics ; *Gastrointestinal Microbiome ; Sequence Analysis, DNA ; Antioxidants ; Genome, Bacterial/genetics ; Bacterial Typing Techniques ; *Eubacteriales/classification/isolation &amp; purification/genetics ; }, abstract = {Two novel Gram-stain-positive, anaerobic, and non-motile bacterial strains, designated M3-R-103[T] and C3-R-101[T], were isolated from human faecal samples and subjected to comprehensive taxonomic characterization together with evaluation of selected functional properties. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain M3-R-103[T] is affiliated with the genus Bifidobacterium, whereas strain C3-R-101[T] belongs to the genus Blautia. Strain M3-R-103[T] exhibited the highest 16S rRNA gene sequence similarity (98.9%) to Bifidobacterium pseudocatenulatum DSM 20438[T], while strain C3-R-101[T] showed 98.6% similarity to Blautia hominis KB1[T]. The draft genome sizes of strains M3-R-103[T] and C3-R-101[T] were 2.08 Mbp and 6.40 Mbp, respectively, with DNA G+C contents of 56.3 mol% and 46.7 mol%. Both strains demonstrated tolerance to simulated gastrointestinal stress conditions, including exposure to acidic pH (2.0) and bile salts (0.3%). In vitro assays revealed measurable antioxidant, α-amylase inhibitory, and anti-inflammatory activities. Specifically, DPPH radical scavenging activity ranged from 38.28 ± 8.35% to 58.83 ± 9.35%, α-amylase inhibition ranged from 47.12 ± 2.76% to 69.19 ± 3.83%, and inhibition of albumin denaturation ranged from 52.99 ± 2.70% to 58.16 ± 8.00%. Based on combined phylogenetic, genomic, and phenotypic evidence, strains M3-R-103[T] and C3-R-101[T] represent two novel species within their respective genera. We therefore propose the names Bifidobacterium intestinale sp. nov. (type strain M3-R-103[T] = KCTC 25443[T] = CGMCC 1.19415[T]) and Blautia caeci sp. nov. (type strain C3-R-101[T] = KCTC 25440[T] = CGMCC 1.17981[T]).}, }
@article {pmid42199064, year = {2026}, author = {Goobie, GC}, title = {Molecular mechanisms of environmental risk factors for interstitial lung disease.}, journal = {Current opinion in pulmonary medicine}, volume = {}, number = {}, pages = {}, doi = {10.1097/MCP.0000000000001286}, pmid = {42199064}, issn = {1531-6971}, abstract = {PURPOSE OF REVIEW: Interstitial lung disease (ILD) comprises a diverse group of conditions characterized by lung inflammation and fibrosis. Cumulative lifetime exposures (i.e. the exposome) contribute to ILD onset and progression by interacting with genetic susceptibility and influencing multiple molecular pathways. This review summarizes current evidence evaluating how environmental exposures interact across the genome, epigenome, transcriptome, proteome, metabolome, and microbiome to drive ILD pathogenesis.<br><br>RECENT FINDINGS: Environmental exposures, including air pollution, influence ILD risk through interactions with genetic factors that modify disease susceptibility. Epigenetic mechanisms, particularly DNA methylation, reflect key pathways through which exposures may contribute to ILD onset and progression and serve as sensitive biomarkers of environmental injury. Exposure-associated molecular alterations can be detected across multiple omic layers, including transcriptomic, proteomic, and metabolomic profiles. In parallel, exposures like cigarette smoking, silica, and air pollution influence the respiratory microbiome, with potential downstream effects on immune responses and fibrogenesis. Integrating these findings highlights environmentally-sensitive pathways that may represent novel targets for therapeutic modulation.<br><br>SUMMARY: Integration of exposomic and multiomic molecular frameworks offers new opportunities to improve ILD risk stratification, prognostication, and precision therapeutic development, while also strengthening our mechanistic understanding of environmentally-mediated disease.}, }
@article {pmid42199152, year = {2026}, author = {Zhang, W and Song, Y and Li, C and Luo, Y and Shao, M and Guo, F and Wei, F and Fan, X and Guo, W and Xu, F and Sang, Y and Zhang, D and Zhou, Y and Wang, L and Kang, Z and Yang, Y and Song, C and Liu, Y and Ma, X and Wang, J and Li, C and Ma, S and Zhao, L and Qin, Z and Xing, G and Zhao, Q and Li, J and Song, S and Zhao, D and Huang, T and Wang, Q and Zhao, Y and Qin, G}, title = {Canagliflozin Alleviates Diabetic Glomerular Endothelial Injury via Melibiose in a Microbiota-Dependent Manner.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e17222}, doi = {10.1002/advs.202517222}, pmid = {42199152}, issn = {2198-3844}, support = {82170839//National Natural Science Foundation of China/ ; U23A20414//National Natural Science Foundation of China/ ; 82470876//National Natural Science Foundation of China/ ; 82300930//National Natural Science Foundation of China/ ; 251111311500//Key Research and Development Program of Henan Province/ ; 242300421272//Natural Science Foundation of Henan Province/ ; LHGJ20230200//Henan Joint Construction Program/ ; SBGJ202301006//Science and Technology Research Project of Henan Province/ ; }, abstract = {Canagliflozin reduces albuminuria in patients with diabetic kidney disease (DKD) beyond its glucose-lowering effect, but the mechanisms remain unclear. We analyzed 85 patients treated with canagliflozin and 85 controls over 26 weeks to explore whether the gut microbiome and its metabolites contribute to renoprotection. Canagliflozin remodeled the gut microbiota, notably enriching Roseburia intestinalis and increasing plasma melibiose levels. In mice, canagliflozin alleviated glomerular endothelial injury and albuminuria. Similar effects were replicated by fecal microbiota transplantation, Roseburia intestinalis, or melibiose administration. Mechanistically, melibiose bound to and activated glyoxalase 1, reduced methylglyoxal, and suppressed the AGE-RAGE pathway, preserving glomerular endothelial integrity. Furthermore, oral melibiose precursor supplementation reduced albuminuria in patients with early-stage DKD. These findings suggest the involvement of a gut-kidney axis in the renoprotective effects of canagliflozin and indicate that melibiose may serve as a potential therapeutic strategy for DKD.}, }
@article {pmid42199216, year = {2026}, author = {Suchowiecki, K and Corr, PG and Schurr, A and Asemani, A and Frame, LA}, title = {Evaluating the gut microbiome, dietary patterns, and cognition: a sub-study protocol from the brain health and the gut microbiome study in cognitive decline (bMicrobiome study).}, journal = {Gut microbiome (Cambridge, England)}, volume = {7}, number = {}, pages = {e8}, pmid = {42199216}, issn = {2632-2897}, abstract = {The aim of this study is to describe the development and implementation of a novel Readiness to Change Nutritional Habits (RCNH) survey for use along with dietary assessment and gut microbiome profiling in a proof-of-concept study in individuals with early Alzheimer's disease dementia (eAD), mild cognitive impairment (MCI), and healthy controls (HC). Overall, this methods paper contributes to emerging research examining how behavioural readiness for change can be integrated with dietary assessment and gut microbiome profiling to better understand the microbiome's influence on the nervous system. This is a sub-study embedded within a multi-prong proof-of-concept, observational study mapping the gut microbiome in 45 participants (15 HC, 15 MCI, 15 eAD) at baseline, 3 months, and 6 months. The parent study collects gut microbiome profiles, dietary patterns, and cognitive assessments. The sub-study develops and administers the 32-item RCNH survey to characterize participants' readiness to adopt nutritional change. This manuscript reports the RCNH survey, its development process, the sub-study protocol including data collection procedures, and planned exploratory analyses. This protocol presents a novel intervention to assess the gut microbiome, individual dietary patterns, and readiness to make lifestyle changes related to diet.}, }
@article {pmid42199361, year = {2026}, author = {Song, S and Han, M and Moon, K and Lee, H and Ha, S and Seo, J and Lee, S and Jang, S and Lim, SK and Kim, N and Ko, G}, title = {Bifidobacterium stercoris KC84 attenuates IBS-D-like symptoms via modulation of serotonin-related pathways and dendritic cell-mediated IFN-β induction.}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100603}, pmid = {42199361}, issn = {2666-5174}, abstract = {Irritable bowel syndrome with diarrhea (IBS-D) is a prevalent disorder that significantly impairs quality of life, yet therapeutic advances remain limited. Serotonin dysregulation, primarily driven by enterochromaffin cells in the intestinal epithelium, is central to IBS-D pathogenesis. We hypothesized that targeted modulation of enterochromaffin cell activity through microbiome-based interventions could provide a novel treatment approach. Here, we screened 128 Bifidobacterium isolates and identified B. stercoris KC84 as a promising candidate. KC84 alleviated IBS-D-like symptoms in both chemically and stress-induced models, accompanied by changes in serotonin-related markers. Transcriptomic analysis revealed activation of type I interferon (IFN)-associated pathways, consistent with ex vivo evidence of KC84-induced IFN-β secretion, predominantly from CD11b[-] dendritic cells. Furthermore, IFN-β treatment attenuated contractile activity in colonic smooth muscle cells. Collectively, these findings suggest that KC84 mitigates IBS-D-like symptoms, potentially through modulation of serotonin-related pathways and activation of a KC84-IFN-β-smooth muscle regulatory axis, supporting KC84 as a mechanism-guided probiotic candidate for IBS-D therapy.}, }
@article {pmid42199372, year = {2026}, author = {Vijayakumar, K and Paul, BC}, title = {Virulence factors of the microbiome: A functional toolkit for cancer progression (Review).}, journal = {Molecular and clinical oncology}, volume = {25}, number = {1}, pages = {48}, pmid = {42199372}, issn = {2049-9469}, abstract = {The paradigm of cancer biology has shifted to recognize tumor as a complex ecosystem inhabited by a diverse microbiome. Beyond mere association, the molecular mechanisms driven by microbial virulence factors are critical for understanding how these microorganisms contribute to malignancy. The present review describes a virulence factor-centric framework to deconstruct the microbial 'toolkit' and illustrate its role in enabling the Hallmarks of Cancer. The major classes of virulence factors were systematically analyzed, detailing how each contributes to tumor progression. It was described how bacterial adhesins (for example, Fusobacterium adhesin A and Fap2) initiate oncogenic signaling and mediate immune evasion; how secreted toxins drive genomic instability (Colibactin and CDT) and corrupt cellular signaling pathways (CagA and Bacteroides fragilis toxin); how degradative enzymes (gingipains and collagenases) dismantle the extracellular matrix to facilitate physical invasion; how viral oncoproteins (Human Papillomavirus E6/E7 and Epstein Barr virus latent membrane protein 1) hijack core cell cycle machinery; and how microbial structural components (lipopolysaccharides and extracellular vesicles) and metabolites (secondary bile acids) sustain a pro-tumorigenic environment. This analysis reveals a pattern of functional convergence, where diverse microbial agents repeatedly target core host pathways such as NF-κB, Wnt/β-catenin and p53. This mechanistic understanding reframes the microbiome as an active orchestrator of malignancy and reveals a new frontier of therapeutic targets. Strategies aimed at neutralizing specific virulence factors or modulating the tumor ecosystem represent a novel and promising pillar in oncology.}, }
@article {pmid42199404, year = {2026}, author = {Zhu, M and Li, R and Wu, S and Chen, J and Sun, K}, title = {Multi-omics insights into spondyloarthritis and psoriatic arthritis: integrating genomics, transcriptomics, proteomics, and the microbiome for immunological and clinical translation.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1831823}, pmid = {42199404}, issn = {1664-3224}, mesh = {Humans ; *Arthritis, Psoriatic/diagnosis/immunology/genetics/metabolism/microbiology ; Multiomics ; *Proteomics/methods ; *Genomics/methods ; *Microbiota/immunology ; *Spondylarthritis/diagnosis/genetics/immunology/metabolism ; Biomarkers ; Transcriptome ; Gene Expression Profiling ; Translational Research, Biomedical ; Animals ; }, abstract = {Spondyloarthritis (SpA) and psoriatic arthritis (PsA) are interrelated, immune-mediated inflammatory diseases characterized by significant clinical heterogeneity. Early differential diagnosis, accurate disease activity assessment, and the development of personalized treatment strategies remain significant clinical challenges. Single-omics approaches have provided only a limited view of this complexity, highlighting the need for integrative strategies. This review systematically synthesizes findings from multi-omics studies-including genomics, transcriptomics, proteomics, and microbiomics-in SpA and PsA. We focus on their application in three key areas: (i) elucidating shared and distinct immunopathological mechanisms, (ii) facilitating differential diagnosis, and (iii) discovering novel biomarkers. By comparing their molecular landscapes, we explore the shared and distinct immunological foundations of SpA and PsA. Furthermore, we critically evaluate the translational potential of integrated multi-omics strategies for advancing early diagnosis, precision monitoring, predicting treatment responses, and identifying novel therapeutic targets. This integrated, multi-omics framework promises to refine disease taxonomy and guide personalized therapeutic decisions, paving the way for precision medicine in SpA and PsA.}, }
@article {pmid42199424, year = {2026}, author = {Zhao, L and Wang, Q and Chen, J and Wang, J}, title = {Multi-omics analyses reveal significant differences in the gut microbiota and metabolites in children with Kawasaki disease in Northwest China.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1767902}, pmid = {42199424}, issn = {1664-3224}, mesh = {Humans ; *Mucocutaneous Lymph Node Syndrome/microbiology/metabolism ; Female ; Multiomics ; Male ; *Gastrointestinal Microbiome ; Child, Preschool ; Metagenomics/methods ; China/epidemiology ; *Metabolome ; Metabolomics/methods ; Infant ; Feces/microbiology ; Bacteria/classification/genetics ; Child ; }, abstract = {BACKGROUND: Kawasaki disease (KD) is a systemic vasculitis characterized by mucocutaneous lymph node syndrome and aberrant immune activation. Previous studies have indicated substantial disruptions in the gut microbiota during the acute phase of KD. However, the detailed characteristics of the gut microbiota and metabolome in children with KD, as well as their clinical relevance, remain poorly understood.<br><br>METHODS: 31 children with KD (KDs) and age/sex-matched healthy controls (HCs) were enrolled to collect their fecal and blood samples. Shotgun metagenomic sequencing and untargeted metabolomic analyses were conducted on these samples.<br><br>RESULTS: Significant reductions in alpha diversity and microbial richness were observed in the gut microbiota of KDs at both species and genus levels. Pathogenic species including Enterococcus avium, Streptococcus peroris and Clostridioides difficile were significantly abundant in the KDs group, while beneficial species containing Faecalibacterium prausnitzii, Anaerostipes hadrus, Akkermansia muciniphila, Eubacterium hallii, Agathobaculum butyriciproducens, Ruminococcus bicirculans, and Roseburia intestinalis were markedly decreased. A total of 49 metabolic pathways were differentially enriched between the two groups, with 22 pathways including nucleotide, carbohydrate, energy, and amino acid metabolism being abundant in KDs, while the other 27 pathways were enriched in HCs. For metabolites, both fecal and blood metabolomes exhibited significant alterations. Notably, fecal metabolites including indole, L-tryptophan, L-lactic acid, 5-HETE, indol-3-acetamid, tetraethylammonium and dopaquinone were elevated in KDs, whereas butyrate, methylxanthine, phosphocholine, methylhistidine, ADP-ribose, vitamin A acid, and chenodeoxycholic acid were reduced. In plasma, cholesterol, phosphocholine, porphobilinogen, pantothenate, cortisol, bile acids and related compounds were enriched in KDs, while amino acids, indole and tryptamine derivatives, nucleotides, nucleic acids, and sugar metabolites were more abundant in HCs.<br><br>CONCLUSIONS: This study represents the first systematic multi-omics investigation of KD in a pediatric population from Northwest China. It establishes a foundational resource characterizing the gut microbiome and metabolome in KD, offering novel biological insights, suggesting potential therapeutic targets, and supporting further mechanistic and clinical research.}, }
@article {pmid42199468, year = {2026}, author = {Groß, VE and Cheng, KO and Cristóvão, B and Gürel, E and Himmel, M and Fernández-Fernández, C and Schuchardt, JV and Dietschmann, A and Montaño, DE and Gresnigt, MS}, title = {An In Vitro A-431 Epithelial Cell Infection Model for Studying Fungal Pathogenicity and Immune Responses Associated With Vulvovaginal Candidiasis.}, journal = {Bio-protocol}, volume = {16}, number = {10}, pages = {e5693}, pmid = {42199468}, issn = {2331-8325}, abstract = {Vulvovaginal candidiasis (VVC), also known as vaginal thrush, is an infection of the vulvovaginal mucosa caused by fungi of the Candida genus. Particularly for patients suffering from recurrent infection, the disease has a significant impact on their quality of life. The still unknown aspects of disease pathogenesis, as well as factors driving the development of infections and recurrence, represent a challenge for both clinical practitioners and patients. Mouse models and patient studies have suggested important roles of the microbiome, deployment of fungal pathogenicity mechanisms in the vagina, and dysregulated immune responses for VVC pathology. Dissecting their individual contributions can reveal specific processes associated with infection and may inspire novel therapeutic strategies. Epithelial in vitro infection models have been playing a key role in dissecting a crucial interaction during VVC, the invasion and infection of the vaginal mucosa. They have been instrumental in characterizing candidalysin as a fungal toxin that damages epithelial cells and elicits initial inflammatory responses to catalyze downstream inflammation. Moreover, they have also revealed potential protective immune pathways. Such a standardized epithelial cell infection model offers high versatility and compatibility with different downstream assays to link epithelial responses with other processes during VVC. This protocol describes a general A-431 vulvovaginal epithelial cell-Candida infection model in detail and provides several adaptations, such as live-cell imaging and mRNA silencing, as well as possible follow-up readouts, like the quantification of cytokine release, cytotoxicity, and neutrophil recruitment to study diverse processes relevant to VVC research. Key features • This protocol describes the use of the A-431 epidermoid carcinoma cell line as an in vitro infection model of vulvovaginal candidiasis. • The protocol can be adapted to answer research questions relevant to vulvovaginal candidiasis (epithelial damage, release of inflammatory cytokines, recruitment and activation of neutrophils). • Live-cell imaging can be used to study dynamic infection processes. • mRNA silencing can be applied to interrogate the function of genes of interest in the host-pathogen interaction. This protocol is used in.}, }
@article {pmid42199542, year = {2026}, author = {Cycoń, M}, title = {Bioaugmentation as microbiome engineering: a framework for evaluating functional performance, persistence, and safety.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1835468}, pmid = {42199542}, issn = {1664-302X}, abstract = {Bioaugmentation is increasingly applied to enhance the degradation of contaminants in environmental and engineered systems, yet its effectiveness is often evaluated using endpoints that do not establish whether the introduced microbial function was expressed, sustained, or responsible for the observed outcome. This review considers bioaugmentation as an approach to microbiome engineering rather than a discrete inoculation step. It outlines an evaluation framework based on three complementary criteria: functional performance, functional persistence, and safety. Emphasis is placed on the microbiological determinants of successful implementation, including pathway completion, expression of terminal transformation steps, functional redundancy, ecological compatibility, and the maintenance of introduced activity under variable environmental conditions. The analysis also examines how inoculum design, delivery, selective pressure, retention, and biomonitoring influence the establishment of degradative functions within complex microbial communities. A central theme is the need to distinguish genuine inoculum-driven effects from outcomes generated by biostimulation, modified mass transfer, or changes in contaminant bioavailability. Available evidence indicates that robust interpretation requires an integrated assessment of substrate-to-product relationships, functional and activity markers, community-level responses, and, where appropriate, indicators of biological effect. Microbiological safety considerations are also reviewed, including selective pressures and resistance-related consequences in systems exposed to biologically active contaminants. Bioaugmentation should therefore be evaluated as a controlled microbiotechnological intervention in which function, persistence, mechanistic attribution, and safety are assessed collectively.}, }
@article {pmid42199545, year = {2026}, author = {Wang, Z and Guo, X and Shi, Y and Ma, N and Ma, Y and Pei, Y and Li, Y and Xu, H and Ma, F and Li, Y and Li, J and Gao, Y}, title = {Impacts of off-flavor on microbial community structure, nutritional traits and metabolite profiles in whole-plant corn silage.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1827817}, pmid = {42199545}, issn = {1664-302X}, abstract = {Off-flavor in corn silage compromises feed quality and animal performance, yet the microbial-metabolic changes driving its formation remain poorly understood. In this study, microbiome profiling, metabolomics, and sensory evaluation were integrated to elucidate the changing factors driving off-flavor formation. Silage samples from 10 dairy farms were classified by sensory score into control (CON, 15-20) and abnormal silage groups (ASG, <15). The bacterial community structure was analyzed, metabolites were identified and quantified using gas chromatography-mass spectrometry (GC-MS), and the associations between microorganisms and metabolites were explored via Spearman correlation analysis. Compared with the CON, the ASG exhibited significantly lower concentrations of dry matter (p = 0.01), starch (p = 0.04), lactic acid (p = 0.03), and acetic acid (p = 0.04), while those of neutral detergent fiber (p = 0.02), acid detergent fiber (p = 0.03), propionic acid (p = 0.01), and butyric acid (p = 0.02) were significantly higher. The pH value of the ASG was increased to 4.99 compared to that of the CON (3.74), with a significant difference observed between them. Meanwhile, the abundances of phylum Firmicutes (p-Firmicutes) and genus Lactobacillus (g-Lactobacillus) in the ASG were both significantly lower than CON. After further screening from the 32 differentially abundant metabolites (excluding 16 redundant metabolites and 2 that remained unannotated due to database limitations), a total of 14 core differential metabolites associated with off-flavor in silage were identified. Among these, compounds contributing acetic and waxy aromas were enriched in the ASG. Spearman correlation analysis showed Corynebacterium and JC017 were positively correlated with fatty and waxy compounds (methyl linoleate, oleic acid), while Massilia and Paenibacillus_D were negatively correlated with phenylacetic acid. These findings demonstrate that off-flavor in corn silage arises from Lactobacillus decline, aerobic spoilage bacteria overgrowth, and subsequent accumulation of phenylacetic acid coupled with gallic acid depletion. This microbiome-metabolomics interaction provides a mechanistic framework for developing targeted strategies to control silage off-flavors.}, }
@article {pmid42199549, year = {2026}, author = {Wang, Y and Zhao, H and Sun, Y and Mi, M and Hu, X and Ye, D and Wang, X and Dou, L and Wang, J and Yang, Z}, title = {Prevalence of Lawsonia intracellularis and characteristics of gut microbiomes of the infected pigs in Shaanxi province, China.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1834533}, pmid = {42199549}, issn = {1664-302X}, abstract = {OBJECTIVES: Lawsonia intracellularis is an obligately intracellular enteric bacterium that infects intestinal epithelial cells and causes porcine proliferative enteropathy (PPE). This study aimed to investigate the epidemiological prevalence of L. intracellularis in large-scale pig farms in Shaanxi Province, China, and analyze the differences in fecal microbial communities of growing pigs with natural L. intracellularis infection.<br><br>METHODS: A total of 672 fecal samples and 300 serum samples were collected from five intensive pig farms in Shaanxi during 2022-2023. Quantitative PCR (qPCR) was used to detect L. intracellularis in feces and quantify its fecal load, while enzyme-linked immunosorbent assay (ELISA) was employed to detect the seroprevalence of anti-L. intracellularis antibodies in serum. 16S rRNA gene sequencing was performed on fecal samples from L. intracellularis-positive and -negative growing pigs.<br><br>RESULTS: The results showed an overall fecal positive rate of 15.3% (95% CI: 12.7-18.3%) and a serum seroprevalence of 14.7% (95% CI: 11.0-19.3%) for L. intracellularis in the surveyed farms, with growing pigs exhibiting the significantly highest positive rate and fecal pathogen load (p&#x202f;<&#x202f;0.05). Tongchuan exhibited a significantly lower fecal positive rate than the other surveyed regions (p&#x202f;<&#x202f;0.05). Fecal microbial diversity analysis revealed that L. intracellularis-positive fecal samples exhibited significantly higher bacterial species richness. LEfSe analysis indicated a significant enrichment of Lactobacillus in L. intracellularis-positive feces relative to negative samples. Network analysis demonstrated a positive correlation between Desulfovibrionaceae and Lachnospiraceae, and random forest analysis identified Erysipelotrichaceae_UCG.003 as the critical microbial biomarker for L. intracellularis infection.<br><br>CONCLUSION: This study elucidates the epidemiological characteristics of L. intracellularis in Shaanxi and its interaction with the porcine gut microbiome, thereby providing a theoretical basis for the precise prevention and control of PPE, as well as for further investigations into the interactions between the gut microbiota and L. intracellularis.}, }
@article {pmid42199803, year = {2026}, author = {Liu, Y and Yang, M and Liao, Y and Hu, Z}, title = {Global research trends, reporting and handling of missing data in observational studies of type 2 diabetes mellitus with mild cognitive impairment from 2020 to 2025: a systematic review.}, journal = {Frontiers in endocrinology}, volume = {17}, number = {}, pages = {1649881}, pmid = {42199803}, issn = {1664-2392}, mesh = {*Diabetes Mellitus, Type 2/complications/epidemiology ; *Cognitive Dysfunction/epidemiology/complications ; Humans ; *Observational Studies as Topic ; Bibliometrics ; }, abstract = {BACKGROUND: Missing data is common in observational studies, and even more so in type 2 diabetes mellitus with mild cognitive impairment(T2DM-MCI), which limits the completion of assessments. We evaluated the extent, current reporting, and handling of missing data, as well as the prevailing research trends in observational studies related to T2DM-MCI.<br><br>METHODS: A systematic search of PubMed, Embase, and Cochrane Library was conducted from January 2020 to April 2025 to identify observational studies related to T2DM-MCI. Bibliometrics was performed using VOSviewer and CiteSpace to evaluate publishing trends, authors, journals, and keywords. The reporting and handling of missing data were assessed according to the guidelines recommended by STROBE and Sterne et&#xa0;al., with a focus on the recording, causes, mechanisms, processing methods, and sensitivity analysis of missing data. Data analysis was conducted using SPSS 26, and visualization was performed using Origin Pro 2024.<br><br>RESULTS: Among the 4,471 screened records, 88 studies (78 in English and 10 in Chinese) were included in this analysis. Among the 78 English articles, the annual publication volume exhibited fluctuations, peaking in 2024. Chinese institutions and authors led in research output. Diabetes, Metabolic Syndrome, and Obesity had the highest publication volume (7, 8.97%). Keyword identified five clusters: 1) resting-state functional magnetic resonance imaging, 2) metabolic disorders, 3) clinical assessment tools, 4) molecular mechanisms, and 5) emerging fields such as the gut microbiome.<br><br>MISSING DATA: Only 22.7% (n = 20) of the studies quantified the missing data, with an average of 9.1%. Among studies with missing data (n = 23), 52.2% (n = 12) provided reasons for missing data, primarily citing poor quality of data collection (41.7%) and loss to follow-up (41.7%). Complete case analysis was the predominant method for addressing missing data (93.3%). No study articulated the hypothesized mechanisms underlying the missing data, and only 4.4% (n = 1) performed a sensitivity analysis.<br><br>CONCLUSION: In the domain of T2DM-MCI, research outcomes post-COVID-19 pandemic indicate a rebound, with China maintaining a leading position in scientific research output. However, the reporting of missing data remains ambiguous, and the methods employed to handle such data are insufficient, which may potentially introduce bias.<br><br>https://doi.org/10.17605/OSF.IO/EZDXM.}, }
@article {pmid42199861, year = {2026}, author = {Xu, T and Roy, SP and Hadia, R and Annu,  and Bhowmik, S and Panchal, A}, title = {The gut-brain axis in pharmacology: microbiome-driven modulation of CNS drugs and neuropsychiatric outcomes.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1826681}, pmid = {42199861}, issn = {1663-9812}, abstract = {BACKGROUND: The gut-brain axis has emerged as a critical regulator of Central Nervous System (CNS) pharmacology, significantly influencing drug response and neuropsychiatric outcomes through complex interactions between the gut microbiota and host systems.<br><br>OBJECTIVE: This review aims to examine the role of gut microbiota in modulating the pharmacokinetics and pharmacodynamics of CNS drugs, and to explore their implications in neuropsychiatric disorders.<br><br>KEY FINDINGS: Accumulating evidence indicates that microbial enzymes and metabolites can alter drug absorption, metabolism, and bioavailability, particularly for antidepressants such as Selective Serotonin Reuptake Inhibitors (SSRIs) and Tricyclic Antidepressants (TCAs). In turn, psychotropic medications can modify gut microbial composition, leading to dysbiosis and variability in therapeutic outcomes. Microbiota-derived metabolites, immune signaling pathways, and host genetic factors (e.g., cytochrome P450 polymorphisms) collectively contribute to interindividual differences in drug efficacy and safety.<br><br>CONCLUSION: Integration of microbiome profiling into pharmacological research holds significant potential for advancing precision medicine in neuropsychiatry. However, challenges such as methodological heterogeneity, limited longitudinal clinical data, and lack of standardized biomarkers must be addressed to enable clinical translation.}, }
@article {pmid42200243, year = {2026}, author = {Li, J and Lian, Z and Wang, Y and Meng, H and Fu, F and Qu, Y}, title = {[Association of acute kidney injury with gut microbiota: a study integrating Mendelian randomization and real-world clinical cohort].}, journal = {Zhonghua wei zhong bing ji jiu yi xue}, volume = {38}, number = {4}, pages = {337-345}, doi = {10.3760/cma.j.cn121430-20250903-00472}, pmid = {42200243}, issn = {2095-4352}, mesh = {Humans ; *Acute Kidney Injury/microbiology ; Mendelian Randomization Analysis ; Polymorphism, Single Nucleotide ; Genome-Wide Association Study ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S ; Cohort Studies ; Female ; Male ; }, abstract = {OBJECTIVE: To investigate the association between acute kidney injury (AKI) and the gut microbiota by integrating 16S sequencing analysis with mendelian randomization (MR).<br><br>METHODS: 1) MR analysis: The genome-wide association study (GWAS) dataset for AKI from the FinnGen consortium and the GWAS dataset for gut microbiota composition from the Dutch Microbiome Project were selected to screen single nucleotide polymorphism (SNP) associated with AKI as instrumental variable (IV) for genetic variation, using AKI as the exposure factor. Potential causal associations between AKI and gut microbiota were analyzed using a two-sample, one-way MR analysis with the primary analysis method of inverse variance weighted (IVW). Heterogeneity analysis was performed using the Cochran Q test. Potential pleiotropy was assessed using the MR-Egger intercept test. Sensitivity analysis was performed using the leave-one-out test. 2) Clinical cohort study: Consecutive patients admitted to the intensive care unit (ICU) of Qingdao Municipal Hospital between December 2024 and March 2025 were prospectively enrolled. Patients were classified into the AKI group or the non-AKI group based on the occurrence of AKI during their ICU stay, according to the diagnostic criteria from Kidney Disease: Improving Global Outcomes (KDIGO) clinical practice guidelines (2012). Baseline clinical data were collected within 48 hours of ICU admission, including gender, age, height, weight, body mass index (BMI), major comorbidities, vital signs, serum creatinine (SCr), blood routine, C-reactive protein (CRP), interleukin-6 (IL-6), etc. Anal swabs were collected from patients within 48 hours of ICU admission for 16S rDNA high-throughput sequencing. Significant difference analysis and linear discriminant analysis effect size (LEfSe) were performed to characterize the gut microbiota profile in AKI patients and to further validate the findings from the MR analysis.<br><br>RESULTS: 1) MR analysis results: Using the GWAS summary statistics for gut microbiota and AKI, the MR analysis revealed that the genetic liability to AKI was associated with decreased abundance in six gut microbial taxa and increased abundance in one taxon. IVW analysis showed that at the genus level, genetic susceptibility to AKI was associated with lower abundance of Collinsella (&#x3b2;=-0.144, P=0.029), Lachnospiraceaenoname (&#x3b2;=-0.131, P=0.040), Roseburia (&#x3b2;=-0.126, P=0.047), and Parasutterella (&#x3b2;=-0.198, P=0.023). At the species level, AKI genetic susceptibility was linked to reduced abundance of Parasutterellaexcrementihominis (&#x3b2;=-0.197, P=0.024) and Roseburia unclassified (&#x3b2;=-0.280, P=0.012), while being associated with increased abundance of Bacteroidesintestinalis (&#x3b2;=0.358, P=0.013). Cochran Q test showed no heterogeneity, MR-Egger intercept test revealed no pleiotropy, and leave-one-out analysis verified the robustness of the results. 2) Clinical cohort study results: A total of 129 patients were initially enrolled. After excluding 25 patients with incomplete clinical data and 10 whose samples failed to generate sufficient 16S rDNA gene amplification for sequencing, 94 patients were included in the final analysis comprising 72 cases in the AKI group and 22 cases in the non-AKI group. Apart from higher SCr levels in the AKI group than those in the non-AKI group, no statistically significant differences were observed in other baseline clinical characteristics between the two groups. 16S rDNA high-throughput sequencing yielded 6 868 647 high-quality reads, which were clustered into 13 025 amplicon sequence variant (ASV). Significant difference analysis at the species level showed that, compared with the non-AKI group, patients in the AKI group had a relative enrichment of Streptococcus anginosus and Novosphingobium sp. B0.09-8. Conversely, the relative abundances of uncultured Prevotellasp., Alistipesshahii, uncultured Coprococcussp., Collinsellatanakaei, Streptococcus equinus, Alistipesindistinctus, Klebsiellasp. GRB36, and uncultured Oscillospirasp. were significantly lower in the AKI group. LEfSe analysis identified Veillonella unclassified, Ligilactobacillus unclassified, Collinsellatanakaei, Atopobium unclassified, and Streptococcus anginosus as potential biomarkers for the AKI group, whereas Alistipesshahii, uncultured Prevotella sp., and Agathobacter unclassified were more characteristic of the patients in the non-AKI group.<br><br>CONCLUSIONS: The MR analysis suggests that the occurrence of AKI exerts an influence on the gut microbiota profile, characterized by a reduction in the abundance of the genus Collinsella. Findings from the real-world study further indicate significant differences in gut microbiota composition between patients with and without AKI. Overall, the gut microbiota of AKI patients is characterized by an enrichment of pro-inflammatory bacteria and a depletion of commensal symbionts. The genus Collinsellamay may serve as a potential biomarker for AKI.}, }
@article {pmid42200271, year = {2026}, author = {Vázquez-Reyes, S and Esposito, E and Rosell, A and Lizasoain, I and Lo, EH and Moro, MA and Hayakawa, K}, title = {Immune System of the Ischemic Brain: Old Paradigms Revisited.}, journal = {Stroke}, volume = {}, number = {}, pages = {}, doi = {10.1161/STROKEAHA.125.051471}, pmid = {42200271}, issn = {1524-4628}, support = {R01 NS137979/NS/NINDS NIH HHS/United States ; }, abstract = {The central nervous system was once viewed as immunologically privileged, but it is now recognized that brain-immune interactions are dynamic and critical. After central nervous system injury or disease, microglia and perivascular macrophages survey the damaged tissue, while diverse immune cells infiltrate through various barriers, driving neurovascular dysfunction and neuroinflammation. Depending on timing and phenotype, systemic immune responses can also promote brain repair and recovery. Recent studies show that brain-peripheral organ communication profoundly affects both injury progression and healing. These insights redefine the neurovascular-immune interface and the concept of the brain's immune system. This review examines immune cell infiltration and highlights emerging brain-peripheral circuits that regulate neuroinflammation and recovery after stroke.}, }
@article {pmid42200417, year = {2026}, author = {Lin, L and Gao, G and Sun, S and Wu, X and Fan, S and Wang, H and Zhou, F and Zhang, X}, title = {Host-independent metagenomics reveal gut bacteria contribution to Delia antiqua growth by vitamin B6 provision.}, journal = {Insect molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/imb.70046}, pmid = {42200417}, issn = {1365-2583}, support = {2024KJI002//Young Innovation Team Project of Higher Education in Shandong Province/ ; 2024ZDZX10//QLU Major Innovation Projects of Education-Industry Integration Pilot/ ; SDAIT-31-04//Shandong Province Key Agricultural Project for Application Technology Innovation/ ; 32272530//National Natural Science Foundation of China/ ; }, abstract = {Insect guts host a diverse and abundant array of microorganisms. These microbes improve host fitness by extensively involving in a range of crucial physiological processes, which have mainly been revealed by high-throughput sequencing, particularly metagenomics. However, it is almost impossible to make an accurate and complete distinction between the genetic functions of microbial symbionts and insect hosts without host genome data. By comparing metagenomic data from gut germ-free and nonaxenic larvae, we accurately identified the data belonging to the gut microbiome of the onion maggot Delia antiqua (Diptera: Anthomyiidae). Besides, a correlation between bacteria of the genus Wohlfahrtiimonas (Gammaproteobacteria: Pseudomonadaceae) and vitamin B6 metabolism was detected through collinearity analysis. Furthermore, in vitro tests confirmed that the gut bacterium Wohlfahrtiimonas larvae contributed to the growth of D. antiqua larvae via the independent synthesis of vitamin B6. This study provides a comprehensive view of the gut bacterial diversity in D. antiqua and reveals a functional profile that is strictly specific to the gut microbiota of this species. It has preliminarily revealed the functional differentiation between insect hosts and their symbiotic microorganisms. This study also offers a technical reference for the study of microbial symbiotic functions in other insect-microbe symbioses without host genomic data.}, }
@article {pmid42200499, year = {2026}, author = {Plocek, MR and Dunham, NT and Amato, KR}, title = {Comparative Analysis of Fecal Microbiome Composition in Zoo-Housed Colobines: The Influence of Dietary Macronutrients, Browse Provisioning, and Phylogeny.}, journal = {American journal of primatology}, volume = {88}, number = {5}, pages = {e70169}, doi = {10.1002/ajp.70169}, pmid = {42200499}, issn = {1098-2345}, support = {(CS2020-028)//Cleveland Metroparks/ ; }, mesh = {Animals ; *Feces/microbiology ; *Animals, Zoo/microbiology ; *Diet/veterinary ; Phylogeny ; Nutrients/analysis ; *Colobinae/microbiology/physiology ; RNA, Ribosomal, 16S/analysis ; *Gastrointestinal Microbiome ; Animal Feed/analysis ; Male ; Female ; Feeding Behavior ; }, abstract = {This study investigated the interplay between dietary macronutrient composition, browse provisioning frequency, and host phylogeny in shaping the gut microbiome of zoo-housed colobine monkeys. We focused on four species (Colobus guereza, Colobus angolensis, Trachypithecus cristatus, and Trachypithecus francoisi) housed across 20 AZA-accredited institutions and integrated detailed dietary records with fecal microbiome profiling. Diets were categorized using Partition Around Medoids clustering based on macronutrient content, while browse offerings were classified by provisioning frequency (low, moderate, and high). Microbial diversity and community composition were evaluated using high-throughput 16S rRNA sequencing. The results revealed that browse provisioning frequency was the strongest predictor of microbiome alpha diversity, with moderate and high browse categories supporting significantly greater microbial richness and evolutionary breadth than low browse frequency. While diet cluster and phylogeny did not significantly affect alpha diversity metrics, all three factors significantly influenced the overall microbiome composition, as indicated by the unweighted and weighted UniFrac analyses. Notably, diet clusters with the highest relative crude fat (16.33%) or protein (23.27%) content, as well as sugar-rich diets promoted distinctive shifts in microbial community structure and function, fostering bacteria linked to dietary macronutrient processing, and in low-fiber contexts, reduce the abundance of key fiber-degrading taxa. These findings emphasize the necessity of frequent browse provision and an appropriate fiber balance to maintain gut microbial diversity and ecosystem stability in zoo-housed colobines. These results provide evidence-based recommendations for husbandry practices to promote nutritional and microbiome health in managed primate populations.}, }
@article {pmid42200521, year = {2026}, author = {Wright, RJ and Fisher, BR and Comeau, AM and Langille, MGI}, title = {From classification to confirmation: verifying taxonomic classifications by mapping metagenomic reads to reference genomes.}, journal = {Microbial genomics}, volume = {12}, number = {5}, pages = {}, doi = {10.1099/mgen.0.001739}, pmid = {42200521}, issn = {2057-5858}, mesh = {*Metagenomics/methods ; Humans ; *Metagenome ; *Bacteria/classification/genetics ; Genome, Bacterial ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Microbiota/genetics ; }, abstract = {Obtaining high precision while maintaining high recall is an ongoing problem for metagenomic taxonomic classification in microbial ecology research. Parameter adjustments can achieve this in simulated samples, but in real samples - especially from environments like marine and soil - the proportion of classified reads drops sharply with precision increases. We, therefore, suggest verification of metagenomic taxonomic classifications obtained from a tool like Kraken by mapping their assigned reads to reference genomes to assess genomic coverage. In simulations, filtering the identified species to only those with ≥0.5% reference genome coverage removed 99.7% of false-positive taxa. Applying this method to samples from real datasets requires a more nuanced approach that considers sequencing depth, whether the samples are high- or low-microbial biomass, and database completeness with respect to the sampled environment. Nevertheless, we show that clinically relevant Kraken-identified taxa, such as Helicobacter pylori identified in human stool samples, lack any reads mapping to their reference genome and are likely false positives driven by contaminating phage sequences within reference genomes. Similarly, in human blood and lung tumour datasets, only 18 and 11 species, respectively, have ≥1% reference genome coverage and likely represent sample collection or sequencing contaminants. Marine and soil samples pose additional challenges due to lower representation in reference databases, leading to low nucleotide identity between sequenced reads and reference genomes and similarity only at higher taxonomic ranks. We recommend genome coverage checking to researchers in all fields of microbial ecology and provide an open-source pipeline on GitHub (GeCoCheck): https://github.com/R-Wright-1/GeCoCheck.}, }
@article {pmid42200614, year = {2026}, author = {Hourigan, D and Draper, L and Leahy, SC and Attwood, GT and Kelly, WJ and Stanton, C and Hill, C and Ross, RP}, title = {The Hungate1000 prokaryotic culture collection encodes a wide variety of bacteriocins.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0019526}, doi = {10.1128/msystems.00195-26}, pmid = {42200614}, issn = {2379-5077}, abstract = {Bacteriocins are antimicrobial peptides/proteins that are widely distributed among bacteria and are gathering traction as natural alternatives to antibiotics, modulators of the microbiota, and interbacterial signaling peptides. The Hungate1000 is a culture collection of isolated prokaryotic microorganisms and their genomes from ruminant animals that aims to expand the knowledge base of rumen ecology. In this study, 410 rumen-isolated prokaryotes within the collection were mined to expand upon the bacteriocin-producing potential of the rumen. A total of 408 novel bacteriocin gene clusters were identified across 308 genomes. Bacteriocins in novel species within the Hungate1000 were identified, such as Pseudobutyrivibrio sp. UC1225, which has two novel natural nisin variants, Clostridium sp. DSM 8431 with a novel peptide 81% identity to amylocyclicin and Lachnobacterium C7 encoding a novel circular bacteriocin with 55% identity to the circular bacteriocin NKR-5-3B. A novel class II lanthipeptide gene cluster was also identified containing eight distinct core peptides encoded within the genome of a novel Butyrivibrio species. Bacteriocin biosynthetic potential was noted within species unknown to produce bacteriocins, such as Lachnobacterium bovis DSM 14045, Lachnospira multipara D15d, Eubacterium callanderi NLAE-zl-G225, Eisenbergiella tayi NLAE-zl-G231, and Muricomes contorta NLAE-zl-C134. The frequency of putative bacteriocin production within ruminal strains was 30%, doubling the frequency previously suggested in the mammalian gastrointestinal tract. This number increases to ~70% when encompassing groups of peptides with limited knowledge of antibacterial activity, such as ranthipeptides and auto-inducing peptides. We also show that the bacteriocin core peptides mined from the Hungate1000 culture collection are found in the microbiomes of other ruminant animals and the human gut microbiome. These findings highlight the Hungate1000 as a rich biosynthetic reservoir of cultured strains that can be experimentally explored for functional antimicrobial activity. The presence of diverse bacteriocin-producing lineages in rumen-associated microbes provides a foundation for future strategies aimed at targeted microbiome modulation, including approaches to improve rumen function and potentially mitigate enteric methane emissions using bacterial strains or their natural products.IMPORTANCEBacteriocins are gathering traction as a possible alternative to antibiotics in some instances. Therefore, it is crucial to discover novel bacteriocins to expand the bacteriocin knowledge base if these peptides are to be translated to the clinic for use in humans or developed as veterinary interventions to modulate rumen function. Here, we use in silico methods to identify the biosynthetic potential of the Hungate1000 culture collection of rumen bacterial strains. We discover 408 novel bacteriocin gene clusters across 308 genomes and identify that the frequency of bacteriocin gene clusters is over 30%, which is double the incidence rate from previous studies of the mammalian gastrointestinal tract. This number increases to approximately 70% when including bacteriocin classes such as ranthipeptides and cyclic-lactone-autoinducer peptides. Together, these findings position the rumen microbiome as a rich and underexplored reservoir of antimicrobial diversity, with potential for the development of targeted microbiome-modulating therapeutics, livestock interventions aimed at improving rumen function, and strategies aligned with One Health goals, including antimicrobial stewardship and methane mitigation.}, }
@article {pmid42200648, year = {2026}, author = {Gomez, A and Tisa, LS}, title = {A longitudinal roadside study of the New Hampshire alder root nodule microbiome.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0044626}, doi = {10.1128/aem.00446-26}, pmid = {42200648}, issn = {1098-5336}, abstract = {UNLABELLED: Actinorhizal plants are pioneer plants that colonize harsh environments and have been used for land reclamation. Their ability to thrive under these harsh conditions is due to their symbiotic association with the nitrogen-fixing bacterium Frankia and forming a root nodule structure. Although the plant root nodule primarily contains the symbiont Frankia, other members of the nodule community have been identified. This study represents an investigation of the effects of different environments on the nodule microbiome of Alnus rugosa, a shrub actinorhizal tree found at different locations within New Hampshire over a 3-year period. We utilized 16S rRNA and ITS amplicon sequencing to map the seasonal bacterial and fungal communities in the A. rugosa root nodule microbiome compared to rhizosphere and bulk soil communities. The relative abundance of Frankiaceae in root nodules fluctuated seasonally and by site. Sites with lower relative abundance of Frankiaceae in nodules had higher relative abundances of fungal nodule occupants. The roadside bacterial communities were distinct from those at the rural site, with Chitinophagaceae and Nitrosomonadaceae being characteristic members of the roadside rhizospheres and bulk soils, respectively. Soil zinc significantly affected all microbial communities. Our results indicate that the A. rugosa root nodule and soil microbiomes are responsive to different environmental variables like roadways and other microorganisms, and these responses need to be further elucidated for the optimization of future in situ actinorhizal projects.<br><br>IMPORTANCE: Actinorhizal plants like alders are important ecologically and economically as pioneering plants. The symbiotic association with Frankia greatly accelerates the growth of the host plant and indirectly does the same for neighboring plants. Actinorhizal trees provide an excellent mechanism to restore disrupted environmental sites and have been used to reclaim land that has been used for strip-mines, gravel pits, and soil stabilization of other landscapes disturbed by the effects of erosion and water runoff. Actinorhizal plants are found on coastal lands around the estuaries, and some are proven to be salt tolerant. Elucidating the dynamics of microbial community structure of the alder root nodules will help our understanding of the ability of these pioneering plants to reclaim degraded lands and to survive in diverse harsh environments. The role that other members of actinorhizal plant root nodule plays may be important to that survival ability. This field study reports on the influence of soil variables, habitats, and seasons on the dynamics of the actinorhizal microbiome.}, }
@article {pmid42200649, year = {2026}, author = {Peng, Y and Wu, J and Zhang, X and Wang, X and Wang, B and Zhang, C and Wang, C and Zhang, H and Liu, F and Lian, K and Li, Y and Liu, Q and Wang, H}, title = {A horizontal connectivity mode in coastal oceans: transport overrides stratification to govern microbiome network stability.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0044826}, doi = {10.1128/aem.00448-26}, pmid = {42200649}, issn = {1098-5336}, abstract = {UNLABELLED: Coastal ecosystems are critical biogeochemical reactors and biodiversity reservoirs, yet the mechanisms governing the community connectivity and stability of their foundational microbiomes remain poorly understood, particularly in anthropogenically influenced coastal oceans. Here, we systematically analyzed prokaryotic and microeukaryotic communities along both vertical and horizontal gradients in the Bohai-Yellow Sea, a model anthropogenically influenced and multi-stressed coastal ocean. We found that horizontal gradients, primarily driven by distance to coastline and latitudinal transitions, surpassed vertical gradients as the principal force governing microbial community assembly, connectivity, and stability. These horizontal factors overwhelmingly shaped microbial diversity, niche breadth, and biogeographic patterns, with prokaryotes displaying broader environmental adaptability and stronger cross-regional dispersal potential than microeukaryotes. Consequently, prokaryotes maintained higher spatial connectivity than microeukaryotes across both dimensions. This prokaryotic connectivity advantage was most pronounced within intermediate water masses. In contrast, vertical connectivity weakened with intensified water column stratification from the well-mixed Bohai Sea to the hydrographically complex South Yellow Sea. Horizontal gradients directly steered microbial co-occurrence network properties, driving a depth-dependent decline in network complexity and stability. This regional disparity was further underscored by distinct stability trade-offs: the semi-enclosed Bohai Sea fostered robust, modular networks, whereas the Yellow Sea systems formed highly connected but less modular, and thus more vulnerable, network architectures. Our findings reveal a dominant horizontal connectivity mode in coastal microbiomes, establishing a mechanistic link between large-scale environmental gradients and microbial network stability. This is a crucial advance for predicting ecological responses to anthropogenic and climate perturbations in vulnerable coastal zones.<br><br>IMPORTANCE: Coastal microbial communities drive global biogeochemical cycles, yet the principles governing their large-scale connectivity and microbial network stability remain elusive, particularly in anthropogenic disturbances regions. Focusing on the Bohai-Yellow Sea system, we establish that horizontal transport processes, modulated by land-sea exchange and latitudinal gradients, override vertical stratification as the dominant force structuring microbial assembly and interaction networks. We demonstrate that prokaryotes possess a stronger horizontal dispersal advantage than microeukaryotes, sustaining higher connectivity through intermediate water layers. This horizontal connectivity governs microbial network stability. Networks shift from robust, prokaryote-driven modular architectures in shallow coastal waters to fragile, microeukaryote-dominated patterns in deeper, stratified regions. These findings define a "horizontal connectivity mode" as a central organizing principle for coastal microbiomes, moving beyond descriptive biogeography to provide a mechanistic framework for predicting community resilience to anthropogenic and climate forcing.}, }
@article {pmid42200658, year = {2026}, author = {Blanchard, JL}, title = {Learning R with generative AI in a metagenomic data science course.}, journal = {Journal of microbiology &amp; biology education}, volume = {}, number = {}, pages = {e0034325}, doi = {10.1128/jmbe.00343-25}, pmid = {42200658}, issn = {1935-7877}, abstract = {Generative artificial intelligence (AI) tools are increasingly used by students in introductory coding courses; however, evidence-based guidance for integrating these tools into biology education remains limited. We examined student experiences with generative AI in a beginner R programming course focused on metagenomic data analysis. An anonymous survey (n = 43) captured quantitative ratings and qualitative reflections on how AI influenced learning, productivity, and problem-solving practices. Most respondents entered the course with little to no prior coding experience (79%) and reported frequent AI use throughout the semester, indicating that AI quickly became embedded in students' workflows. Students rated AI as highly helpful for suggesting R code, explaining syntax and logic, and brainstorming analyses, with over 70% endorsing each use case. However, AI errors were common: over 90% of students encountered incorrect output at least sometimes, including domain-specific misinterpretations and overcomplicated or syntactically incorrect code. Notably, students identified a need for clearer instructional support in core AI-mediated practices. The most frequent recommendation for course redesign was to introduce foundational R concepts prior to AI use, highlighting a threshold-competency principle for effective AI integration. Together, these findings suggest that generative AI can support novice coders but does not substitute for foundational instruction. Effective AI integration requires deliberate pedagogical scaffolding and reflection rather than code generation alone. These principles are likely to remain critical as AI tools become more capable and more widely adopted in undergraduate biology education.}, }
@article {pmid42200660, year = {2026}, author = {Guo, C and Yang, A and Zhang, X and Bai, W and Zhang, W-H}, title = {Leaf- and root-associated bacterial communities differ in their resistance and resilience to N disturbance in a temperate steppe.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0033226}, doi = {10.1128/aem.00332-26}, pmid = {42200660}, issn = {1098-5336}, abstract = {Enhanced deposition of nitrogen (N) has great impacts on grassland ecosystems. A decline in N deposition has occurred in many regions across the globe. Changes in N deposition alter the structure and functions of grassland ecosystems and bacterial community of soil and rhizosphere. However, the responses of plant microbiomes to N deposition and cessation of N input in terms of resistance and resilience have not been systematically evaluated. We examined the effects of N addition and cessation of N addition on leaf- and root-associated bacterial communities through a consecutive N addition and cessation of N addition experiment in a temperate grassland. We found that leaf-associated bacterial community exhibited lower resistance to N enrichment than root-associated bacterial community, which was mainly steered by leaf soluble sugars and leaf morphology via regulating functional taxa. In contrast, the root-associated bacterial community showed stronger resilience to cessation of N addition than leaf-associated bacterial community, which may be explained by the high N accumulation in roots and root morphology via regulating functional taxa. The greater resistance and resilience in the root-associated bacterial community may be attributed to the presence of host-related factors. Additionally, N enrichment-induced suppression of beneficial symbiotic microbes associated with the N cycle in the leaf-associated bacterial community was not readily recovered after cessation of N input. Conversely, microbes involved in carbon cycle and ecological restoration in the root-associated bacterial community showed a quick recovery after cessation of N enrichment. Our results offer valuable insights into the mechanisms by which changes in N input influence the plant microbial community.IMPORTANCEAs an integral component of ecosystems, the plant microbiome plays an important role in the response of grassland ecosystems to enhanced N deposition. Changes in N deposition influence bacterial communities of soil and rhizosphere of grassland ecosystems. However, whether and how the N deposition and cessation of N input impact microbiomes of plant species of temperate grasslands remain unexplored. Based on a long-term N-addition experiment in a temperate steppe, we discover that leaf- and root-associated bacterial communities respond differently to N addition and subsequent cessation of N addition. The leaf-associated bacterial community exhibits lower resistance to N enrichment than the root-associated bacterial community due to the unique environment of the phyllosphere, whereas the root-associated bacterial community shows stronger resilience to cessation of N addition than the leaf-associated bacterial community due mainly to the higher root N accumulation and morphology. These findings offer valuable insights into the impact and mechanism of N interference on the plant microbial community.}, }
@article {pmid41826827, year = {2026}, author = {Duduk, B and Galic, I and Stanojević, N and Stankovic, N and Rekanović, E}, title = {Microbial diversity of plant pathogens and insect endosymbionts in Reptalus artemisiae.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41826827}, issn = {1471-2180}, support = {451-03-136/2025-03/200214//Ministarstvo Prosvete, Nauke i Tehnolo&#x161;kog Razvoja/ ; 451-03-136/2025-03/200042//Ministarstvo Prosvete, Nauke i Tehnolo&#x161;kog Razvoja/ ; }, abstract = {BACKGROUND: Phloem-sap-feeding planthopper Reptalus artemisiae is an emerging vector of rubbery taproot disease (RTD) and syndrome basses richesses (SBR) in sugar beet, diseases associated with 'Candidatus Phytoplasma solani' and 'Candidatus Arsenophonus phytopathogenicus', respectively. Despite studies on related cixiids, the microbiome of R. artemisiae remains uncharacterized. Using a PCR-free metagenomic long-read shotgun sequencing approach, this study investigates the bacterial diversity associated with R. artemisiae, and provides genomic insight into two plant pathogens 'Ca. P. solani' and 'Ca. A. phytopathogenicus'.<br><br>RESULTS: Taxonomic assignment revealed six prokaryotic taxa in R. artemisiae: two plant pathogens ('Ca. P. solani' and 'Ca. A. phytopathogenicus') and four insect endosymbionts &#x2013; three primary endosymbionts ('Candidatus Vidania', 'Candidatus Purcelliella', and 'Candidatus Karelsulcia') and a secondary endosymbiont (Wolbachia). Community profiles showed a consistent presence of all four endosymbionts across five evaluated R. artemisiae individuals. Phylogenetic analyses of 16S rRNA gene sequences of primary endosymbionts confirmed strong congruence with the cytochrome oxidase subunit I phylogeny of the insect host, indicative of long coevolution and vertical transmission. In contrast, plant pathogen presence in R. artemisiae varied, with 'Ca. P. solani' and 'Ca. A. phytopathogenicus' each detected in three individuals. Genome assembly yielded a complete 774&#xa0;kb circular chromosome for 'Ca. P. solani' with streamlined metabolism featuring limited biosynthetic pathways, but a full arsenal of genes related to host&#x2013;pathogen interactions and pathogenicity typical for this biotrophs. The draft genome of 'Ca. A. phytopathogenicus' comprising 18 scaffolds totalling 3.11&#xa0;Mb and two plasmids shows a self-sufficient metabolism with several missing metabolic modules and presence of genomic islands, virulence factors, and a dynamic mobilome indicating a bacterium in transition that is reorganizing its genetic material, possibly in response to host interactions.<br><br>CONCLUSION: These findings represent the first in-depth characterization of R. artemisiae microbiome, highlighting a stable endosymbiont consortium and variable pathogen presence that emphasize ecological complexity in vector-pathogen-endosymbiont interactions. The assembled genomes enhance the understanding of microbial ecology, pathogen adaptation and transmission, offering resources for comparative genomics and potential applications in disease management strategies.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04915-x.}, }
@article {pmid41975251, year = {2026}, author = {Zhang, Y and Lai, W and Wang, M and Lai, S and Liu, Q and Luo, Q and Chen, Z and Zhao, D and Wang, Z and Yang, F}, title = {Gut microbial metabolic disorder in depression: insights from computational modeling and mediation analysis.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41975251}, issn = {1471-2180}, support = {62102065,62272321//National Natural Science Foundation of China/ ; 2022J05055//Joint Funds for the Innovation of Science and Technology, Fujian province/ ; XRCZX2022003//Fujian Medical University Research Foundation of Talented Scholars/ ; 24ywa61//Science and Technology Plan Project of Taizhou/ ; }, abstract = {UNLABELLED: Depression is increasingly recognized as a disorder not only of the brain but also of systemic metabolic dysfunction, particularly involving the gut microbiota. Integrating multi-cohort gut microbiome data with constraint-based metabolic modeling, this study investigates how microbial metabolic fluxes mediate depressive symptoms. Significant alterations in microbial pathways, notably those related to amino acid metabolism and neurotransmitter precursors, were identified. Causal mediation analysis showed that gut microbial composition influenced depressive symptoms, significantly mediated by specific metabolites including butyrate, Cu[2+], and tryptophan-derived compounds. This study, employing systems biology and mediation analysis, suggests that microbial metabolic activity mediates the gut-brain axis’s role in depression development and severity. These results enhance our understanding of microbiota-related mechanisms in mental health and highlight potential metabolic targets for depression treatment.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04991-z.}, }
@article {pmid42183319, year = {2026}, author = {Barzi, SM and Naderi, P and Haririzadeh Jouriani, F and Torkamaneh, M and Siadat, SD and Shamkani, F and Javadian, S and Ebrahimi-Rad, M and Saghiri, R and Nojoumi, SA}, title = {Impact pattern of heavy metals on gut microbiota in the polluted city of Tehran.}, journal = {Iranian journal of microbiology}, volume = {18}, number = {2}, pages = {204-216}, pmid = {42183319}, issn = {2008-3289}, abstract = {BACKGROUND AND OBJECTIVES: This article focuses on the effects of six heavy metals on gut microbiota, which plays a key role in human health. Gut microbiota plays a key role in metabolism, immunity, and maintaining homeostasis. Heavy metals can affect microbiota composition and function, with health consequences. Consuming large amounts of heavy metals may have harmful impacts, including alteration in microbial composition and bacterial population changes.<br><br>MATERIALS AND METHODS: Six heavy metals-cadmium, chromium (toxic metals), copper, zinc, iron, and selenium (beneficial trace elements)-were detected in peripheral blood, serum, or urine, while feces were used for 16S rRNA sequencing. Serum samples from 100 volunteers from Tehran (polluted area) and Firoozkooh (clean city) were collected. Subjects were analyzed for the presence of Escherichia coli, Bacteroides fragilis, Bifidobacterium longum, Lactobacillus acidophilus, Clostridium clostridioforme, Faecalibacterium prausnitzii and Akkermansia muciniphila to evaluate correlations between metals and microbial composition using biochemical, microbial, and molecular methods.<br><br>RESULTS: Escherichia coli and Bifidobacterium longum levels in polluted areas were not significantly different from those in unpolluted areas. Bacteroides fragilis in polluted areas was significantly higher compared to non-polluted locations. Clostridium, Akkermansia, Faecalibacterium, and Lactobacillus acidophilus were significantly lower in polluted areas, amounting to less than half the levels in clean areas. Heavy metal concentrations showed no gender differences in either location.<br><br>CONCLUSION: Some heavy metals change intestinal microbiota composition and metabolic profiles, potentially resulting in metabolic diseases and environmental risks.}, }
@article {pmid42183324, year = {2026}, author = {Karimi Behnagh, A and Bourbour, M and Moghaddam Shiri, S and Asadi, O and Honardoost, M}, title = {Microbiome and thyroid diseases: future precision studies of the gut-thyroid axis to facilitate the adjuvant treatment.}, journal = {Iranian journal of microbiology}, volume = {18}, number = {2}, pages = {172-185}, pmid = {42183324}, issn = {2008-3289}, abstract = {BACKGROUND AND OBJECTIVES: The gut microbiome is a key determinant of overall health, impacting numerous bodily functions, such as those of the endocrine glands. The effect of the microbiota on thyroid function has become a matter of interest, more so since the revelation of the possible link between intestinal disease and autoimmune thyroid disorders (AITDs). This review aims to provide an in-depth insight into the possible link between gut microbiota and thyroid diseases and metabolism of thyroid hormones.<br><br>MATERIALS AND METHODS: A set of online sources including, PubMed, Scopus, Google Scholar and CENTRAL were comprehensively searched to find the studies relevant to the topic of the review. Only reports in English were included in this review.<br><br>RESULTS: It has been proposed that damage to the intestinal barrier is a key element in the passage of antigens from the lumen into the bloodstream and their subsequent contact with the immune system. In addition to AITDs, dysbiosis has been shown to be linked with thyroid cancers, in which higher counts of certain bacteria associated with inflammation and carcinogenesis have been identified.<br><br>CONCLUSION: The majority of the available literature is focused on the differences in the microbial strain composition in individuals with thyroid disorders compared to that of healthy controls. Nonetheless, the current body of evidence has implied on possible role gut microbiome in the development of thyroid diseases.}, }
@article {pmid42183327, year = {2026}, author = {Abd El Rahmen, RA and Alghamdi, KS}, title = {Gut microbiome signatures associated with iron-deficiency anemia in young adults.}, journal = {Iranian journal of microbiology}, volume = {18}, number = {2}, pages = {186-196}, pmid = {42183327}, issn = {2008-3289}, abstract = {BACKGROUND AND OBJECTIVES: Iron is vital for both the body of the host and the metabolism of microbes. Pathogenic Enterobacteria need iron to grow and cause disease, but many good gut bacteria, like lactobacilli, do not require as much iron. Changes in the amount of iron available in the gut may therefore affect the makeup of the gut microbiome. Iron-deficiency anemia (IDA) represents the most prevalent nutritional disorder globally, concerning about 1.24 billion, mostly women and young people in low- and middle-income countries. This cross-sectional study looked at the link between iron-deficiency anemia and the makeup of the gut microbiome in young adults aged 18 to 30.<br><br>MATERIALS AND METHODS: We looked at hematological and iron status parameters as well as gut microbiota profiling using 16S rRNA gene sequencing. Differences in microbial diversity, taxonomic composition, and the relative abundance of bacteria that make short-chain fatty acids between people with IDA and healthy controls were investigated.<br><br>RESULTS: The results show that iron-deficiency anemia is linked to different gut microbiome signatures. This suggests that there may be connections between iron levels and the structure of microbial communities.<br><br>CONCLUSION: These results show how important it is to study the gut microbiome to understand iron-deficiency anemia. They also show how important it is to do long-term, interventional studies to figure out how these associations work and what they mean for health.}, }
@article {pmid42183373, year = {2026}, author = {Petty, CJ and Isaman, M and Perez, LP and Millard, S and Ortiz, M and Freeman, LR}, title = {Sex differences in hedonic feeding and characterizing the effects of antibiotic-induced microbiome disruption.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-9557496/v1}, pmid = {42183373}, issn = {2693-5015}, abstract = {Background Obesity continues to be a public health issue in our country. Additionally, there continues to be a higher incidence of severe obesity for women compared to men. Among the proposed causes of obesity is increased hedonic feeding: food intake driven by pleasure and palatability rather than physiological hunger. While hedonic feeding is not the sole culprit for the obesity epidemic, it is a major contributing factor. Emerging evidence shows that the gut microbiome impacts feeding behavior and studies have shown that individuals with obesity exhibit an altered gut microbiome. Methods Here, we used a novel behavioral economics (BE) approach to evaluate hedonic feeding in male and female Sprague-Dawley rats for a high-fat palatable (HFP) reward pellet, before and after antibiotic administration. Specifically, we measured demand elasticity (α), the rate at which demand falls when the price or effort required increases, and demand at null cost (Q 0), a prediction of consumption at null effort extrapolated from the animals' consumption at low price. Results We determined a higher demand at null cost (Q 0) for the HFP reward pellet for females compared to males, as we have observed previously. Next, we administered an antibiotic cocktail in the drinking water to disrupt the gut microbiome and investigate a role of the gut microbiome in hedonic feeding. Female rats administered antibiotics continued to have a higher demand at null cost compared to male control rats, but no statistically significant differences were determined between male and female rats administered antibiotics. We characterized the fecal microbiome genus-level composition and short chain fatty acid (SCFA) levels before and after antibiotic administration. We also characterized serum SCFA and bile acid levels at the end of the study. Conclusions We did not determine a significant effect of antibiotics on hedonic feeding, despite disruption to the fecal microbiome. Additionally, we did not observe striking baseline sex differences in fecal microbiome diversity and composition. This brings to question whether the gut microbiome contributes to sex differences in hedonic feeding. More research will be necessary for network factors such as microbiome - bile acid effects on feeding that exhibit sex differences.}, }
@article {pmid42184156, year = {2026}, author = {Sumner, JT and Hartmann, EM}, title = {Uncovering Mechanistic Determinants of Host Phenotypes Using Microbial Systems Biology.}, journal = {Integrative and comparative biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/icb/icag052}, pmid = {42184156}, issn = {1557-7023}, abstract = {Host phenotypes are caused by a multitude of interacting factors, including but not limited to the microbiome. The advent of high throughput sequencing technology revolutionized our ability to characterize host-associated microbial communities. Early microbiome profiling studies often focused on strategies such as 16S rRNA gene amplicon sequencing to assess the relative abundance of host-associated microbiota. Waves of technological improvement and an ever-increasing knowledge base led to accessible multiomic profiling (i.e. integration of multiple different 'omics assays). Rather than just associating phenotypes with patterns of microbial taxa, we can leverage multiple omics to advance mechanistic explanations for how microbiota cause or are affected by host phenotypes. However, it is still challenging to determine which assays (or combinations of assays) to use and how best to integrate their results. We review bioinformatic strategies for integrating diverse microbiome sequencing data and experimental approaches for validating correlative findings. We also present perspectives on how systems biology connects observational and experimental microbiology. We analyze the strengths of different 'omics methods and how complementary combinations economically improves biological discovery. Augmenting relative abundance data with absolute quantitation (i.e. exact measurement of microbial biomass) can dramatically change the resulting insights. Functional profiling (i.e. measurement of microbial gene content or expression using high-throughput sequencing) ultimately enables linking microbial profiles with phenotypic trait expression. Finally, while many sequencing studies are observational and thus limited to correlative findings, it is critical to integrate experimental validation to mechanistically explain relationships between the microbiome and host phenotypes. Host-associated microbial ecosystems are complex. Confounded microbial and host factors make it challenging to determine the mechanisms underlying host-microbiome dynamics. Innovative experimental systems, including non-model organisms, synthetic consortia, and tissue-culture models, enable high-throughput manipulation of microbiomes to test hypotheses generated from correlative results and advance translational research.}, }
@article {pmid42184295, year = {2026}, author = {Wong, SH}, title = {The human microbiome at translational crossroads: an ecological and causal perspective.}, journal = {Singapore medical journal}, volume = {67}, number = {5}, pages = {279-287}, pmid = {42184295}, issn = {2737-5935}, mesh = {Humans ; *Translational Research, Biomedical ; Probiotics/therapeutic use ; *Microbiota ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Ecology ; }, abstract = {The human microbiome has emerged as a central focus of biomedical research, driven by interest in its translational potential for chronic diseases. Although compelling associations link microbial alterations to gastrointestinal, metabolic, neuropsychiatric and systemic conditions, successful clinical translation remains limited. This perspective contends that the principal barrier is not biological relevance but the application of reductionist thinking to an inherently complex ecological system, compounded by an incomplete understanding of causality. This review examines the gradient of causal confidence across gut-organ axes, from established roles in digestive disorders to less established distal associations, as well as highlights the epistemological challenges underlying microbiome research. A critical appraisal of current strategies, including probiotics, live biotherapeutics and faecal microbiota transplantation, suggests that progress requires ecological reasoning, causal rigour and systems-level integration. Moving from association to intervention demands approaches that account for host-microbiome complexity rather than oversimplified microbial targeting.}, }
@article {pmid42184480, year = {2026}, author = {Sihra, N and Malde, S}, title = {Pathophysiological mechanisms underlying the overactive bladder.}, journal = {Autonomic neuroscience : basic &amp; clinical}, volume = {266}, number = {}, pages = {103440}, doi = {10.1016/j.autneu.2026.103440}, pmid = {42184480}, issn = {1872-7484}, abstract = {Overactive bladder is a heterogenous condition, with several phenotypes, and a complex pathophysiology. The principal pathophysiological mechanisms for the development of OAB are based on the urotheliogenic, myogenic, neurogenic and urethrogenic theories. The most well-described contributors to these pathophysiological mechanisms are metabolic syndrome, sex hormone deficiency, altered urinary microbiota, functional gastrointestinal disorders, affective disorders, autonomic nervous system dysfunction, and bladder outflow obstruction. This review describes the normal physiology of the lower urinary tract, and summaries the pathophysiological mechanisms behind overactive bladder.}, }
@article {pmid42184529, year = {2026}, author = {Wang, R and Chen, H}, title = {Metagenomic insights into vertical migration of soil antibiotic and metal(loid) resistance genes under long-term organic fertilizer application and irrigation.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142479}, doi = {10.1016/j.jhazmat.2026.142479}, pmid = {42184529}, issn = {1873-3336}, abstract = {Agricultural irrigation is associated with antibiotic resistance gene (ARG) transmission and resistome succession through the integration of exogenous and indigenous soil communities. However, the long-term field-scale impacts of organic irrigation on vertical resistome migration and its ecological consequences remain underexplored. This study employed metagenomic analyses and field surveys to bridge these knowledge gaps. The results showed that ARGs and metal(loid) resistance genes (MRGs) were most abundant and diverse at 0-20 cm depth, with distinct characteristics in deeper layers depending on manure type. Cattle manure-irrigated soils exhibited a greater potential for vertical ARG diffusion than chicken manure-irrigated soils, despite lower surface-level enrichment. ARG distribution was more strongly associated with groundwater and soil background factors than with organic fertilizer inputs. Mobile genetic elements (MGEs) and heavy metal concentrations were key factors associated with resistome succession. Compared to the control, contigs associated with both ARGs and MRGs increased 5.8-fold and 3.1-fold in chicken and cattle manure-irrigated soils, respectively, suggesting a potentially important role for prophages. While control contigs were distributed in deeper layers, irrigated soils showed pronounced surface enrichment. Irrigation was linked to increased network density and complexity, with chicken manure-irrigated soils exhibiting higher levels of antibiotic-resistant bacteria (ARB). Notably, opportunistic pathogens carrying ARGs, including Ralstonia pickettii and Stenotrophomonas maltophilia, were enriched in irrigated profiles. Microbiome, MGEs, and abiotic factors were collectively associated with resistome succession, with deterministic processes contributing substantially to community assembly. This study provides new insights into the vertical distribution and inferred succession of the resistome in organically irrigated soils.}, }
@article {pmid42184614, year = {2026}, author = {Pradhan, S and Nischay,  and Shivay, YS and Sharma, S}, title = {Transplantation of rhizosphere microbiome from tomato enhances salinity stress tolerance in chilli and bell pepper.}, journal = {Plant physiology and biochemistry : PPB}, volume = {235}, number = {}, pages = {111323}, doi = {10.1016/j.plaphy.2026.111323}, pmid = {42184614}, issn = {1873-2690}, abstract = {Salinity stress adversely affects plant growth and development, leading to reduced quality and yield. Traditional approaches, including chemical amendments and bioinoculants, often show limited effectiveness under natural conditions. To overcome these limitations, this study employed a top-down rhizosphere engineering approach through rhizosphere microbiome transplantation (RMT) to mitigate salinity stress. First, a salt stress-acclimatized microbiome was generated by repeated plant growth cycles (PGCs) through RMT by ramping up salinity levels along the PGCs in a salt-susceptible tomato cultivar. Then, the generated salt stress-acclimatized rhizosphere microbiome was transplanted to mitigate salinity stress in chilli and bell pepper. RMT effectively increased various plant growth parameters in both plant model systems under salinity stress (150 mM in chilli and 170 mM in bell pepper). In rhizosphere microbiome treated plants, there was a reduction in stress markers, viz., malondialdehyde and proline levels. Further, the K[+]/Na[+] ratio increased by 1.94- to 3.47- fold in plants with RMT + salt stress. In addition, the expression level of salt stress-responsive gene, SlHKT1;1, increased in RMT plants under salt stress in both chilli and bell pepper compared to only salt treated plants. Our study showed that salt stress-acclimatized RMT from tomato is an effective and sustainable strategy to enhance salinity tolerance in other plants of the Solanaceae family, under natural conditions.}, }
@article {pmid42184623, year = {2026}, author = {Su, Y and Mai, X and Wang, Z and Feng, C and Huang, Z and Li, Z}, title = {Multi-omics-based characterization and differentiation of fecal microbiota and metabolite profiles in high- and low-yielding laying hens.}, journal = {Poultry science}, volume = {105}, number = {9}, pages = {107003}, doi = {10.1016/j.psj.2026.107003}, pmid = {42184623}, issn = {1525-3171}, abstract = {Egg-laying rate is a crucial economic trait that significantly contributes to the poultry industry. Compelling evidence has clearly demonstrated that gut microbiota is closely associated with production performance in chickens. Given that suboptimal egg production performance has become one of the bottlenecks constraining the development of the indigenous layer industry in China, the present study aimed to systematically compare the fecal microbiome and metabolome data from high-yielding (HR) and low-yielding (LR) Tianfu powder-shell laying hens, and further evaluate the potential interactions between microbes and metabolites. Our results revealed that fecal microbiota diversity and composition in HR chickens were significantly different from those in LR chickens. Moreover, Lactobacillus, Bacillus, and Bacteroides were highly enriched in HR chickens and exhibited a significantly positive correlation with laying rate. In contrast, Romboutsia and Aerococcus were more abundant in LR chickens, and Aerococcus was significantly negatively correlated with laying rate. The KEGG pathway enrichment analysis suggested that the fecal microbiota of HR chickens was mainly enriched in phosphotransferase system, glycerophospholipid metabolism, and amino sugar metabolism. Through untargeted metabolomics analysis, we observed that the abundances of L-glutamic acid, L-threonine, L-valine, curcumin, fumaric acid, and L-glutamine were obviously higher in HR chickens and were significantly positively correlated with laying rate. Furthermore, the correlation analysis revealed that the abundances of Akkermansia, Bacteroides, Christensenellaceae_R-7 group, and Parabacteroides were positively correlated with most of the identified key metabolites. These findings offer a promising strategy to manipulate the gut microbiota and metabolites, ultimately improving egg production in the poultry industry.}, }
@article {pmid42184640, year = {2026}, author = {Fang, L and Zhang, H and Sun, C and Hu, X and Wright, D and Zhou, H}, title = {The current and future perspective of ChickenGTEx project and its applications in precision breeding.}, journal = {Poultry science}, volume = {105}, number = {9}, pages = {107132}, doi = {10.1016/j.psj.2026.107132}, pmid = {42184640}, issn = {1525-3171}, abstract = {The Chicken Genotype-Tissue Expression (ChickenGTEx) project was established to systematically characterize the regulatory landscape of the chicken genome and to accelerate the translation of functional genomics into precision breeding. By integrating whole-genome sequencing with multi-tissue transcriptomic profiling, ChickenGTEx provides a comprehensive atlas of gene expression regulation across diverse tissues and physiological systems. Current findings demonstrate that complex production traits are governed by coordinated regulatory networks rather than isolated loci, with substantial contributions from tissue-specific gene expression, structural variation, and genotype-by-sex interactions. Sex-dependent regulatory effects further refine the genetic architecture of metabolic, immune, and reproductive traits, highlighting the importance of incorporating sex as a biological variable in genomic analyses. Application of integrative omics frameworks within elite layer populations has revealed multilayer regulatory mechanisms underlying extended laying performance, feed efficiency, metabolic health, and eggshell quality. By partitioning phenotypic variance into genetic, regulatory, and host-microbiome components, these approaches move beyond association-based mapping toward causal inference and biological interpretation. Importantly, validated regulatory loci identified through ChickenGTEx and related analyses provide actionable markers for genomic selection and rational targets for precision genome modification. Looking forward, continued expansion of regulatory atlases, incorporation of single-cell and longitudinal data in diverse environmental conditions, and integration of functional annotation into breeding pipelines will further enhance prediction accuracy and sustainable genetic improvement. The ChickenGTEx project thus represents a foundational platform bridging functional genomics and practical poultry breeding.}, }
@article {pmid42184718, year = {2026}, author = {El-Sehrawy, AAMA and Soleimani Samarkhazan, H}, title = {The silent pharmacist: Harnessing the gut microbiome to improve therapy in hematologic malignancies.}, journal = {Translational oncology}, volume = {70}, number = {}, pages = {102833}, doi = {10.1016/j.tranon.2026.102833}, pmid = {42184718}, issn = {1936-5233}, abstract = {The gut microbiome, a complex ecosystem of microorganisms, is now recognized as a key determinant of drug efficacy and toxicity, giving rise to the field of pharmacomicrobiomics. This review decodes the profound influence of the gut microbiome on treatment outcomes for hematologic malignancies. We explore the tripartite mechanistic pathways through which gut microbes act: the direct enzymatic biotransformation of chemotherapeutic agents, the indirect immunomodulation of systemic and anti-tumor responses, and the preservation of mucosal barrier integrity to prevent devastating complications like graft-versus-host disease (GVHD). The manuscript details how the microbiome interacts with specific drug classes, from conventional chemotherapies like cyclophosphamide to cutting-edge immunotherapies like immune checkpoint inhibitors and CAR-T cells, shaping their clinical success. Furthermore, we discuss the translational potential of targeting this "silent pharmacist" through fecal microbiota transplantation, next-generation probiotics, and dietary interventions. Finally, we highlight the main translational opportunities, current limitations, and future clinical priorities for integrating microbiome science into hematology, paving the way for more personalized and improved cancer care.}, }
@article {pmid42184757, year = {2026}, author = {Azadi, S and Fadaei-Kenarsary, M and Sahebi, K and Baneshi, M and Tajbakhsh, A and Niknahad, H and Negahdaripour, M}, title = {Metformin as a promising therapeutic option for reducing substance withdrawal syndromes: A narrative review.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {200}, number = {}, pages = {119553}, doi = {10.1016/j.biopha.2026.119553}, pmid = {42184757}, issn = {1950-6007}, abstract = {Substance withdrawal syndromes pose significant challenges in addiction treatment, often leading to poor treatment adherence and high relapse rates. This review evaluates metformin's potential as a therapeutic option for substance withdrawal syndromes, focusing on its mechanisms (AMPK activation, neurotransmitter modulation, gut microbiome effects) and clinical implications. Proposed mechanisms of action, including the involvement of signaling pathways, neurotransmitter regulation, and gut microbiome modulation, are also discussed. The study also highlights key areas requiring further investigation, such as the need for well-designed clinical trials, exploration of metformin dosage and treatment duration, and a deeper understanding of the specific molecular pathways underlying metformin's impact on withdrawal syndromes. Preclinical and clinical evidence suggest that metformin alleviates withdrawal symptoms and reduces relapse risk, but further research is needed to optimize dosing and validate efficacy. Overall, this review supports metformin's potential as a promising therapeutic option for managing substance withdrawal syndromes, offering improved treatment outcomes and reduced relapse rates and vulnerabilities.}, }
@article {pmid42184815, year = {2026}, author = {Bełkot, Z and Adamski, MG and Strzałkowska, ZJ and Domańska, ED and Kłosińska, D and Kunstman, G and Skoczek, D and Pławińska-Czarnak, J}, title = {Full-Length 16S and 18S rRNA Long-Read Sequencing Reveals Gut Microbiome Diversity in the European Brown Hare (Lepus europaeus).}, journal = {Environmental microbiology reports}, volume = {18}, number = {3}, pages = {e70358}, doi = {10.1111/1758-2229.70358}, pmid = {42184815}, issn = {1758-2229}, mesh = {Animals ; *Hares/microbiology ; *Gastrointestinal Microbiome/genetics ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *RNA, Ribosomal, 18S/genetics ; Phylogeny ; Sequence Analysis, DNA ; Biodiversity ; }, abstract = {The European brown hare (Lepus europaeus) is a declining wildlife species of ecological and epidemiological importance, yet its intestinal microbiome remains poorly characterized. Here, Oxford Nanopore long-read sequencing was used to analyse full-length 16S and 18S rRNA genes from pooled large-intestine contents of 30 healthy hares divided into three groups. Comparative taxonomic assignment at 95% and 80% sequence identity thresholds revealed striking differences in diversity estimates, with the lower threshold uncovering up to ten-fold more taxa. Across all samples, 40 phyla, 360 families, 1027 genera, and 3373 species were identified, including 30 taxa not previously reported in lagomorphs. These included Monoglobus pectinilyticus, Ruminococcus champanellensis, Odoribacter splanchnicus, Butyricimonas virosa, and Akkermansia muciniphila, associated with pectin degradation, cellulose hydrolysis, butyrate production, mucin degradation, bile acid transformation, and nitrogen recycling. Several taxa relevant to both animal and human health were also detected, supporting hares as sentinels of environmental microbiota within a One Health framework. These findings show that analytical parameter selection strongly shapes microbiome interpretation and provide the most comprehensive gut microbiome profile of the European brown hare to date. The study expands lagomorph microbial ecology and highlights long-read sequencing as a valuable tool for wildlife microbiome surveillance in undercharacterized host species globally.}, }
@article {pmid42184816, year = {2026}, author = {Miao, J and Zhang, C and Jiang, Q and Yao, Z and Cao, K and Chen, J and Wang, H and Liu, N}, title = {Complete Genome of an Alkali-Resistant Rhizobium anhuiense Symbiont of Pea Reveals Species-Specific Plasmid Fusion and Genomic Plasticity.}, journal = {Environmental microbiology reports}, volume = {18}, number = {3}, pages = {e70366}, doi = {10.1111/1758-2229.70366}, pmid = {42184816}, issn = {1758-2229}, support = {//Team development funding from Xianghu Laboratory, the Xiaoshan District Government and the Zhejiang Provincial Government/ ; //2025 Special Cooperation Program between Xianghu Laboratory and Chinese Academy of Agricultural Science/ ; }, mesh = {*Plasmids/genetics ; *Genome, Bacterial ; *Pisum sativum/microbiology/growth &amp; development ; Symbiosis ; Phylogeny ; *Rhizobium/genetics/isolation &amp; purification/classification/physiology/drug effects ; *Alkalies/pharmacology ; Root Nodules, Plant/microbiology ; Gene Transfer, Horizontal ; }, abstract = {The rhizosphere microbiome is crucial for plant growth and stress resilience in sustainable horticulture. Here, we report the complete genome assembly and functional characterisation of Rhizobium anhuiense Xianghu001, a nitrogen-fixing symbiont isolated from pea (Pisum sativum) root nodules. A hybrid assembly strategy combining PacBio reads and Illumina reads yielded a 7.36 Mb high-quality assembly comprising one chromosome, one megaplasmid and four accessory plasmids, encoding 6899 protein-coding genes, of which 66.64% are located on the chromosome. Phylogenomics and synteny confirmed its placement within R. anhuiense. We detected a lineage-specific plasmid fusion forming the megaplasmid, while three accessory plasmids appear to be strain-specific and potentially acquired via horizontal gene transfer. Insertion sequence profiling suggests genome rearrangement shaping plasmid structure. To explore intraspecies diversity, we sequenced six additional local R. anhuiense isolates from pea. Despite their close geographic origin, genomic comparison revealed extensive divergence. Phenotypic assays demonstrated that Xianghu001 significantly promotes pea growth under nitrogen-deficient conditions, increasing chlorophyll content and nitrogen accumulation. It synthesises high levels of IAA (~184 mg/L), tolerates mild salinity (≤ 0.15% NaCl) and grows optimally at alkaline pH (8.0-10.0). Our findings provide a comprehensive genomic and functional framework for R. anhuiense Xianghu001 and underscore its potential as a biofertiliser.}, }
@article {pmid42184901, year = {2026}, author = {Green, JB and Haykal, D}, title = {AI and longevity medicine: unlocking predictive and preventive strategies for healthy aging.}, journal = {Presse medicale (Paris, France : 1983)}, volume = {}, number = {}, pages = {104359}, doi = {10.1016/j.lpm.2026.104359}, pmid = {42184901}, issn = {2213-0276}, abstract = {Longevity medicine is transforming healthcare by shifting the focus from disease treatment toward the preservation of function, resilience, and healthspan. In parallel, artificial intelligence (AI) has emerged as a powerful catalyst accelerating this transition through the integration and interpretation of multidimensional biological and behavioral data. AI-driven systems can now analyze genomics, epigenomics, proteomics, microbiome signatures, digital biomarkers, lifestyle metrics, and environmental exposures to identify early deviations from healthy aging trajectories before clinical disease manifests. These predictive capabilities enable personalized preventive strategies tailored to an individual's biological aging profile rather than chronological age alone. AI-supported longevity medicine therefore facilitates precision prevention through adaptive interventions involving nutrition, metabolic optimization, sleep regulation, stress management, continuous biosensing, and targeted therapeutics. Moreover, AI contributes to the evolution of healthcare systems from reactive episodic care toward adaptive and continuously monitored models emphasizing long-term physiological resilience. However, the integration of AI into longevity medicine also raises important scientific, ethical, and societal challenges, including data fragmentation, unequal access to preventive technologies, risks of overmedicalization, and concerns regarding privacy and governance. Bridging siloed biomarker ecosystems through interoperable data infrastructures, federated learning, and digital twin technologies will be essential for clinically meaningful predictive models. Ultimately, AI has the potential to redefine modern preventive medicine by enabling proactive, personalized, and age-resilient healthcare. The future success of AI-enhanced longevity medicine will depend on ensuring that technological innovation remains accurate, ethically grounded, clinically relevant, and equitably accessible across populations.}, }
@article {pmid42184963, year = {2026}, author = {Riben Grundström, C and Lund, B and Bostanci, N and Silbereisen, A and Pennhag, A and Koistinen, IS and Zha, Y and Damdimopoulos, A and Belibasakis, GN and Hultin, M}, title = {Systemic Antibiotics in the Surgical Treatment of Peri-Implantitis: Impact on the Salivary Microbiome.}, journal = {Journal of clinical periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jcpe.70143}, pmid = {42184963}, issn = {1600-051X}, support = {//Region Uppsala/ ; //Swedish Dental Association/ ; //Public Health Agency of Sweden/ ; //Steering Group for Collaborative Odontological Research at Karolinska Institutet and Stockholm City County/ ; //Centre for Innovative Medicine (CIMED)/ ; //Folktandv&#xe5;rdens Region Uppsala/ ; }, abstract = {AIM: To exploratorily compare the shifts in the salivary microbiome composition after administration of two combined systemic antibiotic regimens used in the surgical treatment of peri-implantitis.<br><br>MATERIALS AND METHODS: A subset of 27 patients treated surgically for peri-implantitis with an adjunctive 7-day course of systemic antibiotics were included (group A, amoxicillin and metronidazole; group B, phenoxymethylpenicillin and metronidazole). Unstimulated saliva was collected before surgery followed by 8&#x2009;days, 14&#x2009;days, 6 months and 12 months post surgery. Microbiome profiling was performed using standardised and automated pipelines for DNA extraction and whole genome shotgun sequencing (WGS).<br><br>RESULTS: WGS identified 498 species across 194 genera and 16 phyla, with Firmicutes and Actinobacteria being the most abundant. A distinct decrease in alpha diversity was observed on Day 8 relative to baseline across both antibiotic regimens, with signs of richness recovery by Day 14. Alpha and beta diversity analyses showed no statistically significant differences between interventions over the 12-month observation period.<br><br>CONCLUSION: Both adjunctive antibiotic regimens applied in the surgical treatment of peri-implantitis caused comparable ecological disturbances in the salivary microbiome, with no microbiological or clinical evidence supporting the superiority of one regimen over the other.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov identifier: NCT02185209.}, }
@article {pmid42185030, year = {2026}, author = {Gould, AAM and Walsh, NP and Tipton, MJ and Zurawlew, MJ and Robson, SC and Shute, JK and Watts, JEM and Tyson, HC and Robinson, MR and Roberts, AJ and Rawcliffe, AJ and Hemingway, R and Corbett, J}, title = {Gastrointestinal microbiota and barrier integrity in individuals who develop exertional heat illness and pair-matched controls: A prospective observational cohort study.}, journal = {Experimental physiology}, volume = {}, number = {}, pages = {}, doi = {10.1113/EP093100}, pmid = {42185030}, issn = {1469-445X}, support = {//Ministry of Defence/ ; }, abstract = {It has been hypothesised that the composition of the gastrointestinal (GI) microbiota contributes to exertional heat illness (EHI) aetiology, but relevant empirical data in humans are lacking. Utilising a unique prospective study design, stool samples and resting blood samples were obtained from 550 individuals prior to (within 3 days) undertaking a 6.4-mile/10.3 km loaded march (median (IQR) duration = 66 (1) min), during which 79 individuals developed an EHI (mild, n = 55; severe, n = 24). These individuals were pair-matched for body mass index and cardiorespiratory fitness to individuals who did not develop an EHI during the same exercise (non-EHI). Our primary outcome measure was the composition of the gut microbiota, determined using 16S ribosomal RNA (rRNA) amplicon sequencing of stool samples. Secondary outcomes included the concentration of baseline blood biomarkers of GI barrier integrity (intestinal fatty acid binding protein, claudin 3, zonulin, lipopolysaccharide binding protein, and soluble cluster of differentiation 14). No significant differences in the composition of the GI microbiota (α-diversity, β-diversity, relative abundance, differential abundance) were observed between EHI cases and matched non-EHI controls (P > 0.05). Similarly, no significant between-group differences in biomarkers of GI barrier integrity were observed. These findings persisted when conducting additional sub-group analysis of severe EHI cases only, and additional sensitivity analysis excluding individuals who reported non-steroidal anti-inflammatory drug use and/or GI disorders. In conclusion, when potential confounding factors are controlled for, the composition of the GI microbiota and baseline GI barrier integrity do not appear to predispose to increased EHI risk during strenuous exercise.}, }
@article {pmid42185048, year = {2026}, author = {Gibson, OR}, title = {The gut microbiome and thermoregulatory response: Relevance of the microbiota in heat-related illness?.}, journal = {Experimental physiology}, volume = {}, number = {}, pages = {}, doi = {10.1113/EP093905}, pmid = {42185048}, issn = {1469-445X}, }
@article {pmid42185250, year = {2026}, author = {Dar, HY and Fang, J and Patil, S and Roy, NK and Agarwal, S and Weitzmann, MN and Jones, RM and Bilezikian, JP and Pacifici, R}, title = {Bacterial specificity of the gut microbiome predicts bone density in primary hyperparathyroidism.}, journal = {Bone research}, volume = {14}, number = {1}, pages = {}, pmid = {42185250}, issn = {2095-4700}, support = {DK124821//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; DK124821//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Bone Density/physiology ; Animals ; *Hyperparathyroidism, Primary/microbiology/physiopathology ; Female ; Male ; Middle Aged ; Mice ; Th17 Cells/immunology ; Aged ; Tumor Necrosis Factor-alpha/metabolism ; }, abstract = {Primary hyperparathyroidism causes mild-to-severe bone loss, but the reason for this heterogeneity is unclear. We investigated the role of the microbiome in 50 primary hyperparathyroidism patients. Microbiome transfers from primary hyperparathyroidism patients with and without osteoporosis to germ-free mice replicated the human bone phenotype and regulated TNF[+] T cells and Th17 cells in mice. Accordingly, circulating TNF[+] T cells and Th17 cells and TNF/IL17 production predicted bone density in primary hyperparathyroidism patients. Bifidobacterium longum, TNF[+] T cells, and Th17 cells were mediators of bone loss in primary hyperparathyroidism patients, while Bifidobacterium longum supplementation caused PTH to expand TNF[+] T cells and Th17 cells and induce bone loss in mice. Our findings link Bifidobacterium longum-induced TNF[+] T cells and Th17 cells to bone loss in patients with primary hyperparathyroidism. Bifidobacterium longum abundance may determine the skeletal phenotypes of patients with primary hyperparathyroidism and allow prediction of their risk of bone loss. Microbiome modifications by antibiotics or precision probiotics might offer novel preventive approaches for the skeletal complications of primary hyperparathyroidism.}, }
@article {pmid42185302, year = {2026}, author = {Nishisaka, CS and Quevedo, HD and Pellegrinetti, TA and de Almeida Godoy, F and Rossmann, M and Mendes, LW and Mendes, R}, title = {Bacterial inoculation drives microbiome-mediated resistance to a soil-borne pathogen in wheat.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01021-8}, pmid = {42185302}, issn = {2055-5008}, support = {2020/06077-9//S&#xe3;o Paulo Research Foundation (Fapesp)/ ; 2025/11610-1//S&#xe3;o Paulo Research Foundation (Fapesp)/ ; 402654/2023-4//National Council for Scientific and Technological Development (CNPq)/ ; }, abstract = {Soil microbiomes are fundamental to plant health, mediating nutrient cycling, stress tolerance, and pathogen defense. However, soil-borne pathogens such as Bipolaris sorokiniana severely constrain wheat productivity. Despite growing interest, the mechanisms by which beneficial bacterial inoculation reshapes rhizosphere microbial communities to enhance disease resistance remain poorly understood. Here, we isolated three bacterial strains, Streptomyces virginiae CMAA1738, Paenibacillus ottowii CMAA1739, and Pseudomonas inefficax CMAA1741, with antagonistic activity against B. sorokiniana, and evaluated their effects on wheat under controlled conditions. Through plant bioassays, bacterial inoculation reduced disease severity by ~60% and promoted root growth. Metataxonomic and metagenomic analyses revealed shifts in the structure and functional potential of the rhizosphere microbiome. Structural equation modeling indicated that inoculation was the primary driver of microbiome restructuring and disease suppression. Notably, inoculation restored the diversity of plant growth-promoting genes and biosynthetic gene clusters reduced by pathogen infection, enriching functions associated with stress tolerance, nutrient metabolism, and secondary metabolite production. In addition, Random Forest analysis revealed that variation in disease severity under pathogen pressure was associated with differences in bacterial community composition. Together, these findings demonstrate that bacterial inoculation can restructure the rhizosphere microbiome and restore key functional traits linked to plant resilience.}, }
@article {pmid42185318, year = {2026}, author = {Nguyen, UT and Salamzade, R and Sandstrom, S and Swaney, MH and Townsend, EC and Wu, SY and Cheong, JZA and Sardina, JA and Ludwikoski, I and Rybolt, M and Wan, H and Carlson, CM and Ferro, J and McArthur, O and Suh, WS and Zarnowski, R and Andes, DR and Currie, CR and Kalan, LR}, title = {Large-scale investigation for antimicrobial activity reveals newly-identified defensive species across the healthy skin microbiome.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73524-z}, pmid = {42185318}, issn = {2041-1723}, support = {U19AI142720//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R35GM137828//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, abstract = {The skin microbiome forms a protective barrier to pathogens, including through the production of antimicrobial metabolites. Here, we present EPIC[HHS], a large and taxonomically diverse skin microbiome culture collection of 968 strains from eight body sites. EPIC[HHS] captures >95% of cumulative species-level abundance across 268 skin metagenomes. It includes isolates present at <0.1% relative abundance and the cultured representatives for eight species not previously isolated, markedly expanding current skin microbiome resources. A contact-independent screen assaying ~14,000 pairwise interactions against 22 pathogens revealed widespread antagonism with striking enrichment for antifungal activity. Finally, functional genomic analysis, including 287 EPIC[HHS] isolate genomes, demonstrated a diverse landscape of skin-associated biosynthetic gene clusters that are mostly uncharacterized. Together EPIC[HHS], its functional and genomic characterization, establishes the skin microbiome as a reservoir for specialized metabolism and provides a platform for microbiome-based antimicrobial discovery.}, }
@article {pmid42185319, year = {2026}, author = {Lima, RD and Bauer, OR and Pauer, H and Hajiarbabi, K and Moreira, DA and Parente, TE and Ferreira, RBR}, title = {Cutibacterium acnes inhibits Staphylococcus lugdunensis biofilm formation through inhibition of autolysis and purine biosynthesis.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01014-7}, pmid = {42185319}, issn = {2055-5008}, abstract = {Cutibacterium acnes is a key member of the human skin microbiome that contributes to host homeostasis. Staphylococcus lugdunensis, while also a resident of the skin microbiota, is an opportunistic pathogen capable of causing severe infections, associated with its ability to form biofilms. We previously showed that C. acnes secretes molecules that inhibit S. lugdunensis biofilm formation without affecting planktonic growth. Here, we demonstrate that C. acnes-derived molecules also significantly reduced S. lugdunensis adherence to and invasion of human epithelial cells, as well as adhesion to keratinocytes. Transcriptomic analysis revealed repression of genes involved in S. lugdunensis purine biosynthesis and induction of the autolysis negative regulators, lrgA and lrgB. Functional assays confirmed that exposure to C. acnes molecules inhibits autolysis and extracellular DNA (eDNA) release and decreases intracellular guanine levels in S. lugdunensis. Crucially, the addition of exogenous guanine suppressed the effect of C. acnes molecules on both biofilm formation and lrgA gene expression. Collectively, our data indicate that C. acnes molecules inhibit S. lugdunensis biofilm formation by depleting the intracellular guanine pool, leading to repression of autolysis, and reduced eDNA release, a key component of biofilm structural integrity. These findings underscore the importance of interspecies microbiome interactions in pathogen exclusion.}, }
@article {pmid42185548, year = {2026}, author = {Guo, X and Wang, Y and Wang, L and Lei, Y and Sa, RN and Li, L and Xia, S and Lin, X and Liu, C and Shao, Y}, title = {An integrated multi-omics approach for deciphering podophyllotoxin-induced nephrotoxicity via the microbiome-gut-kidney (MGK) axis based on the toxicological evidence (TEC) concept.}, journal = {Journal of molecular histology}, volume = {57}, number = {3}, pages = {}, pmid = {42185548}, issn = {1567-2387}, support = {Grant 24A360023//he Key Scientific Research Projects of Henan Higher Education Institutions/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Podophyllotoxin/toxicity ; *Kidney/drug effects/pathology/metabolism ; Male ; *Metabolomics/methods ; Mice, Inbred ICR ; *Kidney Diseases/chemically induced/pathology/metabolism ; Dysbiosis ; Multiomics ; }, abstract = {Podophyllotoxin (PPT), a potent antitumor natural lignan, is clinically limited by nephrotoxicity, with the microbiome-gut-kidney (MGK) axis's role unclear. Guided by the Toxicological Evidence Chain (TEC) framework, this study used multi-omics approaches in ICR mice (control, low/high-dose PPT) to explore mechanisms. The physiological indices of mice, health status, renal pathological changes, injury and proinflammatory biomarkers, gut microbiota, metabolism, and transcriptional changes were determined to collect toxicity evidence. Besides, an integrated multi-omics approach, including 16S rRNA gene sequencing, metabolomics coupled with LC-MS/MS, and transcriptomics, was employed to systematically elucidate the potential nephrotoxicity mechanism of PPT. Results showed that PPT significantly induced health deterioration, including reduced activity and body weight, hemorrhage, hunched posture, and severe diarrhea. The dose-dependent nephrotoxicity caused, including decreased kidney organ index, pathological structural changes, and elevated renal injury indices, particularly BUN, Cr, KIM-1, IL-18, and mAlb. Furthermore, gut microbiota dysbiosis (enriched Escherichia-Shigella, depleted Lactobacillus), disrupted tryptophan/ascorbate metabolism, and downregulated key metabolic genes were also observed after PPT intervention. Integrated analysis confirmed gut microbiota dysbiosis mediates PPT-induced nephrotoxicity via the MGK axis. Our research evidence chain implies that PPT promotes intestinal flora dysbiosis, thereby redirecting tryptophan metabolism toward the kynurenine pathway and suppression of the ascorbate and aldarate metabolism pathway abolishes its renoprotective effects simultaneously, triggering amplified inflammatory cascades and ultimately leading to renal dysfunction and nephrotoxicity. This study identifies a novel mechanism, actionable mitigation targets, and supports TEC's application in toxicological assessment.}, }
@article {pmid42185684, year = {2026}, author = {Miyake, T and Kojima, M and Tani, S and Muramoto, K and Maehira, H and Kaida, S and Shimizu, T and Tani, M}, title = {Gut microbiota profiles in reactive and metastatic lymphadenopathy in colorectal cancer: a tumor location-stratified analysis.}, journal = {International journal of colorectal disease}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00384-026-05154-2}, pmid = {42185684}, issn = {1432-1262}, abstract = {PURPOSE: Preoperative lymphadenopathy in colorectal cancer may represent nodal metastasis or reactive change. We aimed to compare gut microbiota profiles between reactive and metastatic lymphadenopathy and to explore microbial features associated with nonmetastatic lymph node enlargement.<br><br>METHODS: We conducted a retrospective observational study of colorectal cancer patients with radiological lymphadenopathy who underwent resection at Shiga University of Medical Science Hospital between 2018 and 2021. For the primary analysis, we included patients with radiological lymphadenopathy on preoperative CT. An additional analysis restricted to right-sided colon cancer compared no lymphadenopathy without pathological lymph node metastasis (NN), lymphadenopathy without pathological lymph node metastasis (PN), and lymphadenopathy with pathological lymph node metastasis (PP).<br><br>RESULTS: Pathological nodal metastasis was identified in 34 patients, whereas 29 had reactive lymphadenopathy. Fecal samples showed higher alpha diversity than tumor tissues. In left-sided colorectal cancer, no notable bacterial taxa exceeded the predefined LDA threshold. In right-sided colon cancer, Proteobacteria were enriched in metastatic cases, whereas Firmicutes were more abundant in reactive lymphadenopathy. Predicted pathway analysis suggested distinct metabolic profiles between the two groups. In the additional right-sided analysis, alpha and beta diversity did not significantly differ among NN, PN, and PP, although taxon-level differences were observed between NN and PN.<br><br>CONCLUSION: Gut microbiota profiles differed between reactive and metastatic lymphadenopathy in colorectal cancer, with more distinct findings in right-sided tumors. These findings suggest an association between microbial patterns and reactive lymphadenopathy.}, }
@article {pmid42185899, year = {2026}, author = {Wang, Z and Wang, Z and Ji, X and Zhao, L and Zheng, K and Yu, W and Zhang, H and Chang, H and Liu, F}, title = {CR1(+) tumor-associated macrophages orchestrate an immunosuppressive niche in hepatocellular carcinoma: a genetic and multi-omics dissection.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-08301-z}, pmid = {42185899}, issn = {1479-5876}, abstract = {BACKGROUND: Hepatocellular carcinoma (HCC) remains a major global health burden and a leading cause of cancer-related mortality. Advanced disease is characterized by a profoundly immunosuppressive tumor microenvironment (TME) and limited durable responses to therapy. However, the upstream genetic determinants that drive tumor-associated macrophage (TAM) dysfunction in HCC remain poorly defined. Using an integrative genetic and multi-omics framework, we investigated complement receptor 1 (CR1) as a candidate regulator of this immunosuppressive niche.<br><br>METHODS: We combined Mendelian randomization (MR) and metabolite mediation analyses with bulk, single-cell, and spatial transcriptomics to define the role of CR1 in HCC. Public datasets included the TCGA-HCC cohort, a single-cell RNA-sequencing dataset comprising 53,474 high-quality cells from 21 samples, and two spatially profiled HCC sections. Clinical validation was performed in 30 paired HCC and adjacent liver tissues. Functional assays were conducted in THP-1-derived macrophages using CR1 gain- and loss-of-function approaches, phagocytosis assays, and macrophage-CD8[+] T-cell co-culture experiments.<br><br>RESULTS: MR analyses implicated CR1 in HCC susceptibility at both the protein and transcript levels. pQTL analysis linked genetically predicted circulating CR1 levels to HCC risk (IVW OR&#x2009;=&#x2009;1.403, p&#x2009;=&#x2009;0.017), and mediation analysis identified specific metabolites as candidate intermediates. Integrative multi-omics analyses showed that CR1 was preferentially enriched in TAMs, spatially co-localized with the M2 marker CD206, and associated with reduced CD8[+] T-cell infiltration, enhanced T-cell exhaustion signatures, advanced clinicopathological features, and poorer survival. In 30 paired clinical samples, CR1-high tumors exhibited increased M2-like macrophage accumulation and reduced CD8[+] T-cell infiltration. Functionally, CR1 overexpression drove macrophages toward an M2-like phenotype, enhanced phagocytic activity, increased PD-L1 expression, and suppressed CD8[+] T-cell proliferation as well as IFN-gamma and granzyme B production, whereas CR1 knockdown produced the opposite phenotype.<br><br>CONCLUSIONS: Our study provides the first integrated genetic, spatial, and functional evidence that CR1[+] TAMs constitute a clinically relevant immunoregulatory axis in HCC. These findings extend current understanding of complement-associated immunosuppression beyond canonical complement cascade activity and support CR1 as a candidate biomarker and therapeutic target for macrophage reprogramming, with potential translational relevance for combination strategies involving immune checkpoint blockade.}, }
@article {pmid42186042, year = {2026}, author = {Salgueiro, AM and Ferreira-Marques, M and Ribeiro, RFN and Lopes, SM and Pereira, D and Costa, DG and Santana, MM and de Almeida, LP and Cavadas, C}, title = {Ketogenic diet as a therapeutic strategy for neurodegenerative diseases: from mechanisms to translational challenges.}, journal = {Translational neurodegeneration}, volume = {15}, number = {1}, pages = {}, pmid = {42186042}, issn = {2047-9158}, support = {UIDB/04539/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDP/04539/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; LA/P/0058/2020(JPND/ 0001/2022//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; DOI: 10.54499/JPND/0001/2022; JPND/0002/2022//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; DOI: 10.54499/JPND/0002/2022//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH/BD/120023/2016; 2020.04850.BD//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2022.11293.BD//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; GeneT project-The Gene Therapy CoE at the Center of Portugal (Project ID: 101059981//HORIZON EUROPE Widening participation and spreading excellence/ ; DOI: 10.3030/101059981); GCure - From Gene to Cure//HORIZON EUROPE Widening participation and spreading excellence/ ; ID: 101186929//HORIZON EUROPE Widening participation and spreading excellence/ ; DOI:10.3030/101186929; GeneH - Excellence Hub for Advancing Innovation in Gene Therapy//HORIZON EUROPE Widening participation and spreading excellence/ ; ID: 101186939//HORIZON EUROPE Widening participation and spreading excellence/ ; DOI: 10.3030/101186939//HORIZON EUROPE Widening participation and spreading excellence/ ; }, mesh = {Humans ; *Diet, Ketogenic/methods ; *Neurodegenerative Diseases/diet therapy/metabolism ; Animals ; *Translational Research, Biomedical/methods ; Gastrointestinal Microbiome/physiology ; Oxidative Stress/physiology ; }, abstract = {The ketogenic diet (KD) is increasingly recognized as a promising therapeutic strategy for neurodegenerative disorders because of its multifaceted impacts on key pathophysiological mechanisms. This review explores the molecular pathways through which KD may protect against neurodegeneration, including the use of ketone bodies as alternative energy substrates, reduction of oxidative stress and inflammation, modulation of autophagy and protein aggregation, and impact on the gut microbiome. The potential benefits of KD are explored across neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, and multiple sclerosis, based on both preclinical and clinical evidence that supports its feasibility. However, challenges in long-term safety, patient adherence, and clinical practicality limit its widespread adoption. This review underscores the potential of KD for treating neurodegeneration on the basis of current scientific evidence while highlighting the need for further research to optimize its application and address existing gaps.}, }
@article {pmid42186076, year = {2026}, author = {Liping, Y and Xingzhi, Y and Jie, T and Xiaohua, D}, title = {Yajieshaba extract improves alcohol‑induced liver injury by regulating hepatic lipid metabolism and gut microbiota.}, journal = {BMC complementary medicine and therapies}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12906-026-05421-3}, pmid = {42186076}, issn = {2662-7671}, support = {202101AZ070001-321//he Joint Special Project of Traditional Chinese Medicine of Basic Research Program of Science and Technology Department of Yunnan Province/ ; 202101AZ070001-321//he Joint Special Project of Traditional Chinese Medicine of Basic Research Program of Science and Technology Department of Yunnan Province/ ; 202101AZ070001-321//he Joint Special Project of Traditional Chinese Medicine of Basic Research Program of Science and Technology Department of Yunnan Province/ ; 202101AZ070001-321//he Joint Special Project of Traditional Chinese Medicine of Basic Research Program of Science and Technology Department of Yunnan Province/ ; }, abstract = {BACKGROUND: Yajieshaba, a commonly used Dai medicine formula, is renowned for its hepatoprotective properties. This study aimed to investigate the therapeutic effects and underlying mechanisms of Yajieshaba on alcoholic liver disease (ALD) in mice, focusing the gut-liver axis.<br><br>METHODS: Male C57BL/6 mice were pair-fed the Lieber-DeCarli control or ethanol-containing diet for 8 weeks, with or without Yajieshaba co-administration. Serum biomarkers were assessed using biochemical kits. Liver pathology was evaluated by hematoxylin and eosin (H&amp;E) and Oil Red O staining. Intestinal barrier integrity was assessed by H&amp;E staining and immunofluorescence of tight junction proteins (occludin, ZO-1). Hepatic lipid composition was analyzed by liquid chromatography-mass spectrometry (LC-MS), and gut microbiota diversity was profiled by 16&#xa0;S rRNA sequencing.<br><br>RESULTS: Yajieshaba significantly attenuated ethanol-induced liver injury, steatosis, and intestinal barrier disruption. Multi-omics integration revealed that Yajieshaba mitigated ALD progression by restoring gut microbial homeostasis and regulating hepatic lipid metabolism.<br><br>CONCLUSION: This study elucidates the therapeutic mechanism of Yajieshaba from the perspective of the gut microbiome-lipid metabolism axis, providing a novel perspective and experimental basis for further ALD management.}, }
@article {pmid42186163, year = {2026}, author = {Eterovick, PC and Glos, J and Burkart, F and Overmann, J and Ruthsatz, K}, title = {Interplay of Diet, Heat Stress, and the Microbiome Shapes Health and Escape Behaviour in Amphibian Larvae.}, journal = {Environmental microbiology}, volume = {28}, number = {6}, pages = {e70331}, doi = {10.1111/1462-2920.70331}, pmid = {42186163}, issn = {1462-2920}, support = {546565602//Deutsche Forschungsgemeinschaft/ ; 459850971//Deutsche Forschungsgemeinschaft/ ; 101151070-AMPHISTRESS//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; }, mesh = {Animals ; Larva/microbiology/physiology/growth &amp; development ; *Diet ; *Rana temporaria/microbiology/physiology/growth &amp; development ; *Gastrointestinal Microbiome ; *Heat-Shock Response ; Hot Temperature ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Microbiota ; }, abstract = {Diet influences animal health and their microbiomes, potentially affecting how they cope with environmental stressors such as rising temperatures and altered food quality associated with climate change. Using a multifactorial experiment, larvae of the frog Rana temporaria were reared on three diets differing in protein, fat, and animal-derived components (low-, intermediate-, and high-quality), at two temperatures (18°C and 24.5°C), and either exposed or not to a simulated heatwave (28°C for 48 h). We examined how these treatments and associated shifts in gut bacterial indicators and predicted microbial metabolic pathways related to nutrient assimilation, host health (body condition and developmental rate), and escape behaviour. Larvae maintained body condition and developed faster at 24.5°C, with higher diet quality further accelerating development. An intermediate-quality diet reduced responsiveness to an aversive stimulus at 24.5°C, although this effect disappeared following heatwave exposure. Heatwave conditions were associated with increased abundance of Klebsiella and a predicted increase in the myo-inositol degradation pathway, which may influence membrane dynamics and signalling and may increase attention levels. Despite microbial shifts, host performance remained similar across most treatments, suggesting substantial microbiome plasticity and the presence of functionally redundant enterotypes that help buffer environmental stress.}, }
@article {pmid42186183, year = {2026}, author = {Wang, H and Jin, Z and Di, S and Alizadeh, H}, title = {Exercise-Induced Exerkines: Multi-Nodal Suppression of the NLRP3 Inflammasome and Translational Potential.}, journal = {Medicinal research reviews}, volume = {}, number = {}, pages = {}, doi = {10.1002/med.70063}, pmid = {42186183}, issn = {1098-1128}, abstract = {Chronic low-grade inflammation driven by persistent NLRP3 inflammasome activation is a unifying pathophysiological feature of most non-communicable diseases (NCDs). Whereas single-target pharmacological inhibitors exhibit limited breadth and durability, regular moderate-intensity exercise confers robust multi-system protection through a diverse network of exerkines. This narrative review synthesizes evidence that exercise-released myokines (irisin, Metrnl, context-reprogrammed IL-6), hepatokines/adipokines (FGF21, adropin, adiponectin), metabolites (lactate, β-hydroxybutyrate), microbiota-derived factors (SCFAs, betulinic acid), and extracellular vesicle (EV)-delivered non-coding RNAs converge on every regulatory node of the canonical NLRP3 inflammasome to achieve multi-nodal suppression that is currently unmatched by any single pharmacological approach based on available evidence. Acute high-intensity exercise transiently activates NLRP3 via canonical danger signals, whereas chronic moderate-intensity training (150-300 min·wk[-1], 60%-75% HRmax) induces profound basal suppression through NF-κB attenuation, mitochondrial protection, direct interference with NEK7-NLRP3 interaction and ASC oligomerization, post-transcriptional silencing, and enhanced autophagic clearance. These mechanisms are supported by preclinical structural data and human biomarker studies across cardiovascular, metabolic, neurodegenerative, and musculoskeletal disorders. We propose a precision exercise medicine framework integrating exerkine/genetic/microbiome profiling to minimize non-responders, together with emerging mimetics, RNA therapeutics, and synergistic pharmacology, to deliver scalable systems-level modification of NLRP3-driven metaflammation.}, }
@article {pmid42186196, year = {2026}, author = {Smith, RE and Holtappels, D}, title = {The role of phages in plant-associated microbial communities.}, journal = {Essays in biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1042/EBC20250035}, pmid = {42186196}, issn = {1744-1358}, support = {NE2335//USDA | National Institute of Food and Agriculture (NIFA)/ ; }, abstract = {Microbial communities deliver essential functions in ecosystems. In plant environments, the plant microbiome facilitates nutrient uptake, supports plants during abiotic stress, and counteracts disease. As implementation of synthetic microbial communities becomes more of a realistic strategy for mitigating the effects of biotic and abiotic stressors on plant productivity, it is increasingly important to understand how interactions between microbes, which are essential for ecosystem function (hub microbes), are maintained. Recent research highlights the ecological role of bacteriophages, the viruses of bacteria, in host-associated microbial communities. Current evidence demonstrates the influence of the phageome on microbiomes, ranging from effects on an individual (transduction, lysogenic conversion, and evolutionary pressure) to entire populations and communities, such as Kill-the-Winner dynamics. These dynamics appear to affect the overall function of microbial communities and support plant growth. In this review, we lay out recent insights on the role of bacteriophages in plant-associated microbiomes through an eco-evolutionary lens and future directions of research to broaden our understanding of the ecological implications of bacteriophages.}, }
@article {pmid42186200, year = {2026}, author = {Diaz-Amigo, C and Bartolomé Del Pino, LE and Lejeune, J and Pinto Ferreira, J and Bessy, C}, title = {Antimicrobial resistance and the human gut microbiome-a food safety perspective.}, journal = {Critical reviews in food science and nutrition}, volume = {}, number = {}, pages = {1-29}, doi = {10.1080/10408398.2026.2629533}, pmid = {42186200}, issn = {1549-7852}, abstract = {The gastrointestinal environment is where the resident gut microbiome encounters foodborne microorganisms, antimicrobial resistance genes (ARGs), and bioactive substances from food, all of which may influence the acquisition and dissemination of antimicrobial resistance (AMR). Although resistant bacteria and ARGs are frequently detected in food and food production environments, their contribution to the gut resistome remains unclear. Most ingested microbes are transient and constrained by ecological barriers; however, the conditions that enable horizontal gene transfer in vivo are not well characterized. Multiple factors (e.g., microbial composition and density, the presence of mobile genetic elements, antimicrobial residues, and host physiology) can modulate ARG persistence and mobility, but their relative impact within the gut ecosystem and its associated resistome needs to be better understood. Resistance acquisition also depends on fitness costs and adaptive responses within complex microbial communities. Methodological variability and limited in vivo data further limit comparability and interpretation. This review summarizes current knowledge of AMR dynamics in the gut following dietary exposure and highlights significant knowledge gaps that limit our understanding of factors influencing ARG transfer and persistence in the gastrointestinal environment. Reducing these uncertainties is crucial for strengthening AMR risk assessment and designing more effective mitigation strategies.}, }
@article {pmid42186240, year = {2026}, author = {Jiang, K and Saha, S and Peterson, CB}, title = {Bayesian Sparse Regression for Microbiome-Metabolite Data Integration.}, journal = {Statistics in medicine}, volume = {45}, number = {13-14}, pages = {e70607}, doi = {10.1002/sim.70607}, pmid = {42186240}, issn = {1097-0258}, support = {R01 HL158796/NH/NIH HHS/United States ; CCSG P30CA016672/CA/NCI NIH HHS/United States ; //Andrew Sabin Family Fellowship/ ; }, mesh = {Bayes Theorem ; Humans ; Colorectal Neoplasms/microbiology/metabolism ; Computer Simulation ; *Gastrointestinal Microbiome ; *Microbiota ; Models, Statistical ; Regression Analysis ; *Metabolome ; }, abstract = {Numerous studies have shown that microbial metabolites, which represent the products of bacteria in the human gut, play a key role in shaping cancer risk and response to treatment. However, metabolite data typically contain a large proportion of missing values, which may result from either low abundance or technical challenges in data processing. Moreover, given the compositionality of microbiome data, where the observed abundances can only be interpreted on a relative scale, standard variable selection methods are not applicable. In this project, we propose a novel Bayesian regression method to address these challenges in the integration of metabolite and microbiome data. Key features of our proposed model include modeling the two different mechanisms of missingness for the metabolite data and adopting a Bayesian prior designed to address the compositional characteristics of microbiome data. We demonstrate on simulated data that our proposed model can accurately impute the unobserved true metabolite values and correctly select the relevant microbiome predictors. We further illustrate our method using real data from a study focused on understanding the interplay between the microbiome and metabolome in colorectal cancer.}, }
@article {pmid42186272, year = {2026}, author = {Kris-Etherton, PM and Rogers, CJ and Oh, ES and West, SG and Sandhu, AK and Burton-Freeman, B and Huang, Y and Proctor, DN and Petersen, KS}, title = {Cardiometabolic and Microbiome Effects of Spices and Herbs.}, journal = {Nutrition reviews}, volume = {84}, number = {Supplement_1}, pages = {70-75}, pmid = {42186272}, issn = {1753-4887}, support = {//McCormick Science Institute/ ; /TR/NCATS NIH HHS/United States ; UL1 TR002014/NH/NIH HHS/United States ; }, mesh = {Humans ; *Spices ; *Cardiovascular Diseases/prevention &amp; control ; *Gastrointestinal Microbiome/drug effects ; Cardiometabolic Risk Factors ; *Plants, Medicinal/chemistry ; }, abstract = {This article appears as part of the supplement "The Role of Spices and Herbs on Supporting Healthy Diets and Improving Nutritional Status," sponsored by the McCormick Science Institute. Studies conducted at Penn State University to evaluate the effects of spices and herbs (S&amp;H) on risk factors for cardiovascular disease (CVD) are summarized herein. We also report effects of S&amp;H on phytochemical metabolites and the microbiome. Results demonstrate beneficial effects of S&amp;H on postprandial endothelial function, insulin and triglycerides, pancreatic lipase, inflammatory markers, and measures of oxidative defense. In a controlled-feeding trial that evaluated 3 doses of S&amp;H (0.5, 3.3, and 6.6 g/d per 2100 kcal) in the context of an average American diet, the high-S&amp;H diet improved 24-hour blood pressure after 4 weeks, the moderate-S&amp;H diet decreased proinflammatory cytokines, and the high-S&amp;H diet reduced monocyte adherence. Our research also identified polyphenol metabolites that may have important functional properties for CVD risk reduction. Finally, we report benefits of S&amp;H on gut bacterial composition, which suggests possible benefits on CVD risk.}, }
@article {pmid42186275, year = {2026}, author = {Diacova, T and Heber, D and Li, Z}, title = {Spices Beyond Antioxidants: From the Gut to the Brain.}, journal = {Nutrition reviews}, volume = {84}, number = {Supplement_1}, pages = {52-69}, pmid = {42186275}, issn = {1753-4887}, mesh = {Humans ; *Spices ; *Antioxidants/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Brain/drug effects ; Gastrointestinal Tract/microbiology ; }, abstract = {OBJECTIVES: The objective of this review was to summarize evidence of the effects of select spices/herbs on human health with a focus on the work conducted at the University of California-Los Angeles (UCLA) Center for Human Nutrition.<br><br>BACKGROUND: Herbs/spices have been used in various countries around the world for centuries. The purposes for using herbs/spices include improvement in food organoleptic properties and use as food preservatives and medicine. As interest in ethnic cuisines is gaining popularity, more Americans are interested in adding spices/herbs to their daily diets for health benefits. Health benefits conferred by herbs/spices include protection against oxidative stress, neurodegeneration, cardiovascular disease among others and may be at least partially due to their high (poly)phenolic content. (Poly)phenols are not accessible by the human digestive enzymes and are metabolized by the gut microbiome, earning them the status of "prebiotics." This is confirmed by a vast body of evidence pointing to the herbs'/spices' ability to affect gut microbiota composition/functionality.<br><br>METHODS: In vitro experiments and human trials conducted at the UCLA Center for Human Nutrition were collated and results summarized. Reference lists of these publications were scanned and relevant literature extracted. Multiple additional searches relating to the select herbs/spices and their effects on human health were conducted in PubMed.<br><br>RESULTS: A total of 8 human trials and 12 in vitro experiments were conducted at the UCLA Center for Human Nutrition between 2010 and 2024. These experiments included interventions with individual herbs/spices, including cinnamon, chili pepper, and turmeric, as well as spice mixes. Additional relevant original research and reviews/meta-analyses were identified and included to supplement the discussions.<br><br>CONCLUSION: While further research of herbs/spices is undeniably warranted, several considerations should be kept in mind. These include the relatively small amounts of herbs/spices consumed by the general population on a daily basis, cooking methods, as well as effects of digestive/metabolic processes on the bioavailability of herb/spice (poly)phenols. While much is already known, there are still substantial gaps in knowledge that need to be addressed.}, }
@article {pmid42186278, year = {2026}, author = {Crowe-White, KM and Senkus, KE and DiNatale, JC}, title = {Spices for Targeting the Gut Microbiome to Improve Cardiometabolic Health.}, journal = {Nutrition reviews}, volume = {84}, number = {Supplement_1}, pages = {49-51}, pmid = {42186278}, issn = {1753-4887}, support = {//McCormick Science Institute/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Spices ; Prebiotics ; Polyphenols/pharmacology ; Cinnamomum zeylanicum/chemistry ; *Cardiovascular Diseases/prevention &amp; control ; Zingiber officinale/chemistry ; Fatty Acids, Volatile/metabolism ; }, abstract = {The intricate balance between the gut microbial ecosystem and cardiometabolic health underscores the importance of cultivating a healthy gut microbiome. A noteworthy strategy for harnessing the potential of this ecosystem is the consumption of prebiotics-non-digestible compounds promoting the growth of beneficial bacteria. While dietary polyphenols are emerging as significant modulators of microbial proliferation and systemic therapeutic effects, the prebiotic functionality of spice polyphenols remains understudied. It is, however, hypothesized that metabolism of spice polyphenols by intrinsic microflora in the colon may elicit downstream cardiometabolic effects resulting from the stimulated release of gut-derived metabolites, specifically short-chain fatty acids. This brief article highlights research on the functionality of spices, namely cinnamon and ginger, to influence microbial proliferation, the production of gut-derived metabolites and hormones, and prospective health outcomes.}, }
@article {pmid42186489, year = {2026}, author = {Dong, X and Guo, L and Chen, H}, title = {Phosphorus availability enriches Massilia in the root microbiome to enhance resistance against Sclerotinia sclerotiorum in rapeseed.}, journal = {Molecular breeding : new strategies in plant improvement}, volume = {46}, number = {6}, pages = {53}, pmid = {42186489}, issn = {1572-9788}, abstract = {UNLABELLED: Phosphorus is an essential macronutrient for plant growth and development, especially in P-sensitive crops such as rapeseed (Brassica napus). However, the role of phosphorus (P) availability in plant disease resistance mediated by the root-associated microbiome remains poorly understood. Here, we investigated how P homeostasis regulates rapeseed resistance to Sclerotinia sclerotiorum through modulation of the root-associated microbiome. P deficiency significantly inhibited plant growth and increased susceptibility to S. sclerotiorum in multiple rapeseed ecotypes, including spring, semi‑winter, and winter types. Microbiome profiling revealed that Massilia was a key P-responsive biomarker genus significantly enriched under P-sufficient conditions. Both foliar application and root inoculation with Massilia effectively suppressed S. sclerotiorum infection in rapeseed. Mechanistically, Massilia colonization strongly activated the expression of pathogenesis‑related (PR) genes, antioxidant genes, and jasmonic acid (JA) signaling genes. Overall, this study establishes a P-mediated tripartite interaction linking root microbiota assembly and plant immunity. These results highlight that optimizing P supply to enrich beneficial microbes such as Massilia can enhance rapeseed resistance to S. sclerotiorum, providing a sustainable strategy for disease management.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11032-026-01669-2.}, }
@article {pmid42186656, year = {2026}, author = {Kimura, M and Taketani, T}, title = {Hemoglobin Response to a Low-Iron Dose in Infantile Anemia.}, journal = {Cureus}, volume = {18}, number = {4}, pages = {e107641}, pmid = {42186656}, issn = {2168-8184}, abstract = {INTRODUCTION: Iron-deficiency anemia (IDA) is common during infancy, especially among infants exclusively breastfed after six months of age. The recommended therapeutic iron dose is 3-6 mg/kg/day; however, excessive iron load can be harmful due to alteration of the gut microbiome and oxidative stress to the developing organs. Lower doses of iron have shown efficacy in treating IDA in adults. This retrospective study evaluated the hemoglobin (Hb) response to a lower iron dose in infantile anemia.<br><br>METHODS: During health checkups for 9- to 10-month-old infants, anemia screening was conducted for those who were exclusively breastfed. Clinical parameters, including birth date, gestational age, birth weight, and body weight at the start of iron supplementation, were recorded. Venous blood samples were collected for a complete blood count (CBC). Infants with either Hb levels below 11.0 g/dL or mean corpuscular volume below 70 fL received a therapeutic iron trial. From March 2016 to November 2018, a fixed dose of elemental iron (soluble ferric pyrophosphate) 15 mg/day was administered (reference group), and from November 2018 to December 2023, a dose of 1 mg/kg/day was given (low-dose group). CBC measurements were repeated after four weeks, and Hb responses were compared between the two regimens.<br><br>RESULTS: A total of 26 children in the reference group and 27 in the low-dose group were finally analyzed. The fixed 15 mg/day dose in the reference group corresponded to 1.8 (1.6-1.9) (median (interquartile range) mg/kg/day). Baseline clinical variables showed no statistically significant differences between the two groups.&#xa0;The median Hb increase was 1.6 g/dL and 1.5 g/dL, with 69% (18/26) and 70% (19/27) of children achieving an Hb level &#x2265; 1 g/dL, in the reference and low-dose&#xa0;groups, respectively. All 15 children (15/27, 56%) in the low-dose group, who met the new WHO anemia definition at the age of 6-23 months of Hb < 10.5 g/dL, had an Hb response &#x2265; 1.0 g/dL, with a median Hb response of 2.2 g/dL.<br><br>CONCLUSION: An iron dose of 1 mg/kg/day was as effective as 15 mg/day (median: 1.8 mg/kg/day) in the Hb response. In all children with Hb < 10.5 g/dL, the iron dose of 1 mg/kg/day showed substantial Hb responses. These findings suggest that therapeutic iron doses lower than conventional recommendations may be effective for managing IDA and mitigating the harmful effects.}, }
@article {pmid42186662, year = {2026}, author = {Mueller, MK and Rousseau, SR and Hark, GM and Shaffer, LR and Rizvanović, BF and Nuelle, JAV}, title = {The Role of the Gut Microbiota in Functional Recovery after Peripheral Nerve Injury: A Narrative Review.}, journal = {Orthopedic reviews}, volume = {18}, number = {}, pages = {162156}, pmid = {42186662}, issn = {2035-8164}, abstract = {INTRODUCTION: While researchers have previously pointed to the peripheral nervous system as a method of transportation for the gut microbiota metabolites to distant organs, researchers have more recently studied the impact of gut microbiota on the peripheral nerves. The purpose of this review was to synthesize the literature on how modulation of the gut microbiota impacts functional recovery following peripheral nerve injury.<br><br>METHODS: Electronic searches were conducted in Ovid/Medline and PubMed to identify articles that discuss gut microbiome interventions following peripheral nerve injury in sciatic nerve chronic constriction injury or crush injury animal models and the effects on peripheral nerve regeneration and functional recovery.<br><br>RESULTS: Twelve articles met inclusion criteria; all were prospective studies in animal models. Four interventions were identified by the twelve studies, including probiotics, antibiotics, intermittent fasting, and naturopathic compounds. Probiotic treatment and dietary interventions targeted at modulating the gut microbiota improved histological, sensory, and motor outcomes following peripheral nerve injury. While antibiotic treatment negatively impacted recovery after peripheral nerve injury, co-treatment with probiotics or reconstitution of the gut microbiota through fecal microbiota transplantation was able to rescue these negative effects.<br><br>CONCLUSION: Alterations in the gut microbiota, whether induced by antibiotics, probiotics, intermittent fasting, or dietary interventions, impact functional recovery, neuropathic pain, and inflammatory processes. However, future research should focus on identifying the specific microbial taxa responsible for neuroregenerative effects and developing standardized protocols for probiotic treatment to optimize improvement in peripheral nerve recovery after injury.}, }
@article {pmid42186771, year = {2026}, author = {Zhang, Y and Li, X and Zhang, X and Wang, Y and Chen, Z and Lin, X and Zheng, X and Hao, H and Zhang, X}, title = {Ketogenic Diet Modulates Depressive-Like Behavior via Gut Bacterial Metabolism of Tyrosine.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {40}, number = {10}, pages = {e71966}, doi = {10.1096/fj.202504666RRR}, pmid = {42186771}, issn = {1530-6860}, support = {2024YFA1308200//MOST | National Key Research and Development Program of China (NKPs)/ ; 2021YFA1301300//MOST | National Key Research and Development Program of China (NKPs)/ ; 82321005//MOST | National Natural Science Foundation of China (NSFC)/ ; BK20240095//JST | Natural Science Foundation of Jiangsu Province (Jiangsu Natural Science Foundation)/ ; }, mesh = {Animals ; *Diet, Ketogenic/methods ; *Gastrointestinal Microbiome/physiology ; Mice ; *Depression/metabolism/diet therapy/microbiology ; Male ; Mice, Inbred C57BL ; *Tyrosine/metabolism ; Behavior, Animal ; Brain/metabolism ; }, abstract = {Emerging evidence suggests the therapeutic potential of ketogenic diet (KD) for mood disorders such as depression, yet the underlying mechanisms are poorly understood. Here we report a gut microbe-to-brain signaling pathway through which KD protects against depressive-like behavior in mice. We show that KD feeding triggers a prompt and dynamic remodeling of the gut microbiome, the depletion of which abrogates the protective effect of KD against depressive-like behavior in stressed mice. Colonization with Roseburia intestinalis (R. intestinalis), which is enriched by 1-week KD, sustains the protective effect of KD against depressive-like behavior in mice. The protective effect of KD is linked to the reduction of a host-microbe co-metabolite p-Cresol sulfate (p-CS), the supplementation of which negates the protective effect of KD against depressive-like behavior. Mechanistically, p-CS enters the brain and activates lateral habenula (LHb) to counteract the protective effect of KD. Our findings uncover a gut microbiota-brain axis mechanism for KD consumption to protect against depressive-like behavior.}, }
@article {pmid42187072, year = {2026}, author = {John, JM and Manjarres, Z and Zulkifly, NI and Plumb, AN and Pratt, ML and Sadler, KE}, title = {Male-specific analgesic effects of minocycline in sickle cell disease are mediated by microglia and the microbiome.}, journal = {Pain}, volume = {}, number = {}, pages = {}, doi = {10.1097/j.pain.0000000000004008}, pmid = {42187072}, issn = {1872-6623}, abstract = {Over 50% of individuals with sickle cell disease (SCD) experience chronic pain that is phenotypically distinct from their acute, vaso-occlusive crisis pain. Chronic SCD pain is commonly managed with opioid-based drugs that are associated with unwanted side effects, incomplete pain relief, and-in this population-accessibility issues. Thus, new treatments for chronic SCD pain are desperately needed. Here, we examined the analgesic efficacy of acute minocycline treatment in transgenic SCD mice. Sickle cell disease mice exhibit gut dysbiosis and chronic inflammation. Therefore, we hypothesized that minocycline would provide robust analgesia in this model given the drug's antibiotic and anti-inflammatory properties, respectively. Six days of minocycline treatment reversed chronic mechanical hypersensitivity only in male SCD mice. We identified 2 potential mechanisms underlying these sex-specific effects. First, we observed increased microgliosis only in the dorsal horn of male SCD mice. Minocycline treatment had opposite effects on microglial number in male and female SCD spinal cords. Second, minocycline treatment altered the gut microbiota in a sex-specific fashion; fecal microbiota transplant (FMT) from minocycline-treated female SCD mice induced widespread pain in recipients, whereas FMT from minocycline-treated male SCD mice did not. In summary, these experiments highlight novel sex-specific mechanisms of minocycline analgesia and support future exploration of minocycline use for SCD pain management, but only in male patients.}, }
@article {pmid42187337, year = {2026}, author = {Cheng, X and Shi, H}, title = {Melatonin-Mediated Alleviation of Plant Response to Heavy Metals: From Integrative Mechanisms to Potential Applications.}, journal = {Journal of pineal research}, volume = {78}, number = {4}, pages = {e70150}, doi = {10.1111/jpi.70150}, pmid = {42187337}, issn = {1600-079X}, mesh = {*Melatonin/pharmacology/metabolism ; *Metals, Heavy/toxicity/metabolism ; *Plants/metabolism/drug effects ; Biodegradation, Environmental ; Plant Growth Regulators/metabolism ; }, abstract = {Global heavy metal (HM) stresses pose serious threats to environmental plants and animals. Melatonin has shown potent effects on improving plant stress resistance and phytoremediation upon HM stress, however, the systematic discussion of these extensive mechanisms and the gaps to practical applications remain elusive. This review aims to systemically provide the mechanistic understanding and environmental implication of melatonin integrative effects on alleviating HM toxicity. On the one hand, melatonin modulates HM homeostasis, induces HM detoxification, keeps photosynthesis and nutrient balance, and activates antioxidant defense systems to improve plant defense resistance to HM. On the other hand, melatonin triggers multiple transcriptional gene networks and extensive phytohormone crosstalks in plant defense responses. Notably, melatonin and melatonin-producing microbes exhibit potential applications in keeping plant growth and improving phytoremediation under HM conditions, indicating their effects on plant-microbiome-soil synergistic feedbacks. Finally, the current challenges and future perspectives of melatonin integrative mechanisms and applications are elucidated, highlighting that basic scientific questions and combined technologies should be further integrated to promote its practical applications. In summary, this review clarifies the multifaceted mechanisms of melatonin-integrated plant responses and potential remediation applications for environmental HMs, providing relative broad-spectrum and long-term strategies.}, }
@article {pmid42187510, year = {2026}, author = {Burjanivova, T and Buday, T and Mokra, D and Hanzlikova, Z and Babusikova, E and Podlesniy, P and Holubekova, V and Budis, J and Szemes, T and Plevkova, J}, title = {Challenges and Solutions in Low-Biomass Respiratory Microbiome Profiling: A Workflow for Bronchoalveolar Lavage Fluid Sequencing in Guinea Pigs.}, journal = {Physiological research}, volume = {75}, number = {2}, pages = {337-348}, pmid = {42187510}, issn = {1802-9973}, mesh = {Animals ; Guinea Pigs ; *Bronchoalveolar Lavage Fluid/microbiology ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; Workflow ; *DNA, Bacterial/genetics ; Male ; }, abstract = {Accurate profiling of the respiratory microbiome in low-biomass samples remains technically challenging due to host DNA contamination and limited microbial yield. This study aimed to optimize a methodological workflow for 16S rRNA sequencing of bronchoalveolar lavage fluid (BALF) obtained from guinea pig models with differing microbial statuses-specific pathogen-free (SPF) and conventionally bred (CON) animals. Using a comparative approach, we evaluated six commercial DNA extraction kits and tested different input DNA concentrations (1 ng vs. 0.5 ng) to enhance microbial detection while minimizing host DNA interference. Among the tested kits, only the ZymoBIOMICS DNA Microprep Kit yielded sufficient microbial DNA for downstream analysis. Real-time PCR and droplet digital PCR confirmed the microbial origin of the extracted DNA. Sequencing libraries were prepared from the V1-V3 regions of 16S rRNA genes and sequenced using the Illumina iSeq 100 platform. Taxonomic assignment and diversity metrics were analyzed using the MicrobAT pipeline. Our findings revealed significant differences in microbial composition between SPF and CON animals, notably in Mycoplasma abundance, which dominated the microbiota in CON but was nearly absent in SPF animals. Alpha and beta diversity metrics showed consistent stratification by animal group and input DNA concentration. However, a high proportion of unclassified reads-particularly in SPF samples-correlated strongly with sequences mapping to the Cavia porcellus genome, indicating substantial host DNA contamination. This study demonstrates the feasibility of microbiome profiling from low-biomass BALF samples in guinea pigs while highlighting the limitations of current sequencing and bioinformatic tools in distinguishing microbial from host-derived DNA. Our optimized workflow supports future respiratory microbiome studies in animal models and provides a foundation for improving host DNA depletion and reference databases tailored to non-human species.}, }
@article {pmid42187628, year = {2026}, author = {Scocca, V and Sarnelli, G and Pesce, M and Navarro-Cuéllar, C and Dell'Aversana Orabona, G}, title = {Oral Manifestations in Patients with Inflammatory Bowel Disease: A Systematic Review and Meta-Analysis.}, journal = {Dentistry journal}, volume = {14}, number = {5}, pages = {}, pmid = {42187628}, issn = {2304-6767}, abstract = {Background/Objectives: Oral manifestations are recognized extra-intestinal features of inflammatory bowel disease (IBD); however, their prevalence and clinical relevance remain controversial. This study aims to quantify the prevalence of individual oral outcomes in IBD patients and to evaluate their association with the disease compared with healthy controls. Methods: A systematic review was conducted in accordance with PRISMA guidelines. Eligible studies were identified through searches of PubMed/MEDLINE, Cochrane Library, Scopus, Ovid MEDLINE, and EMBASE. Studies reporting oral signs and symptoms in IBD patients were included. A single-arm meta-analysis was performed for oral ulcerations, dry mouth, halitosis, tongue alterations, oral aphthae, stomatitis, and taste changes. Risk of bias was assessed using the Newcastle-Ottawa Scale. Results: Twenty-one studies including 7791 participants (5914 IBD patients and 1877 controls) were analyzed. The pooled prevalence of oral ulcerations was 20% (95%CI11-33), dry mouth 32% (95%CI14-59), halitosis 22% (95%CI7-51), and tongue alterations 11% (95%CI4-24). Comparative analyses showed no statistically significant differences between IBD patients and controls for these outcomes. Conclusions: Although oral manifestations are frequently reported in IBD patients, their prevalence does not significantly differ from that of the general population. Standardized, multicenter studies are required to clarify disease-specific associations.}, }
@article {pmid42187670, year = {2026}, author = {Bordbar-Khiabani, A}, title = {Simulated Body Fluids for Dental Implant Corrosion: A Practical Guide.}, journal = {Dentistry journal}, volume = {14}, number = {5}, pages = {}, pmid = {42187670}, issn = {2304-6767}, abstract = {Background/Objectives: Electrolytes used in in vitro corrosion testing critically determine the behavior inferred for metallic dental implants, yet formulations and their justifications are inconsistently reported across the literature. This review compiles and compares electrolytes employed to simulate the oral cavity and the bone-implant interface, linking their chemical composition to the corrosion mechanisms they target. Methods: This structured narrative review synthesized peer-reviewed literature on simulated electrolytes used for in vitro corrosion testing of metallic dental implants and implant-related alloys. Literature was identified using database searches and targeted reference screening, with emphasis on artificial saliva formulations, physiological simulated fluids, challenge chemistries, protein-containing media, hydrodynamic conditions, and microbiological models. Relevant formulations were standardized to grams per liter and grouped according to application domain and targeted corrosion mechanisms. Results: The analysis maps electrolyte selection to corresponding corrosion modes, including uniform dissolution, pitting, crevice, galvanic, and microbiologically influenced corrosion. Consolidated composition tables highlight how pH, halide concentration, calcium-phosphate balance, proteins, gas control, and flow conditions modify passive-film stability and metal-ion release. Dental-specific gaps are identified, notably the lack of a standardized fluoride-pH matrix and limited guidance for microbiome-integrated assays. Conclusions: Aligning electrolyte formulations with the research question enhances reproducibility and mechanistic interpretation. However, current in vitro corrosion data should be interpreted cautiously because quantitative links between simulated-fluid testing and clinical outcomes such as peri-implantitis, peri-implant bone loss, and implant failure remain insufficiently established. The adoption of shared reporting standards, dynamic programmable chemistries, and interoperable datasets may improve the translational value of future corrosion studies.}, }
@article {pmid42187679, year = {2026}, author = {Guzmán-Flores, JM and Meza-Rodríguez, S and Vázquez-Jiménez, SI and Medrano-González, IDC and Gallegos-García, BL and Hernández-Villalobos, AL and Yañez-Acosta, MF and Alonso-Sanchez, CC}, title = {In Silico Identification of Dual-Action Compounds Targeting TLR2 and Streptococcus mutans Proteins for the Prevention of Early Childhood Caries.}, journal = {Dentistry journal}, volume = {14}, number = {5}, pages = {}, pmid = {42187679}, issn = {2304-6767}, abstract = {Background/Objectives: Early childhood caries (ECC) remains a major public health concern, with Streptococcus mutans as a primary etiological agent. Current treatments rely on broad-spectrum antimicrobials, which can disrupt the oral microbiome and promote resistance. This study applied a structure-based in silico pipeline to identify molecule modulators of Toll-like receptor 2 (TLR2), a key host receptor implicated in ECC, and to explore their binding potential against major S. mutans proteins. Methods: ECC-related genes were collected from public databases and analyzed by functional enrichment and protein-protein interaction (PPI) network analysis. Hub genes were ranked using centrality algorithms. Virtual screening on TLR2 (DrugCLIP) was followed by molecular docking of selected compounds against the TLR1/TLR2 heterodimer and 50 S. mutans proteins, complemented by in silico absorption, distribution, metabolism, excretion, and toxicity (ADMET) profiling. Results: Fifty-four ECC-related genes and nine hub genes were identified, with TLR2 and cathelicidin antimicrobial peptide (CAMP) as central nodes. Virtual screening yielded five lead compounds fulfilling drug-likeness and toxicity criteria. Docking to TLR1/TLR2 showed favorable binding energies, with Z7684613096 showing the most consistent binding. V026-2549 displayed the highest number of strong interactions with S. mutans targets, including dTDP-glucose 4,6-dehydratase (rmlB), NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (gapN), glucosyltransferase C (gtfC), and 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase (metE). Conclusions: Five candidate compounds with promising dual activity against TLR1/TLR2 and S. mutans proteins were prioritized for experimental validation, including TLR2 functional assays and in vitro anti-biofilm studies.}, }
@article {pmid42187718, year = {2026}, author = {Wen, F and Chen, X and Chen, Q and Li, L and Zhao, Y and You, Y and Niu, S and Xia, Z}, title = {Nutrient Supply Gradients Modulate Cultivation-Driven Restructuring of Microbial Communities in Desert Soils.}, journal = {Biology}, volume = {15}, number = {10}, pages = {}, pmid = {42187718}, issn = {2079-7737}, abstract = {Understanding how cultivation conditions influence the recovery of microbial diversity is critical for interpreting cultivation-derived communities in relation to in situ microbial ecology, particularly in nutrient-limited environments such as desert soils. In this study, we investigated how an oligotrophic nutrient gradient shapes cultivation outcomes and enrichment-derived bacterial community structure in soils from the Taklimakan Desert. Three enrichment treatments representing decreasing nutrient availability-standard low-nutrient medium (R2A), diluted medium (DR2A), and sterile water-were used to compare enrichment-derived communities with the original soil microbiome. Amplicon sequencing revealed that cultivation substantially altered community composition and reduced both taxonomic richness and diversity relative to the original soil. Across enrichment treatments, bacterial communities were dominated by a limited number of taxa, whereas the original soil contained a broader range of low-abundance lineages. Within the enrichment system, variation in nutrient supply influenced the relative abundance of specific taxa, with differential responses observed at the genus level. In contrast, beta diversity analysis showed only limited separation among enrichment treatments, and co-occurrence network analysis indicated generally simple and weakly connected community structures across all conditions. Overall, our results demonstrate that cultivation represents the primary selective force shaping enrichment-derived bacterial communities, while nutrient supply intensity acts as a secondary modulator of taxon-specific enrichment. These findings highlight the importance of incorporating nutrient gradients into cultivation strategies to improve ecological interpretation and facilitate the recovery of oligotrophy-associated microorganisms from desert soils.}, }
@article {pmid42187725, year = {2026}, author = {Ma, R and Lu, H and Zhang, S and Ji, H and Xin, F and Wang, G}, title = {Gut Microbiota Mediates Host Responses to Microplastic Exposure in Artemia salina.}, journal = {Biology}, volume = {15}, number = {10}, pages = {}, pmid = {42187725}, issn = {2079-7737}, support = {3160190//National Natural Science Foundation of China/ ; ZR2022MC167//the Natural Science Foundation of Shandong Province/ ; }, abstract = {BACKGROUND: Microplastics, derived from plastic degradation and industrial sources, are widely detected in aquatic environments and food systems, posing increasing environmental and ecological risks.<br><br>AIMS: This study aimed to investigate how microplastics affect host physiology and gut microbiota, as well as determine whether microbiota changes actively modulate host responses.<br><br>METHODS: Using A. salina as a model organism, we combined physiological assays, oxidative stress analysis, gut microbiome profiling, and bacterial functional validation under chronic polystyrene microplastics exposure.<br><br>RESULTS: Polystyrene microplastics accumulated in the gut and significantly impaired growth and survival, accompanied by reduced digestive enzyme activity and immune function, as well as increased oxidative stress, indicating disruption of physiological homeostasis. Microplastic exposure also induced microbial dysbiosis, characterized by decreased diversity and compositional shifts. Functional assays demonstrated that a bacterium enriched under exposure, Pseudomonas knackmussii, partially restored host growth and physiological functions while reducing oxidative stress.<br><br>CONCLUSIONS: These findings demonstrate that gut microbiota are not only altered by microplastic exposure but also actively modulate host responses to environmental stress, providing new insight into microbiota-mediated resilience under pollutant stress.}, }
@article {pmid42187733, year = {2026}, author = {Sui, J and Wang, N and Wang, H and Li, Y and Wang, J and Duan, M and Liao, M and Jiang, Y and Zhou, X}, title = {Soil-Nutrient Depletion and Microbial Community Restructuring in Continuous Celery Cropping: Opposing Responses of Bacteria and Fungi.}, journal = {Biology}, volume = {15}, number = {10}, pages = {}, pmid = {42187733}, issn = {2079-7737}, support = {32001929//National Natural Science Foundation of China/ ; K25LD351//Development of Compound Microbial Inoculant for Soil Microecological Regulation Based on Wheat-maize Rotation/ ; K26LD069//Creation and Demonstration of Microbial Remediation Agent for Rhizosphere Regulation in Wheat on Saline-Alkaline Soil/ ; 202510447005//National College Student Innovation Training Program/ ; }, abstract = {Continuous cropping obstacles represent a major constraint in agricultural production, yet the underlying microbial mechanisms remain incompletely understood. This study systematically compared soil physicochemical properties, microbial diversity, community composition, and nutrient-microbe relationships between continuous cropping (CC) and non-continuous cropping (CK) celery rhizospheres using high-throughput sequencing, soil physicochemical analysis, and Mantel tests. The results revealed that CC soils exhibited severe depletion of available potassium (AK, 69.9% decreased) and alkali-hydrolyzable nitrogen (AN, 65.9% decreased), accompanied by a modest but statistically significant accumulation of total phosphorus (TP, 8.0% increased). Strikingly, bacterial and fungal communities displayed diametrically opposed diversity responses: CC significantly reduced bacterial α-diversity (Shannon: 5.66 vs. 6.67, p < 0.01) and richness (ACE: 2018 vs. 2623, p < 0.01), whereas fungal diversity and richness more than doubled under CC (ACE: 619 vs. 296, p < 0.01; Shannon: 4.13 vs. 3.34, p < 0.01). β-diversity analyses (NMDS and ANOSIM) confirmed fundamental community restructuring in CC soils for both microbial domains. At the taxonomic level, CC soils showed significant depletion of beneficial plant growth-promoting rhizobacteria (PGPR), including Bacillus (↓89.3%), Mesobacillus (↓72.8%), and Pseudomonas (↓30.8%), coupled with dramatic enrichment of the phytopathogenic genus Fusarium (10.9-fold increase, 8.81% vs. 0.81%, p < 0.001). LEfSe analysis identified Fusarium, Arrhenia, and Mortierella as specific biomarkers of CC soils, whereas Bacillus, Mesobacillus, Cladosporium, and Alternaria were biomarkers of CK soils. Mantel tests further revealed that CC significantly altered nutrient-microbe coupling relationships, with bacterial communities significantly correlated with TP, AN, and OC, and fungal communities with TP, TK, AP, and AN. Collectively, these findings demonstrate that continuous celery cropping shifts the rhizosphere microbiome from a bacterial-dominated profile associated with beneficial taxa (e.g., Bacillus, Pseudomonas) toward a fungal-enriched profile dominated by the pathogen Fusarium, suggesting a potential transition from a putatively disease-suppressive to a disease-conducive microbial state.}, }
@article {pmid42187739, year = {2026}, author = {Ernstberger, H and Palmieri, G and Sun, JS}, title = {How Drosophila suzukii Acquires and Interacts with Its Microbiome Across Ecological Contexts.}, journal = {Biology}, volume = {15}, number = {10}, pages = {}, pmid = {42187739}, issn = {2079-7737}, support = {Presidential Postdoctoral Research Fellowship//Rutgers, The State University of New Jersey/ ; Goyette Family Endowment//Rutgers, The State University of New Jersey/ ; }, abstract = {Spotted wing drosophila (Drosophila suzukii; SWD) has become a globally invasive pest by ovipositing in ripening, intact fruit rather than decaying material, a niche distinct from most other drosophilids. An expanding body of work implicates microbes and microbially derived chemistry as key drivers of this ecology, shaping fly biology across life stages. However, much of this evidence is derived from microbiome surveys and observational comparisons, further constrained by uncontrolled diet history, laboratory rearing, and insufficient ecological context. We examine how the SWD microbiome differs in which taxa are present (composition), how flies pick up those taxa from fruit and maternal sources (acquisition), how long those taxa are retained across life stages (persistence), and how each of these varies with diet, geography, season, and host crops. We then address how microbial cues and fermentation state function as context-dependent drivers of adult attraction, avoidance, and oviposition, and how microbe-mediated interspecific interactions reshape substrate suitability and competition among drosophilids. Throughout, we critically evaluate experimental designs and identify gaps that impede causal inference. These include limited strain-level resolution, incomplete fungal characterization, and weak linkages between microbial community structure and host phenotypes. Key unresolved questions include how SWD maintains performance across diverse hosts, how microbes modulate sensory processing during seasonal shifts, and which microbial metabolites drive attraction, avoidance, and competition. Resolving these questions is a direct prerequisite for field-stable integrated pest management (IPM), including microbially informed behavioral lures, oviposition deterrents derived from pathogen- and competitor-associated volatiles, and competitor-mediated suppression strategies. The experimental priorities identified here translate directly into a roadmap for the next generation of mechanistically grounded, ecologically realistic SWD management tools.}, }
@article {pmid42187885, year = {2026}, author = {Albusta, N and Isa, S and Alrahma, H}, title = {Lean Metabolic-Dysfunction-Associated Steatotic Liver Disease (MASLD): Pathophysiology, Diagnostic Challenges, Clinical Outcomes, and Management.}, journal = {Diseases (Basel, Switzerland)}, volume = {14}, number = {5}, pages = {}, pmid = {42187885}, issn = {2079-9721}, abstract = {BACKGROUND/OBJECTIVES: Lean metabolic dysfunction-associated steatotic liver disease (lean MASLD) is an increasingly recognized phenotype occurring in individuals with normal body mass index (BMI), despite clinically important hepatic and cardiometabolic risk. This narrative review summarizes current evidence on its epidemiology, pathophysiology, diagnostic challenges, clinical outcomes, and management.<br><br>METHODS: A narrative literature review was conducted using PubMed, Embase, and Cochrane Library from database inception to March 2026. Relevant studies on lean MASLD/lean NAFLD, including cohort studies, meta-analyses, clinical trials, consensus statements, and practice guidelines, were prioritized.<br><br>RESULTS: Lean MASLD reflects interactions between visceral adiposity, insulin resistance, genetic susceptibility, sarcopenia, dietary and lifestyle factors, vitamin D deficiency, and gut microbiome alterations. Diagnosis is challenging because BMI and aminotransferase levels may underestimate metabolic vulnerability, MASH, or clinically significant fibrosis. Available data suggest increased liver-related events, liver-related mortality, and all-cause mortality compared with individuals without steatotic liver disease, although comparisons with non-lean MASLD remain heterogeneous. Resmetirom and semaglutide have expanded treatment options for noncirrhotic MASH with moderate to advanced fibrosis, but lean patients are underrepresented in pivotal trials.<br><br>CONCLUSIONS: Lean MASLD is an underrecognized but clinically important phenotype. Earlier recognition, fibrosis risk stratification, sarcopenia assessment, cardiometabolic optimization, and lean-specific therapeutic research are needed to improve outcomes.}, }
@article {pmid42187995, year = {2026}, author = {Schauer, IE and Kuhn, K and Bradford, AP and Fought, AJ and Frank, DN and Kotter, CV and Robertson, CE and Duffy, K and Santoro, N}, title = {Effects of a Reprometabolic Syndrome-Inducing Eucaloric High-Fat Diet on Insulin Sensitivity, Body Composition, the Lipidome, and the Microbiome.}, journal = {Metabolites}, volume = {16}, number = {5}, pages = {}, pmid = {42187995}, issn = {2218-1989}, support = {R01HD087314//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; }, abstract = {Background: We previously demonstrated recapitulation of the relative hypogonadotropic hypogonadism of obesity, the Reprometabolic Syndrome (RMS), in women of normal BMI with a one-month high-fat, eucaloric diet (HFD). Objective: Assess effects of HFD on sleep, body composition and lifestyle and metabolic secondary outcomes and correlate insulin sensitivity changes with the RMS. Methods: A total of 18 normally cycling women aged 18-38 with BMI 18-24 kg/m[2] were enrolled for a four-month study including a eucaloric HFD (48% calories from fat) for one menstrual cycle. Activity, sleep, body composition, and the lipidome were measured in all participants. Fecal microbiome was analyzed in the last nine participants, and insulin sensitivity by two-stage hyperinsulinemic euglycemic clamp was measured before and after HFD in 15 participants. Results: Relative to the pre-diet period, BMI, activity and sleep measures did not change, except for waking after sleep onset (WASO), which appeared to decrease during and post HFD. DXA revealed statistically significant decreases in total percent fat, total fat mass, visceral fat volume, and trunk fat volume. Whole-body insulin sensitivity decreased with the HFD while adipocyte insulin sensitivity was unaffected. Insulin sensitivity changes did not correlate with change in gonadotropins or response to gonadotropin releasing hormone (GnRH). Multiple significant changes in plasma lipids were observed, including increased ceramides and glucosylceramides. Microbiome analysis revealed increased microbial diversity. Conclusions: A one-month eucaloric HFD that induced RMS in normal-weight, reproductive-aged women also induced whole-body insulin resistance (IR) and multiple lipidomics changes potentially associated with IR. These changes in IR occurred despite overall stable activity, BMI and sleep, but did not correlate with the HPO axis defects. The unexpected decrease in body fat and increase in microbial diversity may be related to specific dietary elements of the HFD.}, }
@article {pmid42188006, year = {2026}, author = {Zhang, Y and Feng, T and Dong, Z and Ke, T and Storebakken, T and Cai, W and Shi, B and Huang, L}, title = {Lysolecithin Improves Lipid Metabolism and Gut Microbiota: An Integrated Transcriptome and Microbiome Analysis in Largemouth Bass (Micropterus salmoides) Fed Stearin-Based High-Lipid Diets.}, journal = {Metabolites}, volume = {16}, number = {5}, pages = {}, pmid = {42188006}, issn = {2218-1989}, support = {2025SNJF091//Zhejiang 'San-Nong Jiu-Fang' Agri-Tech Cooperation Initiative/ ; }, abstract = {Background: Supplementing aquafeeds with emulsifiers can enhance lipid utilization, yet the physiological effects of lysolecithin, derived from enzymatic lecithin conversion, remain under-explored. Objectives: This study examined the effects of lysolecithin supplementation on hepatopancreatic transcriptome and gut microbiota in largemouth bass (Micropterus salmoides) fed stearin-based high-lipid diets. Methods: Two diets were formulated: a control containing 130 g kg[-1] stearin fish oil (SO), and in the experimental diet (SL), 3.1 g kg[-1] rapeseed oil was replaced with 3.1 g kg[-1] lysolecithin oil. Each diet was fed to three replicate groups for 56 days. Hepatopancreas and distal intestine were sampled for transcriptome profiling, and gut microbiota were characterized at 28 and 56 days. Results: Lysolecithin supplementation resulted in 424 differentially expressed genes compared with the control (322 up- and 102 downregulated). KEGG enrichment indicated major effects on lipid metabolic processes, notably activation of the PI3K-AKT signaling pathway, enhanced adipocyte lipolysis, and modulation of adipocytokine signaling, suggesting improved insulin sensitivity and lipid mobilization. Histological analysis showed mild distal intestinal inflammation in the SO group. Gut microbiota composition shifted over time; lysolecithin increased the relative abundance of Cetobacterium and reduced potential opportunistic taxa compared with the control. Conclusions: Overall, dietary inclusion of lysolecithin improved lipid utilization in largemouth bass, likely by enhancing lipid metabolism and promoting beneficial gut microbial profiles. These findings support lysolecithin as a promising feed additive for optimizing high-lipid aquafeeds.}, }
@article {pmid42188162, year = {2026}, author = {Tao, M and Zhang, J and Fan, Y}, title = {Metagenomic Analysis of Gut Microbiome Across Developmental Stage of Asian Corn Borer (Ostrinia furnacalis).}, journal = {Insects}, volume = {17}, number = {5}, pages = {}, pmid = {42188162}, issn = {2075-4450}, support = {Grant No. 32402469//National Natural Science Foundation of China/ ; }, abstract = {Ostrinia furnacalis is one of the most important agricultural pests in Asia. Previous studies utilizing 16S rRNA sequencing have established a foundational understanding of the taxonomic composition of its gut microbiota; however, the dynamic functional transitions across the host's entire life cycle remain poorly understood. In this study, we used metagenomic sequencing to systematically characterize the gut microbiome across six groups representing different life stages and sexes of O. furnacalis: first-instar, third-instar, and fifth-instar larvae, pupae, and adults (both males and females). Microbial richness and evenness vary significantly across six groups representing different life stages and sexes. Species richness is highest in the first-instar larvae (L1D2), while evenness is relatively high in both first- and third-instar larvae (L1D2 and L3D2). Additionally, no sex-based differences were observed in either indicator during the adult stage. Enterococcus mundtii is the primary species driving community succession and rapidly achieves dominance after the third-instar stage. Co-occurrence network analysis revealed that the first-instar larval network exhibits the highest complexity, with positive correlations accounting for 96.6% of all edges. Conversely, the fifth-instar larvae exhibits the greatest proportion of negative correlation edges at 29.13%, while the pupal stage network is the most dispersive, indicating microbial reorganization during metamorphosis. Functional annotation reveals that carbohydrate and amino acid metabolism pathways are significantly enriched during the larval stage. In contrast, the pupal stage is characterized by enrichment in environmental information processing and a notable increase in polysaccharide lyases (PLs). This shift indicates that the microbiota transitioned from degrading plant polysaccharides to foraging host-derived glycans. The number of resistance genes in the first-instar larvae is significantly higher than that in all other groups representing different life stages and sexes. Collectively, this study systematically reveals the dynamic succession patterns of the gut microbiome throughout the life cycle of O. furnacalis and provides a theoretical foundation for the development of microbiome-based pest management strategies.}, }
@article {pmid42188320, year = {2026}, author = {Mustika, A and Gorica, E and Harbuwono, DS and Kurniawati, EM and Hadinata, E and Hidayat, AA and Siahaan, SCPT and Hendarto, H and Santini, A and Nurkolis, F}, title = {Algae-Derived Bioactives Reprogram the Gut-SIRT1-Kisspeptin Axis in Polycystic Ovary Syndrome.}, journal = {Marine drugs}, volume = {24}, number = {5}, pages = {}, pmid = {42188320}, issn = {1660-3397}, mesh = {*Polycystic Ovary Syndrome/drug therapy/metabolism/physiopathology/microbiology ; Humans ; Female ; *Sirtuin 1/metabolism ; Animals ; Gastrointestinal Microbiome/drug effects ; Signal Transduction/drug effects ; }, abstract = {Polycystic ovary syndrome (PCOS) is increasingly recognized as a complex, multi-system disorder involving interactions among metabolic dysfunction, chronic low-grade inflammation, and neuroendocrine dysregulation, rather than a condition confined to the ovary. While current management strategies primarily target symptomatic manifestations, such as menstrual irregularity, hyperandrogenism, and insulin resistance, they do not directly address the underlying integrative pathways linking the gut microbiome, cellular energy sensing, and hypothalamic reproductive control. This review proposes a mechanistic framework in which algae-derived bioactives modulate a gut-SIRT1-kisspeptin axis, thereby offering a systems-level perspective on PCOS pathophysiology and intervention. Gut dysbiosis in PCOS contributes to altered bile acid signaling, disrupted microbial metabolite profiles, and increased inflammatory tone, all of which may impair both metabolic and reproductive functions. Concurrently, reduced activity of the NAD[+]-dependent deacetylase SIRT1 has been documented across ovarian, endometrial, and metabolic tissues, linking energy imbalance to oxidative stress, inflammation, and impaired steroidogenesis. At the neuroendocrine level, dysregulated kisspeptin signaling contributes to abnormal gonadotropin-releasing hormone pulsatility and luteinizing hormone hypersecretion, key features of PCOS. Algae-derived compounds, including polysaccharides, phlorotannins, fucoidan, fucoxanthin, and microalgae bioactives, exhibit prebiotic, anti-inflammatory, and metabolic regulatory properties that intersect with these pathways, particularly through modulation of gut microbiota and activation of AMPK/SIRT1 signaling. The central proposition of this review is that algae-derived bioactives may act across interconnected biological layers: reshaping gut microbial ecology, restoring SIRT1-mediated metabolic balance, and retuning kisspeptin-driven neuroendocrine activity. While individual components of this axis are supported by substantial evidence, direct experimental validation of the complete pathway remains limited. Therefore, this framework is positioned as a translationally grounded but hypothesis-driven model that integrates currently fragmented findings into a coherent and testable paradigm. Future research should prioritize multi-level experimental and clinical studies that simultaneously assess microbiota composition, metabolic signaling, and reproductive neuroendocrine outcomes to establish the therapeutic potential of algae-based interventions in PCOS.}, }
@article {pmid42188693, year = {2026}, author = {Morozan, VP and Stancu, M and Ionescu, MI and Catrina, AM and Mocanu, A and Suhăianu, V and Iacovache, AV and Chirilă, AT and Bordeianu, A and Zăgrean, L and Zăgrean, AM and Moldovan, M}, title = {Prolonged Antibiotic Exposure During Gestation Increases the Severity of Perinatal Asphyxia as Measured by EEG Reactivity in Rodents.}, journal = {Neurology international}, volume = {18}, number = {5}, pages = {}, pmid = {42188693}, issn = {2035-8385}, support = {PSCD NEURO_Depress//Ministry of National Defence/ ; }, abstract = {BACKGROUND/OBJECTIVES: Birth asphyxia is a frequent neonatal complication in humans. Its outcome is variable, and the factors underlying this variability remain incompletely understood. Maternal gut microbiome impairment has been proposed as one factor that may influence offspring neurodevelopment, especially when the immature brain is exposed to additional vulnerability such as perinatal asphyxia (PA). Building on our previous maternal microbiome disruption model and on our prior observation that electroencephalography (EEG) reactivity to photic stimulation under deep anesthesia detects functional impairment two months after PA, we assessed whether this reactivity was further impaired after prolonged gestational antibiotic administration and whether probiotics modulated this effect.<br><br>METHODS: Wistar dams received antibiotics, probiotics, antibiotics with probiotics, or control treatment, and offspring underwent PA. Adult EEG reactivity to photic stimulation was assessed during chloral hydrate-induced burst suppression. Burst count reactivity (BCR) was used as the primary event-based readout of stimulus-evoked burst recruitment and was compared with the suppression-ratio-based burst-suppression reactivity index (BSRi).<br><br>RESULTS: Burst suppression remained reactive to photic stimulation in all groups. BCR was lower after gestational antibiotic treatment than in controls. The magnitude of the effect was attenuated by probiotics coadministration. BSRi showed the same overall pattern.<br><br>CONCLUSIONS: Prolonged gestational antibiotic exposure increased the severity of perinatal asphyxia as measured by EEG reactivity in the adult offspring. The converging BCR and BSRi results support burst-suppression reactivity as a functional neurophysiological readout in this PA model and support further methodological development of EEG reactivity measures for translational studies of hypoxic-ischemic brain injury.}, }
@article {pmid42188886, year = {2026}, author = {Yi, C and Nicolas, CS and Sun, Z and Wang, Q and Dong, T and Wu, Y}, title = {Effects of a Novel Prebiotic and Postbiotic Dietary Supplement on Gut Microbiota, Intestinal Barrier Markers, and Inflammation in Healthy Dogs.}, journal = {Veterinary sciences}, volume = {13}, number = {5}, pages = {}, pmid = {42188886}, issn = {2306-7381}, support = {202404810411350//Virbac China/ ; }, abstract = {Although prebiotics and postbiotics support gastrointestinal health, evidence for their combined effects in dogs remains limited. This study evaluated a novel prebiotic and postbiotic supplement in healthy dogs undergoing a dietary transition. Thirty-six healthy adult dogs were randomly assigned to control group (CON, high-protein basal diet with placebo chew) or treatment group (TRT, the same basal diet with chew containing prebiotics [baobab fruit pulp and acacia gum] and postbiotics [inactivated Lactobacillus acidophilus and selected yeast fractions]) for a 28-day formal trial following a 7-day adaptation period. The primary outcomes evaluated included clinical fecal scores, specific biomarkers of intestinal barrier function and inflammation, fecal short-chain fatty acids, and microbiota structure. Following the 7-day adaptation, formal trial baseline, fecal scores were already within the healthy range and remained optimal without differing between groups throughout the study. Compared with CON, the TRT group showed lower fecal calprotectin and serum diamine oxidase levels, and higher fecal butyrate (p < 0.05). Metagenomic analysis revealed increased abundances of Bacteroidota, Oscillospiraceae, Prevotellaceae, and Prevotella in TRT (p < 0.05). Overall, in healthy dogs, this supplementation was associated with favorable microbiota modulation and modulated biomarkers of intestinal barrier and inflammation within normal ranges, without altering clinical fecal endpoints.}, }
@article {pmid42189287, year = {2026}, author = {Candeliere, F and Busi, E and Cerri, S and Sola, L and Lombardi, M and Greco, S and Pedroni, S and Amaretti, A and Raimondi, S and Chiavelli, C and Vitale, MG and Bertolini, F and Depenni, R and Franchini, G and Dominici, M and Rossi, M}, title = {Enterotype-specific microbial biomarkers of immune checkpoint inhibitor response revealed by large-scale integrated metagenomic analysis.}, journal = {Cancer immunology, immunotherapy : CII}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00262-026-04432-w}, pmid = {42189287}, issn = {1432-0851}, support = {PE00000019//NextGenerationEU/ ; }, abstract = {The gut microbiota appears to play a critical role in modulating antitumor immune responses and influencing the efficacy of cancer immunotherapy drugs such as immune checkpoint inhibitors. However, the identification of consistent microbial biomarkers of response remains a significant challenge. This lack of consensus is largely driven by multi-source heterogeneity, including geographic variations in lifestyle, and high inter-individual variability. We hypothesize that these inconsistencies arise because microbiome composition is not uniform but organized into distinct enterotypes. To address this, we performed an integrated metagenomic analysis of 569 fecal samples from oncological patients affected by different tumor types treated with immunotherapy. The samples were clustered into two main enterotypes, E1 and E2, each of them containing two subclusters. A total of 166 species (e.g., Collinsella spp., Blautia spp., Bacteroides spp.) were identified as enterotype-specific biomarkers. A preliminary independent concordance assessment of these biomarkers was conducted in 19 oncologic patients with exceptional response to immunotherapy, providing an initial confirmation of selected enterotype-associated signals. Furthermore, we evaluated the predictive potential of gut microbiota profiles for immunotherapy outcomes through machine learning techniques. The models showed encouraging, albeit moderate, performance in the heterogeneous full dataset, supporting the potential of microbiome-based stratification as an exploratory framework for patient classification, while indicating that further validation is needed before clinical application.}, }
@article {pmid42189338, year = {2026}, author = {Önal, A and Ayaz, F and Aydemir, E}, title = {Cancer immunotherapy: mechanisms, clinical applications, resistance and future directions.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {42189338}, issn = {1573-4978}, mesh = {Humans ; *Neoplasms/therapy/immunology ; *Immunotherapy/methods/trends ; Tumor Microenvironment/immunology ; Cancer Vaccines/therapeutic use/immunology ; Animals ; Immune Checkpoint Inhibitors/therapeutic use ; Oncolytic Virotherapy/methods ; }, abstract = {Cancer immunotherapy has revolutionised oncology by utilising immune-mediated mechanisms to achieve durable anti-tumour responses and long-term clinical benefits. Unlike traditional cytotoxic therapies, immunotherapeutic approaches modulate host-tumour interactions and restore immune surveillance, thereby enabling sustainable tumour control. This review provides a comprehensive synthesis covering the biological foundations and clinical development of cancer immunotherapy, cancer-immunity system interactions, tumour immunoediting, and the cancer-immunity cycle as a conceptual framework for therapeutic intervention. Major immunotherapeutic approaches, including immune checkpoint inhibitors, adoptive cell therapies, cancer vaccines, cytokine-based therapies, and oncolytic viruses, have been systematically reviewed for their mechanisms of action and clinical applications. Particular emphasis is placed on regulatory agency-approved agents, indication-based clinical use, predictive biomarkers, and rational combination strategies. Furthermore, this review addresses key challenges that limit therapeutic efficacy, including primary and acquired resistance, tumour heterogeneity, immune escape mechanisms, and the immunosuppressive tumour microenvironment. New directions such as personalised immunotherapy, neoantigen-based targeting, microbiome-immune interactions, and artificial intelligence-supported systems immunology are also discussed. By integrating mechanistic insights with clinical evidence and resistance frameworks, this review provides a consolidated perspective on the current state and future trajectory of cancer immunotherapy, offering important implications for translational research and clinical practice.}, }
@article {pmid42189604, year = {2026}, author = {Lopes, F and Martinez-Martinez, D and Späth, MR and Hoyer-Allo, KJR and Strubl, S and Cukoski, S and Knieps, L and Brodesser, S and Göbel, H and Schwarz, G and van den Berg, BM and Rabelink, TJ and Schermer, B and Benzing, T and Müller, RU and Beyer, A and Cabreiro, F and Koehler, FC}, title = {The Interplay between Gut Microbiota and Diet-Induced Kidney Protection.}, journal = {Kidney360}, volume = {}, number = {}, pages = {}, doi = {10.34067/KID.0000001219}, pmid = {42189604}, issn = {2641-7650}, abstract = {BACKGROUND: On the one hand, dietary interventions are known for their pivotal role in regulating diversity, composition as well as function of the gut microbiome. On the other hand, specific diets show an immense potential in preventing kidney injury from various damaging stimuli in rodents and recent findings, in turn, highlight a central role of gut microbiota in kidney health and disease.<br><br>METHODS: Three protective dietary regimens - a fasting mimicking diet, a diet depleted in sulfur containing amino acids and caloric restriction - were examined in parallel in a rodent model of ischemia-reperfusion injury. To delineate the diet-induced effect on gut microbiota in response to ischemic kidney damage we used comparative shotgun metagenomics for taxonomic as well as functional profiling. We further examined the renal metabolic response using comparative transcriptomics to unravel the interplay between gut microbiota and kidney protection.<br><br>RESULTS: Beneficial dietary preconditioning strategies changed the composition of gut microbiota in an IRI-dependent manner. Using ternary plots to investigate the role of dietary interventions over time before and after ischemic insult, we detected a central role of Lachnospiraceae that commonly expanded in response to renal IRI in dietary-preconditioned mice. Further functional profiling of gut microbiota in our model revealed an increase in plasma levels of bacterial derived short chained fatty acids in diet-induced kidney protection. Comparative bulk transcriptomics in our model, in turn, pointed towards the metabolic use of these bacterial derived short-chained fatty acids in kidneys of protected mice.<br><br>CONCLUSIONS: As proximal tubules lack sufficient glycolytic capacity, products of microbial metabolism may serve as an additional energy source to fulfill their high demands when withstanding ischemic damage. Our data shed light on a close interplay between gut microbiota and diet-induced kidney protection calling for further research at the crossroads of microbiology, metabolism and molecular nephrology.}, }
@article {pmid42189677, year = {2026}, author = {Reiné, J and King, LA and Singh, Y and de Steenhuijsen Piters, WAA and Carniel, BF and Solórzano, C and Mitsi, E and Pojar, S and Nikolaou, E and German, EL and Blizard, A and Marcon, F and Marques, AHC and Voskamp, AL and Chu, ML and Hasrat, R and Hill, H and Hales, C and Brown, L and Horsley, V and Hughes, LP and Zaidi, SR and Connor, V and Morton, B and Collins, AM and Rylance, J and Adler, H and Smits, HH and Mahfouz, A and McNamara, PS and Nakaya, HI and Bogaert, D and Ferreira, DM and Jochems, SP}, title = {Host-microbial interactions at the nasal mucosa in young children and adults: A retrospective, cross-sectional study.}, journal = {Cell reports}, volume = {45}, number = {5}, pages = {117346}, doi = {10.1016/j.celrep.2026.117346}, pmid = {42189677}, issn = {2211-1247}, abstract = {Young children are at increased risk for respiratory tract infections and are frequently colonized by respiratory pathogens. However, how the mucosal immune system differs between children and adults is relatively unknown. We collected nasal samples from 50 young children (aged 1-5 years) and 318 young adults (aged 18-34 years) to study how the mucosal immune system and host-microbe interactions differ with age. We used multi-omics data integration to combine host (immunophenotyping, transcriptomic, and cytokines) and microbial (16S-rRNA amplicon sequencing, viral PCRs, and pneumococcal culture) datasets. Young children had a paucity of mucosal granulocytes, while B and T cell subsets were increased. Children also had increased immune activation and inflammation, which associated with the presence of Haemophilus spp. and pneumococcus, but not viruses. In adults, Haemophilus spp. associated with T cell and monocyte recruitment, while Dolosigranulum negatively associated with neutrophil degranulation. Thus, nasal immune composition and host-pathogen interactions were clearly age dependent.}, }
@article {pmid42189941, year = {2026}, author = {Zhang, Z and Chen, X and Wu, M and Liu, X and Chang, L and Rao, F and Zhou, Y and Tsuda, K and Zhang, C and Cheng, J and Xie, J and Lin, Y and Fu, Y and Jiang, D and Chen, T}, title = {Aesculetin-mediated recruitment of denitrifying microbiota by resistant rapeseed suppresses Plasmodiophora brassicae via nitrate depletion.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag061}, pmid = {42189941}, issn = {1751-7370}, abstract = {Clubroot, caused by the protist pathogen Plasmodiophora brassicae, is a major threat to cruciferous crop production worldwide. Although plant microbiota is known to influence disease outcomes, the mechanisms underlying microbiota-mediated resistance remain unclear. Here, we investigated the role of plant microbiota in clubroot resistance using two Chinese rapeseed cultivars carrying resistance genes introduced through breeding and their susceptible parental lines. Microbiome profiling revealed that P. brassicae infection altered root and rhizosphere bacterial communities, with resistant cultivars displaying distinct assemblages. Functional prediction indicated an enrichment of denitrifying bacteria in the roots of resistant plants following pathogen challenge. Key denitrifying strains were isolated and assembled into a synthetic microbial community (SynCom18), which significantly suppressed clubroot development under both controlled and field conditions. In addition to reducing disease severity, microbial treatments improved agronomic traits, including yield and seed quality. Mechanistic analysis revealed a positive correlation between soil nitrate levels and disease severity. Denitrifying strains and SynCom18 likely suppressed the development of P. brassicae and enhanced plant immunity by reducing soil nitrate levels by approximately 39.4%. Metabolomic profiling revealed that aesculetin, as a dominant metabolite that is produced by resistance roots and excreted into the rhizosphere to recruit denitrifying bacteria. Our findings show that pathogen-infected clubroot-resistant rapeseed cultivars secrete aesculetin to recruit nitrate-depleting bacteria for resistance against P. brassicae. This study elucidates a tripartite microbiota-pathogen-soil nutrient interaction and provides a sustainable biocontrol strategy for cruciferous crops.}, }
@article {pmid42190049, year = {2026}, author = {Verma, S and Gupta, K and Qiao, X and Shen, DL and MacLennan, GT and Suryavanshi, M and Zhang, L and Miller, AW and Gupta, S}, title = {Microbial Differences in Prostate Lesions Between Black and White American Men.}, journal = {The Prostate}, volume = {}, number = {}, pages = {}, doi = {10.1002/pros.70200}, pmid = {42190049}, issn = {1097-0045}, support = {W81XWH-18-1-0618//U.S. Department of Defense/ ; W81XWH-19-1-0720//U.S. Department of Defense/ ; }, abstract = {BACKGROUND: Ethnicity and pathological factors contribute to differences in prostate neoplasm, and this landscape could be influenced by the local microbiome.<br><br>METHODS: To investigate whether prostate tissue harbors race-specific microbiota, we performed 16S rRNA gene sequencing of various hypervariable regions of cancer, inflammation, and non-cancer (benign) tissue from Black and White American men with prostate cancer followed by qRT-PCR for validation. All reported p-values were adjusted for false discovery rate to account for multiple comparisons.<br><br>RESULTS: Comparative analysis revealed marked differences in microbial composition between the two groups. Several species showed significant differential abundance, including Alphaproteobacteria (p&#x2009;<&#x2009;0.001), Bacteroides fragilis (p&#x2009;<&#x2009;0.001), Candidatus Kerfeldbacteria (p&#x2009;<&#x2009;0.001), Flavobacterium frigoris (p&#x2009;<&#x2009;0.0001), Fusobacterium nucleatum (p&#x2009;<&#x2009;0.003), Rhizobiales bacterium (p&#x2009;<&#x2009;0.0001), Sphingomonas glacialis (p&#x2009;<&#x2009;0.0001), and Staphylococcus epidermidis (p&#x2009;<&#x2009;0.05). Lesion-specific analysis further identified Pseudomonadota, Actinomycetota, and Bacilliota as the most abundant phyla in inflammatory lesions of both racial groups. However, Tenericutes were uniquely present in Black American samples, whereas Bacteroidota and Deinococcota were more abundant in the inflammatory lesions of White American men. At the genus level, analysis identified several key bacterial taxa associated with prostate cancer. Streptococcus, Abiotrophia, and Acinetobacter were significantly enriched in the Black American prostate tissues, while Staphylococcus and Corynebacterium were more abundant in tissue from White American men.<br><br>CONCLUSIONS: This is the first study to demonstrate significant microbial diversity and distinct microbial signatures in Black and White American men, suggesting that intra-prostatic bacteria may play a role in disease disparities and pathogenesis.}, }
@article {pmid42190060, year = {2026}, author = {Barbeau, AM and Kincaid, JWR and Hillis, AL and Rashan, EH and Zhang, Y and Oaks, GE and Vander Heiden, MG}, title = {The Influence of Diet on Cancer Progression and Treatment.}, journal = {Annual review of nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-nutr-062122-021518}, pmid = {42190060}, issn = {1545-4312}, abstract = {Growing evidence suggests that dietary interventions can influence cancer progression and patient outcomes. Here, we discuss mechanistic links between diet and cancer biology including those related to systemic hormone signaling, modulation of nutrient availability within the tumor microenvironment, and interactions with the immune system and microbiome, while highlighting their interconnectedness. Further, we review preclinical and clinical data evaluating specific diets, including their use with cancer therapies. Given the interest in diet as an adjunct to cancer care, it is essential to establish evidence-based dietary strategies for optimizing patient outcomes and quality of life.}, }
@article {pmid42190160, year = {2026}, author = {Park, JM and Beckman, I and Delaney, CL}, title = {Could targeting the gut microbiome provide a novel treatment option for intermittent claudication.}, journal = {Current medical research and opinion}, volume = {}, number = {}, pages = {1-14}, doi = {10.1080/03007995.2026.2673710}, pmid = {42190160}, issn = {1473-4877}, abstract = {Peripheral artery disease is a highly prevalent, age-related inflammatory condition. Many patients are asymptomatic, while others progress to chronic limb-threatening ischemia associated with high rates of morbidity and mortality. In between this wide spectrum of disease severity, patients often present with intermittent claudication which can be debilitating and lifestyle-limiting. Targeting the gut microbiome may be a novel strategy to treat patients with claudication, primarily through dietary interventions that promote restoration of microbial homeostasis. A review of the literature suggests that gut dysbiosis, circadian dysrhythmia, and vascular senescence are key interacting contributors to claudication, and each of these factors are amenable to modulation. These may include introducing key SCFA-producing bacteria (e.g. butyrate and propionate) or specific bacterial species that are associated with vigorous exercise in athletic individuals (e.g. Veillonella atypica and Prevotella), natural dietary senolytics (e.g. o-Vanillin), and behavioural changes such as time restricted eating, intermittent fasting and calorie restriction. Furthermore, resistance training provides an important exercise option in this cohort without additional strain on the lower limbs. We propose that an integrated cocktail of selective dietary interventions to restore gut homeostasis, tailored resistance exercise regimes, and entrainment to normalized circadian rhythm will provide a significant beneficial impact on exercise capacity in patients with claudication.}, }
@article {pmid42190264, year = {2026}, author = {Xinlin, L and Gu, H and Li, R and Mao, X and Chen, C}, title = {Association Between Metabolic Clusters and Microbial Age in High-Risk Populations for Diabetes and Their Potential Impact on Cardiovascular Disease Risk: Cross-Sectional Observational Study.}, journal = {JMIR medical informatics}, volume = {14}, number = {}, pages = {e73119}, doi = {10.2196/73119}, pmid = {42190264}, issn = {2291-9694}, mesh = {Humans ; Female ; Middle Aged ; Cross-Sectional Studies ; *Cardiovascular Diseases/epidemiology ; Male ; *Gastrointestinal Microbiome/physiology ; *Diabetes Mellitus/epidemiology/metabolism/microbiology ; Adult ; Cluster Analysis ; Risk Factors ; Aged ; }, abstract = {BACKGROUND: Metabolic multimorbidity is prevalent in high-risk populations for diabetes and is linked to cardiovascular disease (CVD) and gut microbiota composition. The relationship between metabolic clusters (MCs), microbial age (MA), and metabolic markers remains poorly understood.<br><br>OBJECTIVE: This study aimed to investigate the characteristics of MCs and MA in high-risk diabetic populations, focusing on their associations with gut microbiota, metabolic dysregulation, and CVD risk.<br><br>METHODS: Using data from the NIH Integrative Human Microbiome Project, we performed metabolomic and microbiomic analyses. K-means clustering identified MCs, and redundancy analysis examined the relationship between metabolic variables and microbiota. A random forest (RF) model predicted MA and CVD risk, while the linear discriminant analysis effect size identified microbial species associated with MCs and MA. Co-occurrence network analysis explored microbial interactions.<br><br>RESULTS: We included 103 high-risk individuals (56/103, 54.4% female, mean age 50.6, SD 54.6 years). In total, 3 MCs were identified: MC1 (high glucose or blood urea nitrogen), MC2 (relatively healthy), and MC3 (lipid dysregulation). Age explained 3% of gut microbiota variation (R2=0.03; P=.006). The RF model predicting microbial age showed a strong correlation with chronological age in training data (&#x3c1;=0.97, root mean square error=3.33; P<.001) and moderate correlation in test data (&#x3c1;=0.35; P<.001). High microbial age was associated with elevated lipid markers (low-density lipoprotein and triglycerides; P<.001) and higher cardiovascular risk. The RF model for CVD risk prediction achieved excellent discrimination (area under the curve=0.95 for the low-risk and 0.95 for the high-risk groups).<br><br>CONCLUSIONS: This study highlights the relationship between MCs, MA, and gut microbiota, providing insights for early intervention and personalized treatment strategies for diabetes and related metabolic disorders.}, }
@article {pmid42190464, year = {2026}, author = {Yergalyiev, T and Roth, C and Rodehutscord, M and Seifert, J and Camarinha-Silva, A}, title = {Age, strain, and gut section shape the microbiome of commercial laying hens.}, journal = {Poultry science}, volume = {105}, number = {9}, pages = {107152}, doi = {10.1016/j.psj.2026.107152}, pmid = {42190464}, issn = {1525-3171}, abstract = {Gut microbiota, among other factors, may influence the overall performance of laying hens. To investigate how host genetics and age shape microbial communities, we profiled the gut microbiome of two commercial laying hen strains, Lohmann Brown-Classic and Lohmann LSL-Classic, across five anatomical sections (crop, gizzard, duodenum, ileum, caeca) at five ages spanning pullet development through late lay (10, 16, 24, 30, 60 weeks of age). We extracted RNA from the luminal content and performed 16S rRNA gene amplicon sequencing based on complementary DNA. Both strain and age had highly significant effects on community composition. The greatest shifts occurred between early development (10 weeks) and the onset of lay (16-24 weeks). To link taxa to function, we applied shotgun metagenomics to samples taken at 16 and 24 weeks, revealing strain-specific changes in functional profiles associated with the transition into egg production. We identified three groups of bacterial species that increased in abundance during the transition: lactic-acid producers (such as Lactococcus raffinolactis, Ligilactobacillus aviarius, Lactobacillus pontis, etc.), potential probiotic bacteria (Megasphaera stantonii, Megamonas funiformis, Phocaeicola coprophilus, etc.), and opportunistic or egg-associated pathogens (Comamonas testosteroni, Aeromonas caviae, Acinetobacter johnsonii, etc.). Corresponding shifts were also observed in the functional profiles of inositol phosphate metabolism. Moreover, MAG-based analyses reported two bacterial species - Gallibacterium anatis and Megamonas hypermegale, to contain high numbers of myoinositol-related genes. Together, our results demonstrate that genetic background and production phase both drive dynamic, section-specific changes in the gut microbiome of laying hens.}, }
@article {pmid42190486, year = {2026}, author = {Esther, A and Gegout, PY and Auger, C and Petit, C and Huck, O}, title = {3D human cell culture models in periodontal research: A scoping review.}, journal = {Archives of oral biology}, volume = {188}, number = {}, pages = {106636}, doi = {10.1016/j.archoralbio.2026.106636}, pmid = {42190486}, issn = {1879-1506}, abstract = {OBJECTIVE(S): Despite the increasing use of 3D in vitro models in periodontal research, there is currently no comprehensive synthesis explicitly mapping how effectively these models translate structural achievements into functional biological fidelity. Thus, this scoping review aims to map the existing literature while critically evaluating the biological complexity and translational value of current human 3D in vitro periodontal models.<br><br>DESIGN: PubMed, Cochrane Library, and Web of Science databases were searched to identify relevant original studies detailing the development and application of human 3D in vitro models in periodontal research.<br><br>RESULTS: A substantial increase in publications since 2018 was observed, reflecting a growing interest in physiologically relevant in vitro systems. However, our analysis highlights a critical gap between structural innovation and biological fidelity. Most studies (76.2%) employ single-cell-type culture systems, predominantly utilizing periodontal ligament stem cells. Methodologically, conventional fabrication techniques remain dominant (84.8%), particularly solid scaffolds and hydrogels, whereas scaffold-free approaches are less frequent. Only 23.8% of the models incorporate multiple cell types, and the integration of immune components is mostly absent. Furthermore, complex dysbiotic microbial communities, which play a central role in periodontal pathogenesis, are rarely included.<br><br>CONCLUSIONS: While the structural biofabrication of periodontal models has significantly advanced, their functional biological relevance remains restricted. To better recapitulate disease mechanisms and enhance clinical predictivity, future models must shift toward integrating multicellular microenvironments, immune system components, and dynamic host-microbiome interactions.}, }
@article {pmid42190523, year = {2026}, author = {Udobi, ME and Bella-Omunagbe, M and Effiong, PE and Afolabi, IS and Chinedu, SN}, title = {Malaria driven mechanisms shaping cancer risk and aggressiveness in African populations.}, journal = {Cancer treatment and research communications}, volume = {48}, number = {}, pages = {101210}, doi = {10.1016/j.ctarc.2026.101210}, pmid = {42190523}, issn = {2468-2942}, abstract = {Malaria and cancer represent intersecting public health challenges in sub-Saharan Africa, where malaria remains endemic and cancer incidence is rapidly increasing. Emerging evidence indicates that chronic or recurrent malaria infection may influence carcinogenesis and tumour aggressiveness through complex biological mechanisms. This narrative review critically synthesizes data from PubMed, Scopus, and Web of Science to elucidate the mechanistic intersections between malaria and cancer risk, progression, and therapeutic response. The review highlights five principal axes linking malaria to oncogenesis: malaria-induced oxidative stress and chronic inflammation driving genomic instability; gut microbiome dysbiosis altering systemic immunity and tumour microenvironment; exploitation of shared molecular targets such as the endothelial protein C receptor (EPCR) and oncofetal chondroitin sulfate by Plasmodium parasites and cancer cells; cooperative interactions between malaria and oncogenic viruses like Epstein-Barr virus in lymphomagenesis; and malaria-associated vitamin D deficiency impairing immune surveillance. Furthermore, pharmacological evidence reveals that several antimalarial agents, including artemisinin derivatives, chloroquine, and quinacrine, possess anticancer properties, while some anticancer drugs exhibit antimalarial activity, underscoring opportunities for dual-action or repurposed therapeutics. The convergence of malaria and cancer biology underscores the urgent need for integrative, multidisciplinary research spanning molecular epidemiology, immunology, and pharmacology. Unveiling these mechanisms may unveil novel biomarkers and therapeutic targets, guiding context-specific interventions to reduce the disproportionate cancer burden in malaria-endemic African populations.}, }
@article {pmid42190649, year = {2026}, author = {Lobel, L and Fonseca-Pereira, D and Nakatsu, G and Michaud, M and Cao, YG and Bae, S and Krabak, C and Oren, Y and Clay, SL and El Tekle, G and Chun, E and Kon, S and Chan, AT and Clardy, J and Glickman, JN and Ajami, NJ and Day, A and Damania, A and Baruch, EN and White, MG and Diggs, LP and Wargo, J and Riffelmacher, T and Balancio, A and Kronenberg, M and Huttenhower, C and Garrett, WS}, title = {Dietary sulfur amino acids enhance anti-tumor immunity in colon cancer via an NKT cell-XCL1-cDC1 circuit.}, journal = {Immunity}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.immuni.2026.05.001}, pmid = {42190649}, issn = {1097-4180}, abstract = {The efficacy of immune checkpoint inhibitors (ICIs) in colon cancer (CC) is limited by the tolerogenic immune landscape of both the tumor and the intestine. Here, we investigated the impact of microbial metabolic pathways associated with ICI responsiveness on anti-tumor immunity in CC. Sulfur amino acid (Saa) metabolic pathways were enriched in ICI responders and in individuals without CC. In murine models, high-Saa diets restricted CC progression, increased colonic mucus thickness, and promoted the expansion of mucus-dwelling Mucispirillum schaedleri (M. schaedleri). Dietary Saa supplementation increased the frequency of activated intratumoral cytotoxic CD8[+] T cells. The protective effect of high-Saa diets required type 1 conventional dendritic cells (cDC1s) in tumor-draining lymph nodes, where M. schaedleri was sufficient to drive cDC1 expansion and activation. Mechanistically, M. schaedleri stimulated natural killer T (NKT) cell expansion and secretion of the chemokine XCL1, which was essential for cDC1 recruitment and anti-tumor immunity. Dietary modulation of this NKT-XCL1-cDC1 axis in combination with ICIs may open avenues for improved treatments of CC.}, }
@article {pmid42190784, year = {2026}, author = {Qadeer, A and Nazir, MJ and Muhammad, S and Azim, R and Wang, Q and Hussain, MM}, title = {Decoding heavy metal tolerance in rice: Nucleic acid-based technologies shaping global food security.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {152693}, doi = {10.1016/j.ijbiomac.2026.152693}, pmid = {42190784}, issn = {1879-0003}, abstract = {Global rice production is critically threatened by heavy metal contamination, particularly cadmium (Cd) and arsenic (As), which compromises yield, diminishes grain nutritional quality, and exposes billions of consumers to nephrotoxic and carcinogenic risks. Conventional remediation strategies (soil amendments, water management, phytoremediation) are prohibitively expensive, temporally protracted, and fundamentally reactive, while conventional breeding is constrained by linkage drag, polygenic trait architecture, and absence of natural alleles that restrict toxic metal uptake from essential mineral nutrition. This review critically examines how nucleic acid-based technologies have fundamentally reconfigured the discovery-to-deployment pipeline for heavy metal tolerance in rice. We trace the progression from early QTL mapping and positional cloning of transporters through population-scale GWAS and pan-genomics, which have resolved the full allelic series at these loci, to contemporary CRISPR-mediated genome editing, that generated transgene-free, field-validated low-accumulating lines. Transcriptomic, epigenomic, and metagenomic tools have further illuminated the dynamic stress response, non-coding regulatory networks, and rhizosphere microbiome contributions to metal exclusion. Translational case studies including Japan's marker-assisted deployment of OsHMA3 for Cd mitigation and South Asia's development of OsLsi2-edited low-As lines demonstrate that these technologies are not merely academic instruments but operational solutions. However, specificity-versus-essentiality dilemma, multi-metal antagonism (Cd/As redox conflict), and profound regulatory divergence (SDN-1 exemption in the Americas, Japan, and India versus GMO classification in the EU) remain formidable barriers. We conclude that nucleic acid technologies constitute the cornerstone of a second Green Revolution focused on grain quality and safety, contingent upon sustained investment in synthetic biology, digital integration, and internationally harmonized governance frameworks.}, }
@article {pmid42190957, year = {2026}, author = {Rico, JL and Schmidt, A and Ghadermazi, P and Otto, K and Metcalf, JL and Castillo Jaimes, JS and Chan, J and Reardon, KF and De Long, SK}, title = {Higher-order interaction effects among operating conditions and feedstocks shape reactor microbiomes and fatty acid production profiles.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134980}, doi = {10.1016/j.biortech.2026.134980}, pmid = {42190957}, issn = {1873-2976}, abstract = {Arrested anaerobic digestion (AAD) offers a promising route for producing fatty acids (FAs) from organic residues, yet optimal conditions for selectively generating medium-chain fatty acids (MCFAs) remain poorly defined. Here, we systematically evaluated the main and interaction effects of pH (5, 7, 9), feedstock (food waste, manure), temperature (35 and 45 °C), and inoculum source on microbiome composition and FA production. Anaerobic digester sludge and a novel bison rumen inoculum were compared. Significant higher-order interactions among operating parameters governed FA profiles and microbiome structure. Butyric acid production was driven by a three-way interaction among pH, feedstock, and temperature (p < 0.001), with maximum concentrations achieved in food waste reactors at pH 5.0 and 35 °C (1.2 ± 0.1 g L[-1] with sludge and 1.1 ± 0.3 g L[-1] with rumen). MCFA production exhibited significant four-way interactions (p < 0.1 to p < 0.001). At 45 °C and pH 5.0, inoculum source tuned MCFA selectivity: sludge favored pentanoic acid (0.4 ± 0.1 g L[-1]), whereas rumen favored hexanoic and heptanoic acids (up to 0.4 ± 0.2 g L[-1]). Manure reactors produced < 0.2 g L[-1] MCFAs under all conditions. Genera, including Megasphaera, Prevotella, and Lactobacillus, were associated with production of specific MCFAs. PICRUSt2-based pathway predictions were consistent with MCFA production patterns and suggested a potential role for lactic acid-driven chain elongation pathways. This study provides insights into how interacting operating conditions shape AAD microbiomes, their FA profiles, and advances the trajectory of research aimed at engineering robust and controllable microbiomes for waste valorization.}, }
@article {pmid42191017, year = {2026}, author = {Cavone, C and De Paola, D and Naclerio, G and Bucci, A and Caracciolo, AB and Rutigliano, A and Cotugno, P and Rolando, L and Savino, I and Grenni, P and Celico, F and Uricchio, VF and Ancona, V}, title = {Lavandula angustifolia and microbial bioaugmentation synergistically reshape rhizosphere microbiome and enhance heavy metals removal in historically contaminated soils.}, journal = {New biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.nbt.2026.05.013}, pmid = {42191017}, issn = {1876-4347}, abstract = {Heavy metal contamination poses a serious threat to soil ecosystems and requires sustainable remediation approaches capable of restoring both chemical quality and microbial functionality. This study evaluates the effectiveness of plant-assisted bioremediation (Lavandula angustifolia) and bioaugmentation with a selected bacterial consortium of four strains (Gordonia amicalis, Rhodococcus erythropolis, Acinetobacter puyangensis, and A. tibetensis) in soils that have been historically contaminated with multiple pollutants - as heavy metals (HMs) and polychlorinated biphenyls (PCBs). Microcosms were created with four treatments, i.e. Historically Contaminated Soil (HCS), Plant-assisted bioremediation (PLANT), microbial bioaugmentation (BIOAUG) and the combination of plant-assisted bioremediation and bioaugmentation (PLANT+BIOAUG) and monitored over a 90-days period through chemical analyses, 16S rDNA sequencing, diversity metrics, differential abundance tests and functional prediction. The PLANT+BIOAUG combination demonstrated the highest removal efficiency of Pb (44.75%) and Sn (66.87%), suggesting a robust synergistic interaction between plant and microbial inoculum. Microbial α-diversity remained stable across treatments, while β-diversity analyses (Bray-Curtis, PERMANOVA p = 0.001) revealed significant community restructuring. Taxonomic analyses highlighted shifts in key genera and an enrichment of bacterial families associated with metal transformation, redox processes, and stress tolerance. The functional prediction identified 7,959 KEGG functions, with the combined treatment showing the highest functional redundancy in metal efflux systems, siderophore production, electron transport pathways, and EPS/biofilm formation. Overall, integrating L. angustifolia with a metal-resistant microbial consortium could improve both contaminant removal and microbial functional potential, supporting a robust and sustainable strategy for the remediation of multi-contaminated soils. These results provide valuable insights into synergistic plant-microbe processes and offer practical guidelines for in situ bioremediation within the framework of the circular economy and nature-based models.}, }
@article {pmid42191188, year = {2026}, author = {Huijs, E and van der Sman, L and Wirken, L and Delcliseur, HS and Winter, EG and de Roos, NM and van der Molen, RG and Oosterman, JM and Viganò, P and Horne, AW and Dolmans, MM and Hoogstad-van Evert, JS and Nap, AW and , }, title = {Effectiveness of an anti-inflammatory diet intervention and cognitive behavioural therapy in endometriosis: protocol for a randomised controlled clinical trial.}, journal = {BMJ open}, volume = {16}, number = {5}, pages = {e116964}, doi = {10.1136/bmjopen-2026-116964}, pmid = {42191188}, issn = {2044-6055}, mesh = {Humans ; Female ; *Endometriosis/diet therapy/therapy/psychology/complications ; *Cognitive Behavioral Therapy/methods ; Quality of Life ; Adult ; *Inflammation/diet therapy ; Life Style ; Research Design ; Treatment Outcome ; }, abstract = {INTRODUCTION: Treatment for women with endometriosis is only partially or temporarily effective. Moreover, medical hormonal treatment is associated with debilitating side effects and interferes with fertility, while surgery has a relatively high risk of complications. Meanwhile, women with endometriosis show increasing interest in implementing lifestyle interventions to alleviate symptoms and improve health-related quality of life (HRQoL). Integrating these lifestyle interventions can provide a holistic approach to the treatment of this debilitating disease. However, scientific evidence supporting the effectiveness of these interventions is limited. This study is designed to investigate the effectiveness of two lifestyle interventions and the combination of both: an anti-inflammatory diet intervention (AIDI) could improve immune cell function and reduce inflammation, resulting in improved HRQoL and alleviating pain. In addition, the integration of cognitive behavioural therapy (CBT) aims to provide insight into pain mechanisms and coping with pain, and to assist in sustaining dietary adjustments.<br><br>METHODS AND ANALYSIS: The Pain in Endometriosis And the Relation to Lifestyle (PEARL) study is a five-arm randomised controlled trial with a pre-post factorial design with two factors: an AIDI and CBT. The study population will consist of 250 premenopausal women, of whom 200 are diagnosed with endometriosis and experience pain symptoms and 50 are healthy controls (HC). Women with endometriosis will be recruited from one academic tertiary and five secondary hospitals in the Netherlands. They will be randomised (1:1:1:1) among four intervention groups: standard care (SC) (SC group), SC and an AIDI (SC + AIDI group), SC and CBT (SC + CBT group), and SC, AIDI and CBT (SC + AIDI + CBT group). Women with endometriosis will visit the hospital twice during the intervention period, at the start (T0) and end (T2) of the 13-week intervention period. HC will not undergo any of the interventions and will have one hospital visit (T0). Participants will complete questionnaires regarding pain symptoms, HRQoL, physical activity level, sleep, diet quality, pain cognitions, and stress at T0 and T2. Furthermore, they are instructed to collect menstrual effluent, a vaginal swab and a faecal sample. During the study visits, peripheral blood will be drawn and scalp hair samples will be taken. The primary outcome is average pain, measured using a numerical rating scale. Secondary outcomes focus on HRQoL, inflammation, immune system characteristics, vaginal- and gut microbiome, and hair cortisol levels. These are considered to reflect potentially underlying mechanisms of the effect of both interventions on the primary outcome. Biological samples and questionnaires of women with endometriosis and HC will be compared to establish the differences in secondary outcomes.<br><br>ETHICS AND DISSEMINATION: This study protocol has been approved (approval number: NL86247.091.24) by the METC Oost-Nederland from Radboud University Medical Centre on July 11, 2024. Prior to participation, participants are required to provide informed consent. The results will be widely disseminated through scientific peer-reviewed journals, and presentation to a broad audience in scientific meetings, congresses, patient meetings, as well as in policy-relevant forums.<br><br>TRIAL REGISTRATION NUMBER: NCT06332560.}, }
@article {pmid42191634, year = {2026}, author = {Shi, ZJ and Li, HC and Fan, QR and Li, JJ}, title = {[Evolution of Soil Bacterial Community Assembly Mechanisms in Reclaimed Pinus tabuliformis Forests of Xishan Mining Area].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {47}, number = {5}, pages = {3521-3528}, doi = {10.13227/j.hjkx.202503298}, pmid = {42191634}, issn = {0250-3301}, mesh = {*Soil Microbiology ; *Pinus/growth &amp; development ; *Mining ; *Bacteria/classification/growth &amp; development ; Nitrogen/analysis ; China ; Forests ; Ecosystem ; Soil/chemistry ; Carbon/analysis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Soil microorganisms are pivotal drivers of ecological restoration in reclaimed mining areas, regulating critical processes such as nutrient cycling and ecosystem stability. This study investigated Pinus tabuliformis plantations across a 3-25 year reclamation chronosequence in the Xishan Mining Area. By integrating 16S rRNA sequencing, β-nearest taxon index (βNTI), Bray-Curtis based stochastic assembly model (RCbray), and environmental multivariate analysis, the bacterial community assembly mechanisms were elucidated. The bacterial Shannon diversity exhibited a significant unimodal distribution (P<0.001), peaking at intermediate reclamation stages (e.g., YS10). This maximum diversity coincided with elevated total organic carbon (TOC) and higher C/N ratios. Diversity dynamics showed significant positive correlations with both total nitrogen (TN) and C/N ratio (P<0.05). Taxonomic composition shifted substantially during succession: Acidobacteriota abundance surged from 14.8% to 35.9% (P<0.001), ascending to dominance in late-stage reclaimed soils (e.g., YS25). This transition reflected an ecological strategy shift from r-strategists (e.g., Proteobacteria) to K-strategists (e.g., Acidobacteriota), attributable to declining soil C/N ratios and progressive nitrogen enrichment. The βNTI-RCbray framework revealed that stochastic processes (dispersal limitation, 57.14% contribution) dominated overall community assembly. However, deterministic processes (e.g., variable selection) increased substantially (30%-60%) between 8-10 years of reclamation. Both TN and urease significantly explained community variation (19.43% and 19.84%, respectively), driving community succession and altering microbial abundance. Although both dominated the deterministic process, dispersal limitation remained the most important stochastic driver, with its contribution reaching 100% in the later stages of reclamation (e.g., YS25), which was caused by physical barriers and the patchiness of microhabitat resources. These findings elucidate the interplay between stochastic and deterministic forces in shaping microbial succession during habitat restoration, providing theoretical and practical guidance for microbiome-directed management in reclaimed mining ecosystems.}, }
@article {pmid42191702, year = {2026}, author = {Zhao, H and Chi, L and Zhang, Z and Hsiao, YC and Liu, CW and Yang, Y and Balfour Sartor, R and Lu, K}, title = {Activity-guided substructure prioritization accelerates discovery of gut microbiota-derived immune-regulating metabolites.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73030-2}, pmid = {42191702}, issn = {2041-1723}, abstract = {Gut microbiota exert significant influences on host physiology through bioactive molecules such as indole derivatives. The characteristic aromatic heterocycle substructure shared among various indole derivatives is intrinsically associated with the activation of aryl hydrocarbon receptor (AhR), suggesting a potential structure-activity relationship (SAR). Here, we develop a substructure-activity relationship mass spectrometry pipeline aiming at elucidating SAR information encompassed within mass spectrometry data, further applying it to identify the unknown gut microbiome-derived, indole-like derivatives with AhR agonistic potential. A total of 22 metabolites exhibiting activity-related substructures are identified, four of which were previously uncharacterized. Notably, the discovered sulfonated and methylthiolated compounds represent two previously underexplored microbiome-mediated reactions. Subsequent assays validate their AhR agonistic activities and downstream immune regulatory effects in male mice. Overall, this study presents an exploratory framework for MS data mining focusing on activity-guided substructure prioritization, enabling the discovery of bioactive microbiota-derived molecules and distinct microbiome-mediated reactions.}, }
@article {pmid42192146, year = {2026}, author = {Wang, W and Li, Z and Gondowardojo, GR and Tan, L and Wu, C and Liu, R and Xiao, M and Liu, C}, title = {Isolation of novel phages from a resistant Dorea longicatena strain reveals genes associated with phage resistance.}, journal = {Npj viruses}, volume = {}, number = {}, pages = {}, doi = {10.1038/s44298-026-00199-0}, pmid = {42192146}, issn = {2948-1767}, support = {2021YFA0911100//National Key Research and Development Program of China/ ; }, abstract = {The gut bacterium Dorea longicatena has been reported to be closely associated with metabolic disorders and has emerged as a promising target for microbiome interventions aiming at improving metabolic diseases. While phages serve as effective tools for precise modulation of gut bacteria, phage resources against this and other obligate anaerobic gut bacteria remain extremely limited, hindering both therapeutic development and studies of phage-host interactions. To address this gap and the challenge of rapid resistance emergence, we performed sequential screening by first generating phage-resistant D. longicatena mutants using a previously reported set of D. longicatena phages and then using these resistant mutants as hosts to isolate additional phages from environmental samples. This approach yielded two novel lytic phages, CPB1657 and CPB1660, which remained active against 27 of the 30 tested D. longicatena strains, including the wild-type strain and resistant derivatives. Genomic characterization confirmed their lytic properties and absence of virulence or lysogeny genes. In addition, resistance to the initial phage was strongly associated with mutations in the major tail protein-like gene MAG_TPA_asm. Several mutants resistant to all tested phages shared an identical set of seven missense mutations in this gene. Together, these findings expand the currently limited phage resources available for D. longicatena and provide new insight into phage-host interactions in anaerobic gut bacteria.}, }
@article {pmid42192310, year = {2026}, author = {Łaniewski, P and Jimenez, NR and Hurwitz, BL and Herbst-Kralovetz, MM}, title = {Comparative genomics of Sneathia species: insights into pathogenicity and adaptation to the human niche.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05201-6}, pmid = {42192310}, issn = {1471-2180}, support = {RFGA2022-010-05//Arizona Biomedical Research Commission/ ; PF-24-1316926-01-MM//American Cancer Society/ ; U54CA143924/CA/NCI NIH HHS/United States ; }, abstract = {BACKGROUND: Sneathia are urogenital anaerobes linked to bacterial vaginosis, preterm birth, chorioamnionitis, urethritis, and HPV-mediated cervical carcinogenesis. Two species have been identified: Sneathia vaginalis and Sneathia sanguinegens. Yet, due to their fastidious nature, our knowledge of their pathogenicity is limited.<br><br>METHODS: Comparative genomic analysis of 12 Sneathia genomes, including two newly sequenced via whole-genome sequencing, was used to evaluate the pathogenic potential of S.&#xa0;vaginalis and S.&#xa0;sanguinegens.<br><br>RESULTS: Sneathia species have small genomes (1.25-1.35 Mbp) with low (26.7-29.0%) GC content. The genomes of both species harbor a similar number of subsystems, mostly related to protein processing, metabolism, and energy. Both species encode subsystems for glycogen utilization and lactic and mixed acid fermentation. The genomes of S. vaginalis exhibit a higher potential for carbohydrate and carbohydrate derivative metabolism (gluconate and ascorbic acid catabolism, the Entner-Doudoroff pathway) providing a competitive advantage in nutrient-limited environments. S.&#xa0;sanguinegens genomes show a higher potential for amino sugar (hyaluronic acid and N-acetylneuraminic acid catabolism) and sulfur-containing amino acid metabolism. Sneathia species also encode unique subsystems related to stress response, including oxidative stress, heat shock, and antibiotic resistance. Finally, Sneathia genomes encode both core (shared by all strains) and accessory (specific for species or strains) virulence factors, including exotoxin, additional hemolysins, O-sialoglycoprotein endopeptidase, and adhesins.<br><br>CONCLUSIONS: Both S.&#xa0;vaginalis and S.&#xa0;sanguinegens are highly adapted to the urogenital niche and exhibit high pathogenic capacities. Genomic information revealed potential mechanisms by which these pathogens enhance their competitiveness within the urogenital tract and likely facilitate microbe-microbe cooperation in polymicrobial communities.}, }
@article {pmid42192555, year = {2026}, author = {Liu, H and Wang, J and Li, F and Yang, W and Zheng, Y and Yin, Y and Wei, Q and Hong, G and Liu, Z}, title = {Dynamics of facial skin microbiota in female college students during menstruation: comparative analysis between regular and irregular menstrual cycles with identification of phase-specific microbiota.}, journal = {BMC women's health}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12905-026-04567-z}, pmid = {42192555}, issn = {1472-6874}, support = {82202629//the National Natural Science Foundation of China/ ; 3502Z20254ZD1038//the Medical and Health Guidance Project of Xiamen/ ; }, abstract = {Previous studies demonstrate that many women experience menstrual cycle-related skin symptoms during their periods. While the exacerbation of skin conditions during menstruation is well-documented, the underlying biological mechanisms remain incompletely understood. Although an association between skin microbiota and the menstrual cycle have been proposed, to gain clearer insights into this change, we finally enrolled 95 subjects and implemented one-to-one matching in the present study. Facial skin microbial samples were collected from female college students during both menstrual and intermenstrual periods, followed by 16 S rRNA gene sequencing. The facial skin microbiome shifted with menstrual cycle regularity, primarily driven by the irregular menstrual group. Proteobacteria predominated over Firmicutes, Actinobacteria, and Bacteroidetes across all samples. At the genus level, Sphingomonas, Bradyrhizobium, Streptococcus, and Corynebacterium were most abundant. However, Firmicutes and Actinobacteria increased significantly in the irregular menstrual group, with Acinetobacter, Haemophilus, Streptococcus, and Corynebacterium exhibiting peak abundance in this group. Multiclass random forest analysis distinguished irregular menstrual samples from all others, achieving an area under the curve (AUC) of 0.82 using bacterial OTUs; Aeromonas caviae (OTU_423025) and Sphingomonadaceae (OTU_4391560) were identified as the model's most important OTUs. Reduced intra-kingdom interactions were observed in subjects with irregular cycles. Notably, in the irregular menstrual group, three co-occurring OTUs including Streptococcus (OTU_523025), Gemellaceae (OTU_858896), and Staphylococcus (OTU_4345285) were lost. Furthermore, PICRUSt2 analysis predicted upregulation of genes involved in fatty acid, carbohydrate metabolism and signal transduction (e.g., K01462, K01104, K17686) and downregulation of transport (K01991) and antioxidant related genes (K00799) in the irregular menstrual cycle group. The study indicates that irregular menstruation is accompanied by alterations in the structure of the skin microbial community, with such structural changes primarily occurring during the menstrual phase. Additionally, distinctive features of the facial skin microbiota were observed in the Irregular-Menstrual group.}, }
@article {pmid42192558, year = {2026}, author = {Aggad, WS and Ghosh, R and Almohaimeed, HM and Mohammedsaleh, ZM and Saleh, FM and Almars, AI and Jyothi, SR and Panigrahi, R and Kumer, A and Dhara, B}, title = {Exosome-mediated gut-brain axis signaling in neurodegenerative diseases: Mechanisms, experimental evidence, and therapeutic perspectives-A narrative review.}, journal = {Animal models and experimental medicine}, volume = {}, number = {}, pages = {}, doi = {10.1002/ame2.70226}, pmid = {42192558}, issn = {2576-2095}, support = {PNURSP2026R213//Princess Nourah Bint Abdulrahman University/ ; }, abstract = {The stomach and the brain are connected by a sophisticated two-way communication mechanism called the gut-brain axis. Extracellular vesicles, particularly exosomes, that move bioactive substances between the stomach and the brain, such as proteins, lipids, metabolites, and microRNAs, may improve the gut-brain axis. In the past years, the role of exosome-mediated communication has been recognized as significant in relation to the etiology, continued progression, and potential treatment of neurodegenerative disorders. The authors of this review article present a summary of the current understanding of the relationship of gut microbiome, exosome biogenesis, and the pathophysiological development of neurodegenerative diseases. Evidence from laboratory studies, animal studies, and newly emerging human studies suggests that microbiome-based metabolites and inflammatory mediators may modulate how exosomes are produced, what they carry, and how they interact with the blood-brain barrier. These exosomal signals may impact neuroinflammation, neuronal signaling, and the spread of pathological proteins of neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and Huntington's disease. In addition, they examine some possible ways to target the gut-brain axis from a therapeutic perspective, including manipulating the gut microbiome, providing probiotics and/or prebiotics, performing fecal microbiota transplantation, and/or using engineered extracellular vesicles as vehicles for drug delivery. The authors also outline some of the methodological differences that make it difficult to assess the effects of exosomes.}, }
@article {pmid42192564, year = {2026}, author = {Kuerban, M and Gomes, SIF and Erol, O and Bezemer, TM}, title = {Steering root-associated microbiomes via direct and soil legacy effects of neighbors.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02429-2}, pmid = {42192564}, issn = {2049-2618}, abstract = {BACKGROUND: Root-associated microbiomes are widely assumed to be primarily shaped by the host plant. However, other co-occurring plants can also influence the composition of this microbiome. This can be either directly, by stimulating or suppressing microbial recruitment of the focal plant, or indirectly, through soil legacies that shape the microbial pool encountered by the focal plant during establishment. The relative importance of these neighbor effects shaping the focal plant microbiome and the consequences for focal plant growth remain poorly known. Here, we challenge the paradigm that the host plant identity is the main driver of root-associated bacterial and fungal communities.<br><br>RESULTS: Under experimental conditions, we show that the influence of the host plant on root-associated microbiomes is dramatically reduced in the presence of neighbors and their soil legacies. Remarkably, root-associated bacterial communities were primarily shaped by co-occurring neighbor plants, while fungal communities were mainly determined by soil legacies from previously grown plants. Furthermore, culturable microbial communities (NatComs) isolated from the roots of focal plants differed greatly depending on neighbor identity and soil legacies. Inoculating new focal plants with these communities caused strong responses in growth that varied greatly depending on the history of these isolated communities, highlighting the importance of neighbor effects. Finally, we show that metabolites produced by these microbial communities are one mechanistic pathway through which neighbors influence plant growth.<br><br>CONCLUSIONS: Our results stress the often-overlooked ecological and functional importance of both direct and indirect effects of neighbor plants in shaping root-associated microbiomes. By integrating neighbor effects with host identity, this work provides a starting point for understanding how neighboring plants contribute to shaping plant communities, with potential implications for sustainable agriculture. Video Abstract.}, }
@article {pmid42192635, year = {2026}, author = {Storck-Thy, C and Dessing, LB and Jensen, BH and Oxlund-Mariegaard, B and Krogfelt, KA and Jønsson, R}, title = {Role of bacterial dysbiosis in infertility: the BIOME study protocol for a Danish multicentre prospective observational cohort study.}, journal = {BMJ open}, volume = {16}, number = {5}, pages = {e118867}, doi = {10.1136/bmjopen-2026-118867}, pmid = {42192635}, issn = {2044-6055}, mesh = {Humans ; Female ; Denmark ; Prospective Studies ; *Dysbiosis/complications/microbiology ; *Infertility/microbiology ; Multicenter Studies as Topic ; *Microbiota ; Male ; Observational Studies as Topic ; *Vagina/microbiology ; Adult ; Research Design ; Reproductive Techniques, Assisted ; }, abstract = {INTRODUCTION: Microbiome composition across multiple body sites, including the vagina, gut, urinary tract and semen, has been implicated in reproductive health and infertility. Vaginal dysbiosis and reduced Lactobacillus abundance have previously been associated with poorer outcomes in assisted reproductive technologies, yet few studies have simultaneously characterised microbiomes of both partners or compared infertile couples with healthy population controls. The BIOME study, a prospective cohort study, aims to characterise multisite microbiomes in infertile and healthy Danish couples and examine their association with long-term fertility outcomes.<br><br>METHODS AND ANALYSIS: The BIOME study is a multicentre, prospective observational cohort study including 100 couples undergoing fertility treatment following &#x2265;12 months of unsuccessful pregnancy attempts and 100 healthy control couples. Participants provide biological samples from multiple body sites (vaginal swab or semen, faeces, urine and blood) prior to initiation of fertility treatment. Samples will undergo microbial sequencing, quantitative PCR, culture-based analyses, proteomics, metabolomics and microRNA profiling. Questionnaire data, clinical information and electronic medical record data will be collected. Participants will be followed for 5 years after sample collection to assess fertility outcomes. No intervention, randomisation or blinding is performed. Recruitment is planned over 24 months.<br><br>ETHICS AND DISSEMINATION: The study has been approved by the Danish Ethics Committee (#SJ-1033), and all participants provide written informed consent. Data are processed according to the General Data Protection Regulation and the Danish Data Protection Act, with pseudonymisation and restricted-access procedures. Results will be disseminated through peer-reviewed publications and scientific conferences. Sequencing data will be deposited in a public repository (eg, European Nucleotide Archive) with personal identifiers removed, and curated metadata will be available on reasonable request.}, }
@article {pmid42192669, year = {2026}, author = {Nowak, E and Korgiel, M and Pawłuszkiewicz, K and Widelski, J and Cheaib, B and Paluch, E}, title = {Quorum Sensing and Quorum Quenching in Pseudomonas aeruginosa and Staphylococcus aureus Infections: Therapeutic Potential, Limitations and Clinical Challenges.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/antibiotics15050447}, pmid = {42192669}, issn = {2079-6382}, abstract = {Antimicrobial resistance (AMR) represents a major global health threat, largely driven by antibiotic overuse and the protective role of bacterial biofilms. Quorum sensing (QS), a bacterial communication system regulating virulence and biofilm formation, has emerged as a promising therapeutic target. Quorum quenching (QQ), which disrupts QS without directly inhibiting bacterial growth, is considered a potential anti-virulence strategy that may reduce selective pressure for resistance. This review critically evaluates recent advances in QQ research, focusing on its clinical applicability, limitations, and risks. We analyzed studies from the last five years involving natural compounds, synthetic molecules, nanoparticles (NPs), and combination therapies targeting key pathogens such as Pseudomonas aeruginosa and Staphylococcus aureus in models of lung diseases, mainly cystic fibrosis, chronic wounds, burns, and implant-associated infections. While numerous compounds demonstrate significant in vitro anti-biofilm and anti-virulence activity, major challenges remain, including limited in vivo validation, pharmacokinetic constraints, toxicity concerns, microbiome disruption, and the potential development of tolerance or functional resistance. Although QQ offers a promising adjunctive approach to conventional antibiotics, its long-term clinical feasibility requires comprehensive evaluation of evolutionary dynamics, host-microbe interactions, and safety profiles.}, }
@article {pmid42192724, year = {2026}, author = {Skotareva, AE and Sokolova, EA and Voronina, EN}, title = {West Siberian Soil Resistome: Mobile Antibiotic Resistance in Agricultural Microbiomes.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/antibiotics15050502}, pmid = {42192724}, issn = {2079-6382}, support = {125012300671-8//Russian state-funded project/ ; }, abstract = {Background/Objectives: Soil microbiomes in agroecosystems are natural reservoirs of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), creating conditions for horizontal gene transfer (HGT) to clinically relevant bacteria. Southern West Siberia-a globally significant grain-producing region-lacks metagenomic characterization of its soil resistome. This study aimed to establish the first baseline profile of resistome and mobilome composition for West Siberian agricultural soils. Methods: Twelve composite soil samples were collected from agroecosystems under seven crop types across diverse soil types in southern West Siberia (September 2022). Shotgun metagenomics was performed on an Illumina NovaSeq 6000 platform. Taxonomic profiling used Kraken2/Bracken; ARG annotation used Prokka/DeepARG (identity ≥ 70%, probability score ≥ 0.8); while MGE characterization used Platon, HMMER v3.3.2, and Prokka-based integrase annotation. Resistome load was normalized to the single-copy housekeeping gene rpoB; ARG-MGE associations were defined as co-localization within 10 kb on the same contig. Results: Microbial communities were dominated by Pseudomonadota and Bacillota, with a stable core of Streptomycetaceae, Nitrobacteraceae, and Sphingomonadaceae. Normalized resistome load (N/rpoB 2.30-5.37) indicated moderate anthropogenic pressure. Dominant ARGs included efflux pumps (emrA, drrA, tetA, bcr, fsr), target modification (lnrL), and lipid A modification (arnA) genes. Class 1 integron integrase (intI1/rpoB 0.64-1.59) was detected in all 12 samples, exceeding unity in 9 of 12. ARG-MGE co-localizations were found in 11 of 12 samples. In sample Mg_155, genes emrA-emrB and bcr (NODE_16) and arnA and lnrL (NODE_6) were each independently associated with distinct prophage IntA integrase copies within Pseudomonas contigs, documenting multiple parallel horizontal transfer events encompassing resistance to five antibiotic classes. Conclusions: This work establishes the first metagenomic baseline of resistome and mobilome for West Siberian agroecosystems. The obtained data indicate moderate anthropogenic pressure on soil microbiomes, consistent with temperate agricultural systems with limited organic fertilizer input. The detected ARG-MGE co-localizations and evidence of prophage-mediated transfer of resistance determinants beyond their natural hosts suggest that mobilization potential in the region warrants consideration in future AMR monitoring programs.}, }
@article {pmid42192865, year = {2026}, author = {Liu, Z and Ang, MY and Kue, CS}, title = {Multi Omics Integration in Colorectal Cancer: From Molecular Insights to Precision Oncology.}, journal = {Cancers}, volume = {18}, number = {10}, pages = {}, doi = {10.3390/cancers18101504}, pmid = {42192865}, issn = {2072-6694}, abstract = {Colorectal cancer (CRC) is a biologically heterogeneous disease in which single-omics analyses incompletely capture the cross-layer mechanisms underlying tumor progression, immune evasion, and therapeutic resistance. This review critically examines how the integration of genomics, transcriptomics, proteomics, metabolomics, and microbiome profiling is redefining CRC biology and precision oncology. Landmark integrative efforts, including TCGA analyses of 276 colorectal cancer samples, CPTAC proteogenomic profiling of 95 tumors, and recent whole-genome sequencing studies of 2023 CRC cases, have refined molecular subtyping, expanded the driver landscape, and revealed clinically relevant discordance between mRNA abundance and protein activity. Integrative studies further show that oncogenic signaling may be driven by post-transcriptional and post-translational regulation, while spatially resolved profiling and microbiome-metabolite analyses are uncovering previously obscured tumor-microenvironment interactions. We also discuss how artificial intelligence-based approaches, including factor analysis, deep learning, graph-based models, and explainable AI, are improving subtype classification, biomarker discovery, and treatment-response prediction, with particular relevance to microsatellite instability-high and early-onset CRC. Finally, we critically evaluate the principal barriers to clinical translation, including batch effects, cross-platform variability, limited external validation, regulatory constraints, and cost, and outline priorities for building reproducible, clinically deployable multi-omics pipelines for CRC management.}, }
@article {pmid42193098, year = {2026}, author = {Zhong, L and Wang, T and Tang, L and Han, J and Zhao, Q and Lin, N}, title = {Microbial Dysbiosis in Photodermatoses: Formation, Pathogenesis and Intervention Strategies.}, journal = {Current issues in molecular biology}, volume = {48}, number = {5}, pages = {}, doi = {10.3390/cimb48050493}, pmid = {42193098}, issn = {1467-3045}, abstract = {Recent studies have reported skin microbiome dysbiosis in patients with photodermatoses, featuring enriched Staphylococcus aureus colonization and decreased microbiome diversity. We propose that ultraviolet radiation (UVR), along with atypical antimicrobial peptides, may exert selective pressure on the skin microbiome, while cytokine dysregulation and a reduction in commensal bacteria amplify microbial dysbiosis. Dysbiotic microorganisms further release pathogen-associated patterns and virulence factors, and activate tissue-resident memory T cells, which collectively contribute to local inflammation. These mechanisms establish the skin microbiome as a potential target for early intervention. Potential therapeutic strategies may include antibiotics, phototherapy, bleach baths, phage therapy, and microbiota-based therapies. This review integrates current findings from microbial ecology, molecular biology, and host immunology to outline a conceptual framework linking UVR exposure, microbiome alterations, and cutaneous immune responses, while emphasizing the current limitations and evidence gaps in this field.}, }
@article {pmid42193107, year = {2026}, author = {Bilal, H and Khan, I and Yaseen, A and Zhang, X and Liu, X and Zhao, J and Li, J and Rehman, AU and Sun, L and Yu, X}, title = {Sodium Butyrate Attenuates Isoprenaline-Induced Myocardial Injury via Restoring the Gut-Heart Axis and Suppressing TLR4/NF-κB Signaling.}, journal = {Current issues in molecular biology}, volume = {48}, number = {5}, pages = {}, doi = {10.3390/cimb48050501}, pmid = {42193107}, issn = {1467-3045}, abstract = {The gut-heart axis plays a role in cardiac injury due to the disruption of barriers, endotoxemia, and inflammatory signaling; yet, it is not clear whether sodium butyrate (SB) is capable of alleviating isoprenaline-induced myocardial injury through coordinated intestinal, microbial, and metabolic restoration. This study used male Sprague-Dawley rats, which were grouped into control, control + SB, isoprenaline (ISO)-induced myocardial injury, and ISO + SB groups. We evaluated cardiac biomarkers of injury, oxidative stress, histopathologic, intestinal barrier (16S rRNA sequencing), and serum metabolomics (LC-MS). SB treatment decreased serum cardiac troponin I, creatine kinase-MB, and lactate dehydrogenase; relieved oxidative stress; and lowered myocardial necrosis and fibrosis. It re-established colonic architecture, upregulated the expression of ZO-1 (zonula occludens-1) and claudin-1, and reduced endotoxin in the bloodstream. SB also prevented the production of proinflammatory cytokines such as TNF-α, IL-6, and IL-1β; cardiac TLR4; IκBα degradation; and NF-κB p 65 phosphorylation. In addition, SB altered the gut microbiota in favor of beneficial commensals, including Ligilactobacillus and Bifidobacterium, and reduced Desulfovibrio. It normalized key circulating metabolites and enriched cardiometabolic pathways, and the patterns of correlation suggested the coordinated remodeling of the microbiome-metabolome. These findings reveal that SB prevents myocardial injury caused by ISO through strengthening gut barrier protection, alleviating endotoxemia, inhibiting TLR4/NF-κB, and remodeling the microbiome-metabolome axis, indicating its potential for use as a gut-targeted cardioprotective intervention.}, }
@article {pmid42193119, year = {2026}, author = {Tavartkiladze, A and Tavartkiladze, L and Reiter, RJ and Burnier, M and Kasradze, D and Okrostsvaridze, N and Revazishvili, P and Turmanidze, R}, title = {Nocturnal Melatonin Amplitude Collapse Is Associated with Age-Independent Convergence of Microbiome and Glymphatic Biomarkers.}, journal = {Current issues in molecular biology}, volume = {48}, number = {5}, pages = {}, doi = {10.3390/cimb48050515}, pmid = {42193119}, issn = {1467-3045}, abstract = {Circadian desynchronization is increasingly linked to metabolic, immune, neurocognitive, and oncological disease, but integrated clinical phenotyping across endocrine, microbiome, metabolic, and neuroimaging domains remains limited. We conducted a prospective, single-centre, observational study in 179 symptomatic patients referred for chronic multisystem features consistent with circadian dysregulation and 107 practically healthy controls. Circadian melatonin status was assessed using fractionated 24 h urinary 6-sulfatoxymelatonin (aMT6s) and standardized dim-light plasma sampling at daytime (14:00-16:00) and nocturnal (02:00-04:00) windows. Microbiome composition was assessed by 16S rRNA sequencing, urolithin A by targeted metabolomics, and putative glymphatic/perivascular clearance by MRI-derived DTI-ALPS index, perivascular space scoring, and white-matter-hyperintensity (WMH) volumetry. Patients showed markedly reduced nocturnal melatonin output and loss of day-night contrast (night aMT6s 10.2 vs. 40.6 ng/mL; urinary aMT6s day/night ratio 0.81 vs. 0.14; plasma nocturnal melatonin 12.7 vs. 54.4 pg/mL; all p < 0.0001), accompanied by altered cortisol day-night patterning. Patients also showed reduced microbiome diversity, depletion of Gordonibacter and Ellagibacter, lower plasma urolithin A, higher WMH volume and perivascular space scores, and a lower DTI-ALPS index. Age distributions broadly overlapped in the individual-level dataset, and key biomarkers were not significantly correlated with chronological age within the patient cohort; however, this finding is interpreted as an exploratory absence of detectable age gradient within the symptomatic cohort, not as proof of biological age-independence. Overall, the data support a coherent cross-sectional association among blunted nocturnal melatonin rhythmicity, dysbiosis/urolithin depletion, and MRI markers compatible with impaired perivascular clearance. The MGM axis framework should be regarded as hypothesis-generating; causal direction, melatonin receptor involvement, and AQP4-related mechanisms require longitudinal and mechanistic validation.}, }
@article {pmid42193156, year = {2026}, author = {Barakat, H and Sakr, SS and Alfheeaid, HA and Alsaleem, KA and Alhomaid, RM and El-Messery, TM and Ebeid, TA and Abdul-Hafeez, EY}, title = {Oxidative Stress-Gut Microbiome Crosstalk: Intestinal Redox Imbalance and Probiotics Therapeutic Potential.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/antiox15050533}, pmid = {42193156}, issn = {2076-3921}, support = {QU-APC-2026//Qassim University/ ; }, abstract = {Oxidative stress and gut microbiota dysbiosis establish a self-perpetuating loop that disrupts epithelial barrier integrity and fuels chronic inflammatory and metabolic disorders, including inflammatory bowel disease (IBD), metabolic syndrome (MS), and chronic kidney disease (CKD). This systematic review synthesizes mechanistic, preclinical, and clinical evidence linking reactive oxygen species (ROS), microbiota-derived metabolites, and host redox homeostasis, with a focus on probiotic-based interventions. Comprehensive searches of PubMed, Scopus, Web of Science, and Google Scholar (2000-March 2026) identified in vitro, animal, and human studies, as well as systematic reviews and meta-analyses, assessing oxidative biomarkers, microbiome profiles, and barrier function outcomes. Probiotic strains, predominantly Lactiplantibacillus, Bifidobacterium, and emerging next-generation taxa, attenuate oxidative stress by inducing antioxidant enzymes [superoxide dismutase (SOD), glutathione peroxidase (GPx)], activating Nrf2 signaling, and restoring short-chain fatty acid (SCFAs) production, thereby lowering malondialdehyde (MDA) and 8-hydroxy-2'-deoxyguanosine (8-OHdG) while enhancing total antioxidant capacity (TAC). At the mucosal interface, probiotics strengthen tight junction proteins, suppress NF-κB-mediated cytokine release, and mitigate dysbiosis, contributing to clinically meaningful improvements in disease activity, insulin sensitivity, and uremic toxin burden along gut-liver, gut-kidney, and other gut-organ axes. Overall, current evidence supports probiotics and synbiotics as promising adjuncts for nutrition-driven redox modulation, while highlighting the need for strain-resolved, multi-omics, multicenter trials with standardized redox and microbiome endpoints to optimize dosing strategies and long-term safety.}, }
@article {pmid42193157, year = {2026}, author = {Kim, G and Park, Y and Lim, YK and Lee, JW and Kang, D and Lee, DK and Lee, JH and Song, MS and Lee, BH}, title = {Understanding Spaceflight-Induced Oxidative Stress and the Critical Role of Diet and Microbiome.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/antiox15050534}, pmid = {42193157}, issn = {2076-3921}, support = {#RS-2023-00212567 and #RS-2025-02307158 (to B.H.L.), #RS-2023-00219399 (to B.H.L. and D.K.) and #RS-2025-24152978 (to M.S.S.)//National Research Foundation/ ; }, abstract = {Spaceflight exposes astronauts to multiple environmental stressors that promote oxidative stress, including ionizing radiation, microgravity, circadian rhythm disruption, and psychological stress. These factors increase the production of reactive oxygen species (ROS) and disturb redox homeostasis, potentially affecting multiple physiological systems during long-duration missions. In addition to environmental challenges, nutritional factors may further influence oxidative balance in space. Space food systems rely on long-term storage and processing, which can lead to degradation of antioxidant nutrients and alterations in dietary composition. Furthermore, spaceflight conditions may modify eating behaviors and disrupt gut microbiome composition, both of which are closely linked to host redox regulation. This review examines current knowledge on oxidative stress during spaceflight and discusses how space food systems, dietary composition, and microbiome alterations interact with spaceflight stressors to influence redox homeostasis. Potential strategies to mitigate oxidative stress are also discussed, including preservation of antioxidant nutrients, optimization of dietary composition, reduction in pro-oxidant exposures, and microbiome-targeted approaches to support astronaut health during long-duration missions.}, }
@article {pmid42193159, year = {2026}, author = {Daff, K and Han, Y and Feng, Z and Upadhyay, M and Sivampeta, V and Rajasekaran, A and Sangwan, N and Cresci, GAM}, title = {Role of L-Arginine in the Gut-Liver Axis of Female Mice: Mediating Ethanol's Alterations in Hepatic Steatosis and Oxidative Stress.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/antiox15050537}, pmid = {42193159}, issn = {2076-3921}, support = {R01AA028043//National Institute of Health/ ; }, abstract = {Ethanol exposure causes microbial imbalance, damages the gut barrier, and increases oxidative stress along the gut-liver axis, leading to the development and progression of alcohol-associated liver disease (ALD). Arginine is a conditionally essential amino acid that may play a key role in maintaining redox homeostasis and mediating host-microbiota crosstalk. We hypothesized that supplemental arginine provided during chronic ethanol exposure in mice would mitigate oxidative damage via the gut-liver axis. Our findings suggest that arginine supplementation mediated hepatic steatosis, preserved body weight and fat, and reduced oxidative stress in the gut-liver axis. These changes were associated with alterations in gut microbiota composition and function. These data support a potential role for arginine supplementation in mitigating ethanol-induced oxidative damage via the gut-liver axis.}, }
@article {pmid42193165, year = {2026}, author = {Liang, Y and Wang, H and Wang, Z and Zhang, Y and Tu, W and Zhou, J and Diao, Y and Pei, H and Huang, J and Zhou, X and Tan, Y}, title = {High-Fiber Diet Supplemented with N-Carbamylglutamate Modulates Uterine Microbiota, Metabolites, and Transcriptome to Improve Reproductive Efficiency in Sows.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/antiox15050542}, pmid = {42193165}, issn = {2076-3921}, support = {No.2023ZD04046//Biological Breeding-National Science and Technology Major Project/ ; 2025M780240//China Postdoctoral Science Foundation/ ; NO.2025(05)//Livestock and Poultry Breeding and Healthy Farming Technology/ ; }, abstract = {Uterine microbiome homeostasis and antioxidant capacity are critical for sow fertility. While high-fiber diets and N-carbamylglutamate (NCG) individually enhance sow fertility, their synergistic effects on the antioxidant status, microbiota, metabolites, and transcriptome remain unclear. Here, sows were assigned to the low-fiber (3.73%) or high-fiber (7.46% crude fiber) group, each without or with 0.05% NCG, throughout the 114-day gestation. Sex hormones and antioxidants in serum were detected. Multi-omics approaches were employed to investigate the impact of a high-fiber diet supplemented with NCG (H + N) on uterine microbiota, metabolites, and gene expression profiles. The study revealed that H + N significantly increased total antioxidant capacity (T-AOC) level in serum. Metagenomic analysis revealed an increased abundance of Clostridium disporicum in the uterine microbiota. Plasma metabolomics identified hydroxylysine as a key metabolite mediating this effect, and this metabolite was positively correlated with elevated abundance of Clostridium disporicum. Subsequent transcriptomic profiling revealed activation of the PI3K-Akt signaling pathway, closely linked to improved T-AOC level. Overall, these findings demonstrated that H + N could modulate the uterine microbiota (specifically Clostridium disporicum), increase hydroxylysine production, and activate the PI3K-Akt signaling pathway. These effects further enhanced hormonal activity and antioxidant capacity, ultimately improving sow reproductive efficiency.}, }
@article {pmid42193259, year = {2026}, author = {Zhang, MY and Ke, ZZ and Deng, PL and Qin, YY and Mo, SL and Qiu, LT and Xu, JJ and Tong, CX and Song, JL}, title = {Rhamnocitrin Ameliorates the Intestinal Fibrosis in DSS-Induced Colitis Mice by Modulating Host-Metabolites and Remodeling the Gut Microbiome.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/antiox15050639}, pmid = {42193259}, issn = {2076-3921}, support = {82273630//National Natural Science Foundation of China/ ; 81960590//National Natural Science Foundation of China/ ; 81760589//National Natural Science Foundation of China/ ; 81560530//National Natural Science Foundation of China/ ; }, abstract = {Ulcerative colitis (UC) is characterized by barrier disruption, microbiota dysbiosis, fibrosis, and impaired autophagy. We investigated the effects of Rhamnocitrin (Rha) in dextran sulfate sodium (DSS)-induced chronic UC mice using histological analysis, molecular assays, and multiomics profiling. Rha alleviated weight loss and colon shortening; improved mucus secretion and tight junction protein expression; suppressed NLRP3 inflammasome activation; activated autophagy via AMPK activation and consequent Akt/mTOR inhibition; and attenuated colonic fibrosis. Multiomics analysis integrating 16S rRNA sequencing, metagenomics, and metabolomics revealed that Rha remodels the gut microbiota and is associated with elevated levels of beneficial metabolites, including butyrate in the colon, glutamate and γ-aminobutyric acid in the liver, and α-linolenic acid in the serum. Correlation analysis revealed close associations between microbiota and metabolite alterations, and improved barrier integrity, reduced inflammation, and attenuated fibrosis. These findings suggest that Rha ameliorates chronic UC by modulating autophagy, microbiota composition, and host metabolism across the gut-liver axis.}, }
@article {pmid42193296, year = {2026}, author = {Pinton, P}, title = {Microbiome-Based Therapies in Ulcerative Colitis: Mechanisms, Clinical Evidence, and a Precision-Medicine Framework.}, journal = {Biomedicines}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/biomedicines14050969}, pmid = {42193296}, issn = {2227-9059}, abstract = {Microbiome-based therapies are reshaping the therapeutic landscape for ulcerative colitis (UC), offering new avenues for disease management beyond conventional immunomodulatory and biologic treatments. UC remains a chronic, relapsing condition with significant unmet clinical needs, as many patients fail to achieve sustained remission or experience adverse effects with current therapies. The gut microbiome has emerged as a central contributor to UC pathogenesis, influencing epithelial barrier integrity, immune homeostasis, and metabolic signaling. Interventions such as fecal microbiota transplantation (FMT) and defined microbial consortia have demonstrated proof-of-concept efficacy in early-phase clinical trials, each leveraging distinct mechanistic strategies. FMT, as a broad ecological intervention, restores microbial diversity and functional redundancy, potentially addressing multiple pathogenic mechanisms simultaneously. In contrast, defined consortia enable precise targeting of specific metabolic and immunological pathways, including short-chain fatty acid production, bile-acid remodeling, epithelial barrier reinforcement, immune modulation, and succinate degradation. Recent clinical evidence suggests that consortia with broader mechanistic coverage may achieve more consistent biological activity than narrowly focused designs. This review synthesizes mechanistic and clinical insights across broad and defined microbial consortia, integrates evidence from randomized controlled trials and early-phase LBP studies, and outlines a precision-medicine framework to guide therapy selection. We highlight the importance of aligning therapeutic mechanisms with patient-specific microbial, metabolic, and immune profiles, and discuss future directions including biomarker-guided stratification, hybrid consortia, and adaptive trial designs. Advancing both broad and defined approaches, while incorporating ecological principles, mechanistic understanding, and patient stratification, will be essential to realizing the full therapeutic potential of microbiome-based therapies in UC.}, }
@article {pmid42193302, year = {2026}, author = {Marchitto, SA and Abbatecola, G and Zeidan, RS and Morgan, L and Calvani, R and Picca, A and Schlögl, M and Tosato, M and Leeuwenburgh, C and Anton, SD and Landi, F and Marzetti, E and Cacciatore, S}, title = {The Gut-Muscle Axis in Sarcopenia: Mechanisms, Evidence Gaps and Translational Challenges.}, journal = {Biomedicines}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/biomedicines14050976}, pmid = {42193302}, issn = {2227-9059}, support = {D1.2024//Universit&#xe0; Cattolica del Sacro Cuore/ ; D1.2025//Universit&#xe0; Cattolica del Sacro Cuore/ ; N/A//Centro Studi Achille e Linda Lorenzon/ ; P30 AG028740/AG/NIA NIH HHS/United States ; 2022YNENP3//Ministero dell'universit&#xe0; e della ricerca/ ; }, abstract = {Sarcopenia is an age-related skeletal muscle disorder characterized by reduced muscle mass, strength, and physical performance, as well as increased risk of disability, hospitalization, and mortality. Emerging evidence suggests that gut microbiota alterations may contribute to muscle decline via a microbiota-gut-muscle axis, acting as a context-dependent modulator rather than a primary causal driver. This narrative review synthesizes mechanistic, clinical, and translational evidence linking gut dysbiosis to sarcopenia. Preclinical studies show that microbiota modulation (e.g., antibiotics, probiotics, prebiotics, postbiotics, fecal microbiota transplantation) affects muscle mass, strength, and metabolism through pathways including inflammation, mitochondrial dysfunction, altered short-chain fatty acid production, and impaired anabolic signaling. In humans, observational studies associate lower microbial diversity and reduced short-chain fatty acid-producing taxa with poorer muscle outcomes, but findings are heterogeneous and non-causal. Interventional trials remain limited and characterized by small sample sizes, with effects more consistent for functional outcomes than muscle mass. Overall, the gut microbiota represents a modifiable contributor within the complex biology of sarcopenia. Future studies should integrate microbiome profiling and multi-omics approaches within well-designed clinical trials to identify responder phenotypes and define the role of microbiota-targeted strategies within multimodal interventions.}, }
@article {pmid42193322, year = {2026}, author = {Lin, Y and Lu, P and Ding, Q and Tao, X and Tan, Q and Liu, M}, title = {Opioid-Induced Constipation: Mechanistic Insights, Experimental Models, and Future Perspectives.}, journal = {Biomedicines}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/biomedicines14050995}, pmid = {42193322}, issn = {2227-9059}, support = {82300689//Youth Fund of the National Natural Science Foundation of China/ ; }, abstract = {Opioid-induced constipation (OIC) represents a prevalent adverse effect of opioid analgesics, affecting 60-90% of patients and significantly compromising quality of life. This review delineates the multifactorial pathogenesis of OIC. Peripheral μ-opioid receptor (MOR) activation suppresses enteric neuronal excitability, inhibits intestinal motility and secretion, and impairs rectoanal function. Notably, the colon appears to exhibit a distinctive lack of tolerance to opioids. Enteric glial cell activation has been implicated in neuroinflammation, while interstitial cells of Cajal show impaired pacemaker function. Central mechanisms are increasingly recognized to involve the brain-gut axis. Furthermore, opioid-induced barrier disruption, microbiota dysbiosis, and LPS/TLR4-mediated inflammation are proposed to interact and may contribute to a self-reinforcing cycle. Animal models have been instrumental in dissecting these mechanisms. However, they present limitations in reproducibility, clinical phenotype fidelity, and translational validity, particularly regarding microbiome composition and neuroimmune responses. Future research should prioritize the development of standardized, physiologically relevant animal models incorporating multi-omics approaches, and validate mechanism-based therapeutic strategies, including peripherally acting MOR antagonists and microbiota-targeted interventions, for precision management of OIC.}, }
@article {pmid42193390, year = {2026}, author = {Tomassini, L and Pacifico, T and Monteleone, G and Stolfi, C and Laudisi, F}, title = {From Gut Homeostasis to Colorectal Cancer: Spatial and Temporal Reprogramming of Microbial Inosine Signaling.}, journal = {Biomedicines}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/biomedicines14051065}, pmid = {42193390}, issn = {2227-9059}, support = {MFAG-27142//F.L. (Federica Laudisi) was supported by the Italian Association for Cancer Research (AIRC), [MFAG-27142]./ ; }, abstract = {Microbial metabolites are increasingly recognized as critical regulators of gut homeostasis, mediating the interaction among gut microbiota, host tissue, and immune response. Among them, inosine, which was previously considered just a byproduct of the adenosine catabolism, was recently discovered as an important bioactive purine metabolite with distinctive context-dependent signaling function. Indeed, inosine supports intestinal barrier integrity and modulates the immune response under physiological conditions. However, this scenario completely changes when chronic inflammation, dysbiosis, and colorectal cancer (CRC) develop, leading to a profound alteration of its spatial distribution and biological function. This review summarizes the biochemical properties, signaling, and sources of inosine and its role in the maintenance of gut homeostasis. We will also discuss the dynamic regulation of host-microbiota interaction, driven by inosine during CRC development and its progression following its spatial redistribution and temporal reprogramming. In particular, we will describe how inosine can shift from a tumor-supportive role to a trigger of anti-tumor immunity by promoting T cell function and macrophage polarization, becoming a critical modulator of host-microbiota crosstalk in health and disease and a promising therapeutic target for microbiome-based strategies and combined clinical approaches.}, }
@article {pmid42193404, year = {2026}, author = {Herawati, F and Az'zahra, F and Anggeraini, M and Ayumuyas, NP and Kantono, K and Setiawan, E and Yulia, R}, title = {Quantifying the Silent Selection Pressure: Antimicrobial Stewardship and Gut Microbiome Integrity in the NICU and PICU.}, journal = {Biomedicines}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/biomedicines14051080}, pmid = {42193404}, issn = {2227-9059}, abstract = {Background: Antimicrobial stewardship in Neonatal (NICU) and Pediatric Intensive Care Units (PICUs) is complicated by rapid physiological maturation and the high vulnerability of the developing gut microbiome. Traditional metrics fails to capture the true utilization density of antibiotics in these settings. This study evaluated antimicrobial consumption patterns and alignment with the WHO AWaRe framework in two Indonesian hospitals and its impact towards patients' length of stay. Methods: A retrospective multicenter study was conducted at a public hospital (Haji Hospital) and a private university hospital (HU Hospital) across 2024-2025. The study population includes all admitted patients (n = 315 in NICU and n = 12 in PICU) to calculate utilization density. Consumption was quantified using Defined Daily Dose (DDD)/100 bed-days, and qualitative assessment was performed using the WHO AWaRe classification. Results: Generalized linear modeling revealed that appropriate antibiotic therapy was significantly associated with a 17% reduction in hospital length of stay (β = -0.187, p = 0.035). At HU Hospital, PICU exhibited a seven-fold higher antimicrobial density (37.56 DDD/100) compared to NICU (5.22 DDD/100). At Haji Hospital, NICU density was 4.95 DDD/100 bed-days. Weight-normalized simulations revealed weight-based dosing disparity with low absolute DDD values in neonates mask a significant biological burden and intense selection pressure on the gut resistome due to immature renal clearance. While Haji Hospital maintained high "Access" category adherence (92.21%), HU Hospital's PICU showed a high reliance on "Watch" agents (71.27%), specifically Ceftriaxone and Meropenem, which are known drivers of multidrug resistance. Conclusions: Low absolute dosing in neonates does not equate to low therapeutic density or reduced environmental pressure. The heavy use of broad-spectrum agents in the PICU acts as a primary driver for microbiome disruption. To mitigate the emergence of multidrug-resistant organisms, stewardship must transition from adult-indexed metrics (DDD) to more precise measures like Days of Therapy (DOT) and prioritize "Access" protocols to preserve microbiome integrity.}, }
@article {pmid42193408, year = {2026}, author = {Olaru-Stavila, C and Steinmann, SM and Mester, P and Müller, M and Tcaciuc, E and Gülow, K}, title = {The Gastrointestinal Barrier-Mechanisms of Barrier Dysfunction in Liver Cirrhosis and Spontaneous Bacterial Peritonitis.}, journal = {Biomedicines}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/biomedicines14051084}, pmid = {42193408}, issn = {2227-9059}, abstract = {The gastrointestinal (GI) barrier is a highly coordinated, multilayered defence system that maintains intestinal homeostasis by separating the luminal microbiota from the internal milieu. In liver cirrhosis, this barrier undergoes profound structural and functional disruption, emerging as a central driver of bacterial translocation and infection-related complications. Among these, spontaneous bacterial peritonitis (SBP) represents a major determinant of morbidity, mortality, and disease progression. Barrier failure in cirrhosis is not attributable to a single defect but results from the convergence of multiple interconnected mechanisms. Structural alterations include disruption of epithelial tight junctions and deterioration of the mucus layer, leading to increased intestinal permeability and loss of spatial compartmentalisation. These changes are compounded by microbial dysbiosis, characterised by reduced diversity, depletion of short-chain fatty acid-producing taxa, and expansion of pathobionts. In parallel, cirrhosis-associated immune dysfunction impairs both mucosal and systemic antimicrobial defences, while gut-vascular barrier disruption facilitates systemic dissemination of bacteria and microbial products. The resulting increase in bacterial translocation plays a pivotal role in the pathogenesis of SBP and contributes to systemic inflammation, circulatory dysfunction, and acute decompensation. Importantly, this process establishes a self-amplifying pathogenic loop in which barrier dysfunction, dysbiosis, and immune dysregulation mutually reinforce each other. Recent advances have identified key molecular pathways involved in barrier regulation, including bile acid-FXR signalling and microbiome-derived metabolites, providing novel targets for therapeutic intervention. While current management relies largely on antibiotics and supportive care, emerging strategies aim to restore barrier integrity and modulate the gut-liver axis. A deeper understanding of GI barrier dysfunction offers new opportunities to prevent bacterial translocation and improve clinical outcomes in patients with liver cirrhosis.}, }
@article {pmid42193506, year = {2026}, author = {Blount, AJ and Schneider, K and Bjornsen, AL and Tran, TS and Pendyala, G and Moore, TA}, title = {Biopsychosocial Influences on the Gut Microbiome in Women's Health: Moving Towards Eubiosis.}, journal = {Behavioral sciences (Basel, Switzerland)}, volume = {16}, number = {5}, pages = {}, doi = {10.3390/bs16050627}, pmid = {42193506}, issn = {2076-328X}, support = {NU#55426//University of Nebraska NU Collaboration Initiative/ ; }, abstract = {Research on the human microbiome, particularly the gut microbiome, has expanded rapidly as its influence on health and behavior becomes increasingly evident. Once understood primarily in terms of digestion and immune function, the microbiome is now recognized as a key contributor to brain function, mood regulation, and social behavior. Emerging evidence links microbial dysbiosis to the onset and persistence of mood disorders, opening new pathways for mental health research and intervention. This paper challenges reductionist biomedical models by advancing a biopsychosocial framework for interpreting health outcomes related to microbiome dynamics. The gut-brain axis illustrates the biological complexity of these interactions, with microbial communities shaping neurodevelopment and neurotransmitter production. Psychologically, alterations in microbial composition have been associated with depression, anxiety, and stress responsivity, while social determinants-including early-life environments, socioeconomic conditions, and relationships-structure microbial variation in ways that may reinforce existing health inequities. Focusing on women's health, this narrative review examines how microbial states both influence and are shaped by interconnected biological, psychological, and social factors. Interdisciplinary implications of microbiome research for understanding and achieving eubiosis and holistic models care in both research and clinical practice are discussed.}, }
@article {pmid42193730, year = {2026}, author = {Lin, H and Cui, S and Hao, S and Yu, W and Jin, M and Jin, T and Ren, X and Ma, J and Gu, S and Teng, L and Liu, Z}, title = {Seasonal and Species-Specific Variations in Gut Microbiota of Wild Ungulates in Captivity.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {10}, pages = {}, doi = {10.3390/ani16101437}, pmid = {42193730}, issn = {2076-2615}, support = {202510225369//Northeast Forestry University/ ; None//Helan Mountain National Nature Reserve in Inner Mongolia/ ; }, abstract = {Seasonal variation can strongly restructure the gut microbiota of herbivores, but under captive conditions it remains unclear whether these shifts outweigh host-species effects when diet is standardized. Here, we profiled the gut microbiota of captive mouflon, argali, and blue sheep in summer and winter using 16S rRNA amplicon sequencing, ASV-based compositional beta-diversity analysis, ANCOM-BC2, and PICRUSt2 functional prediction. Across hosts, Chao1 richness decreased in winter, whereas Shannon diversity remained comparatively stable, indicating that seasonal change affected richness more strongly than evenness. CLR-based ordination further showed that the three species were relatively close in summer but became more clearly separated in winter, especially mouflon and blue sheep, consistent with pronounced seasonal restructuring under a common diet. At the phylum level, summer communities were broadly similar and dominated by Firmicutes_A and Bacteroidota, whereas winter brought stronger taxonomic shifts in mouflon and blue sheep, including marked increases in Proteobacteria and Firmicutes_D. Argali showed a narrower and taxonomically different seasonal response. Genus-level analyses similarly indicated that winter restructuring was host-dependent rather than uniform, with winter-associated enrichment of several Bacillales/Planococcaceae-related lineages and Proteobacteria-associated taxa, particularly in mouflon and blue sheep. Predicted functional profiles inferred by PICRUSt2 also shifted between summer and winter within each host species, suggesting that seasonal restructuring extended beyond taxonomy, although these results should be interpreted as inferred functional potential rather than direct metabolic activity. Overall, our findings support seasonality as the primary axis of gut microbiota variation in captivity, while the host species modulates the magnitude and taxonomic features of these seasonal changes. These results highlight the need to consider seasonal effects in captive management and provide a basis for future multi-omics validation of host-microbiome interactions in wild ungulates.}, }
@article {pmid42193732, year = {2026}, author = {Wang, K and Hu, J and Lu, T and Zhang, Y and Zhao, X and Yang, J}, title = {Effects of Different Feeding Regimes on Rumen Microbial Composition, Functional Potential, and Fermentation Characteristics of Longdong Goats (Capra hircus).}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {10}, pages = {}, doi = {10.3390/ani16101441}, pmid = {42193732}, issn = {2076-2615}, support = {24CXNL007//Sino-Gansu Science and Technology Commissioner Program of the Gansu Provincial Department of Science and Technology/ ; KJZC-2023-9//2023 Modern Silk Road Cold- and Arid-Region Agriculture Science and Technology Support Program/ ; 22JR5RA759//Key Project of the Natural Science Foundation of Gansu Province/ ; }, abstract = {The rumen microbiota plays a key role in nutrient fermentation and short-chain fatty acid (SCFA) production in ruminants. However, the impacts of different feeding regimes on rumen microbial composition, functional potential, and metabolic outputs remain unclear. In this study, rumen fluid samples were collected from 12 Longdong goats (Capra hircus), which were divided into four groups based on feeding regime and coat color: housed white goats (n = 3), housed black goats (n = 3), grazing white goats (n = 3), and grazing black goats (n = 3). Samples were analyzed using high-throughput sequencing combined with functional annotation (KEGG and CAZy) and targeted SCFA profiling. Distinct differences in microbial community composition were observed primarily between feeding regimes, with enrichment of taxa related to carbohydrate degradation and fermentation. Functional analyses revealed significant shifts in metabolic pathways, particularly those associated with carbohydrate metabolism, energy production, and glycan biosynthesis. Several glycoside hydrolase and glycosyltransferase families showed differential abundances across groups. Consistently, SCFA concentrations varied significantly among feeding regimes. Correlation analyses further demonstrated strong associations between key microbial taxa, functional pathways, and specific SCFAs. Overall, these results indicate that feeding regime, rather than coat color, plays a dominant role in shaping rumen microbial structure, functional capacity, and fermentation characteristics, providing insights into microbial mechanisms underlying rumen metabolism and informing feeding strategy optimization.}, }
@article {pmid42193750, year = {2026}, author = {Leduc, L and Boucher, L and Mach, N and Leclère, M and Costa, M}, title = {Long-Read Sequencing for Species-Level Resolution of the Equine Gut Microbiota Reveals the Need for Improved Databases.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {10}, pages = {}, doi = {10.3390/ani16101459}, pmid = {42193750}, issn = {2076-2615}, support = {#RGPIN/4514-2018//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Differences in gut microbiota composition related to diet have been reported in horses, but characterization of specific microbial taxa remains limited, particularly at the species level. The objective of this study was to use long-read sequencing of the 16S rRNA gene to provide additional taxonomic insight into the intestinal microbiota in horses. Fecal samples were collected from 12 horses on pasture and from 6 of them after switching to a hay diet. Sequencing yielded low read counts per sample, and the analysis failed to detect statistical differences in alpha- and beta-diversity among dietary groups (p > 0.05). Species-level taxonomic resolution was not substantially enhanced using long-read sequencing, as only 3% of reads were assigned at the species level, and an additional 3% of reads were assigned at the genus level. The majority of reads (49%) were classified at the family level. Accordingly, in this dataset, long-read sequencing did not provide additional biological insight into diet-associated differences in the equine gut microbial community. This limited added value can be explained by the low sequencing depth obtained for several samples and the current incompleteness of reference databases for equine bacterial taxa, highlighting ongoing challenges in achieving high-resolution characterization of the equine gut microbiome.}, }
@article {pmid42193760, year = {2026}, author = {Zhang, Y and Zhang, M and Zhang, T and Jiang, B and Dai, J and Han, W and Huang, X}, title = {Seasonal Dynamics of the Gut Microbiome and Functional Adaptations in Sika Deer (Cervus nippon kopschi).}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {10}, pages = {}, doi = {10.3390/ani16101470}, pmid = {42193760}, issn = {2076-2615}, support = {20232BAB215018//Jiangxi Provincial Department of Science and Technology/ ; 2023521603//Jiangxi Provincial Department of Science and Technology/ ; 2023521606//Jiangxi Provincial Department of Science and Technology/ ; 2024511601//Jiangxi Provincial Department of Science and Technology/ ; }, abstract = {Seasonal environmental variations significantly affect the health and survival of wild ruminants such as sika deer (C. n. kopschi). This study characterized the adaptation of gut microbial communities to these seasonal shifts, supporting the host's physiological needs. We employed high-throughput sequencing on sixty fecal samples collected throughout the four seasons to assess microbial diversity, composition, and potential functions. Our findings revealed significant seasonal fluctuations, with microbial diversity peaking in summer and reaching its nadir in winter. Taxonomic analysis showed that Firmicutes was the dominant phylum during spring (63.43%), summer (78.52%), and autumn (81.99%), whereas winter was dominated by Proteobacteria (50.60%), primarily due to the enrichment of Acinetobacter and Pseudomonas. Although the community structure formed three distinct seasonal enterotypes with dramatic shifts in bacterial taxa, functional profiling based on genomic databases indicated that core biological pathways remained remarkably stable throughout the year. These results demonstrate that sika deer maintain internal functional homeostasis by reorganizing their gut microbial composition to address harsh environmental stressors. This research provides a critical scientific basis for understanding the adaptive resilience of wild animals, offering valuable insights into the conservation and management of wildlife populations in dynamic ecosystems.}, }
@article {pmid42193867, year = {2026}, author = {Hadjigol, S and Shah, BA and Yazdani, N and O'Brien-Simpson, NM}, title = {The Role of Oral Pathobionts' Outer Membrane Vesicles in Cancer Pathology and Therapeutic Development.}, journal = {Cells}, volume = {15}, number = {10}, pages = {}, doi = {10.3390/cells15100855}, pmid = {42193867}, issn = {2073-4409}, mesh = {Humans ; *Neoplasms/pathology/microbiology/therapy ; Animals ; Porphyromonas gingivalis/metabolism ; Tumor Microenvironment ; *Mouth/microbiology ; Fusobacterium nucleatum ; }, abstract = {Cancer remains one of the leading causes of mortality worldwide, with increasing recognition of the host microbiome as a modifiable contributor to tumour initiation and progression. Among microbial mediators, outer membrane vesicles (OMVs) derived from Gram-negative oral pathobionts have emerged as critical effectors of host-microbe interactions. These nanoscale vesicles function as delivery systems for a diverse range of bioactive cargo, including virulence factors, lipopolysaccharides, proteins, and nucleic acids, enabling both local and systemic modulation of host cellular processes. Emerging evidence suggests that OMVs produced by oral pathobionts, particularly Porphyromonas gingivalis and Fusobacterium nucleatum, are associated with tumour-promoting inflammation, immune dysregulation, epithelial transformation, and metastatic progression. Mechanistically, OMVs have been shown to activate key signalling pathways, disrupt mitochondrial function, induce oxidative stress, and reprogram the tumour microenvironment in ways that favour cancer cell survival and immune evasion. In addition, OMV-mediated modulation of host responses has been linked to resistance to anticancer therapies. In this review, we synthesize current evidence on the role of oral pathobionts' OMVs in cancer biology, with a focus on their contributions to tumour initiation, progression, and metastasis. We further discuss emerging clinical associations, the potential of OMV-derived components as diagnostic biomarkers, and the growing interest in engineered OMVs as platforms for therapeutic intervention. Finally, we highlight key challenges and knowledge gaps that must be addressed to advance the translational application of OMV-based strategies in oncology. Overall, OMVs represent a promising but still evolving link between the oral microbiome and cancer, offering new insights into disease mechanisms and potential avenues for diagnosis and therapy.}, }
@article {pmid42193961, year = {2026}, author = {Palumbo, M and Della Corte, L and Conte, MR and D'Angelo, G and Ascione, M and Pollio, A and Giampaolino, P and Bifulco, G}, title = {Is Recurrent Endometriosis a Reprogrammed Disease? Molecular Persistence Beyond Surgical Clearance.}, journal = {Cells}, volume = {15}, number = {10}, pages = {}, doi = {10.3390/cells15100951}, pmid = {42193961}, issn = {2073-4409}, mesh = {Humans ; *Endometriosis/genetics/surgery/pathology/immunology ; Female ; Recurrence ; Epigenesis, Genetic ; }, abstract = {Background: Endometriosis is traditionally conceptualized as a localized gynecological disorder characterized by the presence of ectopic endometrial tissue. However, high recurrence rates following apparently complete surgical excision challenge this lesion-based paradigm and suggest the existence of underlying biological mechanisms that extend beyond residual disease. Increasing evidence indicates that endometriotic cells exhibit persistent molecular alterations, including dysregulated gene expression, epigenetic modifications, and immune dysfunction, which may contribute to disease maintenance and recurrence. Objective: This study aims to critically examine whether endometriosis can be considered a molecularly reprogrammed disease, characterized by persistent cellular and microenvironmental alterations that are not reversed by surgical removal of visible lesions. Methods: A narrative review of the literature was conducted using PubMed, Scopus, and Web of Science databases including studies published from January 2016 to March 2026. Studies investigating molecular, genetic, epigenetic, and immunological mechanisms of endometriosis persistence and recurrence were included. Particular attention was given to pathways involved in cellular survival, inflammation, hormone resistance, and epigenetic regulation. Results: Endometriotic cells demonstrate stable alterations in gene expression profiles, including pathways related to estrogen signaling, progesterone resistance, inflammation, and cellular proliferation. Epigenetic mechanisms, such as aberrant DNA methylation and histone modifications, appear to sustain these changes over time, contributing to a form of "molecular memory." In parallel, the peritoneal microenvironment is characterized by chronic inflammation, immune tolerance, and impaired clearance of ectopic cells. These factors collectively support lesion persistence and may explain recurrence even after complete surgical excision. Emerging evidence also highlights the role of systemic factors, including endocrine-immune interactions and microbiome-related pathways, reinforcing the concept of endometriosis as a systemic rather than purely localized condition. Conclusions: Endometriosis may be more accurately defined as a persistent, molecularly reprogrammed disease driven by stable alterations in cellular behavior and the surrounding microenvironment. This paradigm shift has important clinical implications, suggesting that surgical treatment alone may be insufficient and that future therapeutic strategies should target the underlying molecular and immunological mechanisms responsible for disease persistence.}, }
@article {pmid42193963, year = {2026}, author = {Stavros, S and Gerede, A and Moustakli, E and Zikopoulos, A and Tsakiridis, I and Messini, C and Potiris, A and Anagnostaki, I and Arkoulis, I and Topis, S and Dagklis, T and Loutradis, D}, title = {Extracellular Vesicles in Human Reproduction: Integrating Redox-Mitochondrial Signaling with Multi-Omics and AI-Driven Biomarker Discovery.}, journal = {Cells}, volume = {15}, number = {10}, pages = {}, doi = {10.3390/cells15100955}, pmid = {42193963}, issn = {2073-4409}, mesh = {Humans ; Multiomics ; *Mitochondria/metabolism ; *Biomarkers/metabolism ; *Extracellular Vesicles/metabolism ; Oxidation-Reduction ; *Signal Transduction ; *Reproduction ; Oxidative Stress ; }, abstract = {In the human reproductive system, extracellular vesicles (EVs) have been recognized as playing a vital role in mediating cell-cell communication. They are considered critical for embryo development, implantation, gamete interaction, and fertilization. The various cargoes carried by EVs, depending on the physiological and pathological state of the cell, include proteins, lipids, nucleic acids, and mitochondrial components. EVs are recognized as critical carriers of redox-related signals and mitochondrial components, linking oxidative stress (OS) to reproductive failure and influencing gamete quality and embryo competence. Although considerable progress has been made, research remains poorly integrated, despite individual omics technologies providing valuable molecular insights. The use of multi-omics technologies, including transcriptomics, proteomics, metabolomics, and microbiome analysis, has been proposed as a global approach to understanding the complexities associated with EVs and discovering new biomarkers associated with infertility. ML and AI have been proposed to identify predictive signatures linked to ART effectiveness and reproductive outcomes, with a strong capacity to handle high-dimensional data. The review aims to provide an overview of current knowledge on EV-mediated redox-mitochondrial signaling in human reproduction, while highlighting the importance of emerging multi-omics and AI technologies for EV-mediated biomarker development. The review discusses the promise of EVs in the development of minimally invasive diagnostic approaches and therapeutic interventions, as well as the challenges in the standardization, integration, and clinical translation of EV-mediated research. In addition, the review proposes integrating computational approaches to better understand molecular pathways involved in the development of next-generation precision medicine in human reproduction.}, }
@article {pmid42194001, year = {2026}, author = {Zhao, Z and Wang, J and Wu, Z and Ye, L and Wang, J and Wang, Y and Zhao, Y and Zhang, H and Luo, C and Tong, J}, title = {Integrated Multi-Omics Analysis Explores the Protective Effects and Potential Mechanisms of Pulsatilla chinensis on Canine Antibiotic-Associated Diarrhea.}, journal = {Biomolecules}, volume = {16}, number = {5}, pages = {}, doi = {10.3390/biom16050650}, pmid = {42194001}, issn = {2218-273X}, support = {32272904//National Natural Science Foundation of China/ ; 32373086//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Dogs ; *Diarrhea/chemically induced/drug therapy/veterinary/prevention &amp; control/metabolism ; Multiomics ; *Anti-Bacterial Agents/adverse effects ; *Pulsatilla/chemistry ; Metabolomics ; *Plant Extracts/pharmacology/chemistry ; Cytokines ; }, abstract = {Diarrhea is a common gastrointestinal disorder in animals, often worsened by antibiotic use. Pulsatilla chinensis (PC) is traditionally used for gastrointestinal issues, but its bioactive constituents and mechanisms remain unclear. This study investigated the preventive effects of PC in a canine model of antibiotic-associated diarrhea using an integrated multi-omics approach. LC-MS identified key constituents of PC, including anemoside B4, berberine, stigmasterol, and quercetin. In silico analyses predicted that stigmasterol and quercetin target EGFR and AKT1, modulating inflammation and epithelial repair via PI3K-Akt and IL-17 signaling pathways. In vivo, treatment with PC significantly reduced serum pro-inflammatory cytokines such as TNF-α and IL-6 and elevated immune markers including IgG and IgA compared to the control group. Furthermore, 16S rRNA analysis revealed that PC restored gut microbial diversity, reflected by increased Sobs and Chao1 indices, enriched beneficial Lactobacillus, and decreased the abundance of inflammation-associated taxa such as Proteobacteria, Desulfobacterota, and Escherichia-Shigella. These findings suggest that PC suppresses inflammation and remodels the gut microbiome, providing a mechanistic basis for its use as an herbal alternative to antibiotics. Future studies should include fecal microbiota transplantation and targeted metabolomics to establish causality and optimize therapeutic strategies.}, }
@article {pmid42194034, year = {2026}, author = {Fang, L and Kim, IS and Martin, BR and Sherlock, L and Min, S and Kim, YK and Mok, KH}, title = {Metabolomics and Human Health: Progress, Insights, Challenges and the Concept of a Healthy Metabolome.}, journal = {Biomolecules}, volume = {16}, number = {5}, pages = {}, doi = {10.3390/biom16050683}, pmid = {42194034}, issn = {2218-273X}, support = {Marie Sk&#x142;odowska-Curie Actions Grant Agreement No.721906-TRACT//Horizon 2020/ ; }, mesh = {Humans ; *Metabolomics/methods ; *Metabolome ; Multiomics ; *Health ; Biomarkers/metabolism ; Life Style ; }, abstract = {Health is increasingly recognized as a dynamic state of physiological equilibrium rather than the mere absence of disease. Traditional clinical biomarkers capture only limited aspects of physiology and fail to reflect the multidimensional and dynamic nature of human homeostasis. Metabolomics, by comprehensively profiling small-molecule metabolites downstream of genetic, proteomic, environmental, and lifestyle influences, offers a sensitive and functional readout of an individual's physiological state. This review catalogues current advances in applying metabolomics to characterize metabolic features of health, focusing on the influence of age, sex, body mass index, physical activity, diet, lifestyle behaviors, microbiome composition, and population heterogeneity. Numerous cohort studies have shown that substantial metabolic variability exists amongst individuals within apparent healthy populations, underscoring the need for stratified and contextual reference frameworks. We further discuss major challenges in defining a standardized metabolic baseline, including analytical platform heterogeneity, biofluid specificity, population diversity, and the predominance of cross-sectional study designs. Finally, we highlight the role of large-scale longitudinal cohorts, biobanks, multi-omics integration, and artificial intelligence-driven tools in overcoming these barriers. Establishing robust, dynamic, and personalized metabolic baselines will be critical for redefining health, enabling early intervention, and supporting predictive and preventive medicine.}, }
@article {pmid42194042, year = {2026}, author = {Elshazly, AM and Li, J and Yang, GY and Radhakrishnan, SK}, title = {Mcl1 as a Molecular Switch Linking Inflammatory Bowel Diseases to Colorectal Tumorigenesis.}, journal = {Biomolecules}, volume = {16}, number = {5}, pages = {}, doi = {10.3390/biom16050694}, pmid = {42194042}, issn = {2218-273X}, mesh = {Humans ; *Myeloid Cell Leukemia Sequence 1 Protein/metabolism/genetics ; *Inflammatory Bowel Diseases/metabolism/pathology/genetics ; *Colorectal Neoplasms/metabolism/pathology/genetics ; Animals ; *Carcinogenesis/metabolism/genetics ; Cell Transformation, Neoplastic ; }, abstract = {The maintenance of gastrointestinal homeostasis relies on a tightly coordinated interplay between the intestinal epithelium, the immune system, and the commensal microbiome. Disruption of this balance underlies inflammatory bowel disease (IBD), encompassing Crohn's disease and ulcerative colitis, and is characterized by chronic, relapsing mucosal inflammation driven by genetic susceptibility, environmental factors, immune dysregulation, and microbial imbalance. Persistent inflammation promotes repeated cycles of epithelial injury and aberrant repair, creating a permissive environment for dysplasia and the development of colitis-associated cancer, most notably colorectal carcinoma. Recent evidence identifies the anti-apoptotic regulator myeloid cell leukemia-1 (Mcl1) as a critical determinant of epithelial integrity and cellular turnover during mucosal stress. Loss or destabilization of Mcl1 disrupts epithelial homeostasis, amplifies inflammatory signaling, and accelerates tumor initiation, whereas its adaptive upregulation in established malignancy promotes tumor cell survival, metabolic fitness, and therapeutic resistance. Thus, Mcl1 functions as a context-dependent molecular switch via restraining malignant transformation during chronic inflammation while supporting tumor progression once neoplasia is established. This functional duality positions Mcl1 as both a biomarker of disease progression and a therapeutically actionable vulnerability. In this review, we synthesize recent advances elucidating how Mcl1 integrates epithelial cell-fate decisions, immune signaling and tumor evolution across the IBD-cancer continuum. We further support these concepts through integrative analyses of multiple transcriptomic datasets comparing normal colonic mucosa with colorectal tumors, and we discuss emerging pharmacological strategies targeting Mcl1 in colitis-associated cancer.}, }
@article {pmid42194074, year = {2026}, author = {Li, J and Long, Q and Zhu, B}, title = {Akkermansia muciniphila and Alzheimer's Disease: Mechanisms, Evidence and Translational Potential.}, journal = {Biomolecules}, volume = {16}, number = {5}, pages = {}, doi = {10.3390/biom16050726}, pmid = {42194074}, issn = {2218-273X}, support = {CSTB2025NSCQ-GPX0455//Chongqing Municipal Government/ ; 2026MSXM099//Chongqing Medical Scientific Research Project/ ; }, mesh = {*Alzheimer Disease/microbiology/metabolism ; Humans ; Animals ; *Akkermansia ; Gastrointestinal Microbiome ; Brain/metabolism ; }, abstract = {Akkermansia muciniphila (A. muciniphila) is a bacterium that breaks down mucus and is studied for its effects on metabolism and the immune system. Studies show that it affects Alzheimer's disease (AD) by protecting the gut barrier, reducing inflammation, and influencing communication between the immune system, the brain, and mitochondria. This review summarizes mechanistic, preclinical, and translational evidence connecting A. muciniphila to AD, including products such as short-chain fatty acids (SCFAs), and structural or secreted proteins including Amuc_1100 and extracellular vesicles (AmEVs). We also discuss differences between bacterial strains, differences in research methods, and findings that change under different conditions, which make the results harder to interpret. Animal studies suggest neuroprotective effects, but clinical evidence is still limited. Clinical use will need human studies at the strain level, confirmation in humanized models, and early trials using biomarkers to test safety and causal effects.}, }
@article {pmid42194156, year = {2026}, author = {Baghdadi, ZD}, title = {From Preservation to Precision in Pediatric Dentistry: Evidence-Calibrated Viewpoint and Heuristic Framework for Silver Diamine Fluoride Guidance.}, journal = {Children (Basel, Switzerland)}, volume = {13}, number = {5}, pages = {}, doi = {10.3390/children13050629}, pmid = {42194156}, issn = {2227-9067}, abstract = {Silver diamine fluoride (SDF) is a key preservation-based intervention in pediatric dentistry. It can arrest many cavitated lesions, reduce treatment burden, and expand access for children who cannot receive conventional restorative care. This viewpoint article offers a reasoned, heuristic framework for calibrating SDF guidance to the strength of the underlying evidence. It does not present a systematic review or formal policy standards. Foundational trials support the clinical usefulness of 38% SDF. The 2017 AAPD guidelines provided conditional recommendations based on low-quality evidence. The current challenge is no longer whether to endorse SDF but how to calibrate guidance on its implementation. Later studies addressing intervals and implementation often have open-label designs, small samples, single centers, or overlapping data sources. Mechanistic and microbiome studies support biological plausibility, but policy should not treat them as definitive evidence. We propose a hypothesis-generating framework that separates claims about the existence of an effect (for which there is stronger directional support) from claims about its optimal conditions (which remain more uncertain), highlights dataset overlap, and matches recommendation strength to study quality. The framework supplements GRADE and provides illustrative upgrade pathways. The goal is to preserve SDF access while making guidelines more transparent, credible, and precise.}, }
@article {pmid42194194, year = {2026}, author = {Luca, AC and Mindru, DE and Rosu, ST and Diaconescu, C and Rosu, EV and Țarcă, E and Adumitrăchioaiei, H and Anton-Paduraru, DT}, title = {The Gut Microbiome in Congenital Heart Disease: Dysbiosis, Intestinal Barrier Injury, and Translational Opportunities Across the Childhood-A Narrative Review.}, journal = {Children (Basel, Switzerland)}, volume = {13}, number = {5}, pages = {}, doi = {10.3390/children13050668}, pmid = {42194194}, issn = {2227-9067}, abstract = {Congenital heart disease (CHD) is the most common congenital anomaly worldwide and is associated with substantial infant morbidity and mortality. This narrative review synthesizes evidence linking CHD to alterations in the gut microbiome across neonatal, perioperative, and chronic stages and highlights a gut-heart-immune framework in which microbial imbalance, intestinal barrier dysfunction, and systemic inflammation may interact to influence clinical outcomes. Early infancy represents a potential window for microbiome and immune development, shaped by delivery mode and feeding, with many breastfed infants developing a Bifidobacterium-dominant community supported by human milk oligosaccharides. In CHD, abnormal splanchnic perfusion and hypoxemia, together with intensive care and perioperative exposures (fasting, delayed enteral feeding, antibiotics, acid suppression), may predispose to dysbiosis and impaired barrier function. Cardiac surgery with cardiopulmonary bypass can act as a "second hit," with evidence of increased gut permeability, endotoxemia, inflammatory activation, and biomarker signals of enterocyte injury and tight-junction disruption. Clinically, these mechanisms align with gut-sensitive outcomes including necrotizing enterocolitis (especially in ductal-dependent lesions), feeding intolerance, and postoperative infection-risk phenotypes. Interventions show mixed evidence: human milk exposure appears protective for NEC risk, synbiotics demonstrated outcome benefits in a randomized trial of cyanotic CHD infants, while probiotics may modify dysbiosis without consistently preventing intestinal injury and require careful safety frameworks. Key research gaps include the need for longitudinal stage-based cohorts, integration of microbiome profiling with barrier injury and perfusion markers, and standardized safety monitoring in intervention trials.}, }
@article {pmid42194502, year = {2026}, author = {Najafimakhsoos, N and Pashollari, E and Malavolta, N and Zangari, F and Cesari, C}, title = {Periodontitis and Rheumatoid Arthritis: Shared Pathophysiology, Bidirectional Association, and Therapeutic Implications-A Narrative Review.}, journal = {Healthcare (Basel, Switzerland)}, volume = {14}, number = {10}, pages = {}, doi = {10.3390/healthcare14101411}, pmid = {42194502}, issn = {2227-9032}, abstract = {Periodontitis (PD) and rheumatoid arthritis (RA) are chronic inflammatory disorders that impose substantial individual and societal burdens worldwide. PD is characterized by progressive destruction of the periodontal ligament and alveolar bone, leading to tooth loss, impaired oral function, and sustained systemic inflammatory burden. RA, affecting approximately 0.5-1% of the population, is a chronic autoimmune disease marked by persistent synovial inflammation, progressive joint destruction, disability, and reduced quality of life. Increasing evidence indicates that these conditions are biologically and clinically interconnected. Both diseases share key pathogenic pathways, including microbial dysbiosis, immune dysregulation, chronic inflammation, genetic susceptibility, and aberrant autoantibody responses. Particular attention has focused on keystone periodontal pathogens such as Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans, which may promote protein citrullination and the formation of anti-citrullinated protein antibodies (ACPA), thereby providing a plausible mechanistic bridge between periodontal infection and systemic autoimmunity. Shared genetic risk factors, including HLA-DRB1 susceptibility alleles, further support a common host predisposition. Clinical, epidemiological, and translational studies increasingly support a bidirectional association. Individuals with PD appear to have a higher risk of RA development, whereas patients with RA demonstrate greater prevalence, severity, and progression of periodontal disease. Interventional studies suggest that nonsurgical periodontal therapy may reduce local periodontal inflammation, circulating inflammatory biomarkers, and RA disease activity indices, while effective pharmacological control of RA may also improve periodontal outcomes. This narrative review critically evaluates the PD-RA relationship across four interconnected domains: (i) epidemiological and clinical associations between PD and RA, (ii) key mechanisms underlying RA pathogenesis, (iii) shared biological pathways linking both diseases, and (iv) the extent to which treatment of one condition influences the other. Particular emphasis is placed on major sources of heterogeneity and confounding-including smoking, metabolic comorbidities, disease stage, therapeutic exposure, and variable diagnostic definitions-that may explain inconsistencies across the literature. By integrating current mechanistic and clinical evidence, this review provides a structured synthesis that extends beyond a descriptive overview of association studies. A clearer understanding of the periodontal-rheumatologic axis may facilitate risk stratification, identify novel therapeutic targets, and support integrated multidisciplinary care. Targeting both oral and systemic inflammation may improve outcomes in patients with coexisting PD and RA and may potentially reduce the risk or severity of one condition in individuals already affected by the other.}, }
@article {pmid42194525, year = {2026}, author = {Szymańska, K and Sałasińska, K and Młynarczyk, A and Miszczak, J and Dmoch, W and Maciejewicz, P}, title = {The Gut-Eye Axis and Microbiome in Ophthalmic Diseases: A Narrative Review.}, journal = {Journal of clinical medicine}, volume = {15}, number = {10}, pages = {}, doi = {10.3390/jcm15103563}, pmid = {42194525}, issn = {2077-0383}, abstract = {The gut microbiome regulates host metabolism, barrier integrity, and immune homeostasis through microbe-host signaling and bioactive metabolites. Growing evidence suggests that dysbiosis may also influence ocular immune privilege and blood-retinal barrier stability, supporting the emerging concept of the gut-eye axis. This narrative review aimed to integrate retinal, uveal, and ocular surface disorders within a shared functional framework, with emphasis on recurring mechanistic pathways and their translational relevance rather than on single diseases or isolated taxonomic findings. The review was based on a literature search of PubMed and Scopus and primarily included English-language studies published between 2015 and 2025, with earlier seminal papers included when needed. The search was last updated in March 2026, and 101 sources were included in the final narrative synthesis. Across age-related macular degeneration, diabetic retinopathy, glaucoma, uveitis, dry eye disease, and Sjögren's syndrome, the most consistent microbiome-related signals were functional rather than taxonomic. Recurrent mechanistic themes included Th17/Treg immune programming, barrier dysfunction with microbial product translocation, and systemic metabolite signaling, particularly involving short-chain fatty acids, bile acid receptor pathways, and tryptophan-derived metabolites. Age-related macular degeneration and diabetic retinopathy showed the strongest multi-layered support, whereas uveitis provided a compelling immune-centered biological model that remains limited by treatment-related confounding in human studies. In glaucoma and ocular surface disease, evidence supports biological plausibility, especially in relation to neuroinflammation, mucosal immune dysregulation, and metabolite-dependent anti-inflammatory pathways, although much of the available human literature remains associative. Overall, current evidence supports dysbiosis as a disease modifier that may influence ocular inflammation, angiogenesis, neurodegeneration, and barrier stability. However, clinical translation remains limited by cohort heterogeneity, methodological variability, and incomplete control of confounding factors. Further progress will depend on longitudinal multi-omics cohorts and controlled intervention trials focused on actionable microbial functions.}, }
@article {pmid42194533, year = {2026}, author = {Inglezou, LM and Konstantinidis, T and Skeva, A and Malkots, B and Panagiotopoulos, E and Sakka, V and Spanoudakis, E and Panopoulou, M and Kotsianidis, I and Liapis, K}, title = {The Role of Gut Microbiota in Acute Myeloid Leukemia.}, journal = {Journal of clinical medicine}, volume = {15}, number = {10}, pages = {}, doi = {10.3390/jcm15103571}, pmid = {42194533}, issn = {2077-0383}, abstract = {Gut microbiota plays a crucial role in regulating immune system function and shaping immunological responses to pathogens capable of causing infections. Alterations in the composition of the intestinal microbiome are associated with immune system dysfunction and increased susceptibility to infections. Patients with acute myeloid leukemia (AML) are highly susceptible to infections due to immune system deregulation caused by the disease itself, as well as chemotherapy-induced bone marrow aplasia. In these patients, gut microbiota dysbiosis and reduced microbial diversity (i.e., imbalances in the composition and function of intestinal microbes) result from multiple factors, including the underlying disease, neutropenia, dietary factors, use of antibiotics, chemotherapy regimens and prolonged hospitalization. Chemotherapy, for instance, induces damage to the intestinal mucosa and disrupts the epithelial barrier, resulting in deregulation of the intestinal microbiome. Previous studies have reported alterations in the human intestinal microbiome in patients with AML undergoing chemotherapy. Of particular interest is the capacity of some commensal bacteria to modulate the tumor microenvironment and response to chemotherapy. Moreover, increased mortality and reduced overall survival have been reported in patients who have undergone allogeneic stem cell transplantation and exhibit decreased gut microbiome diversity at the time of transplantation. These findings indicate that the composition of gut microbiota may play an important role in the prognosis of AML, especially in relation to therapeutic response. This narrative review summarizes new research into the role of the intestinal microbiome and the underlying alterations observed in patients with AML, resulting from the disease and therapeutic interventions and outlines strategies to improve its function and outcomes.}, }
@article {pmid42194691, year = {2026}, author = {Duah, OB and Young, L and de La Serre, C and Zhu, H and Xu, H}, title = {Functional Capacity and Gut Microbiota Shifts in Heart Failure Patients Following Cardiac Rehabilitation.}, journal = {Journal of clinical medicine}, volume = {15}, number = {10}, pages = {}, doi = {10.3390/jcm15103729}, pmid = {42194691}, issn = {2077-0383}, abstract = {Background/Objectives: Increased functional capacity is associated with healthy gut microbiota composition and improved heart failure (HF) prognosis. Although cardiac rehabilitation (CR) improves functional capacity in HF patients, the association between CR and gut microbiota in HF patients is not well-studied. We explored the relationships between functional capacity and changes in gut microbiota composition in 41 patients with HF participating in CR, using data from a previous repeated measures clinical trial. Methods: Functional capacity was evaluated using the six-minute walk distance (6MWD), and the gut microbiota composition was analyzed from fecal samples using 16S rRNA sequencing before CR and again after three months of participation. Results: Higher baseline functional capacity (6MWD ≥ 360 m) corresponded with significant shifts in Bacteroidetes abundance after CR. A clinically meaningful improvement in functional capacity (change in 6MWD ≥ 95 m) was associated with increased α-diversity (p = 0.04, statistic = 6.42), increased abundance of Lachnospiraceae UCG 004, Lawsonella, and Ruminococcus gnavus group, and a lower abundance of Microbacterium. Conclusions: These data suggest that cardiac rehabilitation may be associated with differences in gut microbiota composition in HF patients, alongside its association with functional capacity. Additional research is needed to better understand how gut microbial patterns relate to functional capacity in individuals with HF participating in CR.}, }
@article {pmid42194897, year = {2026}, author = {Lau, WL and Li, W and Sumida, K and Kalantar-Zadeh, K}, title = {The Role of Diet and Gut Microbiome in CKD Progression and Therapy.}, journal = {Journal of clinical medicine}, volume = {15}, number = {10}, pages = {}, doi = {10.3390/jcm15103934}, pmid = {42194897}, issn = {2077-0383}, abstract = {There is a bidirectional relationship between chronic kidney disease (CKD) and an altered gut microbiome, with gut-derived uremic toxins contributing to cardiovascular-kidney-metabolic effects. In this review, we summarize the interplay between diet, the intestinal microbiota and systemic sequelae including CKD progression, cardiovascular morbidity and cognitive decline. We discuss the current state of knowledge regarding microbiota-modulating therapies that have the potential to delay CKD complications such as plant-dominant diets, oral adsorbents, prebiotics/probiotics, fecal microbiota transplantation and exercise.}, }
@article {pmid42195053, year = {2026}, author = {Albuz, O and Pirim, D and Akcay, S and Tan, TG and Ekici, S and Akbulut, S}, title = {Host Gene Signatures Associated with Gastric Cancer-Associated Microbial Taxa: A Descriptive Microbiome-Transcriptome Study.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {62}, number = {5}, pages = {}, doi = {10.3390/medicina62050799}, pmid = {42195053}, issn = {1648-9144}, mesh = {Humans ; *Stomach Neoplasms/genetics/microbiology ; *Transcriptome/genetics ; *Microbiota/genetics ; Gene Expression Profiling/methods ; *Gastrointestinal Microbiome/genetics ; }, abstract = {Background and Objectives: Gastric cancer remains a leading cause of cancer-related mortality worldwide and develops through complex interactions between environmental factors, microbial dysbiosis, and host molecular pathways. Although Helicobacter pylori infection is a well-established risk factor, emerging evidence suggests that broader alterations in the gastric microbiome may also contribute to carcinogenesis. However, the associations between gastric cancer-associated microbial taxa and host gene expression profiles remain insufficiently characterized. This study aimed to identify host gene signatures associated with gastric cancer-related microbial taxa through a descriptive analysis integrating microbiome-derived taxa with transcriptome data. Materials and Methods: Microbial taxa associated with gastric cancer were systematically retrieved from the Disbiome database. Taxon set enrichment analysis (TSEA) was performed using the MicrobiomeAnalyst platform to identify host genes associated with gastric cancer-associated taxa. Importantly, TSEA relies on healthy reference data from the Human Microbiome Project and does not establish gastric cancer-specific interactions or causal relationships. Gene expression levels were subsequently evaluated using The Cancer Genome Atlas (TCGA) PanCancer stomach adenocarcinoma (STAD) dataset by comparing tumor and matched normal gastric tissues. Gene interaction network and transcription factor (TF) enrichment analyses were conducted to explore predicted regulatory relationships. Results: Among 64 microbial taxa associated with gastric cancer, 43 were reported as elevated. After removing overlapping taxa across studies, 37 elevated and 21 reduced taxa were retained for analysis. TSEA identified 11 host genes associated with gastric cancer-related microbial taxa. Transcriptomic analysis demonstrated significant downregulation of DPP6 and DLG2, while KDM4D, USP34, and VDR were significantly upregulated in gastric cancer tissues compared with normal controls. Network and TF enrichment analyses revealed predicted co-expression and co-localization patterns among these genes, suggesting their potential involvement in immune-related processes, epigenetic regulation, and cellular organization. Conclusions: This descriptive study identifies distinct host gene expression signatures associated with gastric cancer-associated microbial dysbiosis. This study is purely associative and hypothesis-generating; no causal or mechanistic inferences are made. TSEA used healthy reference data and therefore does not reflect gastric cancer-specific host-microbe interactions. The findings provide a basis for future hypothesis-driven research but require validation in independent cohorts.}, }
@article {pmid42195127, year = {2026}, author = {Samara, M and Thodou, E and Messini, C and Moustakli, E and Anagnostou, M and Zikopoulos, A and Daponte, A and Georgiou, I and Anifandis, G}, title = {The Influence of Sexually Transmitted Bacteria and Human Papillomavirus on Sperm Parameters: Data from a Preliminary Study.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {62}, number = {5}, pages = {}, doi = {10.3390/medicina62050874}, pmid = {42195127}, issn = {1648-9144}, support = {3371/14.06.2024, grant number: 5600.0218//Special Account for Research Grants, University of Thessaly, Greece/ ; }, mesh = {Humans ; Male ; Cross-Sectional Studies ; Adult ; Infertility, Male/microbiology ; *Human Papillomavirus Viruses/pathogenicity ; *Spermatozoa/microbiology/virology ; Greece/epidemiology ; Semen Analysis/methods ; Papillomavirus Infections/complications ; Papillomaviridae/pathogenicity ; Prevalence ; Semen/microbiology ; }, abstract = {Background and Objectives: The microbiome plays a pivotal role in male infertility, with distinct microbial species exerting both beneficial and deleterious effects on reproductive function. Sexually transmitted bacteria and several viruses, including human papillomavirus (HPV), have been identified in semen. This cross-sectional study aimed to examine the prevalence of single and co-infections of sexually transmitted bacteria (STB)-such as Chlamydia trachomatis, Mycoplasma spp., and Ureaplasma spp.-with various HPV subtypes in Greek male partners of infertile couples and to evaluate their potential impact on sperm parameters. In addition, the possible effect of cryopreservation on the maintenance of these pathogens was assessed. Materials and Methods: Eighty-two semen samples were initially collected from 82 individuals undergoing routine sperm analysis. In total, 80/82 (97.6%) participants proceeded to further analysis, as 2/82 (2.4%) were excluded due to poor DNA quality. Results: A total of 18/80 (22.5%) sperm samples tested positive for STB, with Ureaplasma spp. representing the most frequently detected pathogen. Co-infection of Ureaplasma spp. and Mycoplasma hominis was observed in 4/80 (5%) samples. Twelve samples (12/80, 15%) were positive for HPV, including low-risk (LR) and high-risk (HR) types, and HPV 16 was the predominant HR genotype. Notably, a co-infection of STB and HPV was not found in our specimens. STB-positive samples demonstrated significantly higher sperm concentration and improved progressive motility compared with STB-negative samples. HPV-positive samples exhibited lower sperm volume and concentration and increased non-progressive motility compared with HPV-negative samples. Following three months of cryopreservation, LR HPV and STB were no longer detectable, whereas HR HPV types remained detectable. Conclusions: These preliminary findings are interesting, as they could be useful for routine screening of HPV and STB in sperm samples preserved in sperm banks and highlight the need for future research.}, }
@article {pmid42195292, year = {2026}, author = {Hibić Kaknjašević, H and Dervišević, E and Fajkić, A and Hodžić, A and Chupin, A and Sher, EK}, title = {A Focused Comparative Review of Innovative Therapeutics Across Autoimmune and Chronic Inflammatory Diseases.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {5}, pages = {}, doi = {10.3390/life16050736}, pmid = {42195292}, issn = {2075-1729}, support = {No. 060124-0-000 &#xab;Transformation of international economic relations in the context of new geopolitical challenges&#xbb;.//Peoples' Friendship University of Russia, RUDN/ ; }, abstract = {Chronic inflammatory diseases and autoimmune diseases are overlapping but distinct immune-mediated disorders that represent a growing worldwide health concern, characterised by persistent inflammation, tissue damage, and progressive organ dysfunction. In the United States alone, more than $180 billion is spent annually on managing these conditions, yet fewer than 10% of patients achieve long-term remission. These figures highlight the limitations of conventional therapies, which often control symptoms rather than adequately modify the underlying disease process. This review provides a focused and comparative overview of emerging therapeutic strategies across representative immune-mediated disorders, with particular emphasis on mesenchymal stem cells, Janus kinase-signal transducer and activator of transcription (JAK-STAT) inhibitors, chimeric antigen receptor T-cell therapies, therapeutic vaccines, microbiome-modulating interventions, and nanotechnology-based drug delivery systems. In parallel, artificial intelligence (AI) is increasingly contributing to biomarker discovery, drug repurposing, and treatment stratification, thereby supporting the development of predictive and personalised medicine. Overall, these advances support a shift toward mechanism-based, multimodal, and more durable treatment strategies, although further clinical validation remains necessary.}, }
@article {pmid42195307, year = {2026}, author = {Mogoşanu, GD and Biţă, A and Scorei, IR and Pop, MI and Dinu, IR and Gheonea, DI}, title = {Boron as a Molecular Architect of Host-Microbiome Symbiosis: Implications for Dysbiosis and Aging-Related Pathologies.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {5}, pages = {}, doi = {10.3390/life16050750}, pmid = {42195307}, issn = {2075-1729}, abstract = {Boron (B) is increasingly recognized as more than a trace dietary element, emerging as a context-dependent organizer of molecular interactions at the host-microbiome interface. B exhibits reversible covalent chemistry driven by Lewis' acidity and selective affinity for cis-diol-rich biomolecules, enabling dynamic complexation with polyols, glycans, and phenolic ligands that dominate the intestinal mucus environment and shape microbial ecology. We synthesize evidence supporting an architecture-based framework in which B modulates biological function by conditioning the physicochemical context of microbial communication rather than acting as a single-pathway effector. Central to this model is spatial bioavailability, distinguishing plasma-accessible boron from microbiota-accessible boron (MAB), species that persist in the lumen and mucus layer long enough to influence interface-level processes. We propose that insufficient or altered MAB availability may contribute to dysbiosis (DYS) by destabilizing quorum-associated coordination, signal persistence, and mucosal microstructure, thereby promoting barrier dysfunction and inflammaging. Particular attention is given to B-mediated symbiotaxis, a hypothesis-driven concept describing how B-containing molecular assemblies may bias microbial communities toward cooperative, barrier-supportive configurations and reduce ecological volatility. We identify key knowledge gaps and experimental priorities (speciation-aware measurements, signal-centric readouts) necessary to determine when, where, and how B-mediated molecular architecture may counteract DYS and support healthspan.}, }
@article {pmid42195316, year = {2026}, author = {Grigore, I and Hînganu, D and Hînganu, MV and Grigore, AG and Voinescu, DC and Matei, MN and Guțu, C and Daniel, ITF and Amariței, O and Ciobotaru, OR}, title = {Oral Health and Gut-Targeted Microbial Marker Changes Associated with Prolonged Hospitalization in Cardiac Patients: An Integrative Risk Analysis.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {5}, pages = {}, doi = {10.3390/life16050758}, pmid = {42195316}, issn = {2075-1729}, abstract = {Prolonged hospitalization in cardiac patients is associated with increased morbidity and healthcare resource utilization, yet early biological factors linked to extended length of stay remain insufficiently defined. This study aimed to explore an integrative framework combining oral health parameters and targeted gut microbial markers to identify factors associated with prolonged hospitalization in cardiac patients. A comparative observational design was applied, including patients with short-term hospitalization (1-4 days) and prolonged hospitalization (≥25 days). Oral health status was evaluated using a standardized dental protocol at admission and longitudinally in patients with prolonged hospitalization. Targeted qRT-PCR-based quantification of selected gut bacterial markers was performed at admission and reassessed after one and two weeks. Temporal changes were calculated relative to baseline, and multivariate logistic regression models adjusted for age, sex, and major cardiac diagnoses were used to explore associations with prolonged hospitalization. Short-term hospitalized patients (n = 27) exhibited minimal oral health variation (+2%) and stable marker profiles. In contrast, patients with prolonged hospitalization (n = 30 for oral health; n = 18 for microbial markers) showed progressive changes over time. Oral health impairment increased by 3% after one week and 16% after two weeks, while targeted microbial marker variation showed modest directional changes. Integrative models combining oral health parameters and targeted microbial markers suggested potential complementary information alongside clinical variables, within the limits of an exploratory framework and limited sample size. These findings support the relevance of multidomain clinical and biological monitoring in the early identification of patients at risk for prolonged hospitalization.}, }
@article {pmid42195326, year = {2026}, author = {Badale, A and Zdrîncă, M and Maghiar, L and Magyar, I and Zaha, DC}, title = {Multi-Kingdom Synergy of Perilla frutescens-Derived Effector Vesicles and Postbiotics: A Triple-Action Strategy for Atopic Dermatitis.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {5}, pages = {}, doi = {10.3390/life16050769}, pmid = {42195326}, issn = {2075-1729}, support = {//University of Oradea/ ; }, abstract = {BACKGROUND: Atopic dermatitis (AD) is a chronic inflammatory disease characterized by profound microbial dysbiosis, Staphylococcus aureus (S. aureus) colonization, and a compromised epidermal barrier. Current therapies often face safety and compliance limitations, necessitating proactive, steroid-sparing ecological strategies focused on barrier restoration.<br><br>METHODS: This pharmacological review evaluates a synergistic framework combining Lactobacillus and Saccharomyces postbiotic lysates with Perilla frutescens-derived effector vesicles. The analysis focuses on their molecular impact on skin homeostasis and structural protein synthesis.<br><br>RESULTS: In vitro evaluations indicate that Lactobacillus enhances innate immunity, while Saccharomyces-derived metabolites support the microbial ecosystem. Preliminary data demonstrate a significant impact on structural integrity, showing an 87.9% increase in elastin secretion and a 61.4% increase in Type I collagen synthesis. Furthermore, Perilla frutescens-derived vesicles modulate the JAK-STAT pathway, demonstrating a potential reduction of Interleukin-6 (IL-6) by 40% and a downregulation of CYP1A1 expression by up to 49% in cell models, thereby suggesting a capacity to mitigate oxidative stress and pruritus.<br><br>CONCLUSIONS: By integrating these components into a "Triple-Action" framework, focusing on immunomodulation, structural restoration, and precision signaling, this review provides a comprehensive roadmap for promising dermo-cosmetic interventions in atopic skin management.}, }
@article {pmid42195378, year = {2026}, author = {Rab, A and Magdás, A and Frigy, A}, title = {Microbiome-Associated Drug Response Variability in Heart Failure Treatment.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {5}, pages = {}, doi = {10.3390/life16050823}, pmid = {42195378}, issn = {2075-1729}, abstract = {Gut microbiome composition influences cardiovascular drug efficacy and safety, yet its integration into heart failure (HF) management remains underexplored. Alterations in intestinal microbial communities have been linked to atherosclerosis, coronary artery disease, heart failure, and hypertension through multiple mechanisms. Dysbiosis disrupts the balance between commensal and pathogenic bacterial species, impairing gut barrier function and activating inflammatory pathways. The altered microbial ecosystem modulates the production of key metabolites-such as trimethylamine-N-oxide (TMAO), short-chain fatty acids (SCFAs), and secondary bile acids (BAs)-that directly impact cardiovascular function. This narrative review synthesizes current evidence on bidirectional interaction between heart failure pharmacotherapy and gut microbiome composition. Commonly used drugs in heart failure management show microbiome-dependent pharmacokinetics. Digoxin undergoes bacterial inactivation by Eggerthella lenta, while angiotensin converting enzyme inhibitors and beta-blockers demonstrate enhanced efficacy with specific Firmicutes populations. Conversely, certain probiotic strains attenuate drug-induced gut barrier injury and restore gut homeostasis. Sodium-glucose cotransporter 2 inhibitors (SGLT2i), mineralocorticoid receptor antagonists, and angiotensin receptor-neprilysin inhibitors exhibit beneficial microbiome-modulating effects beyond their primary cardiovascular actions. These findings underscore the potential for microbiome-informed precision medicine in heart failure. However, significant methodological challenges must be addressed, including lack of standardization in microbiome profiling, small sample sizes, and limited longitudinal data. Future research should focus on identifying specific microbial signatures that predict drug response, developing targeted probiotic interventions, and conducting prospective clinical trials to validate pharmacomicrobiomics approaches in heart failure management.}, }
@article {pmid42195884, year = {2026}, author = {Olson, D and Muniandy, A and Zhu, L and Zarei, M and Schwarz, M and Bean, S and Smith, B}, title = {Sorghum Starch and Protein Digestibility: Mechanisms, Modifications, and Health Implications.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {10}, pages = {}, doi = {10.3390/foods15101681}, pmid = {42195884}, issn = {2304-8158}, abstract = {This review examines sorghum digestibility from molecular structure to clinical implications, focusing on compositional factors, processing methods, and health outcomes. We evaluate how sorghum's unique protein-starch interactions influence digestibility and explore emerging technologies that can modulate these properties for targeted nutritional benefits. Cooked sorghum generally has lower digestibility than raw sorghum and other cereals due to heat-induced protein-starch cross-linking and the formation of disulfide bonds by sorghum proteins (kafirins), which restrict enzymatic access. Enzyme inhibitors in sorghum further reduce starch hydrolysis. This reduced digestibility may negatively impact malnourished individuals and those relying on sorghum as a dietary staple. However, it can be advantageous to individuals with diabetes by lowering postprandial blood glucose levels. Sorghum consumption may also beneficially influence the gut microbiome. Certain processing methods have been shown to significantly enhance digestibility while preserving beneficial bioactive compounds. Improving digestibility through these strategies may enhance sorghum's value for vulnerable populations while maintaining its metabolic advantages. Balancing increased nutrient bioavailability with preservation of beneficial functional properties is critical for optimizing sorghum as a health-promoting grain across diverse populations.}, }
@article {pmid42195997, year = {2026}, author = {Yaermaimaiti, B and Huang, S and Ayideng, H and Nazhaer, N and Yasen, N and Jing, H and Tayier, B and Mulati, A}, title = {Elaeagnus angustifolia L. Polysaccharide Alleviates High-Fat High-Fructose Diet (HFFD)-Induced Cognitive Impairment by Modulating the Gut-Liver-Brain Axis.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {10}, pages = {}, doi = {10.3390/foods15101794}, pmid = {42195997}, issn = {2304-8158}, support = {2225ZZQRCXM//Department of Human Resources and Social Security of Xinjiang Uygur Autonomous Region/ ; }, abstract = {Cognitive impairment induced by a high-fat high-fructose diet (HFFD) is associated with gut-liver-brain axis dysfunction, yet whether polysaccharide intervention can modulate this axis to achieve cognitive rescue remains unexplored. This study investigated whether Elaeagnus angustifolia polysaccharide (EAP) is associated with protection against HFFD-induced cognitive decline by modulating this axis. Male C57BL/6J mice (n = 15/group) received Control, HFFD, HFFD + LEAP (300 mg/kg/day EAP), or HFFD + HEAP (800 mg/kg/day EAP) for 14 weeks. HEAP improved spatial memory, reducing escape latency by 31.2% on day 5 (p < 0.01). Multi-omics and histopathological analyses revealed that EAP was dose-dependently associated with restructuring of the gut microbiota, expanding Muribaculaceae and other SCFA-producers while suppressing pathobionts, thereby reversing the Firmicutes/Bacteroidota ratio from 1.71 to 0.94 (p < 0.01). Elevated cecal, hepatic, and cerebral acetate, propionate, and butyrate (p < 0.01) were associated with improved intestinal barrier integrity, attenuated systemic LPS translocation, and reduced hepatic inflammation and changes consistent with normalization toward control levels of PPARα/γ signaling. These peripheral improvements were accompanied by changes in the hippocampus, where EAP suppressed IBA-1 microglial activation (from 4.5-fold to 2.1-fold of control, p < 0.01) and IL-6/TNF-α signaling, changes in neurotransmitter balance (Glu, 5-HT, DA), and preserved postsynaptic density ultrastructure and PSD-95 expression (p < 0.01). These findings support a role for EAP in modulating the gut-liver-brain axis and may help prevent diet-related cognitive impairment, supporting its development as a microbiome-targeted functional food ingredient.}, }
@article {pmid42196140, year = {2026}, author = {Dobretsov, S and Rittschof, D and Peng, L and Yang, JL}, title = {Functional Microbiomes at the Interface: Mediators in Marine Biofouling and Larval Settlement.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, doi = {10.3390/ijms27104155}, pmid = {42196140}, issn = {1422-0067}, support = {CL/SQU-SHOU/AGR/24/01//Sultan Qaboos University/ ; }, mesh = {Animals ; *Biofouling ; *Microbiota ; Larva/microbiology ; Biofilms/growth &amp; development ; Quorum Sensing ; Ecosystem ; *Aquatic Organisms/microbiology ; }, abstract = {Natural and artificial marine surfaces are rapidly colonized by microscopic communities, including propagules of some macrofoulers, in a process called biofouling. These microbiomes play an important role in modulating the evolving microbial community, as well as the attachment and settlement of other invertebrate larvae. Microbiomes act as biochemical and biophysical interfaces in marine communities. This review explores the gene-level processes that underlie microbial functions relevant to biofouling and larval settlement, such as quorum sensing, extracellular polymeric substance (EPS), and innate immune system components, as well as biosynthetic and degradative processes that generate signaling molecules. We critically evaluate current knowledge on how microbial metabolites promote or inhibit larval recruitment in corals, barnacles, polychaetes, and bivalves, and how omics-based approaches are uncovering the functional potential of biofilm communities. We evaluate how these interactions influence ecosystem services, such as habitat structuring, reef resilience, and coastal infrastructure maintenance.}, }
@article {pmid42196161, year = {2026}, author = {Awada, A and Charbel, N and Faraj, S and Hassan, M and Awada, D and Issa, A and Nasr, W and El Meski, S and Hatahet, Z and Tarhini, A and Rizkallah, J and Kreidieh, F}, title = {Host Determinants of Immune Checkpoint Inhibitor Efficacy: Immune, Genetic, Metabolic, and Lifestyle Factors.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, doi = {10.3390/ijms27104178}, pmid = {42196161}, issn = {1422-0067}, mesh = {Humans ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Life Style ; *Neoplasms/drug therapy/immunology/genetics/metabolism ; Gastrointestinal Microbiome ; Animals ; Immunotherapy/methods ; }, abstract = {Immune checkpoint inhibitors (ICIs) have revolutionized cancer treatment by enhancing antitumor immune responses; however, clinical outcomes remain highly variable across patients and tumor types. While tumor-intrinsic factors such as PD-L1 expression and tumor mutational burden provide some predictive value, they do not fully explain response heterogeneity. Increasing evidence highlights the critical role of host-related determinants in modulating ICI efficacy. This review provides a comprehensive overview of key host factors, including baseline immune competence, T-cell repertoire diversity, cytokine profiles, and peripheral biomarkers. It further examines the impact of germline genetics, HLA genotype, and epigenetic regulation on immune responses. The role of the gut microbiome and its metabolites is explored, alongside the impact of metabolic status, obesity, nutrition, and lifestyle behaviors. Additionally, the effects of co-medications and comorbidities are discussed. Integrating these host-related factors may improve patient stratification and support the development of personalized immunotherapy strategies.}, }
@article {pmid42196192, year = {2026}, author = {Pavlov, V and Snezhkina, A and Pudova, E and Emelyanova, M and Fedoseeva, E and Filatova, A and Kalinin, D and Kudryavtseva, A and Fedorova, M}, title = {Intratumoral Microbiome of Metastatic Pancreatic Ductal Adenocarcinoma.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, doi = {10.3390/ijms27104210}, pmid = {42196192}, issn = {1422-0067}, support = {24-25-00460//Russian Science Foundation/ ; }, mesh = {*Carcinoma, Pancreatic Ductal/microbiology/pathology/genetics ; Humans ; *Pancreatic Neoplasms/microbiology/pathology/genetics ; *Microbiota ; Neoplasm Metastasis ; Bacteria/genetics/classification ; }, abstract = {Pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal oncological diseases, with a 5-year survival rate of approximately 13%-among the lowest in oncology. Poor survival is driven by aggressive tumor progression and metastasis, which may be influenced by the tumor microbiome. This study aimed to evaluate the role of microbiome in PDAC progression and metastasis. First, we assessed the microbial composition of control samples (surface swabs, empty paraffin, extraction controls, and sequencing controls) and removed contaminant taxa. Overall bacterial biomass was extremely low, with no significant differences in alpha or beta-diversity between tumor and normal tissue. Kocuria rosea was significantly enriched in tumors compared to normal tissue, and this difference persisted after decontamination. Metastatic tumors showed altered abundance of K. rosea and Herbaspirillum huttiense, whereas non-metastatic tumors differed in Lysobacter bugurensis, Caulobacter ginsengisoli, and H. huttiense relative to normal tissue. No global compositional differences were observed between KRAS-mutant and wild-type tumors; however, KRAS-mutant tumors exhibited differential enrichment of K. rosea and L. bugurensis relative to adjacent normal tissue. The PDAC microbiome harbors very low bacterial biomass and does not robustly distinguish tumor from normal tissue at the community level. Nonetheless, K. rosea emerges as a candidate taxon differentially enriched in PDAC, with potential stage- and KRAS-associated patterns. These findings highlight the need for orthogonal validation (qPCR, FISH, culture) and larger prospective cohorts to differentiate true biological associations from residual contamination or stochastic noise in low-biomass settings.}, }
@article {pmid42196214, year = {2026}, author = {Kiouri, DP and Batsis, GC and Messaritakis, I and Souglakos, J and Chasapis, CT}, title = {Mapping of Phenotype Specific Host-Microbiome Protein-Protein Interaction Networks in Colorectal Cancer Using Deep Learning.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, doi = {10.3390/ijms27104232}, pmid = {42196214}, issn = {1422-0067}, mesh = {Humans ; *Colorectal Neoplasms/microbiology/metabolism/genetics ; *Protein Interaction Maps ; *Deep Learning ; Phenotype ; *Gastrointestinal Microbiome ; *Protein Interaction Mapping/methods ; *Host Microbial Interactions ; }, abstract = {Colorectal cancer (CRC) pathogenesis is driven by complex protein-protein interactions (PPIs) between the host and the gut microbiome, yet these molecular dialogs remain largely unmapped. This study utilizes a Deep Learning framework, enhanced by protein structure embeddings, to predict approximately 8.9 billion interspecies PPIs from clinical metagenomic data. The model achieved high accuracy with an AUROC of 0.9960, identifying a high-confidence interactome representing roughly 16% of evaluated protein pairs. Phenotype-specific analysis revealed that while microbial hubs shift-transitioning from metabolic enzymes in healthy states to transport and regulatory proteins in CRC-the primary human targets remain remarkably consistent across both cohorts. These core human interactors are predominantly metalloproteins and regulators of ubiquitination, apoptosis, and zinc transport, suggesting these pathways are primary focal points for microbial manipulation regardless of disease state. Furthermore, co-occurring bacterial genera exhibit over 99% overlap in host target profiles, indicating significant functional redundancy in microbial engagement with the host. These findings suggest that CRC probably arises from network-level perturbations of stable host signaling hubs, offering a blueprint for identifying novel therapeutic targets and biomarkers.}, }
@article {pmid42196259, year = {2026}, author = {Thavasi, V and Choradia, N and Takebe, N and Naito, N and Yeyeodu, S and Sadler, PW and Hougen, D and Velmurugan, S and Metcalf, JP and Tyungu, DL and Venkatesan, T}, title = {Real-Time Breath Diagnostics: Linking Molecular Pathways, Measurement Technologies, and Clinical Translation.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, doi = {10.3390/ijms27104276}, pmid = {42196259}, issn = {1422-0067}, support = {NA//University of Oklahoma Health Sciences Center/ ; }, mesh = {Humans ; Breath Tests/methods/instrumentation ; *Volatile Organic Compounds/analysis ; Translational Research, Biomedical ; Biomarkers/analysis ; Mass Spectrometry/methods ; }, abstract = {Diagnostic latency limits time-sensitive care and early detection, and exhaled breath provides a rapid, repeatable window into metabolic and inflammatory chemistry. We review real-time breath sampling and analytical technologies and evaluate their readiness for clinical adoption, with emphasis on molecular pathways reflected in the breath volatilome and in exhaled breath condensate. Real-time mass spectrometry enables kinetic VOC profiling and targeted quantification, while humidity-aware sensors and wearable condensate platforms extend monitoring beyond the laboratory. Pathway-anchored interpretation links breath readouts to ketone handling, isoprenoid metabolism, nitric oxide signaling, lipid peroxidation, uremic nitrogen handling, and microbiome-host co-metabolism, but performance remains vulnerable to confounding, drift, and non-representative comparators. Translation requires standardized breath fraction control, traceable features, robust quality systems, and governed device algorithm stacks so that breath outputs inform decisions and outcomes.}, }
@article {pmid42196275, year = {2026}, author = {Roncareggi, S and Fioredda, F and Girardi, K and Serrao, S and Capitoli, G and Fumagalli, R and Nobile, M and Fazio, G and Guerra, F and Valsecchi, MG and Rebellato, S and Casillo, M and Fantuz, MR and Savarese, G and Paglia, G and Gambineri, E and Balduzzi, AC and Biondi, A and Saettini, F and , }, title = {A Gut Feeling: An Exploratory Multi-Omics Study of Gut Microbiome Dysbiosis and Metabolome and Lipidome Alterations in GATA2 Deficiency.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, doi = {10.3390/ijms27104294}, pmid = {42196275}, issn = {1422-0067}, mesh = {Humans ; Multiomics ; *Metabolome ; *Dysbiosis/metabolism/microbiology ; *GATA2 Deficiency/metabolism/microbiology/genetics ; *Gastrointestinal Microbiome ; Lipidomics ; *GATA2 Transcription Factor/deficiency ; Female ; Male ; Lipid Metabolism ; }, abstract = {GATA2 deficiency predisposes patients to recurrent infections, myelodysplastic neoplasms (MDSs), and malignancies through disrupted hematopoiesis and immune dysfunction. The role of the gut microbiome (GM) in this condition remains poorly defined. In this multicenter study, we analyzed GM composition, metabolomic, and lipidomic profiles in 12 Italian GATA2-deficient patients, comparing non-HSCT and post-HSCT GATA2-deficient individuals with healthy controls. Non-HSCT patients showed a relative enrichment of Proteobacteria-associated Gram-negative taxa, accompanied by increased levels of metabolites and lipids previously associated with inflammatory processes. Post-HSCT patients displayed profiles with a trend toward partial normalization of GM composition and metabolic features. Overall, our findings suggest the presence of microbiome and metabolic patterns in GATA2-deficient patients, which may reflect underlying immune and hematopoietic alterations, although these observations should be interpreted as descriptive and require validation in larger cohorts.}, }
@article {pmid42196276, year = {2026}, author = {Cho, A and Wu, C and Theodoropoulos, G and Nagarajan, M and Murphy, AM and Heller, KF and Savaraj, N and Lampidis, TJ and Wangpaichitr, M}, title = {The Tryptophan Paradox: From Microbiome-Mediated Homeostasis to Tumor-Driven Immune Escape.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, doi = {10.3390/ijms27104296}, pmid = {42196276}, issn = {1422-0067}, support = {5I01BX004371//United States Department of Veterans Affairs/ ; P30CA240139//University of Miami/Tumor Biology/ ; }, mesh = {*Tryptophan/metabolism ; Humans ; *Homeostasis ; Animals ; *Tumor Escape/immunology ; *Neoplasms/immunology/metabolism/pathology/microbiology ; Receptors, Aryl Hydrocarbon/metabolism ; Indoleamine-Pyrrole 2,3,-Dioxygenase/metabolism ; *Microbiota ; Interleukin-22 ; Tryptophan Oxygenase/metabolism ; Kynurenine/metabolism ; Signal Transduction ; L-Amino Acid Oxidase ; }, abstract = {Tryptophan (Trp) metabolism sits at the intersection of nutrition, the microbiome, mucosal immunity, and tumor adaptation. The broad observation that microbial indoles can support barrier function, whereas tumors exploit kynurenine-pathway metabolism to suppress immunity, is already established in publications. The specific contribution of this review is to organize that literature into a context- and network-based translational framework. Rather than treating indoleamine 2,3-dioxygenase 1 (IDO1) as a single bottleneck, we frame tumor Trp metabolism as a compensatory system linking IDO1, tryptophan 2,3-dioxygenase (TDO2), interleukin-4-induced gene 1 (IL4I1), amino-acid transport, amino-acid stress sensing, and downstream aryl hydrocarbon receptor (AHR) signaling. In healthy tissue, especially the gut, dietary Trp and microbiota-derived indoles can promote epithelial integrity, interleukin-22 (IL-22)-associated programs, and mucosal restraint. In tumors, the same substrate pool is redirected toward Kynurenine, kynurenic acid, indole-3-pyruvate, and related catabolites that impair cytotoxic lymphocytes, expand regulatory T-cell (Treg) and suppressive myeloid compartments, and reinforce invasion and treatment resistance. We also argue that the potential metabolite biomarker interpretation should be context-dependent. Finally, we propose a clinical-context-specific framework for intervention. Dietary and microbiome-based strategies may be most effective in prevention, premalignant states, or supportive care, whereas established cancers are more likely to require biomarker-guided targeting of tumor-associated catabolic pathways and convergent signaling mechanisms. The "paradox" is therefore not that Trp changes chemistry across settings, but that the same nutrient is routed through different cellular contexts, enzymes, ligands, and cell states.}, }
@article {pmid42196281, year = {2026}, author = {Seliger, B and Mantke, R and Naß, N and Dammermann, W and Ocvirk, S and Kah, J and Kalinski, T and Massa, C}, title = {Inflammation and Colorectal Cancer Pathogenesis: Molecular, Immunological, and Environmental Features for Therapy Response and Resistances.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, doi = {10.3390/ijms27104299}, pmid = {42196281}, issn = {1422-0067}, support = {SE 581/34-1 and SE 581/39-1//Deutsche Forschungsgemeinschaft/ ; 86004036 and 86000697//Investitionsbank des Landes Brandenburg/ ; ZS/2024/01/83830//Investitionsbank Sachsen-Anhalt/ ; }, mesh = {Humans ; *Colorectal Neoplasms/therapy/etiology/immunology/pathology/genetics ; Tumor Microenvironment/immunology ; *Inflammation/complications/immunology/pathology ; *Drug Resistance, Neoplasm ; Animals ; Risk Factors ; Gastrointestinal Microbiome ; }, abstract = {Colorectal cancer (CRC) is a significant global health concern, ranking as the third most frequently diagnosed cancer and the second leading cause of cancer-related deaths. Advances in screening, such as the implementation of liquid biopsies (LB), have improved early detection, thus enhancing survival rates. This review summarizes the multifaceted nature of CRC, focusing on its genetic background, the complex tumor microenvironment, and the influence of gut microbiota, nutrition, and metabolic alterations. The development of CRC is influenced by various risk factors, including age, genetics, chronic diseases, and lifestyle choices. The genetic heterogeneity of CRC defines distinct molecular subtypes, characterized by different treatment responses and patient prognoses. Chronic inflammation and dysbiosis in the gut microbiota further contribute to CRC pathogenesis. In addition, nutritional factors play a crucial role in CRC, affecting carcinogenesis and treatment efficacy through direct interaction with the immune system and microbiome. Current therapeutic strategies include surgical interventions, chemo- and radiotherapy, targeted therapies, immunotherapy as well as dietary interventions, and microbiome modulation, highlighting the challenges posed by tumor heterogeneity and treatment resistance. In sum, a comprehensive understanding of CRC's intrinsic and extrinsic drivers, including genetic, metabolic, and dietary influences, is essential for developing personalized treatment strategies and improving patient outcomes.}, }
@article {pmid42196357, year = {2026}, author = {Hsu, SH and Lee, TY and Huang, CW and Bhattarai, BP and Pan, YI and Liao, YC and Chang, HT and Huang, HH and Lin, JS and Zhao, X and Lee, JW}, title = {Dietary Supplementation of a Multi-Strain Probiotic Increases Muscle Mass in Pigs.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, doi = {10.3390/ijms27104381}, pmid = {42196357}, issn = {1422-0067}, support = {1135714-01//Ministry of Education/ ; B112454//SYNBIO TECH Inc/ ; }, mesh = {Animals ; *Probiotics/pharmacology/administration &amp; dosage ; *Dietary Supplements ; Swine ; *Muscle, Skeletal/drug effects/growth &amp; development/metabolism ; Animal Feed ; Gastrointestinal Microbiome/drug effects ; Signal Transduction ; }, abstract = {Pork production is closely linked to skeletal muscle growth and anabolic processes. This study investigated the effects of dietary supplementation with a multi-strain probiotic (Lactiplantibacillus plantarum, Streptococcus thermophilus, and Bacillus subtilis) on the growth performance, carcass traits, gut microbiota, and potential signaling pathways in growing pigs. A total of 144 weaning piglets (28 days old) were randomly allocated to two groups and fed diets with or without probiotics (0.1%) for 18 weeks. Pigs fed with probiotics showed significantly improved feed efficiency (p < 0.05) and greater muscle mass in the loin eye, arm shoulder, and blade shoulder regions. Microbiome analysis revealed significant enrichment of short-chain fatty acid (SCFA)-producing taxa, including Acidaminococcus, Allisonella, Dialister, and Megasphaera, alongside an increased cecal butyrate level in pigs fed probiotics. Integrated fecal microbiome and serum metabolomics analysis demonstrated that the metabolite profile was substantially altered by the supplementation of probiotics. Additionally, serum insulin levels, expression of the bile acid receptor tgr5, and upstream genes in the PI3K/Akt/mTOR pathway (igf1r, insr, and pi3k) were significantly upregulated (p < 0.05). Collectively, these results suggest that a multi-strain probiotic supplementation may be a promising strategy for improving muscle deposition and feed efficiency in commercial pig production.}, }
@article {pmid42196411, year = {2026}, author = {Kim, KH and Yoo, BC}, title = {Circulating Dipeptides in Cancer: Degradation Fragments or Functional Metabolites?.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, doi = {10.3390/ijms27104438}, pmid = {42196411}, issn = {1422-0067}, support = {RS-2025-02243055//Ministry of Health and Welfare/ ; C2024-0023//Kookmin University/ ; }, mesh = {Humans ; *Dipeptides/blood/metabolism ; *Neoplasms/metabolism/blood/pathology ; Animals ; Proteolysis ; Metabolomics/methods ; }, abstract = {Advances in mass spectrometry-based metabolomics have enabled the detection of numerous small molecules in biological systems, revealing complex metabolic alterations associated with cancer. Among these, dipeptides are consistently detected in plasma, serum, and tumor tissue metabolomic profiles, yet their biological significance is not fully understood. In most studies, circulating dipeptides are interpreted as nonspecific byproducts of protein degradation generated during increased proteolysis. However, accumulating evidence suggests that at least some endogenous dipeptides may have biological activities, including antioxidant effects, metabolic modulation, and potential signaling functions. In this review, we examine the possible origins, transport mechanisms, and biological implications of circulating dipeptides in cancer metabolomics. We discuss multiple sources of dipeptide generation, including intracellular proteolysis, autophagy, extracellular matrix remodeling, tumor cell death, host tissue catabolism, and microbiome metabolism. We also summarize current knowledge regarding peptide transport systems and intracellular dipeptide metabolism that may regulate the fate of these molecules within mammalian systems. In addition, evidence supporting the biological activities of certain endogenous dipeptides is reviewed to evaluate the possibility that some circulating dipeptides may function as bioactive metabolites. Finally, we propose conceptual frameworks for interpreting circulating dipeptides in cancer, including their potential roles as indicators of protein turnover, intermediates in amino acid recycling, stress-buffering molecules, metabolic signals, or components of tumor-host metabolic communication. A better understanding of circulating dipeptides may provide new insights into cancer metabolism and reveal previously overlooked metabolite classes with potential biomarker or functional significance.}, }
@article {pmid42196446, year = {2026}, author = {Chobanyan-Jürgens, K and Muhareb, A and Niesert, M and Scherkl, C and Meid, AD and Cannet, C and Pituk, D and Hoffmann, GF and Stingl, JC and Ziegler, A and Blank, A}, title = {Interpretation of Pharmacometabolomics Results: Fingerprint of Drug Exposure or Confounder Effects? Insights from a Urinary Metabolomics Study with Voriconazole in Healthy Participants.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, doi = {10.3390/ijms27104468}, pmid = {42196446}, issn = {1422-0067}, support = {1DH2011115//Dietmar Hopp Stiftung/ ; 1DH1911470//Dietmar Hopp Stiftung/ ; }, mesh = {Humans ; *Voriconazole/urine/administration &amp; dosage/pharmacokinetics ; *Metabolomics/methods ; Female ; Adult ; Male ; Cytochrome P-450 CYP3A/metabolism ; *Metabolome/drug effects ; Young Adult ; *Antifungal Agents/urine ; Healthy Volunteers ; Biomarkers/urine ; Cytochrome P-450 CYP2C19/metabolism ; }, abstract = {Interpretation of pharmacometabolomics results, aiming particularly at biomarker (sets) discovery for drug exposure, remains a major challenge. The metabotyping of drug exposure depends on resolution of specific metabolomics techniques and comprises individual metabolic phenotypes ("metabotypes"), disease-, drug- and microbiome-specific patterns, as well as conditional metabolic states (e. g. fasting). In this clinical trial with 16 healthy participants, an exploratory objective was to evaluate the untargeted urinary metabolomics of voriconazole, administered in four single doses, using proton nuclear magnetic resonance ([1]H-NMR) spectroscopy. Voriconazole is a second-generation triazole and a potent inhibitor of drug-metabolizing enzymes such as cytochrome P450 (CYP) isozymes CYP3A4 and CYP2C19. Therefore, identification of metabolites reflecting acute CYP3A4 inhibition was of particular interest. On two treatment days without and with voriconazole (with background microdosed midazolam and omeprazole administration for CYP3A4 and CYP2C19 phenotyping, respectively), spot urine was collected after overnight fasting (predose) and 4 h later (postdose fasting). In the postdose versus predose fingerprints, most changes at the annotated metabolite level were attributable to fasting metabolomics or potential confounders. [1]H-NMR spectroscopy identified neither a short-term voriconazole-specific signature nor patterns or metabolites potentially reflecting acute CYP3A4 inhibition. Our study emphasizes crucial significance of strict standardization of fasting time and minimization of confounder influences by clinical trial design as well as selection of adequate baselines and high-resolution analytical techniques in pharmacometabolomics research, especially for biomarker discovery.}, }
@article {pmid42196459, year = {2026}, author = {Pan, M and O'Flaherty, C}, title = {Gut Microbial Dysbiosis and Male Reproductive Health: Current Insights and Future Directions.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, doi = {10.3390/ijms27104482}, pmid = {42196459}, issn = {1422-0067}, support = {MI411644//McGill University/ ; MI411644//Pathy Family Foundation/ ; }, mesh = {Humans ; *Dysbiosis/microbiology ; Male ; Animals ; *Infertility, Male/microbiology/etiology ; *Gastrointestinal Microbiome ; *Reproductive Health ; Spermatogenesis ; Testis/metabolism ; }, abstract = {Male infertility contributes to approximately half of all infertility cases, with a substantial proportion remaining idiopathic. Emerging evidence implicates the gut microbiome as a regulator of male reproductive health through a proposed gut-testis axis. Few studies have shown that gut microbial dysbiosis may impair sperm quality via multiple mechanisms, including disruption of endocrine function (e.g., reduced testosterone production), alterations in microbial-derived metabolites, and impaired testicular energy metabolism. Increased intestinal permeability and systemic inflammation may further compromise the blood-testis barrier, while translocation of bacterial endotoxins may also contribute to testicular damage. Collectively, these processes can disrupt spermatogenesis and negatively affect sperm parameters, such as concentration, motility, and morphology. Interventions that restore microbial balance, including dietary modulation, have shown potential in reversing these effects and improving reproductive outcomes. This review summarizes and evaluates current literature linking gut microbial dysbiosis to male reproductive dysfunction. Key methodological limitations and knowledge gaps are highlighted, providing a foundation for advancing the development of gut microbiome-based interventions to improve male reproductive health.}, }
@article {pmid42196499, year = {2026}, author = {Verhaar, BJH}, title = {Gut Microbiota as a Mediator of Dietary Salt Effects on Blood Pressure.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, doi = {10.3390/ijms27104515}, pmid = {42196499}, issn = {1422-0067}, support = {09150162410064/ZONMW_/ZonMw/Netherlands ; }, mesh = {Humans ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Blood Pressure/drug effects ; *Hypertension/microbiology/etiology/metabolism ; *Sodium Chloride, Dietary/adverse effects/metabolism ; Intestinal Barrier Function ; }, abstract = {Dietary sodium excess is a primary driver of hypertension, yet individuals differ markedly in their blood pressure response to salt. This variation, termed salt sensitivity, cannot currently be predicted from clinical variables alone. This review examines three aspects of salt-gut physiology: intestinal sodium handling, salt-induced changes in gut microbiome composition, and microbiota-mediated effects on immune function, metabolite production, and gut barrier integrity. The intestine absorbs dietary sodium through regulated transporters whose activity adapts to luminal and hormonal conditions, making the gut a key regulator of sodium balance. High salt intake consistently alters gut microbiota composition in animal models, most reproducibly depleting Lactobacillus species, with variable effects on overall diversity. These compositional shifts, supported by human data, activate intestinal Th17 cells and deplete short-chain fatty acid producers, contributing to systemic inflammation and elevated blood pressure. The presence of inducible osmoadaptation responses varies substantially across microbes, though activation under dietary sodium conditions has not been demonstrated in vivo. If salt-driven microbial changes contribute causally to hypertension, microbiota-targeted interventions could complement sodium restriction in patients for whom long-term dietary adherence is poor. Controlled sodium intervention studies in animals and humans are needed to establish whether such a causal contribution exists.}, }
@article {pmid42196552, year = {2026}, author = {Jaworska, K}, title = {Special Issue "New Insights into the Effects of Microbiome-Derived Metabolites on Health and Disease".}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, doi = {10.3390/ijms27104575}, pmid = {42196552}, issn = {1422-0067}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Microbiota ; Animals ; }, abstract = {The human gastrointestinal tract is increasingly recognized not merely as a site of digestion, but as a fully integrated metabolic organ [...].}, }
@article {pmid42196562, year = {2026}, author = {Panagodimou, E and Terzopoulou, I and Triantafyllidou, O and Markantes, G and Georgopoulos, N and Vlahos, N and Adonakis, G and Kaponis, A}, title = {The Role of Immunologic Factors in Endometrial Receptivity: An Embryo-Endometrium Dialogue.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, doi = {10.3390/ijms27104588}, pmid = {42196562}, issn = {1422-0067}, mesh = {Female ; Humans ; *Endometrium/immunology/metabolism ; *Embryo Implantation/immunology ; Animals ; Pregnancy ; Signal Transduction ; *Immunologic Factors/metabolism ; Killer Cells, Natural/immunology ; Cytokines/metabolism ; T-Lymphocytes, Regulatory/immunology ; }, abstract = {Successful embryo implantation requires dynamic, bidirectional communication between a developmentally competent blastocyst and a receptive endometrium, integrating hormonal, molecular, and immunologic signals. Increasing evidence indicates that endometrial receptivity is critically dependent on a specialized immune microenvironment that supports trophoblast invasion while maintaining maternal tolerance. This review synthesizes current knowledge on the immunologic regulation of implantation, with emphasis on uterine natural killer (uNK) cells, regulatory T cells (Tregs), macrophages, dendritic cells, and cytokine networks. We further examine intracellular signaling pathways-including JAK/STAT, PI3K/AKT, NF-κB, and MAPK-that integrate immune and decidual responses. The bidirectional embryo-endometrium dialogue is explored through embryo-derived mediators such as human chorionic gonadotropin (hCG), cytokines, growth factors, and extracellular vesicles. The endometrium is increasingly recognized as a biosensor of embryo quality, selectively supporting viable embryos. Disruption of this complex communication network is implicated in recurrent implantation failure and early pregnancy loss. Despite substantial mechanistic advances, clinical translation remains limited. Emerging strategies, including immune profiling, microbiome modulation, and extracellular vesicle-based diagnostics, hold promise for precision reproductive medicine.}, }
@article {pmid42196564, year = {2026}, author = {Gebretsadik, G and Islam, S and Szpendyk, J and Thomas, V and Furuta, S}, title = {The Role of Selected Bacteria in Breast Cancer Initiation and Development.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, doi = {10.3390/ijms27104585}, pmid = {42196564}, issn = {1422-0067}, support = {R01CA248304, R21CA288449/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Breast Neoplasms/microbiology/pathology ; *Microbiota ; Female ; *Bacteria ; Animals ; *Carcinogenesis ; Dysbiosis/microbiology ; }, abstract = {The breast tissue microbiome is increasingly recognized as a contributor to breast cancer development. Both resident and translocated bacteria can influence carcinogenesis through several mechanisms, including chronic inflammation that promotes DNA damage, bacterial toxins with direct genotoxic effects, and microbial metabolites that alter host physiology-particularly estrogen metabolism via the "estrobolome." Disruptions in microbial balance (dysbiosis) may further increase disease risk. Among the taxa most frequently linked to breast cancer are Fusobacterium nucleatum, Escherichia coli, Bacteroides fragilis, Staphylococcus spp., and Clostridium spp., each of which has been associated with distinct but sometimes overlapping roles in tumor initiation and progression. This review summarizes recent findings on these organisms and outlines the mechanisms through which they may contribute to breast carcinogenesis and metastasis. Improved understanding of host-microbe interactions in the breast could support the development of new clinical approaches, including microbial biomarkers for early detection and prognosis, as well as microbiome-targeted therapeutic strategies.}, }
@article {pmid42196569, year = {2026}, author = {De Silva, S and Xu, B}, title = {Beneficial Effects of Natural Bioactive Compounds on Eye Health: A Narrative Review.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, doi = {10.3390/ijms27104592}, pmid = {42196569}, issn = {1422-0067}, support = {UICR0400015-24B &amp; UICR0400016-24B//Beijing Normal-Hong Kong Baptist University/ ; }, mesh = {Humans ; Animals ; *Eye Diseases/drug therapy/metabolism ; Antioxidants/pharmacology/therapeutic use ; *Biological Products/pharmacology/therapeutic use ; Oxidative Stress/drug effects ; Flavonoids/pharmacology/therapeutic use ; *Eye/drug effects/metabolism ; Polyphenols/pharmacology/therapeutic use ; Macular Degeneration/drug therapy ; Fatty Acids, Omega-3/pharmacology/therapeutic use ; Carotenoids/pharmacology/therapeutic use ; }, abstract = {Ocular diseases like age-related macular degeneration (AMD), diabetic retinopathy (DR), glaucoma and cataracts are major causes of visual impairment all over the world and are closely linked to oxidative stress, inflammation and mitochondrial dysfunction. This narrative review critically summarizes the available evidence on how various natural bioactive compounds, such as carotenoids, polyphenols, flavonoids, omega-3 fatty acids and botanical extracts, can affect important molecular pathways associated with ocular degeneration. Their antioxidant, anti-inflammatory, anti-angiogenic and neuroprotective properties are given particular emphasis, especially regarding the Nrf2, NF-κB and VEGF signaling pathways. This review is different from past reviews that simply discuss the potential of bioactives in the general nutritional context; rather, it unfolds the disease-specific mechanisms and compound-specific molecular actions and gives special attention to recent advances in nano-delivery systems and precision nutrition strategies to increase the bioavailability and therapeutic targeting of these nutrients in the eyes. Moreover, it offers a framework for a comparison of evidence between preclinical and clinical studies, as well as identifying current translational gaps, including limited bioavailability and a lack of long-term clinical trials, and suggesting future directions such as genotype-guided nutrition and microbiome-informed interventions. In general, this review provides a mechanistic and translational overview of how dietary bioactive compounds relate to eye health and offers the perspective of their possible use in prevention and complementary treatment for vision-related diseases.}, }
@article {pmid42196583, year = {2026}, author = {Militaru, AM and Pietreanu, AC and Trifu, S and Popa, GL}, title = {Gut Microbiota in Schizophrenia: Taxonomic Shifts, Beta- Diversity Alterations, and Biomarker Potential: A Systematic Review.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, doi = {10.3390/ijms27104606}, pmid = {42196583}, issn = {1422-0067}, mesh = {*Schizophrenia/microbiology ; Humans ; *Gastrointestinal Microbiome ; Biomarkers/metabolism ; Biodiversity ; Dysbiosis/microbiology ; Bacteria/classification ; }, abstract = {Emerging evidence implicates the gut-brain axis in the pathophysiology of schizophrenia, yet literature regarding specific microbiome alterations remains inconsistent. This study aims to synthesize evidence on gut microbiota diversity and taxonomic composition in individuals with schizophrenia compared to healthy controls. Unlike prior meta-analyses, this study integrates quantitative alpha diversity synthesis with cross-taxonomic qualitative analysis and contextualizes findings within functional frameworks of the gut-brain axis, highlighting the methodological heterogeneity that limits biological interpretation. A systematic review and meta-analysis were conducted following PRISMA 2020 guidelines. Electronic databases (Web of Science, PubMed, MDPI) were searched for observational studies published between 2017 and 2025. Forty-eight studies met inclusion criteria for qualitative synthesis, with 14 providing sufficient data for random-effects meta-analyses of alpha diversity. Meta-analyses revealed no statistically significant differences in alpha diversity indices (Shannon, Simpson, Chao1, ACE, Observed) between patients and controls, despite high heterogeneity. Conversely, beta diversity analyses generally demonstrated significant differences in microbial community composition. Taxonomic synthesis identified recurrent but heterogeneous dysbiotic patterns characterized by the depletion of short-chain fatty acid-producing taxa (e.g., Faecalibacterium, Roseburia, Lachnospiraceae) and enrichment of pro-inflammatory taxa (e.g., Proteobacteria, Fusobacterium). Schizophrenia is associated with evidence of compositional alterations and functional shifts rather than a global loss of microbial richness. These findings highlight candidate taxa that may warrant further investigation in biomarker-focused studies and microbiome-based therapeutics. However, these findings should be interpreted cautiously due to substantial heterogeneity and limited control for key confounders such as antipsychotic medication, diet, and life-style factors.}, }
@article {pmid42196841, year = {2026}, author = {Vilkeviciute-Petraite, A and Bruzaite, A and Cebatoriene, D and Zaliuniene, D and Lukosevicius, R and Skieceviciene, J and Kupcinskas, J and Liutkeviciene, R}, title = {The Role of Kynurenine and 5-Hydroxytryptophan in Modulating Microbiota and Their Implications in Exudative Age-Related Macular Degeneration.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {16}, number = {10}, pages = {}, doi = {10.3390/diagnostics16101475}, pmid = {42196841}, issn = {2075-4418}, support = {No. S-MIP-23-96//Lietuvos Mokslo Taryba/ ; }, abstract = {Background/Objectives: This study explores the roles of kynurenine and 5-hydroxytryptophan (5-HTP) in modulating gut microbiota and their potential implications for exudative age-related macular degeneration (AMD). By examining the interplay between these metabolites and the microbiome, we aim to uncover novel pathways that may influence the pathogenesis of AMD. Understanding these associations could lead to innovative therapeutic approaches for managing this leading cause of vision loss in the elderly. To investigate the roles of kynurenine and 5-HTP, alongside the composition of the nasopharyngeal microbiota, in patients with exudative AMD. Methods: Blood metabolite profiling was performed using LC-MS-based metabolomics. Metabolites were extracted with cold methanol/water containing internal standards, filtered through a 10 kDa cutoff filter, separated on a ZIC-HILIC HPLC column, and detected using an Orbitrap mass spectrometer. Metabolites were identified using MZmine 2 software. Results: Patients with exudative AMD exhibited a profound systemic shift in tryptophan metabolism, characterized by significantly lower plasma levels of 5-HTP and higher levels of kynurenine compared to control subjects (p < 0.001 for both). Logistic regression analysis confirmed that both metabolites were independent predictors of AMD status; higher kynurenine levels were associated with increased disease probability, while higher 5-HTP levels demonstrated a protective effect. The kynurenine/5-HTP ratio emerged as a robust biomarker, achieving an area under the curve (AUC) of 0.85 with an optimal threshold of 3.43 (74.1% sensitivity, 84.4% specificity). When integrated with age and gender, the diagnostic performance of the model reached an excellent AUC of 0.92. After adjusting for demographic factors, the kynurenine/5-HTP ratio remained a potent independent risk factor, with each unit increase associated with a 6.30-fold increase in the odds of exudative AMD. Conclusions: Exudative AMD is characterized by a shift in tryptophan metabolism toward the kynurenine pathway, with decreased 5-HTP, increased kynurenine, and an elevated kynurenine/5-HTP ratio. This ratio showed a strong independent association with AMD and excellent diagnostic performance, highlighting its potential as a biomarker and its role in disease pathogenesis.}, }
@article {pmid42196929, year = {2026}, author = {Stergiadou, E and Louizakis, A and Tatsis, D and Antoniou, A and Poulopoulos, K and Poulopoulos, A}, title = {Prevalence and Etiopathogenic Profile of Oral Squamous Cell Carcinoma in Nonsmokers and Nondrinkers: Expanding Risk Determinants Beyond Tobacco Exposure.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {16}, number = {10}, pages = {}, doi = {10.3390/diagnostics16101563}, pmid = {42196929}, issn = {2075-4418}, abstract = {Oral squamous cell carcinoma (OSCC), comprising ~90% of oral malignancies, remains a major global health burden with rising incidence despite declining tobacco use. While tobacco and alcohol are classic dominant risk factors, a distinct subgroup of nonsmoking, nondrinking (NSND) patients is increasingly recognized, accounting for 15-35% of OSCC cases in many cohorts, particularly in developed countries. This emerging epidemic shows striking demographic patterns: strong female predominance (often 65-77% of cases), bimodal age distribution with peaks in young adults (<45 years) and elderly individuals (>70 years), and overrepresentation among non-Hispanic White and certain Asian populations. Unlike traditional habit-related OSCC, which favors the floor of the mouth in older males, NSND tumors predominantly arise on the lateral tongue, gingiva, and buccal mucosa. Etiopathogenesis extends far beyond conventional carcinogens and involves multifactorial mechanisms, including chronic mechanical irritation from dental factors, oral microbiome dysbiosis enriched with periodontal pathogens (e.g., Fusobacterium nucleatum and Porphyromonas gingivalis), limited roles for viruses (minimal HPV contribution, possible EBV or "hit-and-run" HSV effects), genetic susceptibilities (e.g., Fanconi anemia and CDKN2A mutations), epigenetic changes, hormonal influences contributing to female bias, metabolic conditions (diabetes and hyperlipidemia), poor oral hygiene, and chronic inflammation. NSND OSCC frequently exhibits a distinct immunological profile with higher tumor-infiltrating lymphocytes and PD-L1 expression, potentially favoring immunotherapy, though prognosis remains heterogeneous-better in some cohorts due to fewer comorbidities, yet worse in young patients with higher recurrence and second primary tumor risks. Delayed diagnosis is common due to low suspicion in "low-risk" individuals. This review underscores NSND OSCC as a unique entity requiring expanded risk assessment, heightened clinical vigilance for persistent oral lesions regardless of habit history, and targeted research into novel prevention and therapeutic strategies.}, }
@article {pmid42196944, year = {2026}, author = {Mosca, L and Pagano, C and Tafuri, MG and Di Maio, G and Rejano-Gordillo, CM and Della Marca, R and D'Angelo, S and Monda, M and Messina, G and Polito, R and Perrone, P}, title = {The Gut Microbiota-Polyphenol-NLRP3 Inflammasome Axis: A Key Regulatory Network Linking Diet to Chronic Inflammation.}, journal = {Nutrients}, volume = {18}, number = {10}, pages = {}, doi = {10.3390/nu18101483}, pmid = {42196944}, issn = {2072-6643}, mesh = {*NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; Humans ; *Polyphenols/metabolism/pharmacology ; *Inflammasomes/metabolism ; *Gastrointestinal Microbiome/physiology ; Animals ; *Inflammation/metabolism/microbiology ; Chronic Disease ; *Diet ; Signal Transduction ; }, abstract = {Background/Objectives: Chronic low-grade inflammation, underpinned by persistent activation of the NLRP3 inflammasome, is a central pathological mechanism in non-communicable diseases including cardiovascular disease, type 2 diabetes, inflammatory bowel disease, and neurodegeneration. Dietary polyphenols have been consistently associated with reduced inflammatory burden; however, the mechanisms underlying these effects remain incompletely understood. This review aims to characterize the gut microbiota-polyphenol-NLRP3 inflammasome axis as a central regulatory network through which diet modulates innate immune signaling and chronic inflammatory tone. Methods: A comprehensive narrative review of the available literature was conducted, integrating evidence from mechanistic studies in cell culture and animal models, microbiome research, metabolomics, and human epidemiological and interventional data. Results: The gut microbiota emerges as a critical biochemical intermediary that transforms dietary polyphenols into bioactive metabolites, including urolithins, phenyl-γ-valerolactones, protocatechuic acid, and short-chain fatty acids, with enhanced bioavailability and potent inflammasome-modulating properties. These compounds suppress NLRP3 activation through multiple converging mechanisms, including inhibition of NF-κB-dependent priming, mitochondrial quality control via mitophagy, Nrf2-mediated antioxidant responses, and HDAC inhibition. Evidence across cardiovascular, metabolic, neurological, and respiratory disease models supports the translational relevance of this axis. Conclusions: The microbiota-polyphenol-NLRP3 axis functions as an integrated, self-regulated network in which each component simultaneously shapes and is shaped by the others: dysbiosis primes NLRP3 and depletes protective metabolites, while inflammasome hyperactivation further destabilises microbial ecology; polyphenol biotransformation by specific taxa interrupts this feed-forward loop at multiple nodes, restoring homeostasis.}, }
@article {pmid42196960, year = {2026}, author = {Ribačuka, S and Upmale-Engela, S and Vaivode, I and Konrade, I and Rone-Kupfere, M}, title = {The Gut-Skin and Gut-Thyroid Axis in Autoimmunity: Roles of Dysbiosis, Microbial Metabolites, Immune Dysregulation, and Diet in Psoriasis and Hashimoto's Thyroiditis.}, journal = {Nutrients}, volume = {18}, number = {10}, pages = {}, doi = {10.3390/nu18101501}, pmid = {42196960}, issn = {2072-6643}, mesh = {Humans ; *Psoriasis/immunology/microbiology ; *Hashimoto Disease/immunology/microbiology ; *Dysbiosis/immunology ; *Gastrointestinal Microbiome/immunology ; *Thyroid Gland/immunology/metabolism ; *Skin/immunology/metabolism/microbiology ; *Autoimmunity ; Intestinal Barrier Function ; *Diet ; Animals ; Bile Acids and Salts/metabolism ; }, abstract = {Background/Objectives: Psoriasis and Hashimoto's thyroiditis are chronic immune-mediated disorders affecting distinct target organs but sharing overlapping pathogenic mechanisms, including gut dysbiosis, impaired intestinal barrier function, and systemic immune dysregulation. Growing evidence highlights the gut-skin and gut-thyroid axes as important interfaces linking microbial alterations to immune-mediated inflammation. This review aims to synthesize current knowledge on gut microbiota alterations in psoriasis and Hashimoto's thyroiditis, with particular emphasis on intestinal permeability, immune pathways, and microbiome-derived metabolites. Methods: A narrative review of experimental and human observational studies was conducted to evaluate evidence on gut microbiota composition, intestinal barrier integrity, immune regulation, bile acid metabolism, and dietary influences in psoriasis and Hashimoto's thyroiditis. The relevant literature examining mechanistic pathways and clinical associations was included. Results: Both conditions are associated with altered gut microbial composition, including reduced abundance of short-chain fatty acid-producing taxa, which may impair epithelial barrier integrity and promote systemic immune activation. Increased intestinal permeability and enhanced Th17-driven inflammatory responses are reported in both diseases. Recent studies suggest that dysregulated bile acid metabolism may influence intestinal permeability and immune balance along the gut-skin-thyroid axis, although direct clinical data remain limited. Dietary patterns, particularly anti-inflammatory and Mediterranean diets, are consistently associated with increased microbial diversity, improved metabolic profiles, and reduced systemic inflammation. However, most human evidence is observational. Conclusions: The gut microbiome represents a potential mechanistic link connecting diet, intestinal barrier function, immune regulation, and organ-specific autoimmunity in psoriasis and Hashimoto's thyroiditis. While microbiome-targeted interventions show biological plausibility, well-designed, mechanistically informed randomized controlled trials are required to establish causality and clinical relevance.}, }
@article {pmid42196988, year = {2026}, author = {Fernandes, V and Pezzarini, M and Márquez, Y and Marques, CS and Ballesteros, F and Carmona, A and Delgado, PMS and Fernández, J and Heitt, L and Kumar, DM and Magalhães, AC and Rosas, N and Torabi, K and Riera, M and Lannou, JP and Pereira, L}, title = {An Experiment in Personalized Shopping for Optimal Health, with Integration of Nutrigenetics and Gut Microbiome Information.}, journal = {Nutrients}, volume = {18}, number = {10}, pages = {}, doi = {10.3390/nu18101528}, pmid = {42196988}, issn = {2072-6643}, support = {101086523//DRG4Food Project Consortium HORIZON-CL6-2022-GOVERNANCE-01-10/ ; }, mesh = {Humans ; *Nutrigenomics/methods ; *Gastrointestinal Microbiome ; Female ; Male ; Adult ; Middle Aged ; *Consumer Behavior ; *Precision Medicine/methods ; Spain ; *Diet, Healthy ; Digital Health ; Diet ; }, abstract = {Background: An individual's health status is determined by the interaction of genetic, environmental, social, and lifestyle variables. Nutrition plays a fundamental role in disease prevention, a notion widespread among the informed public, which is keen on participating in initiatives for personalized recommendations informed by advanced biological data. Objectives: To evaluate whether a personalized nutrition service can produce measurable changes in nutritional behavior and biological outcomes, we established the GENIE digital platform. This platform delivers personalized online food shopping and recipe recommendation informed by integrated data from (i) biochemical blood markers, (ii) nutrigenetic profiles, (iii) gut microbiota composition, and (iv) consumer preferences. Methods: We conducted a single-arm study in a Spanish cohort that used a specific online retailer for food shopping, totaling 1177 participants. Group 1 (n = 620) had recommendations based only on the biochemical blood test; Group 2 (n = 357) included the nutrigenetic test; and Group 3 had the gut microbiome test (first batch, n = 200; second batch, n = 97). After one month of informed, tailored dietary advice, a quantitative evaluation of the experience was conducted. Results: The GENIE platform led to strong engagement (mean session time 7.07 min; +154% e-commerce use), with 71% of participants following at least part of the recommendations. This was associated with an increase in microbiome diversity in about 70% of participants, after just one month of guided recommendations. Conclusions: The GENIE platform represents a pragmatic model for translating nutrigenetic and microbiome data into actionable dietary recommendations, bridging the gap between scientific evidence and consumer behavior.}, }
@article {pmid42196995, year = {2026}, author = {Shin, D and Lee, S and So, B and Kang, C and Lee, KJ}, title = {Dietary Dried Laver (Porphyra tenera) Modulates Gut Microbiota Composition and Diversity in Older Women with and Without Metabolic Syndrome: An Exploratory Pilot Study.}, journal = {Nutrients}, volume = {18}, number = {10}, pages = {}, doi = {10.3390/nu18101535}, pmid = {42196995}, issn = {2072-6643}, support = {20220027//Ministry of Oceans and Fisheries/ ; RS-2024-00340086//National Research Foundation of Korea/ ; }, mesh = {Humans ; Female ; *Metabolic Syndrome/microbiology/diet therapy ; Pilot Projects ; *Gastrointestinal Microbiome/drug effects ; Aged ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; *Diet ; Edible Seaweeds ; Porphyra ; }, abstract = {Background: Metabolic syndrome (MetS) is a cluster of cardiometabolic abnormalities linked to increased risk of type 2 diabetes and cardiovascular disease. Emerging evidence implicates gut microbiota dysbiosis in MetS pathophysiology; however, human clinical data on seaweed-based dietary interventions remain scarce. Methods: Twenty-four older women were stratified into a MetS group (n = 13) and a control group (n = 11) per NCEP-ATP III criteria with Korean-specific waist circumference cutoffs. All participants consumed 4 g of dried laver (Porphyra tenera) per day for 12 weeks. Fecal DNA was subjected to 16S rRNA gene amplicon sequencing (V4 region; Illumina iSeq 100). Bioinformatic processing used QIIME2 and MicrobiomeAnalyst; alpha diversity was quantified by Chao1 and Fisher indices; beta diversity by Bray-Curtis, Jensen-Shannon, and UniFrac metrics; and differential abundance by LEfSe. Results: The Firmicutes/Bacteroidetes ratio declined 0.81-fold in the control group and 0.54-fold in the MetS group. Alpha diversity (Chao1 and Fisher indices) increased significantly in both groups (p < 0.001 and p < 0.05, respectively). Unweighted UniFrac distance showed significant compositional differences (R[2] = 0.141, p = 0.001). LEfSe identified four FDR-significant genera: CAG_873 in the control group and Muribaculaceae, Paraprevotella, and Tyzzerella in the MetS group. Conclusions: Twelve-week dried laver supplementation produced measurable shifts in gut microbial diversity and community composition in older women, with potentially greater responsiveness in those with MetS. These preliminary findings justify adequately powered randomized controlled trials to evaluate laver as a gut-microbiome-targeted dietary strategy for MetS.}, }
@article {pmid42197000, year = {2026}, author = {Shehata, F and Dwyer, KM and McGee, SL and Rivera, LR}, title = {Gut Microbiome Dysbiosis in Metabolic Syndrome: Current Evidence and Emerging Perspectives.}, journal = {Nutrients}, volume = {18}, number = {10}, pages = {}, doi = {10.3390/nu18101540}, pmid = {42197000}, issn = {2072-6643}, mesh = {Humans ; *Metabolic Syndrome/microbiology/therapy ; *Dysbiosis/microbiology/complications ; *Gastrointestinal Microbiome/physiology ; Probiotics/administration &amp; dosage ; Prebiotics/administration &amp; dosage ; Fecal Microbiota Transplantation ; Synbiotics/administration &amp; dosage ; }, abstract = {The gut microbiota plays a crucial role in human metabolism, and disruptions to its composition, particularly reductions in bacterial diversity, have been increasingly associated with the development of metabolic syndrome (MetS). MetS encompasses a constellation of interrelated metabolic risk factors, including central obesity, insulin resistance, dyslipidemia, and hypertension, which collectively elevate the risk of cardiovascular and cerebrovascular disease. A comprehensive understanding of the mechanisms underlying MetS is therefore critical for the development of effective preventive and therapeutic strategies. Complex interactions between the gut microbiota and host metabolic pathways are mediated by multiple factors, including microbial metabolites, inflammatory signaling, and host immune responses. This narrative review characterizes the clinical manifestations of MetS and alterations in gut microbiota composition, characterized by an overrepresentation of potentially pathogenic taxa and a concomitant decline in beneficial microbial species. In addition, we discuss current and emerging approaches to microbiota modulation, including prebiotics, probiotics, synbiotics, postbiotics, and fecal microbiota transplantation, and evaluate their potential roles in the prevention and management of MetS. We identify critical evidence gaps and propose research priorities for evidence-based clinical strategies for MetS management and prevention.}, }
@article {pmid42197001, year = {2026}, author = {Lupu, VV and Nedelcu, AH and Miron, I and Anton, SC and Sasaran, MO and Frasinariu, OE and Jechel, E and Bozomitu, LI and Chisnoiu, T and Anton, CR and Marginean, CO and Morariu, ID and Mihai, CM and Anton, E and Lupu, A}, title = {Early Gut Microbiota and Neurodevelopmental Trajectories: Implications for Pediatric Neuropsychiatric Vulnerability-A Narrative Review.}, journal = {Nutrients}, volume = {18}, number = {10}, pages = {}, doi = {10.3390/nu18101541}, pmid = {42197001}, issn = {2072-6643}, mesh = {Humans ; Neurodevelopment ; *Gastrointestinal Microbiome/physiology ; *Neurodevelopmental Disorders/microbiology ; Dysbiosis/microbiology ; Child ; Brain/growth &amp; development ; Probiotics ; Prebiotics/administration &amp; dosage ; Neuronal Plasticity ; }, abstract = {Neurodevelopment is a dynamic and multifactorial process, critical in the early stages of life, involving the formation of neural networks, the establishment of synapses, and the maturation of cognitive, social and emotional circuits. In this context, the gut microbiome emerges as an essential regulator of neurodevelopment, exerting influences through multiple biochemical and immunological mechanisms that define the "gut-brain axis". The microbiota modulates neurodevelopment by regulating neurotransmitters (serotonin, dopamine, GABA), the production of microbial metabolites, including short-chain fatty acids, the modulation of inflammatory cytokines, and vagal signaling to the central nervous system. Recent evidence highlights the role of microbiota in modulating microglia, synaptogenesis, dendritic maturation, and neuronal plasticity, emphasizing how these processes are influenced by microbial activity rather than providing a comprehensive treatise on plasticity itself. Gut microbiota disturbances, or dysbiosis, have been associated with various neuropsychiatric and neurodevelopmental disorders, contributing to cognitive, behavioral, and emotional dysfunctions. This article summarizes, in a narrative manner, the main dysbiosis patterns identified in these disorders and the biological mechanisms by which the microbiome influences neuronal development and function, including immune-neuronal interactions, metabolomic modulation, and neuroendocrine signaling. Finally, emerging directions of intervention aimed at adjusting the microbial profile, such as dietary adjustment, the use of probiotics, prebiotics, symbiotics, and fecal microbiota transplantation, are presented with the aim of positively influencing neurodevelopment and preventing or ameliorating associated dysfunctions. This review emphasizes the need for longitudinal, rigorous, and controlled clinical trials to validate the efficacy of microbiota modulation strategies and to substantiate their integration into individualized pediatric management protocols.}, }
@article {pmid42197002, year = {2026}, author = {Cho, YK and Lee, KH and Kang, HM and Lee, IK}, title = {Early Gut Microbiome-Short-Chain Fatty Acid Axis Disruption May Be Associated with Delayed Recovery in Critically Ill Children.}, journal = {Nutrients}, volume = {18}, number = {10}, pages = {}, doi = {10.3390/nu18101543}, pmid = {42197002}, issn = {2072-6643}, support = {ZC25OISI0127//The Catholic University of Korea Seoul St. Mary's Hospital/ ; }, mesh = {Humans ; *Critical Illness ; *Fatty Acids, Volatile/metabolism ; Feces/chemistry/microbiology ; *Gastrointestinal Microbiome/physiology ; Prospective Studies ; Male ; Female ; Intensive Care Units, Pediatric ; Child, Preschool ; Infant ; Length of Stay ; Child ; Severity of Illness Index ; RNA, Ribosomal, 16S ; }, abstract = {Background: The gut microbiome contributes to immune-metabolic homeostasis through microbial-derived metabolites such as short-chain fatty acids (SCFAs). However, whether early disruption of the gut microbiome-SCFA axis identifies impaired clinical recovery in pediatric intensive care unit (PICU) patients remains unclear. Biological markers reflecting the recovery trajectory beyond conventional severity scores remain poorly characterized in pediatric critical illness. We therefore investigated whether early microbiome disruption and fecal SCFA profiles are associated with recovery trajectory in critically ill children. Methods: In this prospective observational study (N = 26), fecal samples were collected within 5 days of PICU admission. Microbial diversity was assessed using 16S rRNA gene sequencing (Shannon index), and fecal SCFAs were quantified using targeted metabolomics. Disease severity was assessed using the Pediatric Index of Mortality 3 (PIM3). The primary outcome was PICU length of stay (LOS) as a pragmatic indicator of metabolic and functional recovery trajectory in critically ill children. Results: Younger age and higher disease severity showed a trend toward reduced microbial diversity (β = 0.066, p = 0.089, and β = -0.054, p = 0.089). Early loss of gut microbial diversity was associated with reduced fecal butyric acid concentrations (r = 0.440, p = 0.024). Importantly, lower microbial diversity in the early sampling window showed a significant inverse correlation with PICU LOS (ρ = -0.428, p = 0.029), whereas fecal butyric acid alone was not directly associated with LOS (p = 0.321). In multivariable regression models adjusting for age, disease severity, and clinical exposures, microbial diversity showed a consistent inverse association with PICU LOS, although statistical significance was not reached. Conclusions: Early disruption of the gut microbiome-SCFA axis, characterized by reduced microbial diversity and lower fecal butyrate, showed trend-level associations with delayed clinical recovery in this pilot cohort. Gut microbial ecosystem integrity may serve as a biologically relevant marker of recovery trajectory beyond conventional severity scoring.}, }
@article {pmid42197004, year = {2026}, author = {Wang, M and Lyu, Y and Zhang, J and Wang, Y and Yang, Y and Mao, YH}, title = {FMT from Exercise and Konjac Glucomannan Preconditioned Donors Rescues Antibiotic-Induced Dysbiosis with Enhanced Ecological Restoration in Mice.}, journal = {Nutrients}, volume = {18}, number = {10}, pages = {}, doi = {10.3390/nu18101544}, pmid = {42197004}, issn = {2072-6643}, support = {2023ZDZX2035; 2024ZDZX2061//Guangdong Scientific Research Platform and Projects for the Higher-educational Institution (Key Area Project)/ ; SL2024A04J01093//the Guangzhou Fundamental and Applied Research/ ; No.82030098//National Natural Science Foundation of China/ ; S202410585045 and 202410585015//the College Students Innovation and Entrepreneurship Training Program/ ; 2023A1515010004//the Guangdong Basic and Applied Basic Research Foundation/ ; }, mesh = {Animals ; *Dysbiosis/therapy/chemically induced/microbiology ; *Fecal Microbiota Transplantation/methods ; *Mannans/pharmacology ; *Anti-Bacterial Agents/adverse effects ; Mice ; *Gastrointestinal Microbiome/drug effects ; Male ; *Physical Conditioning, Animal ; Mice, Inbred C57BL ; }, abstract = {BACKGROUND: Although antibiotics have a wide range of applications in medical clinical practice and possess significant clinical value, their inevitable contribution to gut microbiome dysbiosis warrants attention. Our previous research has confirmed that the combined intervention of exercise and konjac glucomannan (KGM) has a better regulatory effect on gut dysbiosis in mice compared with individual interventions.<br><br>METHODS: This study aims to further investigate whether this effect can be transmitted through fecal microbiota transplantation (FMT), and to compare the recovery effects of autologous FMT (a-FMT), fecal microbiota transplantation after exercise combined with KGM intervention (EK-FMT), and combinative intervention with exercise and KGM (EXE-KGM) on gut microbiome dysbiosis. Sample sizes ranged from five to six animals.<br><br>RESULTS: The results showed that the a-FMT group recovered &#x3b1; diversity the fastest, including Chao, Shannon, and Simpson indices(p < 0.05), within 2 weeks after transplantation when compared with the CTL group. At the end of the experiment, the Bray-Curtis distance of the a-FMT group was closest to the CTL group, while the EXE-KGM group had delayed recovery, there was no significant difference between the EK-FMT group and the EXE-KGM group. Metagenomic analysis and metabolomics analysis indicated that the arginine synthesis and metabolism pathways (KEGG: map00471, map00473, arginine biosynthesis) played a core role in the restoration of the microbiota.<br><br>CONCLUSIONS: The results of this experiment indicate that EK-FMT group can partially transfer the regulatory effects of combined exercise and KGM intervention, a-FMT accelerates the recovery speed of the gut microbiome and arginine metabolism may play an important role in it. This finding provides a theoretical basis and practical direction for special populations to receive special donor fecal treatment.}, }
@article {pmid42197020, year = {2026}, author = {Brzechffa, C and Fleischman, AG}, title = {Leveraging Dietary Interventions to Benefit Patients with Hematologic Malignancies and Clonal Hematopoiesis.}, journal = {Nutrients}, volume = {18}, number = {10}, pages = {}, doi = {10.3390/nu18101562}, pmid = {42197020}, issn = {2072-6643}, mesh = {Humans ; *Hematologic Neoplasms/diet therapy ; *Clonal Hematopoiesis ; Gastrointestinal Microbiome ; Diet, Mediterranean ; Obesity/complications/diet therapy ; Dysbiosis ; *Diet ; }, abstract = {Diet is a modifiable factor that influences multiple pathways relevant to hematologic malignancy, including systemic inflammation, immune cell activity, gut microbiota composition, and cancer cell metabolism. Translation of preclinical findings into clinical practice for hematologic malignancies remains nascent, although momentum is building to evaluate dietary interventions as a component of supportive and disease-modifying care. This review examines the mechanistic rationale for dietary interventions across the spectrum of clonal hematologic disorders and synthesizes current clinical evidence. Anti-inflammatory dietary patterns, particularly the Mediterranean diet, have demonstrated reductions in pro-inflammatory cytokines and may attenuate the inflammatory milieu that fuels clonal expansion. Obesity, which elevates the risk of developing hematologic malignancies and worsens clinical outcomes in diseases such as acute lymphoblastic leukemia (ALL) and acute myeloid leukemia, may be addressed through calorie-restricted, low-fat, or plant-based dietary strategies. Gut microbiota dysbiosis induced by chemotherapy represents another target, with high-fiber and plant-based diets showing promise in restoring microbial diversity and potentially enhancing treatment efficacy. Early-phase clinical trials in multiple myeloma, acute lymphoblastic leukemia, and myeloproliferative neoplasms have established feasibility and yielded preliminary signals warranting larger confirmatory studies. Larger, rigorously designed trials are needed to establish dietary interventions as legitimate therapeutic tools in the management of hematologic malignancies.}, }
@article {pmid42197026, year = {2026}, author = {Alsinani, Y and Rostamkhani, F and Shirvani, H}, title = {Exercise and the Gut Microbiome: From Mechanisms to Clinical Applications.}, journal = {Nutrients}, volume = {18}, number = {10}, pages = {}, doi = {10.3390/nu18101565}, pmid = {42197026}, issn = {2072-6643}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; *Exercise/physiology ; Fatty Acids, Volatile/metabolism ; }, abstract = {Background/Objectives: The gut microbiome is a critical regulator of host metabolism, immunity, and the gut-brain axis. Exercise is a promising non-pharmacological modulator of microbial ecology, yet human evidence remains heterogeneous and the translational gap persists. This narrative review synthesizes mechanisms, human and animal evidence, and future directions for the exercise-gut microbiome axis. Methods: PubMed, Scopus, Web of Science, and SID were searched for articles published between January 2000 and February 2025. Keywords included exercise, physical activity, gut microbiome, gut microbiota, short-chain fatty acids, and gut-muscle axis. From 218 initial records, 89 original studies (47 human, 42 animal) met inclusion criteria and were critically appraised. Results: Exercise modulates the gut microbiome via splanchnic hypoperfusion, hyperthermia, altered transit time, and immune-mediated barrier regulation. Moderate-intensity continuous training consistently increases alpha diversity and enriches butyrate-producing taxa (Faecalibacterium prausnitzii, Roseburia hominis) and mucin-degrading Akkermansia muciniphila. High-intensity interval training transiently increases intestinal permeability in untrained individuals but, following adaptation, stimulates butyrate production via lactate cross-feeding metabolism-a recent breakthrough. Effects are transient and reversible upon detraining. Animal models establish causality through fecal microbiota transplantation; human randomized controlled trials demonstrate modest, intensity-dependent, and highly individualistic responses. Emerging evidence supports the gut-muscle axis in sarcopenia and personalized exercise prescription guided by microbiome profiling. Conclusion: Exercise shows promise as a low-cost modulator of the gut microbiome for enriching health-associated taxa and improving metabolic outcomes. Definitive evidence linking exercise-induced microbial shifts to enhanced athletic performance in humans remains lacking. Future research requires diet-controlled randomized controlled trials with ≥12-week interventions, shotgun metagenomics, and mechanistic validation of the gut-muscle axis in humans.}, }
@article {pmid42197039, year = {2026}, author = {Goluch, Z and Książek, E and Wierzbicka-Rucińska, A and Skawina, I and Dudkowiak, R}, title = {The Effects of Colostrum Bovinum Supplementation on Human Body Fat Content and/or Blood Lipid Profile: A Systematic Review of Clinical Trials.}, journal = {Nutrients}, volume = {18}, number = {10}, pages = {}, doi = {10.3390/nu18101579}, pmid = {42197039}, issn = {2072-6643}, mesh = {Humans ; *Colostrum ; *Dietary Supplements ; Animals ; *Lipids/blood ; Female ; *Adipose Tissue/drug effects/metabolism ; Cattle ; Male ; Clinical Trials as Topic ; Adult ; }, abstract = {Bovine colostrum (COL) is widely used in dietary supplements, and previous studies have suggested its potential benefits for immune function, selected clinical conditions, wound healing, and athletic performance. This systematic review analyzed clinical trials published between 2001 and 2025 that investigated the effects of COL on human body fat and blood lipid profiles. The review was conducted in accordance with PRISMA guidelines, and study quality was assessed using Cochrane risk-of-bias tools. Thirteen studies were included. One study in older adults reported that COL supplementation at 60 g/day for 8 weeks significantly reduced body fat percentage by 0.4% (p < 0.05). Another study found that COL supplementation at 10 g/day combined with plant proteins for 12 weeks significantly attenuated the increase in leg tissue fat percentage compared with placebo (PLA) (0.48 ± 1.29% vs. 1.12 ± 1.27%, respectively; p < 0.05). Changes in blood lipid profiles were reported in two studies. In individuals with type 2 diabetes, COL supplementation at 10 g/day for 4 weeks significantly reduced total cholesterol (TC) and triglyceride levels in both men and women, by 8.27% vs. 7.62% and 11.96% vs. 21.46%, respectively. In another study involving older adults, COL supplementation at 30 g/day for 12 weeks significantly reduced TC (5.88 to 5.38 mmol/L) and low-density lipoprotein cholesterol (LDL-C) (3.68 to 3.28 mmol/L) compared with PLA. Owing to substantial methodological heterogeneity and inconsistent findings, further randomized, double-blind trials are needed in larger groups of overweight or obese participants, with intervention periods lasting at least six months. Future studies should use a standardized COL dose of 20-25 g/day, controlled caloric deficits, and a four-arm design comparing placebo and COL under normocaloric and energy-restricted dietary conditions. Assessments should include blood metabolic biomarkers, body composition measured by dual-energy X-ray absorptiometry, gut microbiome composition, and fecal short-chain fatty acids to determine whether any observed benefits are attributable to COL alone or to its combination with dietary intervention.}, }
@article {pmid42197051, year = {2026}, author = {Procopciuc, LM and Hangan, AC and Lucaciu, RL}, title = {Synbiotics as a Microbiome-Based Strategy in Colorectal Cancer.}, journal = {Nutrients}, volume = {18}, number = {10}, pages = {}, doi = {10.3390/nu18101591}, pmid = {42197051}, issn = {2072-6643}, mesh = {Humans ; *Colorectal Neoplasms/microbiology/therapy ; *Synbiotics/administration &amp; dosage ; *Gastrointestinal Microbiome/physiology ; Animals ; Probiotics ; Tumor Microenvironment ; Signal Transduction ; Prebiotics/administration &amp; dosage ; }, abstract = {Colorectal cancer (CRC) is a multifactorial disease arising from dynamic interactions between gut microbiota, inflammatory processes, metabolic reprogramming, and dysregulated host signaling pathways. Increasing evidence highlights the potential of synbiotics-combinations of probiotics and prebiotics-as promising modulators of these processes. This review explores the mechanisms by which synbiotics influence CRC development and progression, integrating data from preclinical and clinical studies. Synbiotics exert beneficial effects by restoring microbial balance, enhancing the production of short-chain fatty acids (SCFAs), strengthening intestinal barrier integrity, and reducing chronic inflammation and oxidative stress. These functional changes converge on key molecular pathways, including Wnt/β-catenin, NF-κB, and PI3K/Akt/mTOR, which regulate tumor cell proliferation, survival, and immune responses. Preclinical studies consistently demonstrate anti-tumor effects, including reduced tumor growth, increased apoptosis, and modulation of the tumor microenvironment. Clinical evidence suggests that synbiotics may improve postoperative outcomes, reduce chemotherapy-related toxicity, and positively influence microbiome composition, although results remain heterogeneous. Emerging approaches focusing on microbiome profiling and personalized synbiotic interventions offer new opportunities for precision medicine in CRC. Overall, synbiotics represent a promising adjunctive strategy in colorectal cancer management, with potential to enhance therapeutic efficacy and improve patient outcomes. Further large-scale clinical studies are needed to validate their long-term benefits and establish standardized treatment protocols.}, }
@article {pmid42197053, year = {2026}, author = {Zsálig, D and Molnár, &#xc1; and Kerényi, M and Péter, F and Gerencsér, G and Polyák, &#xc9;}, title = {Does Intrarectal Administration of Christensenella minuta DSM22607 Impact Body Weight?.}, journal = {Nutrients}, volume = {18}, number = {10}, pages = {}, doi = {10.3390/nu18101593}, pmid = {42197053}, issn = {2072-6643}, mesh = {Animals ; Male ; Female ; Mice ; *Body Weight/drug effects ; *Probiotics/administration &amp; dosage ; Energy Intake ; Weight Gain ; Anti-Bacterial Agents/pharmacology ; *Bacillota ; Diet ; }, abstract = {BACKGROUND: Christensenella minuta (C. minuta) is a promising next-generation probiotic linked to reduced body weight, inhibition of obesogenic processes, and enhanced metabolic profiles. However, the extent and persistence of these effects, particularly under varying dietary conditions, remain uncertain.<br><br>OBJECTIVE: This study aimed to examine the effects of intrarectal administration of C. minuta on body weight regulation in vivo under different dietary patterns, with or without antibiotic pretreatment, both during the intervention and over the long term. Particular emphasis was placed on exploring the interactions between C. minuta supplementation, dietary background, caloric intake, and body weight gain.<br><br>METHODS: A total of 180 CD1 mice (both sexes equally) were allocated into nine experimental groups based on diet, with and without C. minuta supplementation, and with and without antibiotic pretreatment. The bacterial suspension was administered intrarectally once a week for three consecutive weeks in the treatment groups. Body weight was monitored weekly, and food intake was recorded biweekly over the 12-week study period. Visceral fat mass was measured postmortem.<br><br>RESULTS: Groups treated with C. minuta with antibiotic pretreatment exhibited significantly lower body weight gain than the control groups during the intervention phase in both sexes, irrespective of caloric intake and dietary pattern, indicating that the reduced weight gain was attributable to the effect of C. minuta. Regarding long-term effects following the cessation of administration, sexual dimorphism was observed: while no lasting impact was found in males, the body weight gain inhibiting effect of C. minuta treatment persisted in females. Furthermore, females treated with C. minuta exhibited the lowest levels of visceral fat among all groups. Caloric intake was not significantly associated with body weight gain at any time point in this study.<br><br>CONCLUSIONS: C. minuta exerts a transient, caloric intake-independent inhibitory effect on body weight gain. The absence of sustained effects highlights the necessity for continuous or optimized administration protocols to ensure the attainment of long-term benefits in the future. The results of this study support the hypothesis that C. minuta can act as a modulator of host metabolism and body composition, underscoring the significance of treatment duration in this process.}, }
@article {pmid42197332, year = {2026}, author = {Rath, A and Rautenschlein, S and Rzeznitzeck, J and Lalk, M and Methling, K and Karasova, D and Rychlik, I and Waldmann, KH and Altrock, AV}, title = {Consequences of Campylobacter jejuni and Campylobacter coli Colonisation of Piglets on Gut Microbiota and Microbial Metabolites.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14050945}, pmid = {42197332}, issn = {2076-2607}, support = {411479547//Deutsche Forschungsgemeinschaft/ ; //Deutsche Forschungsgemeinschaft and University of Veterinary Medicine Hannover, Foundation within the funding programme Open Access Publishing/ ; }, abstract = {Campylobacter (C.) jejuni and C. coli are common zoonotic bacteria in pigs, which typically act as asymptomatic carriers. However, the effects of Campylobacter colonisation on the porcine intestinal microbiota and metabolome remain poorly understood. This study investigated microbiome and metabolome alterations associated with co-colonisation by C. jejuni and C. coli in the different intestinal segments of pigs. Thirty-two weaned piglets were assigned to a control group and a group inoculated with C. coli ST5777/CT828 and C. jejuni ST122/CT206. Four weeks post inoculation, jejunal and caecal contents were analysed for Campylobacter counts, metabolite profiles and microbial composition. All animals remained clinically healthy. Both Campylobacter species colonised the jejunum and caecum, with higher C. coli counts in the caecum. Campylobacter-colonised pigs showed significantly altered metabolite profiles, including reduced cysteine and urea and increased glycine in the jejunum, as well as elevated 3-hydroxybutyrate levels in the caecum. In contrast, short-chain fatty acid concentrations in the caecum were unaffected by infection. Microbiota analysis revealed a significant reduction in caecal alpha diversity, whereas jejunal diversity remained unchanged. Infected pigs exhibited increased relative abundances of Lactobacillaceae and Bifidobacteriaceae and a decreased abundance of Pseudomonadota, including Enterobacteriaceae. In conclusion, Campylobacter co-colonisation induces distinct microbiome and metabolome alterations in pigs despite the absence of clinical disease. These findings highlight complex host-microbiota-pathogen interactions that may be relevant for future Campylobacter control strategies in pig production.}, }
@article {pmid42197333, year = {2026}, author = {Zhao, Z and Wang, X and Wen, F and Zhao, F and Zhang, M and Menghe, B}, title = {Integrated Metagenomic and Metabolomic Profiling Identifies Predictive Biomarkers for Overweight Status in a Mongolian Population.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14050946}, pmid = {42197333}, issn = {2076-2607}, support = {2018YFE0123500//Special Funds for International Science and Technology Cooperation of China/ ; }, abstract = {Mongolians have high overweight prevalence linked to their nomadic lifestyle and diet, but gut microbiota studies in this population are scarce. This study used fecal metagenomic and serum metabolomic analyses of 96 Mongolian participants (normal-weight n = 55, overweight n = 41) to characterize gut microbiome alterations and identify weight-related biomarkers. The analyses revealed that Parabacteroides distasonis, Barnesiella intestinihominis, and Alistipes onderdonkii were significantly reduced in overweight individuals (p < 0.05). Concurrently, the metabolites such as beta-cryptoxanthin, p-cresol, and ribothymidine were significantly down-regulated in the overweight group (p < 0.05). Random forest models from the three datasets showed a strong diagnostic ability for microbial families (AUC > 0.70). A subsequent integrated multi-kingdom classifier that combined microbiota and metabolite data achieved the highest performance (AUC = 0.818). Key features with high predictive contributions were identified, including Lactobacillus crispatus, Alistipes onderdonkii, and Parabacteroides distasonis, and metabolites, such as beta-cryptoxanthin, p-cresol, and picolinic acid. These results show the random forest model has high predictive value for distinguishing normal weight and overweight individuals. In summary, this study identified specific gut microbiota and serum metabolomic profiles linked to overweight in Mongolians. Multi-omics integration established a diagnostic biomarker model, laying a theoretical basis for microbiome-targeted weight management interventions.}, }
@article {pmid42197338, year = {2026}, author = {Oelschlägel, L and Klose, J and Glaß, M and Moritz, S and Trojanowicz, B and Kleeff, J and Rebelo, A}, title = {Microbiome Diversity in Pancreatic Surgery: Associations with Preoperative Stenting and Postoperative Outcomes.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14050951}, pmid = {42197338}, issn = {2076-2607}, abstract = {Carcinomas of the pancreas and bile duct remain highly lethal malignancies, with surgical resection representing the only potentially curative treatment. Despite improvements in perioperative mortality, postoperative complications remain frequent and negatively affect long-term outcomes. Recent evidence suggests that the pancreas and bile ducts harbor distinct microbial communities, challenging the traditional concept of sterility in these environments. However, their composition and clinical relevance remain incompletely understood. This study aimed to characterize microbiome profiles across different anatomical sites in patients undergoing pancreatic surgery, evaluate the impact of preoperative biliary stenting, and assess associations between prevalent bacterial species and postoperative outcomes. A total of 224 samples (bile, pancreatic fluid, duodenal tissue, tumor tissue, and healthy pancreatic tissue) from 58 patients with pancreatic cancer, bile duct cancer, chronic pancreatitis, or healthy pancreas were analyzed using 16S rRNA gene sequencing. Microbial diversity was assessed using the Shannon index for alpha diversity and nMDS with PERMANOVA for beta diversity. Distinct microbial profiles were identified across body sites, with significant beta-diversity differences between duodenal, bile, and pancreatic fluid samples and between duodenal and pancreatic fluid samples from the same patient. Preoperative biliary stenting significantly influenced microbial composition. Enterococcus faecalis was associated with a reduced risk of severe postoperative complications (Clavien-Dindo ≥ III). Overall, microbial composition varies across anatomical sites and disease entities, and specific bacteria may influence surgical outcomes, warranting further investigation in larger cohorts.}, }
@article {pmid42197355, year = {2026}, author = {Feletti, R and Mori, A and Zaffagnini, A and Castilletti, C and Pomari, E}, title = {The Human Virome in Infectious Diseases: Insights from Chronic and Acute Infections Across Body Sites-A Narrative Review.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14050969}, pmid = {42197355}, issn = {2076-2607}, support = {PE00000007, INF-ACT//EU funding within the MUR PNRR/ ; 5MIL-VISA L1P17//Italian Ministry of Health/ ; }, abstract = {The human virome, comprising eukaryotic viruses, bacteriophages, and viral genetic material, is a dynamic component of the microbiome with growing relevance in infectious diseases. This narrative review is structured to: (i) summarize the general composition of the human virome and methodological challenges, including the fraction of unclassified viral "dark matter"; (ii) describe virome alterations in chronic infections; and (iii) explore site-specific virome dynamics across respiratory, intestinal, and genito-urinary tracts in both chronic and acute infections. In chronic viral infections such as HIV, HBV, HCV, and HPV, a recurrent feature is the expansion of Anelloviridae-particularly torque teno virus-reflecting impaired immune surveillance rather than direct pathogenicity, suggesting their potential as surrogate biomarkers of immune competence. Evidence on virome changes in chronic bacterial and parasitic infections remains limited, highlighting a critical knowledge gap. Acute infections are associated with compartment-specific shifts in eukaryotic viruses and bacteriophage communities, often paralleling changes in bacterial populations and inflammatory responses, with implications for disease severity. Despite advances in metagenomic approaches, a substantial proportion of viral sequences remains unclassified, limiting functional interpretation. Nevertheless, virome profiling provides an ecosystem-level perspective, offering insights beyond single-pathogen detection and supporting emerging applications in diagnostics, immune monitoring, prognosis, and infectious disease surveillance.}, }
@article {pmid42197356, year = {2026}, author = {Wilson, A and Quach, B and Musa, K and Musa, I}, title = {Gut Microbiome Dynamics in Food Allergy Development Across the Lifespan: Microbial Mechanisms, Host Interactions, and Therapeutic Perspectives.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14050970}, pmid = {42197356}, issn = {2076-2607}, abstract = {Over the past several decades, the gut microbiome (GM) has been the focus of extensive investigation. In recent years, major discoveries such as the role of maternal breastfeeding in infant GM development and mode of delivery on infant GM health have expanded scientific knowledge on this topic. As this is a rapidly expanding field of research, substantial work remains to further elucidate and integrate the existing evidence on its role in allergic response and immunological development. This comprehensive review will examine the latest discoveries in GM research and its role in the development of food allergies across the lifespan. Examining the existing literature may identify knowledge gaps regarding precise mechanisms through which the development of GM influences the maturation of the immune system. Given the abundance of the literature, we conducted a database search for articles published within the past 10 years. A total of 56 original research articles were retrieved, analyzed, and included in our review. This review article aims to integrate the current evidence on understanding how the development of GM impacts the immune system and food allergy response throughout the lifespan. We aim to uncover microbial mechanisms of allergy response, host and microbe interactions, and opportunities for therapeutic intervention. Additionally, we aim to reveal gaps in the current knowledge of the GM's influence on allergy development, offering directions for future research.}, }
@article {pmid42197358, year = {2026}, author = {Luo, XL and Wang, JY and Tang, YQ and Hu, ZH and Liu, H and Li, BL and Li, YY and Ren, XM and Han, H and Chen, Y and Chen, ZJ}, title = {Role of Plant Growth-Promoting Bacteria in Reshaping Rhizosphere Bacterial and Fungal Microbiomes Under Multi-Metal-Microplastic Composite Pollution in Spinach.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14050972}, pmid = {42197358}, issn = {2076-2607}, support = {U2004145//National Natural Science Foundation of China/ ; }, abstract = {Microplastics (MPs) often co-occur with heavy metals (HMs), posing combined stress that inhibits plant growth. While plant growth-promoting bacteria (PGPB) are known to alleviate heavy metal toxicity, their role under MP-HM co-contamination and the differential responses of rhizosphere microbial communities remain unclear. This study evaluated the effects of cadmium (Cd) and lead (Pb), polylactic acid (PLA) MPs, and their combined contamination on spinach growth using pot experiments, and assessed the mitigation potential of two PGPB strains. PGPB inoculation significantly increased plant height and dry weight. High-throughput sequencing revealed that pollution treatments and PGPB altered rhizosphere bacterial and fungal community composition and diversity. Microbial shifts were closely associated with soil chemical properties and plant growth. Notably, bacteria and fungi exhibited distinct response patterns to combined stress and remediation. Functional prediction (PICRUSt2) indicated that microbial communities enhanced metabolic processes and nutrient (N and P) cycling to cope with stress. PGPB inoculation reduced heavy metal toxicity, improved soil nutrient status (P and K), increased microbial diversity, and regulated microbial functions, thereby supporting soil ecological stability. These findings provide insights into rhizosphere microbial mechanisms and support the application of PGPB for remediation of MP-HM co-contaminated soils.}, }
@article {pmid42197369, year = {2026}, author = {Boeraș, I and Benedek, AM and Curtean-Bănăduc, A and Bănăduc, D}, title = {Influence of Tributary Inflows on Sediment Bacterial Community Composition of the River Mainstem.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14050984}, pmid = {42197369}, issn = {2076-2607}, support = {LBUS-IRG-2023//Lucian Blaga University of Sibiu/ ; }, abstract = {River sediment microbial communities are an integral part of fluvial ecosystems, where they play a central role in nutrient cycling. Although these communities share a core group of microorganisms, their overall composition can be influenced by natural environmental conditions and anthropogenic factors. While anthropogenic influences on river microbial communities have been extensively studied, natural drivers have received comparatively less attention. In this study, we evaluated the impact of tributary inflow on the microbial assemblages of a main river stem. Sediment samples were collected from both the main channel and some of its tributaries, and bacterial community composition was characterized using 16S rRNA gene amplicon sequencing. Taxonomic profiling revealed a largely shared core community typical of riverine sediments across all sites. While alpha diversity did not differ significantly between main river and tributary samples, beta diversity analyses demonstrated clear segregation between the two environments, indicating distinct community structures. Correlation analyses further showed that microbial assemblages in the main river downstream of tributary confluences were significantly associated with tributary community composition, highlighting the influence of tributary inflow on bacterial communities in the main river.}, }
@article {pmid42197370, year = {2026}, author = {Yu, S and Tang, W and Song, Z and Wang, Y and Gao, W and Su, Y and Yang, X and Zhao, Y and Dai, T}, title = {Evaluation of Germplasm Resources and Microbial Diversity Among Different Geographical Provenances of Tamarindus indica L.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14050983}, pmid = {42197370}, issn = {2076-2607}, support = {32471873//National Natural Science Foundation of China/ ; 2023ZD0405605//the STI 2030- Major Projects/ ; 2024M751426//the China Postdoctoral Science Foundation/ ; 2023YFD1401304//National Key R&amp;D Program of China/ ; BK20231291//Natural Science Foundation of Jiangsu Province, China/ ; no//the Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; }, abstract = {Tamarindus indica L. is a species of tree with high economic value. However, research on its associated bacterial communities is limited, and no microbial fertilizer has yet been developed specifically for tamarind. In this study, we selected 20 geographical provenances of tamarind as experimental materials, evaluated their germplasm resources, and investigated the correlation between plant traits and associated bacterial communities under grafting conditions. Provenances YM2 and BS21 produced the largest fruits, while all physiological indices showed significant variability among the tested accessions. Microbial samples from the phyllosphere and rhizosphere were collected from these 20 provenances, and 16S rRNA gene sequencing was conducted to compare microbial communities. The differences in rhizosphere microbiota among different samples were more significant than those in phyllosphere microbiota; subsequently, an in-depth investigation was conducted on the relationships between rhizosphere bacterial communities and various traits under these grafting conditions. Through correlation analysis, significant correlations were identified between some microbial phyla and the traits of tamarind under these grafting conditions. Under the current grafting conditions, variations in the rhizosphere microbiome were associated with tamarind provenances. However, due to the constraints of the experimental design, the potential influences of rootstock genotypes and scion-rootstock signal transduction could not be excluded. Nevertheless, through the unification of rootstock sources and the design of correlation analysis, this study has initially verified the dominant association between scion provenances and microbial communities.}, }
@article {pmid42197371, year = {2026}, author = {Yang, L and Li, Z and Wei, S and Dong, Q and Zha, L and Yu, C and Zhao, Y}, title = {Spent Mushroom Substrate Reused as Organic Fertilizer Enhances Lettuce (Lactuca sativa L.) Quality and Soil Nutrients: Insights from Physicochemical and Microbiome Analyses.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14050985}, pmid = {42197371}, issn = {2076-2607}, support = {2024YFD1200204//National Key R&amp;D Program of China/ ; 19390743000//Shanghai Committee of Science and Technology/ ; 2020-02-08-00-12-F01479//Shanghai Agricultural Commission Program/ ; JCYJ251601//Shanghai Academy of Agricultural Sciences/ ; }, abstract = {Returning spent mushroom substrate (SMS) to the field is an effective way to dispose of it. However, given the substantial nutrient consumption associated with Volvariella volvacea SMS, their effects on soil properties and crop performance warrant further investigation. By analyzing the effects of three different application rates of SMS on soil nutrients and lettuce (Lactuca sativa L.) quality, the results showed that the group with 1.5 kg m[-2] SMS addition improved the total nitrogen (+21.2%), and organic content (+27.9%) in soil, and it demonstrated particularly outstanding performance in enhancing the survival rate (+21.9%), average weight (+71.7%), chlorophyll content (+45.6%), and total phenolic content (+25.2%) of lettuce. By comparing the soil microbial communities in the control group, the SMS (1.5 kg m[-2]) treatment group, and the organic fertilizer treatment group, it was found that they were mainly composed of Group S1, S2, and S3 microorganisms, respectively. The microbial community evenness in the treatment groups was greater than that in the control group. Furthermore, the results also revealed that the microbial conversion efficiency of nitrogen and phosphorus in the SMS treatment group was higher than the control group, which promoted nutrient cycling and improved the quality of lettuce. Our analysis provides an environmentally friendly way for Volvariella volvacea SMS disposal.}, }
@article {pmid42197388, year = {2026}, author = {Gao, XY and Wang, Y and Wang, YH and Yu, H and Liu, L and Zhang, XH and Xu, HT and Meng, Y and Johnston, RN and Liu, GR and Liu, SL}, title = {Akkermansia muciniphila NND9 Mitigates Ulcerative Colitis by Ameliorating the Gut Barrier via Suppressing DR5 Expression in a Mouse Model.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14051002}, pmid = {42197388}, issn = {2076-2607}, support = {NSFC82020108022//National Natural Science Foundation of China/ ; }, abstract = {Ulcerative colitis (UC) is a type of inflammatory bowel disease without curative therapeutics. Recent studies demonstrate that Akkermansia muciniphila exerts mitigating effects on UC, but the underlying mechanisms remain unclear. In this study, we isolated a strain of A. muciniphila, designated NND9, from the feces of DSS-induced ulcerative colitis model mice and investigated its effects on UC of the mouse model. NND9 significantly alleviated UC severity in the mice by restoring gut barrier integrity through improving colonic mucus layer thickness, mitigating goblet cell depletion, and halting epithelial cell death. Mechanistically, NND9 suppressed the expression of the Tnfrsf10b gene encoding death receptor 5 (DR5) on the surface of colonic epithelial cells. Additionally, NND9 inhibited the phosphorylation of kinase 3 (RIPK3) and the pseudokinase mixed-lineage kinase domain-like protein (MLKL) associated with the necrotic apoptosis pathway, thereby reducing gut epithelial cell death. NND9 also markedly ameliorated the gut microbiome of the colitis mice. Untargeted metabolomics analysis demonstrated that NND9 modulated both tryptophan and bile acid metabolism. In conclusion, NND9 exhibits curative effects on UC by resolving inflammatory reactions of the gut mucosa through the DR5-RIPK3/p-RIPK3-MLKL/p-MLKL pathway and redressing gut dysbiosis. This study provides valuable information for the development of innovative therapeutic strategies for the treatment of UC.}, }
@article {pmid42197397, year = {2026}, author = {Aleksandravičienė, A and Jarienė, G and Kirvaitienė, J and Volskienė, R and Dambrauskienė, K and Maželienė, &#x17d;}, title = {Bacterial Contamination and Antimicrobial Resistance in Used Eye Cosmetic Products.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14051011}, pmid = {42197397}, issn = {2076-2607}, abstract = {Eye cosmetic products are widely used and applied in close proximity to the ocular surface, making their microbiological safety particularly important. The aim of this study was to assess bacterial contamination in used eye cosmetic products, characterize the antimicrobial resistance profiles of the isolated bacteria, and perform molecular genotypic analysis. A total of 71 samples, including mascara, eyeliner, and eyeshadow, were analyzed. Microbiological analysis revealed that Bacillus spp. and coagulase-negative staphylococci (CoNS) were the predominant microorganisms, while no major pathogens such as Staphylococcus aureus, Escherichia coli, or Pseudomonas aeruginosa were detected. Antimicrobial susceptibility testing demonstrated high susceptibility of isolates to gentamicin, vancomycin, and linezolid, whereas resistance to benzylpenicillin and clindamycin was observed among Staphylococcus spp. Molecular identification based on 16S rRNA gene sequencing confirmed the presence of Bacillus licheniformis, Bacillus subtilis, Staphylococcus epidermidis, and Staphylococcus warneri, with sequences showing high similarity to globally distributed strains. Although the detected microorganisms were predominantly opportunistic, their presence in products applied near the eyes suggests a potential risk of microbial transfer to the ocular surface. These findings highlight the importance of proper hygiene practices, regular product replacement, and effective quality control measures to minimize microbial contamination and associated health risks.}, }
@article {pmid42197398, year = {2026}, author = {Stavros, S and Gerede, A and Zagorianakou, N and Moustakli, E and Potiris, A and Anagnostaki, I and Kozonis, A and Tzeli, M and Vogiatzoglou, AL and Machairoudias, P and Zacharis, K and Zikopoulos, A and Loutradis, D and Domali, E}, title = {The Impact of Endocrine Disruptor Exposure During Pregnancy on Bacterial Complications and Viral Infections: A Narrative Review.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14051012}, pmid = {42197398}, issn = {2076-2607}, abstract = {Endocrine-disrupting chemicals (EDCs) are a diverse group of environmental pollutants capable of interfering with hormonal and immune system regulation. In recent years, increasing concern has been raised about the effects of chemicals, including bisphenols, phthalates, per- and polyfluoroalkyl substances (PFAS), insecticides, and parabens, on maternal and fetal health, primarily due to their widespread exposure in human populations. Pregnancy represents a critical window characterized by tightly regulated hormonal and immunological adaptations. Emerging evidence suggests that EDC exposure during this period may alter maternal microbiota, disrupt immune responses, and interfere with endocrine signaling. These changes may increase susceptibility to bacterial and viral infections, including bacterial vaginosis, urinary tract infections, and intrauterine infections, all of which are associated with adverse pregnancy outcomes. This review summarizes the current evidence on the sources and mechanisms of exposure to endocrine disruptors during pregnancy and examines the potential biological pathways linking endocrine disruption to the development of infections. Particular emphasis is placed on the interactions between immune regulation, hormonal signaling, and changes in the microbiome, which may contribute to increased susceptibility to infections. A deeper understanding of these complex mechanisms is critical to improve risk assessment, develop effective public health strategies, and ultimately protect maternal and fetal health in an environment of increasing chemical exposure. A literature search was conducted using PubMed/MEDLINE, Scopus, and Web of Science, including studies published up to January 2026.}, }
@article {pmid42197400, year = {2026}, author = {Ye, F and Lu, S and Tian, Y and Li, P and Deng, Z and Gao, P and Gao, H and Liu, X}, title = {Continental-Scale Climatic Zones Drive Reorganization of Lake Sediment Microbiome: Diversity, Assembly and Interaction Networks.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14051013}, pmid = {42197400}, issn = {2076-2607}, support = {8182058//Natural Science Foundation of Beijing, China/ ; 21306180//National Natural Science Foundation of China/ ; }, abstract = {Global climate change has altered temperature regimes, hydrological stability, and redox dynamics in inland waters, yet the continental-scale impact of these alterations on sediment microbiomes remains poorly understood. Here, we compiled 562 publicly available 16S rRNA gene datasets from lake sediments across five major climatic zones in China to examine how climatic gradients influence microbial diversity, community assembly, and interaction networks, as well as their associated taxonomic composition and environmental responses. Sediment microbiomes showed clear spatial differentiation in both α- and β-diversity, accompanied by climatic zone-specific taxonomic signatures and biomarker taxa. Community assembly also varied markedly across climatic zones, with stochasticity and dispersal limitation dominating in colder regions, transitional assembly in the south temperate zone, and stronger selective or high-turnover dynamics in the warm subtropics. Importantly, random forest models revealed a clear transition from climate-dominated to anthropogenic-dominated control in sediment microbiome organization: microbial variation in the plateau and temperate regions was primarily associated with climatic and geographic constraints, whereas anthropogenic factors played a more important role in shaping community differentiation in the central subtropical zone. By integrating diversity patterns, taxonomic composition, assembly processes, and network topology, we further propose a three-stage conceptual pattern of sediment microbial community organization along climatic gradients, shifting from a persistence-dominated regime in the cold plateau regions, to an efficiency-dominated regime in the temperate zones, and finally to a plasticity-dominated regime in the warm subtropical regions. These findings would provide a continental-scale framework for understanding sediment microbiome responses to coupled climatic and anthropogenic forcing in inland waters, with implications for future water quality management and ecosystem conservation.}, }
@article {pmid42197422, year = {2026}, author = {Shaik, SM and Schiro, G and Laubitz, D and Madan, JC and Kelley, CP and Daines, M and Rice, SA and Ghishan, FK and Kiela, PR}, title = {Functional Shifts in Gut Microbiota and Associated Metabolites Suggest Gut-Brain Axis Dysregulation in Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal Infections (PANDAS).}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14051036}, pmid = {42197422}, issn = {2076-2607}, support = {NA//Alex Manful Fund/ ; RFGA2022-010-23//Arizona Department of Health Services/ ; }, abstract = {Background: Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal infections (PANDAS) are characterized by neuropsychiatric symptoms linked to immune dysregulation. Emerging evidence highlights the role of host-microbiome interactions in modulating neuro-immune functions via gut-brain axis signaling; however, its contribution to PANDAS pathophysiology remains poorly understood. Methods: We conducted microbiome analysis from samples collected across multiple sites of PANDAS patients including nasal, throat and stool. We performed an integrated multi-omics analysis of stool samples from pediatric PANDAS cases and healthy controls, including discordant twin pairs. Microbial composition and function were assessed using 16S rRNA gene sequencing, shotgun metagenomics, while untargeted metabolomic profiling was performed using ultra-performance liquid chromatography-mass spectrometry (UPLC-MS/MS). Results: PANDAS cases exhibited reduced alpha diversity and significantly altered beta diversity compared to controls, indicating shifts in gut microbial composition. Shotgun metagenomic analysis revealed differential enrichment of functional pathways, including diminished quorum sensing, altered gamma-aminobutyric acid (GABA) biosynthesis, and microbial degradation processes. Multiple gut-brain modules (GBMs) and gut metabolic modules (GMMs) associated with neurotransmission, transport activities and metabolism were significantly perturbed in PANDAS. Metabolomic profiling showed reduced functional diversity and distinct clustering of metabolic profiles, with differential abundance of amino acids, bile acids, and neuroactive compounds. Integrative analysis further identified disrupted microbe-metabolite networks allied to gut-brain signaling. Conclusions: Our findings reveal significant functional shifts in gut microbiota composition, functional capacity and metabolite profile in PANDAS, suggesting dysregulation of the gut-brain axis signaling. This study provides a foundation for development of microbiome-based biomarkers and therapeutic strategies for pediatric neuropsychiatric disorders.}, }
@article {pmid42197444, year = {2026}, author = {Franco-Moreno, A and de Ancos-Aracil, CL and Martínez-Casa-Muñoz, A and Torres-Macho, J and Ruiz-Navío, E and Bustamante-Fermosel, A and Hornero-Vázquez, M and Casado-Suela, M&#xc1;}, title = {Gut Microbiota Dysbiosis and Risk of Venous Thromboembolism: A Systematic Review.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14051059}, pmid = {42197444}, issn = {2076-2607}, abstract = {Gut microbiota dysbiosis has been proposed as a potential contributor to venous thromboembolism (VTE), although its clinical relevance remains uncertain. This review was conducted following the PRISMA 2020 guidelines. We conducted a systematic review of studies evaluating the association between gut microbiota dysbiosis and VTE. MEDLINE/PubMed, Web of Science, EMBASE, and Scopus were searched from the inception to February 2026. Observational studies and Mendelian randomization (MR) analyses assessing microbiota composition, dysbiosis, or related metabolites in relation to VTE were included. Risk of bias was assessed using established tools. Thirteen studies were included (five observational and eight MR). Observational evidence showed heterogeneous findings. Microbial metabolites such as trimethylamine N-oxide and lipopolysaccharides were associated with prothrombotic profiles in some studies, but no consistent association with VTE risk or recurrence was observed. The differences in microbiota composition were reported, although based on small populations. MR analyses identified microbial taxa with potential protective or risk associations, but most findings were modest and not robust after multiple testing correction. Gut microbiota dysbiosis may contribute to VTE through inflammatory and metabolic pathways; however, current clinical evidence is limited and inconsistent. Further prospective studies are needed to clarify causality and clinical implications.}, }
@article {pmid42197459, year = {2026}, author = {Cheng, J and Zhao, Z and Teng, B and Zhang, W and Wang, Y}, title = {Rethinking Microbial Chemical Ecology: Secondary Metabolites as Concentration-Dependent Signaling Hubs with Implications for Anti-Virulence Intervention.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14051074}, pmid = {42197459}, issn = {2076-2607}, support = {52070072, 51879080, 51509129//National Natural Science Foundation of China/ ; 2019YFC1804303//National Key Research &amp; Development Program of China/ ; }, abstract = {Microorganisms construct complex social communities through the exchange and interaction of chemical substances. Traditional research has typically drawn a strict distinction between quorum-sensing (QS) signaling molecules and cytotoxic secondary metabolites; however, this simplistic classification limits our in-depth understanding of microbial chemical ecology and complex collective behavior. Recent studies have shown that many secondary metabolites exhibit dual functions, acting as signaling molecules that facilitate information exchange at low concentrations. This paper proposes an integrated signaling network framework that views secondary metabolites as key nodes linking microbial collective behavior and environmental adaptation. We explore how this network mechanism overcomes the limitations of linear signaling models, thereby elucidating how microorganisms balance cell growth and metabolite synthesis in dynamic environments. We also introduce emerging spatial omics and synthetic biology tools, which hold great potential for precisely deciphering complex chemical signaling networks at the microscopic scale. Translating these mechanisms into technological applications could enable dynamic, autonomous control of bacterial metabolism in industrial biotechnology, significantly enhancing the yield of target products. Finally, we emphasize the critical importance of reframing chemical ecology as a dynamic signaling network. This shift in ecological and evolutionary perspective not only provides novel intervention pathways based on network decoupling to address the increasingly severe crisis of antibiotic resistance (AMR) but also establishes a theoretical foundation for host microbiome regulation, environmental bioremediation, and industrial multi-strain collaborative engineering.}, }
@article {pmid42197462, year = {2026}, author = {Yan, J and Jiang, L and Li, Y and Lv, H and Wu, W and Yang, L and Chen, J and Shi, D}, title = {The Dual Roles of Gut Microbiota in Biliary Atresia: Mechanisms, Biomarker Potential, and Therapeutic Implications.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14051076}, pmid = {42197462}, issn = {2076-2607}, abstract = {Biliary atresia (BA) is a progressive fibroinflammatory cholangiopathy of infancy that rapidly advances to cholestasis, fibrosis, cirrhosis, and liver failure if bile drainage is not restored early. Although Kasai hepatoportoenterostomy (KPE) remains the standard first-line operation, many children still develop recurrent cholangitis, persistent cholestasis, and progressive native liver injury. Increasing evidence indicates that the gut microbiota participates in this clinical course through the gut-liver axis. In BA, dysbiosis may weaken the intestinal barrier, increase translocation of microbe-associated molecular patterns (MAMPs), amplify innate and adaptive immune activation, disturb bile acid signaling, and promote fibrogenic and ferroptosis-related injury. In contrast, beneficial taxa and their metabolites may preserve epithelial integrity, support immune tolerance, maintain bile acid homeostasis, and constrain oxidative stress. This review summarizes current evidence on these contrasting harmful and protective effects, stage-specific microbiome signatures reported before and after KPE, and critically evaluates the present status of microbiota-based biomarkers and interventions. We emphasize that although several microbial signatures and therapeutic approaches are promising, they are not yet ready for routine clinical implementation and require prospective validation with standardized endpoints.}, }
@article {pmid42197464, year = {2026}, author = {Ramkissoon, P and DuCasse, A and Berman, I and Sadanaga, J and O'Neill, I and Gondek, DC}, title = {Prebiotics Enhance Microbiome Recovery Following Antibiotic-Induced Dysbiosis.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14051079}, pmid = {42197464}, issn = {2076-2607}, support = {R15AI144802//National Institute of Health/ ; }, abstract = {Antibiotic-induced dysbiosis disrupts gut microbiome diversity and functionality, often leading to negative health outcomes, including reduced short-chain fatty acid production, increased susceptibility to opportunistic pathogens, and an increased number of bacterial colonies exhibiting antibiotic resistance. This study investigates the effects of prebiotics (inulin-type fructans) and probiotic supplementation on microbiome recovery in a murine model. Broad spectrum antibiotics induced near-total microbiome depletion, significantly reducing microbial diversity and metabolite production. Prebiotic supplementation demonstrated superior efficacy during recovery in restoring microbiome diversity (~180 species), improving microbiome diversity metrics, and promoting metabolites, particularly butyrate and valerate, compared to probiotics or unmanipulated recovery. While effective in suppressing opportunistic bacterial growth, probiotics significantly delayed total microbial diversity recovery and resulted in lower diversity metrics (~50 species). However, prebiotic-treated microbiomes exhibited a wider antibiotic resistance profile in culturable bacteria, highlighting prebiotics' unique impact on the resistome. These findings underscore the potential of prebiotics for recovery from gut dysbiosis while emphasizing the need for further research to address safety considerations regarding their impacts on antibiotic resistance. Importance: This study explores the impact of prebiotic vs. probiotic manipulation of the microbiome in an antibiotic-induced dysbiosis mouse model. Our data demonstrate that prebiotics are more efficacious at enhancing total diversity and limiting the expansion of potentially harmful opportunist bacteria. This is the first study to indicate that prebiotics increase the number of culturable bacterial colonies resistant to antibiotics. These results contribute to our understanding of microbiome manipulation to promote health and limit disease.}, }
@article {pmid42197472, year = {2026}, author = {Zhao, Z and Dong, W and Zhou, Z and Fan, J}, title = {Stand Age-Associated Rhizosphere Bacterial Succession in the Desert Shrub Haloxylon ammodendron.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14051087}, pmid = {42197472}, issn = {2076-2607}, support = {2023E01007//Shanghai Cooperation Organization Science and Technology/ ; }, abstract = {Haloxylon ammodendron is a keystone shrub widely used for ecological restoration in arid regions of Northwest China. However, how rhizosphere bacterial communities reorganize across stand ages remains poorly understood. Rhizosphere soils were collected from one-, three-, and six-year-old stands using full-length 16S rRNA sequencing. Although alpha diversity remained relatively stable, beta diversity revealed pronounced community turnover. The dominant phyla were conserved across stands, whereas genus- and species-level composition shifted systematically along the age gradient. Younger stands were enriched in stress-tolerant and early colonizing taxa, intermediate stands showed increased representation of plant-associated and nitrogen-cycling bacteria, and older stands harbored taxa associated with complex carbon turnover and stress adaptation. Network analysis suggested modular co-occurrence patterns across stand ages and PICRUSt2-based functional inference indicated a conserved core metabolic repertoire accompanied by gradual ecological differentiation in pathways related to resource utilization and environmental response. Together, these findings suggest a stand age-associated pattern of rhizosphere bacterial succession and provide insight into microbial community differentiation in a desert shrub system.}, }
@article {pmid42197474, year = {2026}, author = {Li, B and Zhao, Q and Li, H and Xu, Z and Zhou, T and Guo, X and Zhou, L}, title = {Effects of Different Cropping Patterns on Soil Microbial Community and Function in Ningxia Irrigation-Silted Soil.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14051089}, pmid = {42197474}, issn = {2076-2607}, support = {2023BCF01049//Ningxia Key Research and Development Program/ ; 2026BBF02011//Ningxia Key Research and Development Program/ ; }, abstract = {Irrigation-silted soil in Ningxia represents a unique, anthropogenically modified agroecosystem, beneficial for regional food security. Yet, how different agricultural management techniques influence soil microbiome diversity remains poorly explored. Full-length amplicon sequencing (16S rRNA and ITS) was applied to assess the effects of vegetable and maize cultivation, relative to an uncultivated wasteland control, on soil bacterial and fungal community. Cropping patterns significantly influenced microbial alpha diversity, with contrasting effects on bacterial and fungal communities. Specifically, bacterial diversity peaked in vegetable fields, while fungal diversity was highest in maize fields. Both the bacterial and fungal community structures differed markedly among the three land-use types (p < 0.01). Although Pseudomonadota (among bacteria) and Ascomycota (among fungi) were the dominant phyla across all soils, each land-use type harbored distinct biomarkers. For example, vegetable fields facilitated the enrichment of the genus Fusarium, whereas maize fields were characterized by both Pseudomonadota and diverse saprotrophic fungi. Based on functional prediction, sulfur oxidation and cellulose decomposition were enhanced in soil with vegetable cultivation, while maize cultivation promoted relatively broader metabolic activity and enriched arbuscular mycorrhizal fungi compared with the control. Agricultural practices act as selective filters shaping soil microbial assembly and function, which provide a theoretical foundation for sustainable management strategies aimed at preserving soil health.}, }
@article {pmid42197476, year = {2026}, author = {Yang, EJ and Park, HR}, title = {The Gut-Brain Axis in Post-Traumatic Stress Disorder: From Biological Mechanisms to Microbiome-Based Therapeutic Strategies-A Narrative Review.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14051091}, pmid = {42197476}, issn = {2076-2607}, support = {KSN2225011//KIOM/ ; }, abstract = {Post-traumatic stress disorder (PTSD) is a debilitating psychiatric condition that impairs psychological functioning and increases susceptibility to various chronic illnesses, including inflammatory, metabolic, and cognitive disorders. Recent advances in neuroscience and microbiology have identified the brain-gut-microbiota axis as a key mediator of neuroimmune and neuroendocrine regulations, providing new insight into the pathophysiology of PTSD. This review synthesizes current findings from preclinical and clinical studies on gut microbiome alterations in PTSD, highlighting the underlying mechanistic pathways. Dysbiosis in PTSD is associated with immune dysregulation, altered neuroendocrine signaling, and neurotransmitter imbalances. Animal models, particularly those using the single prolonged stress paradigm, have demonstrated behavioral and microbial changes that mirror the characteristics of human PTSD. Human studies have revealed reduced abundance of beneficial bacterial taxa and increased inflammation-associated genera in patients with PTSD. Although emerging evidence supports the role of gut microbiota in PTSD, further research is needed to establish causal relationships and optimize microbiome-targeted therapies. Overall, the gut microbiome offers a novel and potentially modifiable target for the prevention and treatment of PTSD.}, }
@article {pmid42197478, year = {2026}, author = {Li, Z and Liu, Y and Liu, Z and Jiang, Z and Wang, Y and Xing, B and Mei, C and Wang, H}, title = {Avibacterium paragallinarum: Pathogenesis Mechanisms and Subunit Vaccine Development.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14051093}, pmid = {42197478}, issn = {2076-2607}, support = {KJCX20251102//Beijing Academy of Agricultural and Forestry Sciences/ ; XMS202601//Beijing Academy of Agricultural and Forestry Sciences/ ; }, abstract = {Avibacterium paragallinarum (A. paragallinarum) is the primary causative agent of infectious coryza in chickens. Infection often leads to growth retardation in broilers and a 10% reduction in egg production, reaching over 40% in laying hens. The problem is particularly severe under intensive farming conditions, significantly jeopardizing global poultry health and farming profitability. From a 'One Health' perspective, this not only disrupts the stability of the food supply chain, but also increases antibiotic usage due to disease prevention and control needs, thereby aggravating antimicrobial resistance (AMR) and posing a global public health challenge. This review systematically summarizes advances in the pathogenesis of A. paragallinarum and the protective immunity induced by subunit vaccines. It focuses on the infection mechanisms of A. paragallinarum, emphasizing its colonization strategies in the infraorbital sinus and nasal epithelium of chickens, and analyzes the roles of key virulence factors such as hemagglutinin and capsule in adhesion, colonization, and immune evasion. We integrate the tissue-specific pathogenesis of A. paragallinarum with the role of respiratory commensal microbiota in facilitating infection, providing an in-depth analysis of the bacterium's key immune evasion strategies, thus offering novel insights into host-pathogen-microbiome interactions. Concurrently, to the best of our knowledge, this review provides the first comprehensive overview of current developments in subunit vaccines and their immunoprotective properties, with special attention to limitations in eliciting mucosal immune responses. By delving into the pathogen-host interaction mechanisms, this review aims to inform the optimization of subunit vaccine design and immunization strategies. Ultimately, it seeks to establish a theoretical basis and practical framework for precise control of A. paragallinarum.}, }
@article {pmid42197480, year = {2026}, author = {Duran Yunga, ER and Rodriguez Coyago, ML}, title = {Structure and Function of the Dental Plaque Microbiome in Eubiosis: A Systematic Review of Ethnic-Racial Influences.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14051095}, pmid = {42197480}, issn = {2076-2607}, abstract = {While a conserved core microbiome is shared across healthy individuals, significant interindividual taxonomic variation exists; however, the specific influence of genetic ancestry on supragingival plaque structure in eubiosis remains unclear. This systematic review analyzed evidence regarding taxonomic variations in supragingival plaque associated with ethnicity in systemically healthy populations. A search was conducted in PubMed, Scopus, ScienceDirect, and Scielo following PRISMA 2020 guidelines, covering literature up to October 2025. Cross-sectional studies using genomic sequencing or metagenomics were included, with quality assessed via the GRADE system. Six studies met eligibility criteria. Results identified a universal core microbiome structurally dominated by Corynebacterium spp. and Streptococcus spp. However, distinct ethnic-specific taxonomic signatures emerged, such as the enrichment of Fusobacterium spp. in African Americans and Corynebacterium spp. in Caucasians, alongside the exclusive presence of Sneathia spp. in Burmese individuals. Although a basal microbial architecture necessary for homeostasis exists, ethnicity acts as a biological filter defining distinctive bacterial profiles and differential susceptibilities. These findings suggest that while the core microbiome is conserved, the composition of peripheral species in the dental plaque hedgehog structure varies according to ancestry. This supports a transition from standardized dental care to personalized medicine oriented towards the patient's biological heritage.}, }
@article {pmid42197490, year = {2026}, author = {Feng, J and Huang, J and Zhou, S and Chen, X and Zhou, G and Wang, X and Wen, X and Shi, Q and Guo, P and Li, Q and Xie, X}, title = {Scalp Microbiota Dysbiosis in Seborrheic Alopecia and Restoration Following Herbal Extract Shampoo Intervention.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14051106}, pmid = {42197490}, issn = {2076-2607}, support = {2022GDASZH-2022010101//Guangdong Academy of Sciences/ ; }, abstract = {Seborrheic alopecia (SA) is one of the most common forms of hair loss with a complex pathogenesis involving multiple etiological factors. Although the scalp microbiome has been implicated in various scalp disorders, its specific role in the development and progression of SA remains incompletely understood. To characterize the scalp microbiome in SA, we performed high-throughput sequencing of the 16S rRNA gene and ITS region on scalp samples from 41 Chinese SA participants before and after a 12-week intervention with a shampoo containing herbal extracts (ginger root, Polygonum multiflorum, and Platycladus orientalis leaf) and 29 healthy controls. The untreated SA group exhibited significant microbial dysbiosis compared to the healthy controls, characterized by reduced bacterial and fungal alpha diversity and increased relative abundances of Staphylococcus, Cutibacterium, and Malassezia. LEfSe analysis confirmed the significant enrichment of these three genera. Correlation network analysis revealed a substantial restructuring of microbial interactions in the untreated SA group: Staphylococcus and Malassezia lost all positive correlations with other genera, whereas Cutibacterium displayed relatively stable topological relationships. Following the 12-week intervention, the treated SA group showed significant clinical improvement (reduced hair loss and scalp sebum content), along with a restoration of microbial diversity to levels comparable to the healthy group and a normalization of the abundances of Staphylococcus and Malassezia. Our study confirms the critical role of scalp microecological dysbiosis in SA pathogenesis and identifies Staphylococcus and Malassezia as key taxa strongly associated with this dysbiosis. These findings provide a theoretical foundation for developing microbiome-targeted strategies for SA treatment and support the use of multi-targeted, plant-based interventions to restore microbial homeostasis and promote hair growth.}, }
@article {pmid42197498, year = {2026}, author = {Chacón-Navarrete, H and Barbudo-Lunar, M and Ruiz-Castilla, FJ and Ramos, J}, title = {Debaryomyces hansenii Reshapes the Fungal Community of Iberian Cured Pork Loin: An ITS1 Metabarcoding Approach.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14051113}, pmid = {42197498}, issn = {2076-2607}, support = {Grants Plan Galileo and Plan Propio de Investigaci&#xf3;n 2024 and 2025//University of C&#xf3;rdoba/ ; FPU23//the Spanish Ministry of Science, Innovation and Universities/ ; }, abstract = {Increasing consumer demand for natural and safe food products has led to the exploration of biocontrol alternatives to chemical preservatives, especially in the cured meat industry. The yeast Debaryomyces hansenii has emerged as a promising biocontrol candidate due to its antagonistic properties against spoilage fungi. This study assessed the impact of D. hansenii inoculation on the fungal community structure of Iberian cured pork loin using high-throughput sequencing of the ITS1 region. Ion Torrent ITS1 amplicon sequencing, QIIME2/DADA2 pipeline, and ALDEx2 differential abundance analysis were applied to this study. Pork loin samples inoculated with D. hansenii were compared to non-inoculated controls to evaluate changes in the fungal microbiome. Inoculation resulted in a marked decrease in fungal diversity and evenness, indicating strong competition by D. hansenii against native fungal populations. This effect was reflected in a significant reduction in alpha diversity in inoculated samples (Shannon, p = 0.0042; Pielou p = 0.0075; Gini-Simpson, p = 0.0081). Notably, genera associated with spoilage and mycotoxin production, particularly Aspergillus and Penicillium, were significantly reduced in inoculated samples. Simultaneously, D. hansenii became dominant, reducing other yeasts and filamentous fungi. These findings highlight the powerful competitive and biocontrol potential of D. hansenii, demonstrating its ability to improve microbial safety by potentially reducing mycotoxin-associated risks through the suppression of toxigenic genera. This is the first study to characterise the fungal community of Iberian pork loin using metabarcoding under D. hansenii inoculation. The findings confirm that the inoculation of D. hansenii can substantially reduce fungal contamination risks. Overall, the results contribute valuable insights into microbial interactions during meat curing and underscore the practical benefits of targeted starter cultures for enhancing food safety and quality.}, }
@article {pmid42197517, year = {2026}, author = {Albastaki, A and Smith, J}, title = {Choosing Between Short-Read 16S, Full-Length ONT 16S, and Long-Read Shotgun Metagenomics for Soil Microbiome Studies: A Critical Review of the Benchmarking Evidence.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14051132}, pmid = {42197517}, issn = {2076-2607}, abstract = {Studying soil microbiomes is challenging because soil contains thousands of microbial species at vastly different abundances. The choice of sequencing method has a strong effect on which of these species are detected and how the community is described. Three approaches now dominate soil microbiome research: short-read 16S rRNA amplicon sequencing on Illumina platforms, full-length 16S sequencing on Oxford Nanopore Technologies (ONT) platforms (particularly the R10.4.1 flow cell), and long-read shotgun metagenomics. Each has distinct biases that shape the recovered community, yet researchers routinely select a method based on cost, understanding, or local expertise rather than on a clear knowledge of what each approach methodically over- or under-represents. Here, we review head-to-head benchmarking studies that have applied two or more of these methods to the same soil or directly comparable samples. We show that while long-read and short-read 16S approaches generally converge on dominant taxa and on between-sample differences, they disagree substantially on alpha diversity estimates, rare taxon detection, and the relative abundances of entire phyla. The R10.4.1 flow cell chemistry has narrowed but not eliminated the accuracy gap with Illumina, and shotgun metagenomics reveals systematic biases in both short and long-read assembly that depend on population diversity within the sample. We synthesise this evidence into an evidence-based decision framework tied to specific research questions and recognise the gaps in soil-specific benchmarking that limit current methods. Rather than asking which platform is "best," we argue that method choice should be framed as an important part of study design, with the biases of the chosen method acknowledged and, where possible, controlled for.}, }
@article {pmid42197522, year = {2026}, author = {Li, Y and He, M and Song, Y and Liu, L and Xiao, J and Wang, J and Yang, B and Ouyang, S and Li, X and Peng, D and Zhu, Z}, title = {Herbicide Application Under Co-Cultivation Is Associated with Early Microbiome Assembly Shifts and Later Physiological Decline in Rice.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14051137}, pmid = {42197522}, issn = {2076-2607}, support = {2023YFD1401100//the National Key R&amp;D Program of China/ ; 32402331//National Natural Science Foundation of China/ ; }, abstract = {Herbicides considered selective to rice are generally evaluated based on their direct crop safety and weed suppression effects, yet it remains unclear whether they may also trigger indirect or context-dependent effects on rice under rice-barnyardgrass co-cultivation. To address this question, we compared rice performance and associated microbial dynamics under six conditions: rice-barnyardgrass co-cultivation and rice monoculture, each treated with a water spray control or sublethal doses of propanil (Pro, 66.7 mg a.i. L[-1]) or cyhalofop-butyl (Cyh, 5.86 mg a.i. L[-1]). Barnyardgrass exhibited visible injury and stronger leaf-level oxidative stress responses, whereas rice displayed no discernible phytotoxic symptoms. Nevertheless, under co-cultivation, herbicide treatment significantly suppressed rice growth, with up to 17.8% lower root lengths and 24.8% lower shoot fresh weights, with reductions varying by herbicide and trait. By contrast, comparable suppression was not observed under herbicide exposure or co-cultivation alone, identifying this response as an emergent, context-dependent negative effect. Microbiota reassembly emerged as an early and stage-specific component of the herbicide-associated response under co-cultivation, with the most pronounced changes detected on day 5 and occurring primarily in bacterial communities. Moreover, bacterial community variation was negatively correlated with root length (ρ = -0.664), and urease activity declined under herbicide treatment. Together, these findings indicate that in paddy fields, herbicides act not only on individual plants but also as an external disturbance to the coupled rice-barnyardgrass system, for which microbiota reorganization represents a key component of the ecological response. Our results suggest that herbicide selectivity should be interpreted within a crop-weed-microbiome context, rather than being inferred solely from their direct crop safety and weed suppression effects.}, }
@article {pmid42197523, year = {2026}, author = {Fouad, N and Elzayat, EM and Amr, D and El-Khishin, DA and Radwan, KH and Youssef, A and Khalaf, AA and Ahmed, HA and Radwan, EH and Tawkaz, S and Baum, M}, title = {Rhizosphere Microbiome Engineering for Climate-Smart Agriculture: From Synthetic Consortia to Precision Decision Support.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14051138}, pmid = {42197523}, issn = {2076-2607}, abstract = {Rhizosphere microbiome engineering is a promising approach that can enhance crop resilience and input use efficiency by redirecting plant-microbe-soil interactions toward predictable functions. Here, we review the mechanistic bases underlying rhizosphere assembly and stability, including root exudate-mediated selection, priority effects, keystone taxa, and metabolite-driven signaling, and connect these principles to proposed design rules for microbial inoculants. We present a generalizable Design-Build-Test-Learn (DBTL) framework for engineering synthetic microbial consortia, covering trait-to-module mapping (nutrient acquisition, phytohormone modulation, ACC deaminase activity, stress-protective metabolites, and biocontrol), compatibility screening, minimal yet robust community architectures, and iterative optimization driven by multi-omics and high-throughput phenotyping. Translation to field settings is framed as an engineering challenge defined by formulation and administration limitations, including carrier type, seed coating and encapsulation methods, shelf life, strain invasiveness, and permanence of colonization amid environmental diversity. We also summarize how integrative measurement pipelines (amplicon and shotgun sequencing, transcriptomics, metabolomics, and network or causal analyses) can advance microbiome studies from correlation to actionability. We describe how precision agriculture (sensors, remote sensing, and variable-rate inputs) and AI/ML (split-sample comparisons, transfer learning, and active learning) approaches can accelerate strain discovery, mixture optimization, and adaptive experimentation, driven by the need for stringent controls, metadata-rich reporting, and cross-site comparability. Use cases focus on stress conditions (drought, salinity, thermal extremes, and biotic stress) to demonstrate how microbial functions translate to agronomic outcomes and to highlight critical bottlenecks for reproducible, scalable microbiome products.}, }
@article {pmid42197526, year = {2026}, author = {Xiang, Q and Bu, G and Tang, X and Shi, C and Xiong, B and Wu, L and Xiong, J}, title = {Combined Microbiome and Metabolomic Analyses Reveal That Fine-Root Invasion of Rhododendron auriculatum Sapling Enhances Microbial Decomposition of Sphagnum palustre L.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14051141}, pmid = {42197526}, issn = {2076-2607}, support = {32460293//National Natural Science Foundation of China/ ; MD2020B026//the Doctoral Start-up Fund of Hubei Minzu University/ ; 2025AFD169//the Joint Fund of Hubei Provincial Natural Science Foundation and Enshi of China/ ; }, abstract = {Phenolics in Sphagnum can inhibit its microbial decomposition. Climate warming and drainage have driven vascular plants, such as Ericaceae, to expand into Sphagnum-dominated peatland. However, the impact of fine root invasion by Rhododendron auriculatum Hemsl. on Sphagnum decomposition and changes in phenolic compounds remains unclear. This study compared Sphagnum decomposition in a Sphagnum palustre L.-dominated peatland and an R. auriculatum (Sapling)-S. palustre peatland by examining the microscopic structure of S. palustre and microbial community composition. Decomposition was higher in the R. auriculatum-S. palustre peatland. On this site, bacterial metabolic types such as aerobic chemoheterotrophy and chemoheterotrophy had higher relative abundances, as did fungal trophic modes, including those with combined ectomycorrhizal, ericoid mycorrhizal, and saprotrophic functions. Acid phosphatase, laccase, total nitrogen (TN), C/N ratio (C:N), and pH differed significantly across decomposition stages. Microbial communities are affected by physicochemical factors and enzyme activities. Untargeted metabolomics revealed more downregulated than upregulated phenolics, cinnamic acids, and tannins, indicating loss of phenolic compounds. In summary, R. auriculatum fine root invasion altered enzyme activities and physicochemical properties, driving the restructuring of bacterial and fungal trophic modes and accelerating S. palustre cell wall and hyaline cell decomposition.}, }
@article {pmid41963410, year = {2026}, author = {Tahara, T and Shijimaya, T and Yamazaki, J and Shimogama, T and Kobayashi, S and Nakamura, N and Takahashi, Y and Tomiyama, T and Fukui, T and Shibata, T and Naganuma, M}, title = {Enrichment of T: A→A: T substitutions in the TP53 gene in esophageal carcinoma with high Fusobacterium burden.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41963410}, issn = {2045-2322}, support = {22K08089//Japan Society for the Promotion of Science/ ; }, abstract = {UNLABELLED: Exogenous lifestyle and environmental risk factors impact mutation burden in both benign and cancerous tissues. Moreover, interactions between the mucosa-associated microbiome and such genotoxic changes have been implicated in several cancer types. This study aimed to characterize the TP53 mutation spectrum in esophageal carcinoma (EC) with high amounts of Fusobacterium species. Quantitative PCR analysis of Pan-Fusobacterium species and Fusobacterium nucleatum was performed in 112 EC cases (89 squamous cell carcinomas [SCCs] and 23 adenocarcinomas). Results were correlated with TP53 mutation spectra and clinicopathological features. Both Pan-Fusobacterium species and F. nucleatum were significantly enriched in EC tissues compared with adjacent normal esophagus (both P < 0.001). The TP53 mutation spectrum in Pan-fusobacterium-high EC was characterized by a decrease in C: G→A: T and an increase in T: A→A: T substitutions (P < 0.001). Pan-fusobacterium-high EC was associated with male sex, tumors located in the upper or middle esophagus, and squamous cell histopathology. Cases of EC with detectable levels of Pan-Fusobacterium and F. nucleatum were also associated with more invasive tumors and more advanced cancer stages at diagnosis. These results suggest that EC with high numbers of Fusobacterium species was associated with a distinct mutation spectrum. Future studies should be conducted to investigate the mechanisms of how Fusobacterium species induce specific somatic mutations.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-45806-5.}, }
@article {pmid41975253, year = {2026}, author = {Aquino, CI and La Vecchia, M and Pasolli, E and Sala, G and Ligori, A and Boldorini, R and Ferrante, D and Dianzani, I and Aspesi, A and Surico, D and Remorgida, V}, title = {Decoding the microbial landscape of endometrial cancer: a case-control study.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41975253}, issn = {1471-2180}, support = {IG 2021-ID. 25886//Associazione Italiana per la Ricerca sul Cancro/ ; }, abstract = {BACKGROUND: The human microbiome plays an emerging role in cancer biology, yet its contribution to endometrial cancer (EC) remains poorly defined. This study investigates the microbial composition of the vaginal, rectal, and endometrial sites in women with and without EC, aiming to uncover microbial signatures associated with the disease.<br><br>RESULTS: We performed shotgun metagenomic sequencing on vaginal, rectal, and endometrial samples from 25 patients with EC and 27 control women undergoing hysterectomy for benign conditions. Vaginal and rectal swabs were collected before surgery, while endometrial swabs were obtained post-hysterectomy using a sterile brushing technique to prevent cross-contamination. Vaginal microbiota in patients with EC showed significantly higher microbial diversity and distinct community composition compared to controls. These differences remained significant after adjusting for age and body mass index. Several bacterial species, including Peptococcus niger, Anaerococcus murdochii, Mobiluncus, Porphyromonas, and Prevotella, were more abundant in the vaginal microbiota of patients with cancer. In contrast, Lactobacillus spp. were more abundant in vaginal and rectal samples of control subjects.<br><br>CONCLUSIONS: This work represents one of the few studies to comprehensively examine the relationship between the vaginal, rectal, and endometrial microbiomes in the context of EC, suggesting a potential role for microbial imbalance in disease development. The findings underscore the importance of site-specific microbial analyses in gynecologic oncology and support further investigation into the microbiome as a possible biomarker for early detection and a target for preventive strategies.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-05017-4.}, }
@article {pmid41975427, year = {2026}, author = {Zhang, Z and Bai, J and Liu, Y and Wang, J and Lv, Z and Tang, L and Wang, R and Gao, L and Liu, C and Lu, S and Fu, X and Ni, J and Wan, P}, title = {Effects of synthetic breast milk on the gut metagenome and whole blood transcriptome in lambs.}, journal = {BMC veterinary research}, volume = {22}, number = {1}, pages = {}, pmid = {41975427}, issn = {1746-6148}, support = {NYHXGG.2023AA206-3//Agricultural GG Project of Xinjiang Production and Construction Corps/ ; 2025AB5012//Tacheng Talents Project/ ; 2025AA01504//Project of Major Science and Technology Project of the Corps/ ; 2022TSYCCX0124//Young Science and Technology Top Talent Program of Tianshan Talent Training Program in Xinjiang Province/ ; XJARS-09-26//Xinjiang Agriculture Research System/ ; CARS-39-07//China Agriculture Research System/ ; }, abstract = {UNLABELLED: Early postnatal nutrition is crucial for the growth and development of lambs, and artificial milk formulas are widely used as alternatives to breast milk in intensive sheep production. However, the molecular and microbial mechanisms underlying the differences between breast milk and formula feeding remain unclear. This study aimed to compare the fecal metagenomic and whole blood transcriptomic profiles of lambs fed breast milk (BF group) and commercial formula (FF group) from 4 to 45 days of age, to provide a theoretical basis for optimizing formula compositions. A total of 6 lambs were randomly divided into two groups (n = 3 per group), with body weight and body dimensions measured at 45 days of age, followed by fecal metagenomic sequencing and whole blood transcriptomic sequencing. The results showed that BF lambs had significantly higher body weight, body length, heart girth, and chest width than FF lambs. Metagenomic analysis revealed that at the phylum level, Bacteroidetes was enriched in FF lambs, whereas Firmicutes predominated in BF lambs. Differential abundance was also observed at the genus level (higher Desulfovibrio in FF lambs) and the pathway level, with BF lambs enriched in quorum sensing and FF lambs showing higher abundances of pathways related to ubiquinone and other terpenoid-quinone biosynthesis. Moreover, transcriptomic analysis identified 3290 differentially expressed genes (DEGs) between the two groups, with DEGs mainly enriched in metabolic pathways, mTOR signaling pathway, osteoclast differentiation, B cell receptor signaling pathway and MAPK signaling pathway. Collectively, compared with FF, BF enhanced lamb growth, optimized gut microbiome structure and modulated blood transcriptomic profiles related to metabolism, signaling and immunity. These findings highlight the key microbial taxa and functional pathways modulated by breastfeeding, providing valuable insights for the development of more effective milk formula alternatives.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12917-026-05460-5.}, }
@article {pmid42179543, year = {2026}, author = {de Figueiredo, VSA and Canto Bueno, P and Ponce Fuentes, EA and Dini, C and Alves de Brito Júnior, A and Busato de Feiria, SN and Mattos-Graner, RO and Ricomini Filho, AP and Klein, MI}, title = {Putative Prebiotics Can Disrupt 3D Architecture and Modulate the Microbial Population to Prevent Cariogenic Biofilm Build-Up In Vitro.}, journal = {ACS omega}, volume = {11}, number = {19}, pages = {27942-27957}, pmid = {42179543}, issn = {2470-1343}, abstract = {Background/Objective(s)/Introduction: Prebiotics are substances that metabolically favor certain microorganisms of a microbiome, promoting homeostasis. Dental biofilm microorganisms are enmeshed in a matrix of extracellular polymeric substances that they produce. A diet rich in sucrose can lead to a dysbiotic biofilm associated with microbial acid production and a change in the matrix's composition (mostly water-insoluble glucans), which allows acids to accumulate within biofilms and contribute to teeth demineralization. Thus, the effects of putative prebiotics were evaluated to verify their impact on exopolysaccharides, the microbial population, and biofilm formation. Materials and methods: Five potential prebiotics (N-acetyl-d-glucosamine, arginine, proline, sodium nitrate, and urea) were evaluated compared with a substance-free control. A Streptococcus mutans biofilm model on polystyrene plates was used to determine the concentrations of substances that would inhibit sucrose-derived biofilm formation. Selected concentrations were then used to verify the production of insoluble glucans by glucosyltransferase B. Afterward, S. mutans and mixed-species (S. mutans, Actinomyces naeslundii, and Streptococcus gordonii) biofilms were grown on saliva-coated hydroxyapatite discs with sucrose to evaluate the microbial population and 3D biofilm structure (exopolysaccharides and bacterial biovolume). Lastly, a microcosm biofilm formed on polystyrene plates was used to assess the effects of the substances on biomass and the proportion of distinct viable microbial populations. Results: Only arginine inhibited insoluble glucan production and S. mutans biofilm accretion (≅ 90%). Arginine and proline inhibited a biofilm build-up in mixed-species and microcosm models and modulated microbial counts of species associated with cariogenic biofilms. In the microcosm biofilm, urea hindered biomass accretion in initial biofilms and the counts of aciduric microbiota and fungi, but N-acetyl-d-glucosamine stimulated microbial growth. Sodium nitrate affected the size and shape of microcolonies in S. mutans and mixed-species biofilms. Conclusion(s): Among the substances tested, arginine and proline modulated the microbial population and hindered biofilm accretion, especially arginine, which hampered glucan production. However, urea is the only substance able to impede fungal growth.}, }
@article {pmid42179783, year = {2026}, author = {Chae, S and You, HS and Kim, JG and Cho, JY}, title = {Exploratory Serum Metabolomics Identifies Metabolic Subgroups Across the Gastric Dysplasia-Early Cancer Spectrum.}, journal = {Journal of Cancer}, volume = {17}, number = {5}, pages = {968-978}, pmid = {42179783}, issn = {1837-9664}, abstract = {BACKGROUND: Gastric carcinogenesis involves progressive molecular and metabolic alterations, yet non-invasive biomarkers for early detection and risk stratification remain limited. This study aimed to characterize systemic metabolomic changes across the gastric carcinogenesis spectrum and to investigate potential associations between serum metabolites and gastric microbiome-related pathways.<br><br>METHODS: In this exploratory study, untargeted serum metabolomics was performed on samples from patients with gastric dysplasia or early gastric cancer (n = 40) and healthy controls (n = 14). Differential metabolite analysis, principal component analysis, and k-means clustering were used to identify metabolic alterations and potential metabolic subgroups. Microbial pathway associations were examined using metabolite origin inference based on gastric-resident taxa reported in prior studies.<br><br>RESULTS: Eighteen metabolites were significantly altered in gastric carcinogenesis compared with healthy controls. Six metabolites displayed distinct profiles that suggest two metabolic subgroups, including one subgroup showing a metabolic pattern closer to that of healthy controls, independent of histologic severity. Microbial pathway inference suggested contributions from Pseudomonadota, Actinomycetota, and Bacillota, with ornithine-related metabolites emerging as a key metabolic link previously implicated in dysplasia-to-carcinoma progression. These findings highlight inter-patient heterogeneity and potential metabolic-microbial interactions underlying gastric carcinogenesis.<br><br>CONCLUSION: These findings suggest that serum metabolomic profiling may capture metabolic heterogeneity across the gastric dysplasia-early gastric cancer spectrum and generate hypotheses regarding microbiome-related metabolic alterations. While exploratory in nature, this study provides preliminary evidence supporting the potential of serum metabolites as non-invasive indicators of early gastric carcinogenesis, warranting validation in larger and longitudinal cohorts.}, }
@article {pmid42179876, year = {2026}, author = {Theodorea, CF and Azzahra, NA and Idrus, E and Nurkolis, F and Djais, AA and Mashima, I}, title = {The role of Veillonella species in oral carcinogenesis: is prevalence linked to oral squamous cell carcinoma?.}, journal = {Frontiers in oral health}, volume = {7}, number = {}, pages = {1740043}, pmid = {42179876}, issn = {2673-4842}, abstract = {Oral squamous cell carcinoma (OSCC) remains a significant health challenge because of its aggressive nature and poor survival outcomes. While established risk factors such as tobacco use, alcohol consumption, and human papillomavirus play critical roles, increasing evidence suggests that oral microbial dysbiosis may contribute to carcinogenesis. Among oral commensals, Veillonella species have gained attention because of their ecological role in oral biofilms and metabolic interactions with other microbes, and have also been increasingly identified in altered abundances within OSCC patient samples. This narrative review synthesizes available clinical, epidemiological, and molecular studies investigating the prevalence and biological roles of Veillonella species in OSCC. Relevant English-language publications between 2000 and 2025 were identified through database searches in Pubmed Scopus and Web of Science using keywords related to Veillonella, oral microbiome, dysbiosis, and OSCC. The reviewed evidence reveals a dynamic and stage-dependent shift in Veillonella abundance during oral carcinogenesis. Several studies report enrichment of Veillonella in oral potentially malignant disorders and early tumorigenesis, whereas reduced levels are frequently observed in advanced OSCC. These findings suggest that Veillonella may function as an ecological modulator of tumor-associated microbiota rather than as a single pathogenic driver. Proposed mechanisms include metabolic cross-feeding with lactic-acid-producing bacteria, modulation of inflammatory pathways, biofilm restructuring, and host-microbe metabolic signaling. Overall, current evidence supports a microbial ecological shift model, in which Veillonella participates in early dysbiotic transitions preceding OSCC development but may decline as tumor microenvironments evolve. Further standardized and multiomics studies are needed to clarify its potential as a microbiome-based biomarker and therapeutic target.}, }
@article {pmid42179978, year = {2026}, author = {Chen, S and Xu, B and Lu, M}, title = {Metformin-Associated Gastrointestinal Intolerance: A Narrative Review of Mechanisms and Clinical Management.}, journal = {Clinical medicine insights. Endocrinology and diabetes}, volume = {19}, number = {}, pages = {11795514261453485}, pmid = {42179978}, issn = {1179-5514}, abstract = {Metformin-associated gastrointestinal (GI) intolerance is a frequent clinical problem that can limit treatment initiation, delay dose escalation, and reduce long-term adherence in patients with type 2 diabetes mellitus. Common symptoms include nausea, diarrhea, abdominal discomfort, and bloating, although symptom pattern and severity vary substantially between individuals. This narrative review summarizes current evidence on the determinants, mechanisms, and clinical evaluation of metformin-associated GI intolerance. In routine practice, assessment should begin with potentially modifiable exposure-related factors, including dose, single-dose burden, titration pace, formulation, administration with meals, kidney function, and concomitant medications. If symptoms persist or appear disproportionate to treatment exposure, clinicians should then consider broader host susceptibility, including baseline GI vulnerability, microbiome-related influences, altered bile acid handling, mucosal and neuroregulatory responses, comorbidity burden, and polypharmacy. This exposure-susceptibility framework provides a practical way to interpret metformin-related GI symptoms in routine care. It supports a stepwise clinical approach in which modifiable contributors are addressed first, broader context is reviewed when needed, and premature discontinuation is avoided whenever possible. Despite limitations in the current evidence base, available data support a structured and clinically useful approach to metformin intolerance.}, }
@article {pmid42180143, year = {2026}, author = {Beaulieu, ML and Patel, NB and Wojtys, EM}, title = {The gut microbiome's role in the development and progression of post-traumatic osteoarthritis: A systematic review.}, journal = {Osteoarthritis and cartilage open}, volume = {8}, number = {2}, pages = {100807}, pmid = {42180143}, issn = {2665-9131}, abstract = {OBJECTIVE: Gut microbiome dysbiosis is linked to osteoarthritis (OA), but its specific association with post-traumatic osteoarthritis (PTOA) is less understood. This systematic review synthesizes evidence linking PTOA and the gut microbiome to clarify its role in PTOA pathogenesis.<br><br>METHOD: Literature searches were conducted in PubMed, Embase, SPORTDiscus, and Web of Science through October 2025. Quantitative, original human and animal studies examining associations between the presence/severity of PTOA and gut microbiota composition and diversity were included. These measures were extracted and synthesized. Risk of bias was assessed using ROBINS-I for non-randomized and RoB 2 for randomized studies (PROSPERO registration: CRD42024496152).<br><br>RESULTS: Thirteen studies met inclusion criteria, all utilizing small animal PTOA models. Generally, they found significant gut microbiome differences between PTOA and control groups. Collectively, these preclinical studies provided evidence that the gut microbiome can influence biological processes underlying PTOA, particularly via inflammatory and metabolic pathways, and vice versa. Two studies examined exercise, showing it can reduce PTOA severity by slowing articular cartilage degeneration and subchondral bone loss, increase microbiome diversity, and mitigate negative effects of poor diet.<br><br>CONCLUSIONS: Current literature from animal models suggests the gut microbiome may play a role in PTOA development and progression, emphasizing a bidirectional "gut-joint axis." Traumatic joint injuries may lead to systemic inflammation affecting the gut microbiome, which may exacerbate joint inflammation and PTOA progression. Significant gaps remain, particularly the lack of human studies. Future research should prioritize clinically relevant animal models and human studies to elucidate the gut microbiome's role in PTOA pathogenesis.}, }
@article {pmid42180198, year = {2026}, author = {Nnorom, MA and Du, B and Wang, Z and Tian, Z and Hough, R and Avery, L and Saroj, D and Guo, B}, title = {Dynamics of the Microbiome and Antibiotic Resistome in Hyper-Mesophilic Anaerobic Digestion of Cattle Manure Assisted with Granular Activated Carbon.}, journal = {ACS environmental Au}, volume = {6}, number = {3}, pages = {435-448}, pmid = {42180198}, issn = {2694-2518}, abstract = {The use of conductive materials, such as granular activated carbon (GAC), for optimization of the anaerobic digestion (AD) process has garnered attention in recent years; however, its impact on the dynamics of the microbiome and resistome in continuous AD systems remains unclear, especially under temperature variation. This study combined culture-based bacterial enumeration and shotgun metagenomics to investigate the impact of two GAC application strategies, suspended and packed, on the fate of pathogens (viable Escherichia coli) and ARGs during the AD of cattle manure at 40 and 45 °C. The results show that GAC mitigated the process imbalance and shock induced by temperature transition. The microbial community in the AD sludge was highly impacted by temperature but not GAC, while GAC biofilms showed notably higher archaeal abundance. All AD reactors reduced viable E. coli, with the highest reduction occurring in the packed GAC reactors (95.70-96.24%), followed by the suspended GAC (94.53-95.69%), and then the non-GAC (92.77-94.24%). Culturable tetracycline-resistant bacteria were reduced below the quantification limit in all reactors. Reduction of ampicillin-resistant bacteria showed stochastic trends at 40 °C but improved at 45 °C, indicating limited impact by GAC. ARGs and mobile genetic elements (MGEs) were reduced in all reactors at comparable levels, regardless of GAC addition. Temperature transition exerted a mixed effect, with higher reduction of some resistance classes (MLS, tetracycline, and multidrug) and lower reduction of others (bacitracin, aminoglycoside, beta-lactam, and streptothricin). Mantel test and Procrustes analysis revealed a significant correlation between the resistome and the bacterial community, inferring that shifts in the ARG host population were a major determinant of the fate of ARGs. Overall, GAC was beneficial to reactor stability but had a minimal influence on the reduction of E. coli, ARGs, and MGEs. It is highly recommended to monitor antimicrobial resistance using both culture-based and culture-independent methods.}, }
@article {pmid42180244, year = {2026}, author = {Jiang, Z and Li, G}, title = {Microbiome mediation analysis: methods, assumptions, and practical considerations.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1832981}, pmid = {42180244}, issn = {2235-2988}, mesh = {Humans ; *Microbiota ; Bayes Theorem ; *Mediation Analysis ; }, abstract = {Microbiome mediation analysis provides a principled framework for understanding how environmental, behavioral, or clinical exposures influence human health through microbiomemediated biological pathways. However, its application is complicated by the compositional, sparse, and high-dimensional nature of microbiome data. A growing body of methods has been developed to address these challenges, drawing on structural equation modeling, counterfactual causal inference, distance-based testing, Bayesian variable selection, and nonparametric approaches. This paper reviews methodological developments designed to address these challenges and enable valid and interpretable mediation analysis in microbiome studies with particular emphasis on their underlying assumptions, limitations, and appropriate contexts of use, while also highlighting existing gaps and outlining future research directions.}, }
@article {pmid42180251, year = {2026}, author = {Naorem, RS and Dutta, K and Bora, SS and Teli, AB}, title = {Proton pump inhibitor exposure modulates functional and transcriptional responses in Lactobacillus acidophilus: a comprehensive computational and experimental insights.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1781831}, pmid = {42180251}, issn = {2235-2988}, mesh = {*Proton Pump Inhibitors/pharmacology ; *Lactobacillus acidophilus/drug effects/genetics/metabolism ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Gene Expression Regulation, Bacterial/drug effects ; Gene Expression Profiling ; Pantoprazole/pharmacology ; Probiotics ; Computational Biology ; Bacterial Proteins/metabolism/genetics ; Humans ; }, abstract = {Proton pump inhibitors (PPIs) are among the most widely prescribed medications for gastric acid-related disorders. However, their effect on the gut microbiota remains incompletely understood, despite emerging evidence suggesting potential long-term alterations in microbial composition and reductions in beneficial taxa. In this study, Lactobacillus acidophilus, a well-known probiotic species, was used as a representative model organism to investigate the microbiological effects of PPIs. This specific bacterium is linked to immune modulation, vitamin metabolism, and the preservation of the epithelial barrier. The effects of PPIs on L. acidophilus at the structural and functional levels were elucidated by an integrated framework including subtractive genomics, molecular docking, molecular dynamics (MD) simulations, antimicrobial assays, and transcriptional analysis. Using a multi-criteria scoring system, essential, non-redundant, non-human homologous cytoplasmic proteins were ranked and mapped to important pathways such as ATP synthesis, peptidoglycan biosynthesis, amino-sugar metabolism, nucleotide metabolism, and protein maturation. Molecular docking suggested potential binding of pantoprazole and rabeprazole to targets such as MurA, MurB, MurE, GlmS, NadE, AtpD, Def, and PyrH proteins. MD simulation showed stable protein-PPI complexes with localized flexibility changes near catalytic domains while preserving the global fold. Consistent with in-silico expectations, both pantoprazole and rabeprazole exhibited dose-dependent growth inhibition of L. acidophilus, whereas qRT-PCR revealed transcriptional downregulation of genes involved in cell-wall production, NADH metabolism, and energy generation. Pantoprazole elicited the most uniform transcriptional suppression, whereas rabeprazole had stronger but more varied effects. The present findings provide preliminary insights into potential interactions between PPIs and probiotic bacteria at the molecular and cellular levels. However, the results reflect species-specific responses under in vitro conditions and should be interpreted cautiously, as transcriptional changes do not directly confirm functional inhibition and the concentrations tested may represent upper-range exposure scenarios. Further in vivo and multi-species studies are required to validate this observation and better understand their clinical implications for microbiome stability during PPI therapy.}, }
@article {pmid42180283, year = {2026}, author = {Pazla, R and Antonius, A and Mohd-Aris, A and Ikhlas, Z and Fitri, Y and Bansi, H and Dewi, YL and Hadiatry, MC and Qomariyah, N and Wahyuwardani, S and Yusriani, Y and Rohaeni, ES and Bakrie, B}, title = {The role of tannin-based products in mitigating enteric methane emissions in ruminant livestock: A review.}, journal = {Journal of advanced veterinary and animal research}, volume = {13}, number = {1}, pages = {192-206}, pmid = {42180283}, issn = {2311-7710}, abstract = {Global greenhouse gas accumulation receives significant contributions from methane emitted by ruminant livestock, thereby exacerbating climate change. Tannin-based feed additives are being investigated by researchers as a potential means to alter rumen fermentation and reduce methanogenesis. The researchers build on previous studies on the impact of tannins on methane reduction in the digestive tract and investigate the biological mechanisms of tannins, which are coupled with the potential of animal feed sources. Tannins kill methanogenic archaea by reducing protozoa and altering volatile fatty acid composition. This simultaneously results in reduced methane emissions and improved feed and nitrogen utilization efficiency. As a result, animal production is made more efficient by the reduction of nitrogen excretion and the enhancement of protein metabolism. The use of tannins, essential oils, biochar, and probiotics together is being researched as a way to treat the diet. Yet there are still issues, such as the adverse effects of tannins on nutrition, inconsistent tannin supply across sources, and microbial adaptation over time. The effectiveness of tannins also varies and is connected to the plant source, concentration, and processing methods. Besides, scientists are developing encapsulation methods and selecting optimal feeding protocols to increase tannin effectiveness while minimizing unwanted effects. Future researchers must improve the administration techniques for tannins, develop more efficient delivery systems, and conduct a comprehensive assessment of how tannins affect rumen microbiome health and animal performance. Tannin application emerges as an ecological approach that serves sustainability in livestock management systems and helps environmental adaptation practices.}, }
@article {pmid42180286, year = {2026}, author = {Nguyen, TT and Nguyen, CK and Tran, PD and Duong, KN and Nguyen, HT}, title = {Insights into milk microbiota differences among healthy, mastitis-suspected, and subclinical mastitis cows at dairy farms in Southern Vietnam.}, journal = {Journal of advanced veterinary and animal research}, volume = {13}, number = {1}, pages = {207-220}, pmid = {42180286}, issn = {2311-7710}, abstract = {Objectives: This study aimed to characterize and compare the milk microbiota composition among Holstein Friesian cows with healthy (HU), mastitis-suspected (MSU), and subclinical mastitis (SM) udders in Southern Vietnam. Materials and Methods: Sixty milk samples were collected from two dairy farms and classified based on somatic cell counts (SCC) into three groups: HU (<200,000 cells/ml), MSU (200,000-400,000 cells/ml), and SM (>400,000 cells/ml). Bacterial communities were profiled using Illumina MiSeq sequencing of the 16S rRNA gene. Results: The prevalence of subclinical mastitis was 46.67% (p < 0.05). The core microbiome was dominated by phyla of Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes (>90%); and taxa of Moraxellaceae, Sphingomonadaceae, Enterobacteriaceae, Erysipelotrichaceae, and Streptococcaceae. Analysis revealed significant dysbiosis in the SM group, characterized by elevated relative abundances of mastitis-associated taxa (Mycobacteriaceae, Streptococcaceae, Moraxellaceae, Pasteurellaceae, and Mycoplasmataceae) compared to healthy udders (p < 0.05). Conversely, commensal taxa typical of healthy milk (Rikenellaceae, Lactobacillaceae, Sphingomonadaceae, and Opitutaceae) were significantly depleted in SM samples but remained abundant in both HU and MSU groups (p < 0.05). Notably, the microbial profile of the MSU group was statistically similar to that of the HU group (p > 0.05), with no distinct variation in key bacterial families. Principal coordinate analysis further confirmed that SM samples formed a distinct cluster separate from the HU and MSU groups. Conclusions: Subclinical mastitis drives significant shifts in the milk microbiome. However, mastitis-suspected cows retain a microbiome similar to that of healthy udders, suggesting that SCC thresholds alone may require careful interpretation in borderline cases.}, }
@article {pmid42180552, year = {2026}, author = {Chen, Y and Wei, X and Yi, X and Jiang, DS}, title = {Interactions between the gut microbiome and ferroptosis in degenerative diseases: Novel mechanisms and potential therapeutic strategies.}, journal = {Acta pharmaceutica Sinica. B}, volume = {16}, number = {5}, pages = {2711-2729}, pmid = {42180552}, issn = {2211-3835}, abstract = {Degenerative diseases are a group of medical conditions characterized by the progressive and irreversible deterioration of cells, tissues, and organs over time. Emerging evidence highlights the alteration and functions of the gut microbiome in the development of degenerative diseases. Ferroptosis, a regulated form of cell death characterized by iron-dependent lipid peroxidation, has been implicated as a pivotal factor in the regulatory effect of the gut microbiome on degenerative diseases. Moreover, gut metabolites, particularly short-chain fatty acids and trimethylamine N-oxide, are closely related to iron overload, redox imbalance, and lipid peroxidation. Recently, microbiome-based therapies, such as fecal microbiota transplantation, have been considered novel therapeutic strategies. In this review, we focus on degenerative diseases and explore the interactions between the gut microbiome and ferroptosis, aiming to provide new insights into the underlying mechanisms and clinical implications.}, }
@article {pmid42180556, year = {2026}, author = {Ruhle, M and Espinosa-Maldonado, C and de Anda-Jáuregui, G and Vadillo-Ortega, F and Hernández-Lemus, E}, title = {Leakage-aware machine learning reveals structured clinical and vaginal microbiome patterns associated with preterm birth in a Mexican cohort.}, journal = {Frontiers in global women's health}, volume = {7}, number = {}, pages = {1799518}, pmid = {42180556}, issn = {2673-5059}, abstract = {BACKGROUND: Preterm birth (PTB, <37 weeks of gestation) remains a major cause of neonatal morbidity and mortality worldwide, with Hispanic/Latino populations markedly underrepresented in microbiome-based studies, particularly in intensive data analytics scenarios.<br><br>METHODS: We applied leakage-aware machine learning as a descriptive analytical framework to characterize clinical and vaginal microbiome patterns associated with preterm birth in 43 pregnant Mexican women (110 longitudinal samples, 14 preterm births) recruited from public hospitals in Mexico City. Vaginal microbiome profiles (genus-level 16S rRNA V3-V4 sequencing) were analyzed using centered log-ratio transformation. We evaluated 12 model configurations representing combinations of two algorithms (Random Forest, Elastic Net), three clinical feature selection strategies (minimal DREAM-style adjustment, literature-based comprehensive features, data-driven empirical selection), and two microbiome representations (ANCOM-BC2 differentially abundant taxa, full filtered profiles). Random Forest and Elastic Net models were implemented within a rigorous subject-level nested cross-validation design to prevent data leakage. Model discrimination metrics were interpreted as indicators of internal cohort structure rather than as estimates of clinical predictive performance. Differential abundance analyses were conducted using ANCOM-BC2 both globally and within cross-validation folds to assess feature robustness.<br><br>RESULTS: The best-performing descriptive model (Random Forest with data-driven feature selection and full microbiome) exhibited AUROC 0.813 &#xb1; 0.110 , consistent with structured clinical-microbiome patterning within the cohort. Global differential abundance analysis (ANCOM-BC2, adjusted for maternal age and pre-pregnancy BMI) identified Mycoplasma as the only genus achieving FDR-corrected significance (LFC = + 1.004 , q = 0.049), with ten additional genera reaching nominal significance (p < 0.05). Within-fold feature importance and stability analyses consistently prioritized anthropometric variables (BMI, pre-pregnancy weight) alongside Peptostreptococcus and Mycoplasma, both detected in 100% of cross-validation iterations, indicating relative signal stability despite limited sample size.<br><br>CONCLUSIONS: This study illustrates how descriptive, leakage-aware machine learning can organize, prioritize, and interpret clinical and microbiome signals in small, underrepresented cohorts. At this stage, it does not yet present a clinically deployable predictor for preterm birth, but we are working towards this definite goal in the future, with prenatal screening strategies in mind. The observed internal discrimination reflects, in this sense, cohort-specific structure rather than validated predictive performance and establishes a methodological basis for future externally validated classifiers in Latin American populations.}, }
@article {pmid42180801, year = {2026}, author = {He, Y and Liu, B and Li, W and Zhou, X and Tao, H}, title = {COPD-Lung Cancer Comorbidity: Mechanistic Insights and Precision Oncology Implications.}, journal = {International journal of chronic obstructive pulmonary disease}, volume = {21}, number = {}, pages = {606647}, pmid = {42180801}, issn = {1178-2005}, mesh = {*Pulmonary Disease, Chronic Obstructive/complications/epidemiology ; *Lung Neoplasms/diagnosis/epidemiology/etiology ; Comorbidity ; Humans ; Early Diagnosis ; Biomarkers ; Precision Medicine ; }, abstract = {BACKGROUND: Chronic obstructive pulmonary disease (COPD) and lung cancer frequently coexist, constituting a clinically consequential comorbidity with major implications for precision medicine.<br><br>MECHANISTIC INSIGHTS: Beyond shared environmental exposures such as tobacco smoke and air pollution, COPD has emerged as an independent driver of pulmonary carcinogenesis, mediated through persistent inflammation, genomic instability, epigenetic remodeling, and microbiome-immune dysregulation. Patients with COPD-associated lung cancer exhibit distinct molecular hallmarks, including reduced EGFR mutation frequency, enrichment of LRP1B truncations, and elevated tumor mutational burden, which collectively reprogram tumor immunogenicity and therapeutic responsiveness, favoring immune checkpoint blockade over targeted EGFR-directed therapy.<br><br>Recent advances integrating low-dose CT (LDCT) with spirometry, liquid biomarkers (eg, S100A12, TLR4), and AI-enhanced radiomic algorithms have substantially improved early detection capabilities. In parallel, microbiome-derived signatures provide novel tools for risk stratification and treatment personalization.<br><br>THERAPEUTIC IMPLICATIONS: Preventive and therapeutic strategies, including statin therapy, inhaled corticosteroids, preoperative pulmonary optimization, and microbiome modulation, are emerging as promising approaches to intercept the COPD-lung cancer continuum and improve clinical outcomes.<br><br>CONCLUSION: This review synthesizes current evidence spanning epidemiology, molecular pathogenesis, diagnostic innovations, and comorbidity-tailored interventions, culminating in a "comorbidity-centered precision management" framework. By bridging mechanistic discoveries with clinical implementation, this paradigm may contribute to reducing COPD-lung cancer mortality and could support the advancement of the global precision oncology agenda.}, }
@article {pmid42181048, year = {2026}, author = {Quigley, EMM}, title = {The Gut-Brain Axis-From Science to Clinical Practice.}, journal = {Gastro hep advances}, volume = {5}, number = {7}, pages = {100975}, pmid = {42181048}, issn = {2772-5723}, abstract = {While the idea that the gut and brain communicate has been appreciated for centuries and commented on in many literary works, the formal introduction of the term "gut-brain axis" was much more recent. To the lay person, the operations of this axis are best represented by the effects of stress on gastrointestinal function. Indeed, exactly how stress impacts on such functions as motility and secretion has been extensively studied and its modus operandi revealed. Brain-to-gut communications can be effected via the autonomic nervous system or the hypothalamic pituitary adrenal axis. The recognition that the vagus nerve is predominantly comprised of sensory neurons led to the realization that gut-to-brain traffic is ubiquitous and largely subconscious only achieving conscious recognition at times of alarm or when the gut is injured or diseased. As the field of neurogastroenterology has developed, our understanding of the parallel involvement of "big" and "little" brains by neurodegenerative diseases has increased with Parkinson disease being the exemplar. Of late, the microbiome has entered the fray, and the concept of the microbiome-gut-brain axis emerged. Animal studies have provided considerable evidence to indicate that the gut microbiome can influence brain morphology and function and, thereby, modify behavior. Studies in animal models have also revealed that signals from on high can alter microbiome composition and function. For understandable reasons, it has proven more challenging to explore the microbiota-gut-brain axis and its implications to health and disease in humans. Nevertheless, the possibility that microbiome modulation could exert positive impacts on neurologic and psychological disorders has attracted considerable interest and some hints of efficacy have begun to emerge. For now, pending further studies in humans caution needs to be exerted in assigning pathogenic significance to interactions between the gut microbiome and the brain.}, }
@article {pmid42181089, year = {2026}, author = {Souf, IB and Saidani, M and Mhamdi, L and Darej, C and Ben Larbi, M and M'Hamdi, N}, title = {Nutrigenomics in precision livestock and poultry farming: Enhancing productivity, welfare, and sustainability through gene-tailored diets.}, journal = {Veterinary and animal science}, volume = {33}, number = {}, pages = {100680}, pmid = {42181089}, issn = {2451-943X}, abstract = {Nutrigenomics has emerged as a valuable framework for improving precision livestock and poultry production by elucidating how diet interacts with genetic and molecular pathways to shape animal performance, health, product quality, and sustainability. This review provides a structured synthesis of current research on nutrigenomic applications across major livestock and poultry species, focusing on precision feeding, productivity, disease resilience, reproductive performance, environmental efficiency, and product quality. The review followed a structured narrative approach informed by PRISMA 2020 principles and included peer-reviewed studies published between 2015 and 2026 that examined diet-related genomic, transcriptomic, proteomic, metabolomic, or epigenetic responses in production animals. The reviewed evidence indicates that nutrigenomics can support improvements in feed efficiency, metabolic adaptation, immune function, and environmental outcomes, particularly when integrated with precision nutrition strategies. The manuscript also highlights emerging technologies that are accelerating progress in the field, including multi-omics platforms, microbiome-informed interventions, epigenetic tools, artificial intelligence-based predictive systems, and genome editing for target validation. Despite these advances, translation into commercial practice remains constrained by limited large-scale validation, inconsistent reporting, cost barriers, and regulatory and societal concerns. Nutrigenomics nonetheless represents a promising pathway toward more efficient, resilient, and sustainable animal production systems.}, }
@article {pmid42181191, year = {2026}, author = {Kaminska, H and Wieczorek, W and Pruc, M and Janeczko, M and Siudak, Z and Szarpak, L}, title = {Gut microbiota and the early prevention window in type 1 diabetes and latent autoimmune diabetes in adults: a state-of-the-art narrative review on diet and metabolites.}, journal = {Frontiers in endocrinology}, volume = {17}, number = {}, pages = {1837746}, pmid = {42181191}, issn = {1664-2392}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Diabetes Mellitus, Type 1/prevention &amp; control/microbiology/metabolism ; *Latent Autoimmune Diabetes in Adults/prevention &amp; control/microbiology/metabolism ; *Diet ; Adult ; Autoimmunity ; }, abstract = {Autoimmune type 1 diabetes (T1D) is typically the end point of a prolonged process involving genetic susceptibility, the emergence of islet autoimmunity, and progressive loss of pancreatic beta-cell reserve rather than the day hyperglycaemia is first diagnosed. In parallel, research on the gut microbiome has shifted from searching for single causal taxa to examining ecosystem-level functions, microbial metabolites, and host-pathway interactions. In this narrative review, we synthesise prospective, mechanistic, and translational evidence on the role of the gut microbiome in T1D and latent autoimmune diabetes in adults (LADA) using a stage-aware, function-first framework. Across the current literature, the most consistent signals concern impaired intestinal barrier homeostasis, reduced fermentation-related capacity, altered short-chain fatty acid signalling, perturbations in tryptophan-derived and bile acid-related pathways, and their downstream effects on immune regulation and inflammatory tone. In T1D, evidence from prospective early-life cohorts suggests that microbiome maturation, together with diet, infections, and antibiotic exposure, may influence the risk of islet autoimmunity and the tempo of progression toward clinical disease. In LADA, the available evidence is more limited and largely cross-sectional, but supports an immunometabolic interpretation that includes altered microbiome and metabolomic profiles. We propose that the main translational priority is not taxon-specific manipulation, but identification of stage- and age-specific windows of susceptibility across the life course and alignment of these windows with low-risk, mechanistically plausible dietary and microbiome-modulating strategies. This framework may help guide microbiome-informed counselling, study design, and research prioritisation in autoimmune diabetes.}, }
@article {pmid42181229, year = {2026}, author = {Nakhal, MM and Nafees, F and Mydeen, AB and Baydoun, I and Hamad, MIK}, title = {Gestational dysbiosis is associated with altered early-life microbial seeding and favors pathobiont expansion in offspring.}, journal = {iScience}, volume = {29}, number = {6}, pages = {115925}, pmid = {42181229}, issn = {2589-0042}, abstract = {Maternal gut microbiota shape early-life microbial community assembly, yet how maternal dysbiosis alters microbial inheritance remains poorly defined. Here, we investigated whether antibiotic-induced maternal dysbiosis affects microbial patterns in offspring using a gestational vancomycin mouse model. 16S rRNA profiling revealed that dysbiotic dams exhibited reduced microbial richness and evenness, with the enrichment of pathobionts including Enterococcus faecium and Cronobacter muytjensii. Offspring of dysbiotic dams displayed distinct microbial community structures, lower diversity, and reduced similarity to their mothers (21.5%) compared with controls (61%). Notably, maternal dysbiosis was associated with the enrichment of Gammaproteobacteria pathobionts in offspring, whereas control dyads were characterized by commensal Bacteroidia and Clostridia. These findings indicate that maternal dysbiosis during pregnancy is associated with altered maternal-offspring microbial similarity and shifts in early-life microbial community composition.}, }
@article {pmid42181274, year = {2026}, author = {Akbar, M and Yadav, S and Naseer, A and Hameed, R and Sarkar, A and Nazir, A}, title = {Gut microbiota-derived succinate links proteostasis collapse to α-synuclein pathology and aging.}, journal = {iScience}, volume = {29}, number = {6}, pages = {115941}, pmid = {42181274}, issn = {2589-0042}, abstract = {The gut microbiome profoundly influences brain health, yet the specific microbial metabolites and mechanisms contributing to Parkinson's disease pathology remain poorly defined. Using the Caenorhabditis elegans model expressing human α-synuclein, we systematically tested key microbial fermentation products and identified succinate as a potent driver of pathology. Succinate exposure markedly increased α-synuclein aggregation, disrupted proteostasis, and compromised mitochondrial function - manifesting as oxidative stress, reduced mitochondrial content, and attenuated UPR[mt]. These cellular defects led to dopaminergic neurodegeneration, locomotory impairments, and reduced lifespan, establishing succinate as a pro-neurodegenerative and pro-aging metabolite. Transcriptomic and genetic analyses revealed the involvement of nutrient-sensing pathways, prominently mTORC1, in promoting proteotoxic stress. Together, these findings highlight a direct link between microbial metabolism, proteostasis collapse, and neurodegeneration, establishing succinate as an active modulator of aging. Targeting succinate signaling mechanisms may therefore represent a tractable strategy for microbiome-based interventions in Parkinson's disease and age-associated neurodegeneration.}, }
@article {pmid42181833, year = {2026}, author = {Ren, M and Jia, J and Li, Y and Shen, N and Shi, Y and Wang, Z and Huang, X and Li, G and Xiong, G and Peng, R}, title = {The emerging role of non-Helicobacter pylori microbiome in gastric carcinogenesis: a comprehensive review of pathogenic mechanisms and clinical implications.}, journal = {Gastroenterology report}, volume = {14}, number = {}, pages = {goag033}, pmid = {42181833}, issn = {2052-0034}, abstract = {Gastric cancer remains a leading global health concern, with its etiology shaped by complex interactions between the host and its microbiome. The primary etiological role of Helicobacter pylori (H.pylori) has been well-established, but recent research has pointed to the significant contributions of non-H.pylori pathogens in the onset and progression of gastric cancer. These pathogens contribute to gastric tumorigenesis by directly compromising the gastric epithelial barrier and invading gastric epithelial cells, affecting long-range processes, disrupting microbial balance, and influencing the host's immune microenvironment. In the following, we comprehensively elucidated the potential mechanisms by which Streptococcus anginosus, Methylobacterium, Prevotella, Candida albicans, and Epstein-Barr virus actively participate in gastric tumorigenesis. Beyond this, ongoing investigations seek to identify additional microorganisms that may contribute to gastric cancer development, offering new insights into the multifactorial nature of the disease. Collectively, these findings highlight the critical involvement of diverse non-H.pylori microorganisms at various stages of gastric cancer progression, advancing our understanding of microbe-driven carcinogenesis.}, }
@article {pmid42181960, year = {2026}, author = {Rahimah, S and Tallei, TE and Savitri, M and Yamada, C and Kim, HJ and Choi, M and Park, MN and Ophinni, Y and Kim, B}, title = {Molecular basis of precision nutrition: Food components, microbiome-derived metabolites, and multi-omics modeling.}, journal = {Food chemistry. Molecular sciences}, volume = {12}, number = {}, pages = {100411}, pmid = {42181960}, issn = {2666-5662}, abstract = {Metabolic disorders, including obesity, type 2 diabetes, metabolic syndrome, and fatty liver disease, reflect multifactorial interactions among diet, host genetics, the environment, and the gut microbiome. However, conventional population-level dietary guidance often fails to capture the marked interindividual variability in metabolic responses to identical foods and nutrients. Precision nutrition has therefore emerged as an integrative paradigm that combines genomics, epigenomics regulation, microRNA-mediated control, and microbiome profiling to refine dietary recommendations, with a growing emphasis on targeted functional food-based strategies for metabolic health. This narrative review synthesizes the mechanistic foundations of precision nutrition, emphasizing how functional foods and their bioactive constituents engage nutrient-sensing and regulatory pathways that connect dietary exposures to gene regulation and downstream metabolic phenotypes. We summarize evidence for diet-gene interactions at key metabolic loci, epigenetic programming shaped by early-life nutrition, and diet-responsive microRNAs as candidate biomarkers of nutritional response. We further examine microbiome-derived signaling, specifically short-chain fatty acids and bile-acid metabolism within the gut-liver axis, as a major route by which functional dietary components can influence host pathways and condition metabolic outcomes. We highlight insights from large cohorts and controlled metabolic profiling studies and discuss enabling methodological advances, including multi-omics integration, causal inference, and machine learning models for response prediction. Key limitations remain, notably incomplete reproducibility, heterogeneity in exposure and outcome measurements, data governance challenges, and barriers to clinical implementation. In summary, precision nutrition provides a biologically grounded framework for personalized functional-food and dietary strategies, but robust validation and responsible translation are required before routine adoption.}, }
@article {pmid42182002, year = {2026}, author = {Chen, S and Hu, X and Pan, W and Chen, T and Xie, X and Zhang, Y}, title = {Integrated metagenomic and culture-dependent profiling reveals electric shavers as selective reservoirs for multidrug-resistant opportunistic pathogens.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1839764}, pmid = {42182002}, issn = {1664-302X}, abstract = {INTRODUCTION: Personal care items are commonly viewed as passive vehicles for microbial transfer; however, the physicochemical stresses they impose may actively shape microbial persistence, community composition, and the distribution of resistance-associated determinants. Electric shavers may therefore constitute an underrecognized anthropogenic niche for the enrichment of clinically relevant antimicrobial resistance traits.<br><br>METHODS: We sampled electric shavers from 10 individuals at early (day 2) and mature (day 21) usage stages, generating 8 high-quality metagenomes and recovering 97 viable isolates spanning 16 bacterial species. Deep metagenomic sequencing, combined with whole-genome sequencing of 45 representative isolates, was used to resolve the ecological, functional, and evolutionary features of shaver-associated microbiomes.<br><br>RESULTS: Shaver-associated community assembly was dominated by stringent environmental filtering, which promoted the repeated enrichment of stress-adapted lineages across hosts, notably Acinetobacter ursingii MLST3244 and Klebsiella pneumoniae MLST995 and MLST23. We further identified recurrent mobile genetic element-associated resistance islands and plasmid backbones in different host cohorts, suggesting repeated selection under shared anthropogenic pressures rather than direct evidence of de novo convergent evolution. Importantly, viable Klebsiella pneumoniae isolates co-carried extended-spectrum &#x3b2;-lactamase genes such as bla SHV and major virulence determinants, while metagenomic profiling detected reads assigned to mcr- and tet(X)-like gene variants at the community level, targeted PCR further confirmed the presence of these resistance determinants.<br><br>DISCUSSION: Because routine shaving can generate barrier-disrupting micro-abrasions, electric shavers may function as selective reservoirs for multidrug-resistant bacteria. Our findings reveal a previously overlooked exposure interface through which everyday personal care practices may promote the enrichment and persistence of clinically important resistance and virulence determinants.}, }
@article {pmid42182007, year = {2026}, author = {Brown, AL and McGovern, MJ and Schickle, A and Sharp, KH and Apprill, A}, title = {Controlled temperature-induced dormancy leads to predictable microbial recovery in the temperate coral microbiome.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1799468}, pmid = {42182007}, issn = {1664-302X}, abstract = {INTRODUCTION: Dormancy is a common response to harsh conditions across the tree of life. Increasingly, the animal microbiome is suggested to mediate dormancy, including onset, maintenance and exit or recovery periods. However, it is unclear what triggers dormancy and the consistency of microbial patterns across populations. Because it regularly undergoes dormancy during winter in the northernmost part of its range, the temperate coral Astrangia poculata can serve as a model for studying coral-microbiome dynamics during environmental stress and recovery.<br><br>METHODS: Here, we experimentally manipulated temperature to induce dormancy and measured the microbial community shifts associated with dormancy and during the days that the corals were exiting dormancy in two populations.<br><br>RESULTS: Our treatments successfully induced dormancy, which was maintained through low temperatures. We found consistent and predictable shifts in the microbiome during dormancy and during the recovery period while corals exited dormancy.<br><br>DISCUSSION: We suggest Sulfitobacter, a key genus in tropical corals, may be involved in early recovery in the assembly of the microbiome. Broadly, our results highlight that the inducible, consistent, and persistent microbial restructuring associated with Astrangia dormancy can be applied more generally to tropical coral recovery from stress.}, }
@article {pmid42182016, year = {2026}, author = {Su, S and Li, H and Li, W and Yang, Z and Zhang, Q}, title = {Differences in microbial community structure induced by tillage practices under straw return associated with metabolic functions.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1794771}, pmid = {42182016}, issn = {1664-302X}, abstract = {This study aimed to elucidate the biological mechanisms through which different tillage practices affect wheat yield and nutrient use efficiency under straw return conditions, focusing on rhizosphere microbial communities, metabolite profiles, and their interactions to inform improved agricultural management. The field experiment tested three treatments: no-tillage with all straw mulching (SN), rotary tillage straw return (SR), and plow tillage straw return (SP). Using high-throughput sequencing and liquid chromatography-tandem mass spectrometry, we investigated how different treatments affected the microbial community in wheat rhizosphere soil and metabolic functions through microbiome and non-targeted metabolomics analyses. SN helped to increase the wheat yield, soil nutrient content in the plow layer, and enzyme activity. Compared with SN, the yields were 8.3% and 12.4% lower under SR and SP, respectively, the soil organic carbon contents were 13.2% and 5.6% lower, and the pH values were 2.7% and 1.2% higher. Tillage practices significantly altered the composition and diversity of the bacterial and fungal communities. The species richness of bacterial and fungal communities followed the order of: SP > SR > SN and SN > SP > SR, respectively. The stabilities of the bacterial and fungal communities exhibited the same distribution pattern. Principal coordinate analysis and PERMANOVA indicated that under straw return, different tillage practices led to significant separation of soil bacterial and fungal communities. Furthermore, Actinobacteria and Proteobacteria contributed most significantly to differences in the bacterial community structures, and Ascomycota and Basidiomycota contributed most significantly to differences in the fungal community structures. Under straw return, different tillage practices significantly altered soil metabolite composition. Bacterial communities correlated more strongly with soil metabolites than fungal communities. Compared with SN, metabolic pathways for different metabolites were enriched under SR and SP, and all were related to amino acid metabolism, putatively mainly in the valine, leucine, and isoleucine biosynthesis pathways. Collectively, our findings demonstrate that tillage practice is a key regulator of straw-amended soil ecosystems, and that no-till with straw mulching optimizes yield and nutrient efficiency primarily by enhancing the functional synergy between the rhizosphere microbiome and metabolome.}, }
@article {pmid42182017, year = {2026}, author = {Li, J and Qiu, X}, title = {Neurodevelopmental disorders and the gut microbiome: insights into ADHD and tic disorders.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1779746}, pmid = {42182017}, issn = {1664-302X}, abstract = {This review examines the relationship between tic disorders (TD), attention deficit hyperactivity disorder (ADHD), and the gut microbiota within the framework of the gut-brain axis. We summarize current evidence on the clinical characteristics and neurobiological features of TD and ADHD, and discuss how genetic susceptibility, environmental exposures, and dietary factors may interact with gut microbial composition. We further review studies comparing the gut microbiota of affected individuals and healthy controls, with attention to recurrent taxa-level findings, functional hypotheses, and emerging microbiome-targeted interventions such as probiotics and fecal microbiota transplantation. Importantly, most available human studies remain associative rather than mechanistic, and cross-study comparability is limited by heterogeneity in sequencing approaches, cohort characteristics, medication exposure, and dietary control. Overall, current findings support the gut microbiota as a relevant component of neurodevelopmental disorders such as ADHD and TD, while highlighting the need for larger longitudinal and mechanistic studies to clarify causality and therapeutic potential.}, }
@article {pmid42182018, year = {2026}, author = {Abilda, Z and Isgandarov, I and Kanat, R and Daurov, D and Sapakhova, Z and Zhambakin, K and Daurova, A and Begaliyeva, D and Choi, K and Shamekova, M}, title = {Genome-resolved metagenomics reveals co-selection of antibiotic and metal resistance in chronically polluted industrial soils.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1829529}, pmid = {42182018}, issn = {1664-302X}, abstract = {INTRODUCTION: Chronic heavy metal contamination can restructure soil microbiomes and may co-select for antibiotic resistance, yet genome-resolved evidence from industrial soils remains limited.<br><br>METHODS: In this study, we applied Oxford Nanopore long-read metagenomic sequencing to soil samples collected across industrially influenced sites in East Kazakhstan to characterize strain-level community composition, profile antibiotic resistance genes and metal resistance genes, and relate these patterns to soil physicochemical properties.<br><br>RESULTS: Across all samples, we identified 3,053 strains, with Actinobacteria and Proteobacteria together accounting for 94.1% of the total community. Heavy metal concentrations varied markedly among sites. The resistome comprised antibiotic resistance genes from several drug classes and 238 distinct metal resistant genes, with aminoglycoside, glycopeptide, and multidrug resistance dominating the antibiotic resistance gene profile, while czcA, ruvB, arsM, and arsT were among the most abundant Metal resistant genes. Multivariate analyses showed that heavy metals, particularly Zn, significantly shaped microbial community structure as well as antibiotic resistance gene and metal resistance gene composition, and redundancy analysis identified Zn and soil pH as the principal environmental drivers. Network analyses further revealed that Bradyrhizobium icense and Conexibacter woesei acted as key super-hosts linking ARGs and MRGs, supporting heavy metal-driven co-selection within the soil microbiome.<br><br>DISCUSSION: Together, these findings show that long-read genome-resolved metagenomics can uncover how chronic industrial pollution maintains metal-adapted microbial communities while promoting the persistence and potential dissemination of antibiotic resistance in soil ecosystems.}, }
@article {pmid42182019, year = {2026}, author = {Wu, L and Li, S and Han, F and Guo, J and Zhang, X and Xu, L}, title = {Restoring circadian disrupted gut microbial metabolite rhythms with phytochemicals: a new avenue against metabolic disease.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1801367}, pmid = {42182019}, issn = {1664-302X}, abstract = {The global epidemic of metabolic diseases-encompassing obesity, type 2 diabetes mellitus (T2DM), non-alcoholic fatty liver disease (NAFLD), and cardiovascular disease-represents a defining public health challenge of our era. The traditional model of simple caloric excess vs. expenditure has proven insufficient, giving way to a paradigm that acknowledges complex interactions between genetics, environment, and lifestyle, mediated by intricate physiological systems. Among these, the host circadian timing system and the gut microbiome have ascended as pivotal, deeply intertwined regulators of metabolic homeostasis. The gut microbiome, far from a static collection of microbes, constitutes a dynamic and metabolically active community whose composition and, critically, its functional output exhibit profound and predictable diurnal oscillations. The host's circadian clocks regulate microbial rhythms primarily by controlling the daily cycle of feeding and fasting. Modern life induces circadian disruption (CD) through ubiquitous exposure to artificial light at night, shift work, social jet lag, and erratic eating patterns. It perturbs the rhythmic dynamics of the gut ecosystem, leading to a fundamental dysregulation in the temporal production of key microbial metabolites. These metabolites, including short-chain fatty acids, secondary bile acids (BAs), indoles and other tryptophan derivatives, function as indispensable chemical messengers that coordinate peripheral metabolism, immune responses, and energy homeostasis in a precise, time-of-day-dependent manner. Their desynchronization-manifesting as mistimed, deficient, or incessant signaling-directly instigates the core pathologies of metabolic disease: insulin resistance, adipocyte dysfunction, hepatic lipid accumulation, and chronic low-grade inflammation. This review synthesizes current evidence to delineate the multilevel mechanisms through which CD drives the dysregulation of gut microbiome metabolite rhythms and establishes the causal pathways linking this dysrhythmia to metabolic pathogenesis. Furthermore, we undertake a critical evaluation of the promising therapeutic potential of dietary phytochemicals-a diverse class encompassing polyphenols, glucosinolates, and prebiotic fibers-to act as chrono-therapeutic agents. Through their multifaceted capacity to remodel microbial ecology, calibrate microbial enzymatic output, and reinforce host circadian-metabolic coupling, phytochemicals present a novel, physiologically aligned, and sustainable dietary strategy for the prevention and management of metabolic disorders. We conclude by outlining key translational challenges and propose future research directions essential for harnessing the potential of the "clock-microbiome-metabolite" axis within the framework of precision nutrition and medicine.}, }
@article {pmid42182023, year = {2026}, author = {Duan, J and Chen, Y and Zhang, X and Li, C and Gao, T and Li, K}, title = {Metagenomic analysis suggests that tomato root-knot nematode infestation disrupts rhizosphere microbial networks, consistent with reduced disease suppression.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1798902}, pmid = {42182023}, issn = {1664-302X}, abstract = {INTRODUCTION: The rhizosphere microbiome serves as a critical line of defense for plant health and soil-borne disease suppression. However, the underlying mechanisms by which root-knot nematodes (RKN), a devastating soil-borne pathogen, undermine putative disease-suppressive function through destabilizing microbial interaction networks remain poorly understood.<br><br>METHODS: This study employed metagenomic sequencing coupled with microbial co-occurrence network analysis to systematically compare the community structure, interaction network topology, and functional gene profiles of the rhizosphere microbiome between healthy and RKN-infected tomato plants.<br><br>RESULTS: Our findings revealed that RKN infection significantly altered the community structure of bacteria, fungi, and viruses. This disturbance was associated with a systematic simplification and loss of modularity within microbial interaction networks. Specifically, intra-domain bacterial networks exhibited reduced scale and connectivity, whereas fungal networks showed strengthened internal cohesion. Cross-kingdom interactions (e.g., bacteria-fungi) were severely weakened, resulting in a topological imbalance characterized by "tight within domains, loose between domains." Functional profiling further indicated a distinct metabolic reprogramming in the infected rhizosphere, with a shift in resource allocation from growth and biosynthesis toward core energy acquisition and stress response.<br><br>DISCUSSION: Collectively, our results suggest that the putative decline in disease-suppressive function following RKN infection may be mechanistically rooted in the destabilization of microbial cooperative networks and the consequent loss of functional redundancy. This study provides a novel network-level ecological framework for understanding plant-microbe-pathogen interactions and lays a theoretical foundation for microbiome-based ecological management strategies against soil-borne diseases.}, }
@article {pmid42182024, year = {2026}, author = {Kostelnikova, K and Frejlichova, L and Spetik, M and Sochor, J and Eichmeier, A and Baron, M}, title = {Impact of winemaking technologies on polyphenolic composition and wine microbiome.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1846196}, pmid = {42182024}, issn = {1664-302X}, abstract = {INTRODUCTION: This study investigates how different oenological practices, including spontaneous and inoculated alcoholic fermentation (AF), variations in malolactic fermentation (MLF) and ageing, are associated with changes in microbial diversity and polyphenolic profile of Sauvignon blanc wines.<br><br>METHODS: Microbial composition was investigated through high-throughput DNA sequencing, while polyphenolic compounds were analysed using LC-MS together with total phenolic content through Folin-Ciocalteu assay and antiradical activity by DPPH assay.<br><br>RESULTS AND DISCUSSION: AF was associated with a pronounced homogenization of the microbiota, particularly through the dominance of Saccharomyces and stable epiphytic bacteria. At later stages, microbial communities showed notable compositional divergence, with their development closely linked to technological interventions and the extent of phenolic extraction. The pomace-fermented treatment exhibited the highest polyphenol content along with the greatest compositional heterogeneity, whereas treatments with lower phenolic loads exhibited simpler microbial profiles and the stable dominance of Leuconostoc after malolactic fermentation. Polyphenols appear to act as modulatory factor in microbial succession, with extraction intensity showing a more distinct association with community shifts than the fermentation regime itself. Overall, the study highlights that technological practices affecting phenolic extraction appear to play a notable role in the observed microbial trends and the resulting wine characteristics.}, }
@article {pmid42182071, year = {2026}, author = {Qin, R and Yu, P and Wang, H and Zhou, J and Gong, R and Duan, Y and Jia, H and Xie, M and Zhou, Y and Hu, J}, title = {Gut-bone axis crosstalk: Microbiota-driven immune-metabolic-neural networks in bone disorders and precision interventions.}, journal = {Journal of orthopaedic translation}, volume = {58}, number = {}, pages = {101126}, pmid = {42182071}, issn = {2214-031X}, abstract = {UNLABELLED: The gut microbiota regulates bone metabolism via a complex gut-bone axis involving short-chain fatty acids (SCFAs), immune modulation, and neuroendocrine signals. However, the precise mechanisms remain unclear, and microbiota-targeted interventions (probiotics, prebiotics, fecal microbiota transplantation) are not yet optimized for clinical use. This review systematically synthesizes the immune-metabolic-neural interaction network within the gut-bone axis, highlighting non-linear crosstalk among SCFAs, bile acids, tryptophan derivatives, immune cells (macrophages, Treg/Th17), and vagus nerve signaling. We critically assess translational hurdles, including heterogeneous study designs, confounding factors, and lack of causal evidence. Based on this network perspective, we propose a framework for future research that prioritizes multi-omics approaches, stratified interventions, and rigorous trials. This synthesis advances understanding of how gut dysbiosis drives bone disorders and paves the way for precision skeletal medicine.<br><br>This review identifies microbial markers for risk stratification of bone metabolic disorders and discusses SCFA-based strategies and fecal microbiota transplantation (FMT) in conditions including osteoporosis, impaired fracture healing, rheumatoid arthritis, and glucocorticoid-associated osteonecrosis. It provides testable hypotheses for large-scale randomized controlled trials (RCTs), directly supporting translation of microbiome research into clinical practice for bone disorders.}, }
@article {pmid42182110, year = {2026}, author = {Zhang, Z and Holton, M and Ferrer, DM and Tripp, AD and Richter, A and Dixit, PD and Urtecho, G}, title = {Metagenome-scale Modeling to Assess Microbiome Metabolic Complementarity for Precision Microbiota Transplantation Therapies.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.15.725570}, pmid = {42182110}, issn = {2692-8205}, abstract = {Fecal microbiota transplantation (FMT) holds therapeutic promise beyond recurrent Clostridioides difficile infection, but clinical outcomes remain unpredictable, in part because existing computational models do not fully capture the metabolic compatibility between donor and recipient communities. Here, we present a metagenome-scale metabolic modeling framework that quantifies metabolic niche complementarity between donor and recipient microbiomes to predict transplantation outcomes. Using MICOM-derived community metabolic models, we show that donor taxa whose metabolic flux profiles are more dissimilar from the recipient community engraft at significantly higher rates in both murine and human FMT cohorts. In a human IBS trial, metabolic models accurately predicted post-FMT community composition via leave-one-out cross-validation and recapitulated disease-associated alterations in short-chain fatty acid, sulfur, and gas metabolism. We then performed 2,548 in silico FMT simulations between IBS-D/M patients and donors from the OpenBiome biobank to demonstrate a platform for personalized donor screening. This screen identified super-donors characterized by high taxonomic diversity, broad metabolic niche coverage, and community interaction networks dominated by cross-feeding rather than competition, as quantified by a flux-derived ecological network balance index that strongly predicted engraftment potential. This framework provides a mechanistic, scalable tool for rational donor-recipient matching that could guide personalized microbiome-based therapies.}, }
@article {pmid42182112, year = {2026}, author = {Buchanan, LB and Khan, Y and Vargas, JR and Shao, Z and Biribawa, VM and Ssemunywa, HR and Namuniina, A and Okech, B and Tobian, AA and Park, DE and Liu, CM and Kaul, R and Galiwango, RM and Prodger, JL}, title = {CD11c+ myeloid cells are the predominant CD4+CCR5+ immune population in the foreskin and are increased in men with HIV-associated penile anaerobes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.11.724468}, pmid = {42182112}, issn = {2692-8205}, abstract = {Specific anaerobic species within the penile microbiome - Bacteria Associated with Seroconversion, Inflammation and Immune Cells (BASIC) - have been linked to increased HIV-1 susceptibility. These bacteria can directly disrupt epithelial integrity and are believed to increase local inflammation, resulting in an increased density of HIV-susceptible T cells in the inner foreskin. It is currently unknown whether other immune cells bearing the HIV entry receptors, CD4 and CCR5, are also elevated in individuals with a high abundance of BASIC species. Using inner foreskin tissues and penile swabs from males undergoing voluntary medical male circumcision, we performed a retrospective cross-sectional study to assess the relationship between BASIC species and the tissue density of such immune cells, including CD68+ macrophages, CD11c+ dendritic cells, and CD207+ Langerhans cells. The most abundant cells in the inner foreskin expressing the HIV co-receptors were CD11c+ dendritic cells (48.6% of CD4+/CCR5+ cells), followed by CD68+ macrophages (28.6%), CD3+ T cells (18.8%), and CD207+ Langerhans-like (8.8%) cells. The absolute abundance of BASIC species was associated with elevated tissue densities of both CD4+/CCR5+ T cells (as previously reported) and a heterogeneous population of CD3-/CD4+/CCR5+ cells of myeloid origin. In the dermis, BASIC species abundance was linked to elevated densities of cells expressing CD11c, CD68, and CD207, as well as those co-expressing CD11c and CD207; furthermore, CD11c+ and CD207+ cells were farther from the basement membrane in participants with a high abundance of BASIC species. Myeloid cells were not elevated in participants with a high abundance of control taxa. In an integrated analysis including previously published data from this same cohort, myeloid-cell densities clustered tightly together, positively correlated with BASIC species and pro-inflammatory cytokines, and had trends to negative correlations with control taxa (significant for CD207+ cell density). Overall, our findings suggest that BASIC species are associated with a broader foreskin immune phenotype marked by increased densities of HIV-susceptible myeloid and T cells, alongside epithelial disruption.}, }
@article {pmid42182121, year = {2026}, author = {Hendricks, SF and Tan, AL and Williams, AG and Buckley, KM and Strader, ME}, title = {Environmental microbial communities and host selection shape larval microbiomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.14.725214}, pmid = {42182121}, issn = {2692-8205}, abstract = {UNLABELLED: Ocean warming is altering abiotic environments and biotic interactions experienced by marine organisms, where sensitive early developmental windows occur in biologically complex seawater communities. The impact of these interactions on developmental processes and fitness in hosts is not well understood, but likely contingent on the establishment of a host-associated microbiome. Here, we hypothesize that temperature and microbial exposure during embryogenesis influence larval microbiome assembly and host morphology. Strongylocentrotus purpuratus embryos were raised in low microbial richness (LMR) or high microbial richness (HMR) seawater at ambient (14 °C) or elevated (18 °C) temperature, then collected at 2, 4, and 6 days post-fertilization (dpf) following multiple feedings. Higher microbial diversity was observed in larvae that developed in HMR seawater when compared to LMR. Differences in relative abundances of dominant microbial families between seawater and larvae suggest some degree of host selectivity in microbiome assembly. Temperature did not strongly alter microbiome composition, but both temperature and microbial condition led to differences in larval morphology by 6 dpf, potentially due to enrichment of microbes with chemoheterotrophic functions. By linking how temperature and microbial communities interact with host development, we contribute novel insights into how early-life environmental conditions impact holobiont formation and morphology.<br><br>ONE SENTENCE SUMMARY: Early developmental temperature and microbial conditions shape larval microbiome establishment and morphology.}, }
@article {pmid42182128, year = {2026}, author = {Nguyen, TH and Su, M and Lu, NT and Trotter, V and McKeithen-Mead, SA and Lopez, JA and Sun, J and Hallberg, Z and Shi, H and Ho, PY and DeFelice, BC and Taga, ME and Deutschbauer, AM and Hryckowian, AJ and Huang, KC}, title = {Phage-based microbiome manipulation reveals ecological interactions within gut communities.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.13.724931}, pmid = {42182128}, issn = {2692-8205}, abstract = {Mechanistic understanding of gut ecology is limited by the availability of tools for precise manipulation of microbiome composition. Here, we isolate lytic phages to enable targeted removal of gut commensal Escherichia fergusonii (Ef) from complex, undefined stool-derived in vitro communities. A single phage drove resistance without fitness cost in monoculture, but resistant Ef exhibited reduced fitness in communities, enabling expansion of closely related Proteobacteria. Resistance arose via reversible promoter inversion linked to outer-membrane function. A phage cocktail overcame resistance to achieve Ef knockout across communities with minimal collateral effects. Using knockout communities, we show that Ef is necessary and sufficient for preventing Salmonella invasion. Replacement with an Ef transposon-mutant library revealed that community-specific fitness defects are enriched in genes involved in outer-membrane assembly. Disruption of these genes sensitized Ef to antagonistic community members, highlighting interspecies warfare as a key driver of microbiome ecology. These results establish phage-mediated perturbation as a framework for linking species to community-level function and for enabling precision microbiome engineering.}, }
@article {pmid42182130, year = {2026}, author = {Tossas, KY and Zhu, B and Tyc, KM and Rhodes, C and Strauss, JF and Serrano, MG and Buck, GA}, title = {HPV co-infection burden, vaginal microbiota restructuring, and host context are associated with Cervical precancer risk in a racially restricted observational cohort.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.13.724979}, pmid = {42182130}, issn = {2692-8205}, abstract = {BACKGROUND: High-risk human papillomavirus (HPV) infection is necessary for cervical carcinogenesis, but HPV detection alone does not distinguish transient infection from lesions at greatest risk of progression. We evaluated whether HPV burden, vaginal microbiota structure, and host-context variables jointly characterize cervical intraepithelial neoplasia grade 3 (CIN3) in a Black/African American and White analytic cohort from the Vaginal Microbiome Health Project (VaMHP), integrating L1-based HPV typing, 16S rRNA vaginal microbiota profiling, and linked clinical metadata.<br><br>RESULTS: Among 1181 participants, 75 had CIN3. CIN3 was associated with HPV positivity (55/75, 73.3% vs 431/1106, 39.0%; odds ratio [OR] 4.31, 95% CI 2.55-7.29; Fisher exact p = 7.9 x 10^-9) and with multiple HPV infection among HPV-positive participants (35/55, 63.6% vs 176/431, 40.8%; OR 2.54, 95% CI 1.42-4.54; p = 0.0022). HPV communities in CIN3-positive samples showed higher Shannon diversity, greater observed strain richness, higher evenness, and significant beta-diversity separation. In vaginal microbiota analyses, alpha diversity did not differ by CIN3 status, but community composition did, and Lactobacillus crispatus was the only taxon depleted in CIN3 after multiple-testing correction. Race, age, and metronidazole exposure were central nodes in the host-factor network. In predictive modeling, a full integrated model combining metadata, HPV, and vaginal microbiota features (auROC = 0.745) outperformed both HPV + vaginal microbiota (auROC = 0.670) and HPV-only (auROC = 0.440) models.<br><br>CONCLUSIONS: CIN3 in this cohort was associated with coordinated shifts in virologic burden, vaginal community structure, and host social-clinical context. The results support a structure-function interpretation in which loss of Lactobacillus crispatus-dominant states and enrichment of dysbiosis-associated communities define a host-microbiome context that is more permissive to HPV persistence and precancer. These findings move beyond descriptive omics by showing that microbiome and host-context features add nonredundant discriminatory signal beyond HPV-only models.}, }
@article {pmid42182226, year = {2026}, author = {Sokolik, CC and Sahadeo, K and Vyce, J and Thomas, M and Celeste, C and Gachunga, W and Calixte, T and Ledford, I and Williams, J and Estess, E and Wilder, C and Parker, IK}, title = {Microbiome Composition Regulates Cathepsin Expression in Vaginal Fluid Across BV Diagnoses and Community State Types.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.07.723359}, pmid = {42182226}, issn = {2692-8205}, abstract = {PURPOSE: Bacterial vaginosis (BV) is associated with disruption of the vaginal microbiome and extracellular matrix (ECM) remodeling, yet the contribution of host proteases to this process remains unclear. This study investigated whether expression and activity of cathepsins K, L, S, and V differ by BV diagnosis and community state type (CST). We hypothesized that BV and BV associated CSTs would exhibit increased expression and activity of collagen and elastin-degrading cathepsins.<br><br>METHODS: Vaginal fluid samples were collected and classified by BV diagnosis and CST. Cathepsin expression was evaluated by Western blotting to distinguish inactive and active enzyme forms. Proteolytic activity was assessed using multiplex cathepsin zymography. Statistical analyses compared cathepsin expression and activity across diagnoses and CSTs. Principal component analysis and linear regression were performed to assess associations between cathepsin activity, microbial diversity, and CST.<br><br>RESULTS: Procathepsin K expression was significantly increased in BV-positive and CST IV samples, while total cathepsin L expression was significantly elevated in samples with Nugent-intermediate scores. Cathepsins S and V showed variation in inactive and active forms in Nugent-intermediate and CST III samples. In contrast, total cathepsin activity, including cathepsins K and V, did not significantly differ across BV diagnoses or CSTs. Overall, cathepsin activity varied between individuals rather than by clinical classification.<br><br>CONCLUSIONS: Cathepsin expression and maturation state differ by microbiome composition, suggesting that the vaginal microbiome may regulate post-translational processing of cathepsins. As a result, cathepsin activity appears to be regulated at the individual level rather than strictly by BV diagnosis or CST. These findings link vaginal microbiome composition to ECM remodeling and potential adverse reproductive outcomes.}, }
@article {pmid42182364, year = {2026}, author = {Diaz Olea, X and Beede, K and Pereira, G and Scott, D and Petucci, C and Martens, E and Rodionov, D and Shah, A and Martinez, MP and Kim, H and Sharma, AK and Martin, A and Zhang, T and Faries, MB and Hamid, O and Devkota, S and Osterman, A and Knott, S and Voest, EE and Ajami, NJ and Wargo, J and Ramer-Tait, AE and Ronai, ZA}, title = {Tryptophan degradation by intestinal Bacteroides induces anti-tumor immunity and limits melanoma growth.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.06.723300}, pmid = {42182364}, issn = {2692-8205}, abstract = {Defining mechanisms used by gut microbiota to control anti-tumor immunity may offer novel therapeutic modalities. Here, we demonstrate that Bacteroides rodentium and closely related Bacteroides uniformis species induce anti-tumor immunity and limit melanoma development when colonized in either germ-free (GF) mice, mice with a complex microbiome, or WT mice. Enhanced CD8 [+] T cell infiltration seen in tumors of mice harboring B. rodentium coincided with increased expression of immune-stimulating pathways and activation of bone marrow-derived dendritic cells that were co-cultured with the B. rodentium secretome. Metabolomic analyses of cecal samples from GF mice colonized with Altered Shedlar Flora (ASF) plus B. rodentium revealed lower tryptophan levels than in ASF-colonized controls, and WT mice fed a tryptophan-deficient diet exhibited inhibition of melanoma development. In silico genomic reconstruction of metabolic pathways revealed that both B. rodentium and B. uniformis harbor tryptophanase A (TnaA) and aromatic amino transferase (ArAT) genes, both of which function in tryptophan degradation. Administration of a B. uniformis harboring TnaA mutant failed to inhibit melanoma growth in gnotobiotic mice. Notably, administration of indoles, but not kynurenines, also effectively inhibited melanoma development, increasing immune cell infiltration into the tumors. Correspondingly, levels of bacterially encoded tryptophan-degrading enzymes were higher in cohorts of melanoma patients responding to immune checkpoint blockade. These findings highlight a novel mechanism of anti-tumor immunity and tumor growth inhibition dependent on the tryptophan degradation products, indoles, produced by intestinal Bacteroides species.}, }
@article {pmid42182438, year = {2026}, author = {Fuerte-Stone, J and Ghali, J and Valaitis, S and Mimee, M}, title = {Engineered gut symbionts mediate cross-phylum antagonism to suppress uropathogenic Escherichia coli colonization.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.11.724322}, pmid = {42182438}, issn = {2692-8205}, abstract = {UNLABELLED: Urinary tract infections (UTIs) are among the most common bacterial infections globally and create a large burden on the healthcare system. Uropathogenic Escherichia coli (UPEC) account for the majority of UTIs and increase the risk of recurrence. The standard treatment is antibiotics and, with the rise of multi-drug resistant UPEC lineages, there is a need for alternative treatments and prevention. Colicins, bacteriocins targeting and produced by E. coli , have previously been shown to inhibit the growth of pathogenic E. coli and are a promising alternative. Here, we engineer commensal Bacteroidaceae to secrete colicins via outer membrane vesicle (OMV) targeting signal peptides to suppress E. coli in the mouse gut. Secreted colicins were assessed for their ability to kill primary clinical isolate UPEC strains, including epidemic multi-drug resistant ST131 strains, along with other pathogenic and type strains. Specifically, secreted colicin E7, from Phocaeicola vulgatus fully eliminated of several UPEC strains in culture. In mice, P. vulgatus secreting colicin E7 prevented the extended colonization of two clinical UPEC strains and restored microbiome diversity. Together, this work shows the viability of secreted, heterologous antimicrobials from P. vulgatus as prophylactic treatment against the colonization of pathogenic E. coli utilizing cross-phylum antagonism in the gut.<br><br>SIGNIFICANCE STATEMENT: Recurrent urinary tract infections can be driven by intestinal reservoirs of uropathogenic Escherichia coli that are difficult to eliminate and increasingly recalcitrant to conventional antibiotic therapy. Here, we show that engineered gut symbionts from the Bacteroidaceae family can secrete targeted protein antibiotics to selectively kill these uropathogenic E. coli . Leveraging outer membrane vesicle-based secretion, we demonstrate that bacteriocin secretion can prevent gut colonization by clinically relevant pathogens, while preserving overall microbiome diversity. This work establishes a strategy for programmable, cross-phylum antimicrobial delivery within the gut microbiome, providing a potential alternative to conventional antibiotics for preventing recurrent infections and other enteric diseases.}, }
@article {pmid42182451, year = {2026}, author = {Wei, W and Graf, R and Wang, Y and Oalmann, CJ and Lau, JT and Wang, X and Chien, M and Conrad, MC and Simon, J and Ganguly, S and Yamazaki, T and Harberts, A and Chen, S and Fondevila, MF and Dhar, D and Campbell, SA and Senter, RK and Schnabl, B}, title = {Targeting Microbial Bile Salt Hydrolase Reprograms Bile Acid Metabolism and Ameliorates Metabolic Dysfunction-Associated Steatohepatitis in Mice.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.12.724693}, pmid = {42182451}, issn = {2692-8205}, abstract = {UNLABELLED: Microbial bile salt hydrolase (BSH) plays a central role in shaping bile acid composition and gut-liver metabolic signaling, yet its therapeutic potential in metabolic dysfunction-associated steatohepatitis (MASH) remains incompletely defined. Here, we evaluated the efficacy of the non-absorbable BSH inhibitor GR-7 in a diet induced mouse model of steatohepatitis using early and late intervention strategies with different dosing regimens. GR-7 reduced food intake and exerted stage- and dose-dependent therapeutic effects, with early intervention robustly suppressing hepatic fibrosis even at low dose, whereas late-stage administration of high-dose GR-7 markedly reduced hepatic steatosis and inflammation, as evidenced by decreased liver weight, hepatic triglyceride and cholesterol levels, and plasma ALT. Although late intervention did not result in statistically significant histological reversal of fibrosis, a trend toward improvement was observed, together with suppression of fibrogenic gene expression, suggesting that prolonged treatment may further enhance antifibrotic efficacy. Mechanistically, GR-7 effectively inhibited microbial BSH activity in vivo, leading to reduced cecal unconjugated primary and secondary bile acids-including deoxycholic acid and lithocholic acid, which was associated with improved gut barrier integrity and reduced hepatic inflammation. In parallel, BSH inhibition reprogrammed hepatic bile acid metabolism toward activation of the alternative CYP27A1-mediated synthesis pathway, accompanied by reduced food intake, thereby contributing to improved hepatic lipid accumulation. Furthermore, late-stage high-dose treatment selectively remodeled the hepatic immune landscape rather than fully restoring homeostasis, highlighting immune recalibration as a key component of therapeutic response. Together, these findings identify microbial BSH inhibition as a promising microbiome-targeted therapeutic strategy for MASH.<br><br>HIGHLIGHTS: The non-absorbable BSH inhibitor GR-7 improves steatosis, inflammation, and fibrosis in of Western diet-induced steatohepatitis model in mice in a dose-dependent manner.GR-7 reduces food intake and body weight gain.GR-7 reduces cytotoxic secondary bile acids, including DCA and LCA.GR-7 reprograms hepatic bile acid metabolism and immune responses.}, }
@article {pmid42182456, year = {2026}, author = {Ryu, EP and Keller, CA and Nichols, RG and Tran, HN and Brocious, PR and Harris, LR and Koltun, WA and Yochum, GS and Davenport, ER}, title = {Integrative host transcriptomic and mucosal microbiome profiling reveals region-specific host-microbiome associations across the human intestine.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.13.725025}, pmid = {42182456}, issn = {2692-8205}, abstract = {UNLABELLED: Host genetics shapes gut microbiome composition, yet the physiological mechanisms underlying this relationship remain poorly understood. Characterizing associations between host gene expression and the mucosal microbiome offers a promising route to identifying the host pathways and microbial taxa most likely to interact physiologically. However, existing investigations have been conducted primarily in acute disease contexts and within the colon, leaving host-microbiome associations outside of acute inflammatory contexts and those in undersampled regions such as the terminal ileum poorly characterized. To address these gaps, we profiled paired host gene expression from full-thickness resections and mucosal microbiome data, both from macroscopically non-inflamed tissue from Crohn's disease patients undergoing surgery across three intestinal sites: terminal ileum (n = 32), cecum (n = 35), and right colon (n = 30). Using a multi-level analytical framework including Procrustes analysis, sparse canonical correlation analysis, and elastic net regression, we identified significant associations between the mucosal transcriptome and microbiome. Intestine-wide, genes enriched in immune and intestinal barrier integrity pathways were associated with heritable taxa including Fusicatenibacter , consistent with patterns observed in microbiome genome-wide association studies. Region-specific analysis identified the terminal ileum as a distinct site of host-microbiome interaction, with associations involving metabolic and barrier-related pathways not observed in the large intestine. Notable terminal ileum-specific associations included PCDH20 with Faecalitalea and ACAT1 with Lactococcus , implicating epithelial barrier maintenance and host-microbiome metabolic interactions, respectively. These findings advance our understanding of the physiological basis of host-microbiome interactions across the intestine.<br><br>IMPORTANCE: The human gut is home to trillions of microorganisms that interact with the intestinal lining, yet we have a limited understanding of the specific biological processes involved in these interactions. Most studies characterizing the relationships between host gene expression and the gut microbiome have focused on the colon and on active disease contexts, leaving it unclear whether the associations observed reflect fundamental host-microbiome biology or disease-specific responses. By examining mucosal tissue, where host cells and microbes are in direct contact, across three sites in non-acutely inflamed tissue, we show that expression of immune defense and barrier maintenance genes is broadly associated with the microbiome across the intestine. We also identify distinct classes of associations in the terminal ileum, including host genes involved in metabolic processes. These findings provide a foundation for understanding how host biology and the gut microbiome are linked outside of acute disease.}, }
@article {pmid42182508, year = {2026}, author = {Wang, XW and Huang, D and Yu, P and Weiss, ST and Liu, YY}, title = {Machine learning-based Personalized Dietary Recommendations to Achieve Desired Gut Microbial Compositions.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.12.724618}, pmid = {42182508}, issn = {2692-8205}, abstract = {Dietary intervention is an effective way to alter the gut microbiome to promote human health. Yet, due to our limited knowledge of diet-microbe interactions and the highly personalized gut microbial compositions, an efficient method to prescribe personalized dietary recommendations to achieve desired gut microbial compositions is still lacking. Here, we propose a machine learning framework to resolve this challenge. Our key idea is to implicitly learn the diet-microbe interactions by training a machine learning model using paired gut microbiome and dietary intake data from a population-level cohort. The well-trained machine learning model enables us to predict the microbial composition of any given species collection and dietary intake. Next, we prescribe personalized dietary recommendations by solving an optimization problem to achieve the desired microbial compositions. We systematically validated this Machine learning-based Personalized Dietary Recommendation (MPDR) framework using synthetic data generated from an established microbial consumer-resource model. We then validated MPDR using real data collected from a diet-microbiome association study. The presented MPDR framework demonstrates the potential of machine learning for personalized nutrition.}, }
@article {pmid42182514, year = {2026}, author = {Gallo, H and Bucci, V}, title = {Dynamical Systems-Constrained Metabolic Modeling Enables Forecasting of Host-Microbiome Dynamics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.08.723020}, pmid = {42182514}, issn = {2692-8205}, abstract = {Forecasting how microbiome-host ecosystems evolve through time simultaneously at the compositional and functional level remains a central challenge in biology. While dynamical systems models (DSMs) can infer and predict community composition from longitudinal abundance data, and constraint-based metabolic models (CBMMs) can estimate metabolic fluxes from genome-scale reconstructions, no existing framework unifies these approaches to generate mechanistically grounded, time-resolved forecasts of both microbial abundances and metabolite dynamics from ecological data alone. Here, we introduce the Dynamical Systems Constrained Metabolic Modeling (DySCoMeMo) framework, a new hybrid computational pipeline that integrates ecological DSMs with CBMMs to predict temporal dynamics of biomass and metabolites across microbial communities and hosts. DySCoMeMo leverages parameters inferred from application of DSMs to microbiome time series data to constrain metabolic modeling over time, thereby bridging ecological interaction networks with genome-scale metabolic modeling. DySCoMeMo is able to predict future community and metabolite dynamics in vitro with accuracy that is superior or on-par compared to that achieved with established methods that require actual microbial abundances and/or metabolites data for metabolite network inference or for estimating the per-microbe contribution to the extracellular metabolic pool. DySCoMeMo also generalizes to in vivo data as it is capable of accurately forecasting microbial and metabolite dynamics in response to dietary perturbations even when host metabolism is included. Finally, DySCoMeMo uniquely enables the identification of keystone species by quantifying their contributions to sustaining metabolic environments. Together, our work establishes a generalizable, mechanistically grounded framework for time-resolved forecasting of microbiome-host microbial and metabolic dynamics, bridging ecological interaction inference with genome-scale metabolism of communities.}, }
@article {pmid42182529, year = {2026}, author = {Lai, H and Gao, K and Qiu, L and Huang, M and Yu, W and Li, H and Peng, Z and Wei, S and Wei, F and Zhou, W}, title = {Exploring phylosymbiosis in the skin microbiome of coral reef fish: synergistic effects of environmental and host-specific factors.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag121}, pmid = {42182529}, issn = {2730-6151}, abstract = {The skin is the largest organ in vertebrates, and its microbiome plays a crucial role in immune function and host health. Coral reef fish, characterized by rapid adaptive radiation and complex functional diversity, provide an ideal model for studying the assembly of vertebrate skin microbiomes and the mechanisms that drive this process. In this study, we used 16S rRNA gene amplicon sequencing to investigate the factors influencing the skin microbiomes of coral reef fish across a broad spatial scale. We analyzed 447 skin microbiome samples from 138 fish species, collected from different regions along the latitudinal gradient in coral reef ecosystems of the South China Sea. Our results revealed significant differences in the skin microbiomes of coral reef fish between coastal and offshore habitats in terms of taxonomic composition, diversity, and predicted functional potential. The microbiome structure was influenced by a combination of environmental factors, host traits, and phylogenetic relationships. Notably, we observed a phylosymbiotic pattern in the skin microbiomes of coral reef fish, with more closely related fish exhibiting more similar microbial communities. Temperature and silicate concentration were identified as the primary environmental drivers of microbial community structure, while host-specific factors such as mobility and diet indirectly influenced microbiome assembly by shaping host-associated microenvironment and feeding habitats. Our study highlights the complex interplay between environmental and host-specific factors in shaping coral reef fish skin microbiomes and provides new insights into host-microbe interactions in coral reef ecosystems.}, }
@article {pmid42182532, year = {2026}, author = {Villegas, V and Rajarajan, A and Martínez-Ruiz, EB and Sánchez, KF and Wolinska, J}, title = {Nanoplastic-induced microbiome shifts reduce Daphnia fitness and increase parasite reproduction.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag109}, pmid = {42182532}, issn = {2730-6151}, abstract = {Environmental pollutants can profoundly influence host-associated microbiomes, with cascading effects on host health and susceptibility to disease. Here, we investigated whether nanoplastic particles (NPs), a pervasive contaminant, influence host-parasite interaction by altering the microbiome of the water flea Daphnia magna. Microbiomes from NP-exposed and control Daphnia donors were transplanted to axenic Daphnia recipients, which were subsequently challenged with the fungal parasite Australozyma monospora sp. nov. Host and parasite fitness were then compared across treatments. NP exposure induced marked shifts in bacterial community structure and increased microbial diversity in donor microbiomes. These shifts persisted after transplantation, with recipient microbiomes remaining distinct from controls throughout the host lifespan, despite the absence of direct NP exposure. Microbiome shifts associated with NP exposure corresponded to elevated parasite reproduction and reduced host fecundity, while host survival was unaffected. Our findings demonstrate that NP pollution can indirectly compromise host health by reshaping microbial communities, highlighting microbiome-mediated pathways as important mechanisms through which emerging pollutants may shape ecological and evolutionary dynamics.}, }
@article {pmid42182637, year = {2026}, author = {Cai, X and Pang, S and Tang, C and Li, S}, title = {Relationship between airway stents and airway microorganisms: a literature review.}, journal = {Journal of thoracic disease}, volume = {18}, number = {4}, pages = {418}, pmid = {42182637}, issn = {2072-1439}, abstract = {BACKGROUND AND OBJECTIVE: Airway stent placement is widely used for the management of airway stenosis; however, it can be associated with complications such as granulation, stent migration, and infection, all of which affect patient outcomes. Among these complications, infection is a major concern, yet the relationship between airway stents and microbial colonization remains insufficiently studied. This review aims to summarize the current evidence on the effects of airway stents on the airway microbiome and to discuss their potential clinical implications.<br><br>METHODS: A literature search was conducted in PubMed for relevant studies published from database inception to December 31, 2025. Search terms included "airway stent", "tracheal stent", "bronchial stent", "airway microbiome", "biofilm", and "respiratory infection". Relevant studies were screened according to predefined criteria, and the available evidence was narratively synthesized.<br><br>KEY CONTENT AND FINDINGS: Available evidence suggests that airway stents can alter the airway microenvironment and facilitate microbial colonization, most commonly involving Pseudomonas aeruginosa (P. aeruginosa), Staphylococcus aureus (S. aureus), and Klebsiella pneumoniae (K. pneumoniae). Both metallic and silicone stents lead to similar microbial profiles, dominated by P. aeruginosa and S. aureus. Although microbial colonization frequently occurs after stent implantation, colonization does not necessarily reflect clinically significant infection, and microbiological findings should be interpreted in the clinical context. Most clinical studies report an increased risk of respiratory infection following airway stent placement. In certain specific clinical situations, such as patients with tracheoesophageal fistula, infection rates may decrease after stenting due to restoration of airway integrity. Conventional culture-based methods remain adequate for detecting common respiratory pathogens, while emerging techniques such as metagenomic next-generation sequencing (mNGS) enable broader characterization of airway microbial communities.<br><br>CONCLUSIONS: Airway stents appear to alter the airway's microbial environment by promoting the growth of potentially pathogenic microorganisms. Different stent materials, including silicone stents and self-expanding metallic stents (SEMS), seem to affect the biofilm formation on the stents' surface, which may influence microbial colonization. More studies with larger sample sizes, standardized methodologies, and advanced techniques like metagenomic sequencing are needed to further clarify the microbial changes and improve clinical management.}, }
@article {pmid42182816, year = {2026}, author = {Webber, M and Humphrey, E and van Asselt, A and Chang, A and Morien, E and Simon, ADF}, title = {Diatoms (Bacillariophyta) of the Salish Sea, Northeast Pacific: annotated checklist and new species reports.}, journal = {Biodiversity data journal}, volume = {14}, number = {}, pages = {e189060}, pmid = {42182816}, issn = {1314-2828}, abstract = {BACKGROUND: Diatoms are major primary producers known to respond rapidly to environmental change, making them useful indicators for ecological assessment and monitoring. In the Salish Sea bioregion, diatom records date back to early inventories by Lord (1866) and Bailey and MacKay (1916), followed by scattered surveys throughout the 20[th] and 21[st] centuries. Due to this fragmented record, a consolidated regional baseline has been lacking.<br><br>NEW INFORMATION: We report 924 diatom taxa for the Salish Sea from historical records, voucher specimens and molecular data, forming a curated dataset of 11,469 records. Forty-two species, including six previously unreported genera, are newly recorded for the region, based on combined morphological and molecular evidence. For these taxa, including the recently described Andrzeja fenestrata, we provide taxonomic accounts with diagnostic light and electron micrographs. These data establish a baseline record of diatom diversity in the Salish Sea, setting an example for how collaboration amongst community and academic researchers can help establish data foundations for phytoplankton monitoring.}, }
@article {pmid42182925, year = {2026}, author = {Yin, S and Fu, S and Cheng, J and Wang, M and Zhou, Y and Wei, H and Peng, J}, title = {Functional fiber supplementation improves reproductive performance in sows by reshaping gut microbial functions related to immunity and metabolic health.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1834008}, pmid = {42182925}, issn = {2297-1769}, abstract = {INTRODUCTION: Dietary fiber has been reported to regulate reproductive performance, yet its role in microbial functions during late gestation remains unclear. This study aimed to explore the effect of functional fiber supplementation on the gut microbiome and reproductive performance of sows in late gestation, as well as the potential underlying mechanisms.<br><br>METHODS: A subset of sows from a large-scale feeding trial was selected and assigned to either a control diet (CON, n = 501) or a functional fiber-supplemented diet (DF, n = 409). Relevant indicators including reproductive performance, plasma physiological parameters, and gut microbiome were detected and analyzed.<br><br>RESULTS: Compared with the CON group, DF treatment significantly increased the numbers of total born, born alive and healthy piglets (P < 0.05). Sows in the DF group exhibited higher plasma IL-10 levels, lower plasma reactive oxygen species, reduced insulin resistance and improved insulin sensitivity (higher HOMA-IS) (P < 0.05). Microbiome analyses revealed enrichment of NK4A214_group associated taxa and suppression of Treponema-dominated communities. Further functional profiling showed increased antigen processing and presentation, estrogen signaling pathway, IL-17 signaling pathway, progesterone-mediated oocyte maturation and Th17 cell differentiation pathways, alongside decreased biofilm formation - Pseudomonas aeruginosa pathways. These microbial changes were associated with improved reproductive performance.<br><br>DISCUSSION: Taken together, these results indicate that functional fiber improves reproductive outcomes by functionally remodeling the gut microbiome toward enhanced immune regulation and metabolic homeostasis during late gestation, providing a theoretical basis for the application of functional fiber in late gestation sow feeding.}, }
@article {pmid42183058, year = {2026}, author = {Zhao, X and Zhang, Y and Chu, X and Ma, W and Zhan, R and Wang, Y and Fang, H and Guo, P and Wang, Z and Chen, X and Yang, J and Sun, X}, title = {Gut-engineered Bacillus subtilis-mediated BAMBI delivery for the treatment of thioacetamide-induced liver fibrosis through mechanotransduction inhibition.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {14}, number = {}, pages = {1817519}, pmid = {42183058}, issn = {2296-4185}, abstract = {Liver fibrosis, driven by chronic injury and excessive extracellular matrix (ECM) deposition, lacks effective clinical therapies. This study pioneers a strategy employing genetically engineered Bacillus subtilis (strain Bs-BAMBI-8) to constitutively secrete bone morphogenetic protein and activin membrane-bound inhibitor (BAMBI), which is subsequently delivered to the liver via the gut-liver axis to therapeutically antagonize liver fibrosis. Methodologically, liver fibrosis was induced in mice via 6-week intraperitoneal injections of thioacetamide (TAA), followed by a 19-week daily oral gavage of live Bs-BAMBI-8 (10[9] CFU). This longitudinal intervention achieved sustained intestinal colonization (>10[5] CFU) and BAMBI translocation via the gut-liver axis. This intervention significantly reduced hepatic fibrosis, evidenced by decreased NAFLD Activity Score from six to four and regression of fibrosis stage from S3 to S2. Mechanistically, BAMBI acted as a decoy receptor for transforming growth factor-beta (TGF-β), inhibiting TGF-β signaling and downregulating fibrotic markers (α-smooth muscle actin, collagen I, phosphorylated focal adhesion kinase). This suppression disrupted ECM-mediated mechanotransduction pathways, attenuating hepatic stellate cell activation. Concomitantly, serum markers (alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase, total bilirubin) recovered, while albumin synthesis and platelet count recovered. Crucially, this engineered microbiome-based approach integrates synthetic biology with mechanobiology to simultaneously target biochemical signaling and mechanical transduction. It establishes a potentially translatable paradigm for chronic liver disease therapy.}, }
@article {pmid42183083, year = {2023}, author = {Ke, S and Wang, XW and Ratanatharathorn, A and Huang, T and Roberts, AL and Grodstein, F and Kubzansky, LD and Koenen, KC and Liu, YY}, title = {Association of Probable Post-Traumatic Stress Disorder with Dietary Pattern and Gut Microbiome in a Cohort of Women.}, journal = {Nature. Mental health}, volume = {1}, number = {11}, pages = {900-913}, pmid = {42183083}, issn = {2731-6076}, support = {R01 AI141529/AI/NIAID NIH HHS/United States ; }, abstract = {Post-Traumatic Stress Disorder (PTSD) is a psychiatric condition that may occur in people who have experienced or witnessed traumatic events. The microbiota-gut-brain axis has been suggested to play an important role in mental health. Here we analyzed information on trauma exposure and PTSD symptoms with the gut microbiome data and dietary information in 191 individuals enrolled in a substudy of an ongoing longitudinal cohort of women. We demonstrated that higher PTSD symptom levels were associated with less adherence to the Mediterranean diet pattern, and this association was also linked to specific PTSD putative protective species such as Eubacterium eligens. Moreover, the microbial pathways involved in the biosynthesis of pantothenate and coenzyme A were identified as PTSD putative protective, and these pathways were mainly contributed by PTSD putative protective species such as Akkermansia muciniphila. These findings have the potential to inform dietary- or microbiome-based interventions for PTSD prevention or amelioration.}, }
@article {pmid42183252, year = {2026}, author = {Jin, R and Wang, M and Ke, J and Gao, X and Zhang, L}, title = {Correlation between Staphylococcus aureus colonization and disease severity in atopic dermatitis: a systematic review and meta-analysis of randomized controlled trials.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1820411}, pmid = {42183252}, issn = {1664-3224}, mesh = {*Dermatitis, Atopic/microbiology/diagnosis ; Humans ; *Staphylococcus aureus ; Randomized Controlled Trials as Topic ; Severity of Illness Index ; *Staphylococcal Infections/microbiology ; *Staphylococcal Skin Infections/microbiology ; }, abstract = {BACKGROUND: A positive association between Staphylococcus aureus (S. aureus) colonization and atopic dermatitis (AD) severity has been reported. However, the strength and consistency of this relationship remain unclear.<br><br>METHODS: We systematically searched PubMed, Embase, Cochrane Library, and Web of Science up to July 19, 2025. The reported correlation coefficients of studies have been extracted and converted into Fisher's z-scores. The calculated values have been generated using a random-effects model in RevMan software and the final pooled result was converted to a correlation coefficient (r) with 95% confidence intervals. We tested the heterogeneity between the included studies using I&#xb2;. We also provide sensitivity analyzes and subgroup.<br><br>RESULTS: Seven RCTs with 929 participants were included. The pooled analysis showed a moderate positive correlation between S. aureus colonization and AD severity (r&#xa0;=&#xa0;0.42, 95%CI: 0.31-0.52). The observed heterogeneity was moderate but not significant (I&#xb2;&#xa0;=&#xa0;38%, P&#xa0;=&#xa0;0.14). Sensitivity and subgroup analyzes supported the robustness of the main findings.<br><br>CONCLUSIONS: S. aureus colonization is moderately associated with AD severity. However, it should not be interpreted as evidence of a direct causal relationship.<br><br>https://www.crd.york.ac.uk/prospero/, identifier CRD420251104116.}, }
@article {pmid42183274, year = {2026}, author = {Hu, N and Wang, Z and Liu, M and Guo, D and Jiang, C and Chen, Y and Zhang, Z and Bai, M and Cheng, B and Hsu, JC and Wu, L and Sui, X}, title = {Multi-omics biomarkers for predicting resistance, hyperprogression, and immune-related toxicity during PD-1/PD-L1 therapy in lung cancer: a literature review.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1780459}, pmid = {42183274}, issn = {1664-3224}, mesh = {Humans ; *Lung Neoplasms/drug therapy/immunology/metabolism/genetics ; *Immune Checkpoint Inhibitors/adverse effects/therapeutic use ; *Biomarkers, Tumor/genetics ; *Drug Resistance, Neoplasm/genetics ; *B7-H1 Antigen/antagonists &amp; inhibitors/immunology ; *Programmed Cell Death 1 Receptor/antagonists &amp; inhibitors ; Genomics/methods ; Disease Progression ; Proteomics ; Immunotherapy/adverse effects ; Multiomics ; }, abstract = {Immune checkpoint inhibitors targeting programmed cell death protein 1 (PD-1) and its ligand programmed death-ligand 1 (PD-L1) have transformed the management of advanced lung cancer, yet most patients experience primary resistance, hyperprogressive disease (HPD), or clinically significant immune-related adverse events (irAEs). Multi-omics technologies now enable integrated interrogation of tumor, microenvironmental, host, and clinical determinants of these divergent outcomes. In this review, we first discuss the biological and clinical foundations of PD-1/PD-L1 blockade in non-small cell and small cell lung cancer, and summarize the spectrum of resistance, HPD, and irAEs observed in trials and real-world practice. We then describe multi-omics study frameworks that connect genomics, transcriptomics, epigenomics, proteomics, metabolomics, radiomics, and microbiome profiling with these outcome phenotypes. Building on this foundation, we synthesize evidence for composite biomarkers of primary and acquired resistance, delineate emerging multi-omics signatures of HPD, and examine host- and tumor-derived multi-omics correlates of organ-specific and systemic irAEs. We further propose an efficacy-risk quadrant framework to guide clinical decision-making when favorable efficacy predictors coexist with elevated risk of severe adverse outcomes, and outline a three-step approach for high-efficacy/high-risk patients: joint probability reporting, multi-omics guided mitigation, and dynamic reassessment. Finally, we evaluate translational strategies that integrate multi-omics scores into baseline risk stratification, dynamic monitoring with attention to technical challenges such as distinguishing true progression from ctDNA pseudoprogression, and biomarker-driven trial design, while assessing the evidence level and translational readiness of candidate assays from retrospective discovery to clinical implementation. A clinical case illustrates how multi-omics can link baseline risk stratification, regimen selection, and longitudinal monitoring into a coherent action plan, while acknowledging that artificial intelligence-driven models remain investigational and real-world application still relies on clinician judgment. Collectively, this review defines how integrated multi-omics biomarkers can be leveraged to predict resistance, HPD, and immune-related toxicity, and to refine patient selection and management during PD-1/PD-L1 therapy in lung cancer.}, }
@article {pmid42183282, year = {2026}, author = {Huang, CF and Wang, JY and Karmaus, WJJ and Wang, IJ}, title = {Paradoxical enrichment of Akkermansia in children with poorly controlled asthma: a longitudinal study.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1807949}, pmid = {42183282}, issn = {1664-3224}, mesh = {Humans ; *Asthma/microbiology/diagnosis ; Child ; Male ; Female ; *Gastrointestinal Microbiome ; Longitudinal Studies ; Child, Preschool ; RNA, Ribosomal, 16S/genetics ; *Dysbiosis/microbiology ; Immunoglobulin E/blood ; Prospective Studies ; Taiwan ; Feces/microbiology ; Severity of Illness Index ; }, abstract = {INTRODUCTION: Gut dysbiosis is increasingly recognized as a factor in asthma pathogenesis, yet its relationship with disease severity and specific clinical phenotypes remains unclear. This longitudinal study investigated the dynamic changes in gut microbiota composition associated with asthma control and severity in children.<br><br>METHODS: We identified asthmatic children and matched them with healthy controls within the prospective Taiwan Childhood Environment and Allergic Diseases Cohort Study. Phenotypic data, including childhood asthma control test (C-ACT) scores, clinical severity, serum immunoglobulin E (IgE) levels, and peak expiratory flow (PEF) rates, were collected at the time of fecal sample collection. Gut microbiota composition was assessed using 16S rRNA sequencing and compared between groups. Subgroup analyses and longitudinal paired case comparisons were conducted to track microbial shifts between exacerbation and remission phases.<br><br>RESULTS: A total of 173 children, including 82 children with asthma (mean age: 6.9 &#xb1; 4.1 years) and 91 age- and gender-matched healthy controls (mean age: 7.5 &#xb1; 2.6 years), were recruited. Generally, children with asthma exhibited a lower relative abundance of Akkermansia, Anaerostipes, and Escherichia compared to controls. The relative abundance of Escherichia showed a significant negative correlation with C-ACT scores (&#x3b2; = -0.337, p = 0.016), whereas Akkermansia exhibited a significant negative correlation with PEF (&#x3b2; = -0.325, p = 0.032). Notably, longitudinal paired case comparisons distinguished asthma attack from remission phases, demonstrating a paradoxical enrichment of Akkermansia during exacerbations (LDA = 3.66, p = 0.023).<br><br>CONCLUSION: In contrast to the prevailing view of Akkermansia solely as a beneficial microbe, our study identifies a specific severe asthma-associated gut profile characterized by an unexpected enrichment of Akkermansia in children with poor control. This finding suggests a complex interaction between the gut microbiome and asthma severity, potentially influenced by high-intensity corticosteroid therapy. These results challenge the one-size-fits-all probiotic approach and highlight the need for precision microbiome-based interventions considering asthma phenotypes and medication history.}, }
@article {pmid41865792, year = {2026}, author = {Do, QL and Malau, IA and Nguyen, HT and Liu, J and Chang, JP and Su, KP}, title = {Circulating Short-Chain Fatty Acid (SCFA) profiles as a biomarker of gut-brain axis dysfunction: A meta-analysis for the SCFA signature in major depression.}, journal = {Biomedical journal}, volume = {49}, number = {3}, pages = {100968}, doi = {10.1016/j.bj.2026.100968}, pmid = {41865792}, issn = {2320-2890}, abstract = {BACKGROUND: Major Depressive Disorder (MDD) is increasingly viewed through the lens of the neuroinflammatory hypothesis and gut-brain axis dysfunction. Short-Chain Fatty Acids (SCFAs), the primary metabolites produced by the gut microbiota, are vital signaling molecules that maintain intestinal barrier integrity, modulate peripheral immunity, and influence microglial function. While individual studies suggest altered SCFAs levels in MDD, a definitive, quantitative synthesis establishing a robust biomarker signature is currently lacking. This meta-analysis aimed to precisely characterize the signature of SCFAs (acetic, propionic, butyric, and isobutyric acid) in MDD patients compared to healthy controls.<br><br>METHODS: We systematically searched major databases across PubMed, Embase, and Web of Science databases for studies quantifying SCFAs levels up to September 15, 2025. Studies examining SCFAs levels in depressed patients and depressive-like murine models, as well as studies investigating SCFAs interventions for depressive-like behavior, were selected for synthesis. Risk of bias was evaluated using the Newcastle-Ottawa Scale. The effect sizes were synthesized using a random-effects model and presented as standardized mean differences.<br><br>RESULTS: Eight human and 52 murine studies were included in the meta-analyses. Depressed patients showed significantly lower concentrations in blood (plasma and serum) of propionic (SMD&#xa0;=&#xa0;-0.60, p-value&#xa0;=&#xa0;0.007), butyric (SMD&#xa0;=&#xa0;-0.50, p-value&#xa0;=&#xa0;0.006), isobutyric (SMD&#xa0;=&#xa0;-0.72, p-value&#xa0;=&#xa0;0.020), valeric (SMD&#xa0;=&#xa0;-0.43, p-value&#xa0;=&#xa0;0.040) and isovaleric acids (SMD&#xa0;=&#xa0;-0.75, p-value&#xa0;=&#xa0;0.002). Secondary analysis of MDD patients confirmed consistent reductions. High heterogeneity was observed. In murine models, SCFAs depletion was frequently observed, while supplementation improved depressive-like behaviors.<br><br>CONCLUSION: MDD is characterized by a significant, quantifiable deficit in the circulating SCFAs metabolome, which provides strong empirical validation for the gut-brain axis hypothesis in depression. We advocate for the investigation of SCFAs as novel, measurable peripheral biomarkers and targeted therapeutic agents (e.g., butyrate supplementation) for precision nutritional psychiatry.}, }
@article {pmid42031071, year = {2026}, author = {Ramirez-Posada, M and Guillen-Burgos, HF}, title = {Skin-Brain Axis: Biological Foundations and Clinical Implications.}, journal = {Journal of the Academy of Consultation-Liaison Psychiatry}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jaclp.2026.04.006}, pmid = {42031071}, issn = {2667-2960}, abstract = {BACKGROUND: The skin-brain axis has emerged as a novel conceptual framework describing bidirectional neuroimmune, neuroendocrine, and microbial communication between the skin and the central nervous system. Shared inflammatory pathways, hypothalamic-pituitary-adrenal axis dysregulation, neurotransmitter signaling, neurotrophins, and microbiome-related mechanisms may contribute to the overlap between dermatologic and psychiatric disorders.<br><br>OBJECTIVE: To review the biological and clinical implications of the skin-brain axis in dermatologic and psychiatric disorders.<br><br>METHODS: This perspective review summarizes current evidence regarding the biological foundations and clinical implications of the skin-brain axis. The article integrates findings related to inflammatory skin disorders, psychiatric symptoms, immune signaling, microbial composition, and therapeutic approaches relevant to psychodermatology.<br><br>RESULTS: Evidence from psoriasis, atopic dermatitis, acne vulgaris, chronic urticaria, and prurigo nodularis demonstrates substantial overlap between inflammatory skin diseases and symptoms of depression, anxiety, stress, and suicidality. Emerging data further support the role of cutaneous immune signaling and microbial composition in modulating emotional and cognitive processes. The review also highlights therapeutic convergence between dermatology and psychiatry, including biologic therapies, psychopharmacology, cognitive behavioral therapy, and neuroimmune-targeted interventions.<br><br>CONCLUSIONS: Understanding the skin-brain axis may improve recognition of the bidirectional relationship between dermatologic and psychiatric disorders and support more comprehensive, integrated approaches to patients with complex inflammatory and neuropsychiatric conditions.}, }
@article {pmid42169289, year = {2026}, author = {Li, Y and Liu, X and Li, C and Xu, X and Tang, C and Zhou, G and Liu, Y and Blank, I}, title = {Elucidating microbial succession and aroma-active metabolite formation in hybrid dry-fermented sausage analogues with texturized pea protein: Integrating flavoromics, metabolomics, and metagenomics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {237}, number = {}, pages = {119324}, doi = {10.1016/j.foodres.2026.119324}, pmid = {42169289}, issn = {1873-7145}, mesh = {*Metabolomics/methods ; *Meat Products/microbiology/analysis ; *Odorants/analysis ; Fermentation ; *Metagenomics/methods ; Volatile Organic Compounds/analysis ; *Pea Proteins/metabolism ; Animals ; Gas Chromatography-Mass Spectrometry ; Taste ; Food Microbiology ; Humans ; Microbiota ; Swine ; Tandem Mass Spectrometry ; }, abstract = {Hybrid dry-fermented sausage analogues with texturized pea proteins (TPPs) are emerging, yet flavor formation mechanisms remain unclear. We combined quantitative descriptive analysis with complementary HS-SPME-GC-MS/HS-GC-IMS volatilomics, UHPLC-MS/MS untargeted metabolomics, and marker-gene microbiome sequencing across sausages with different fermentation and ripening stages to map key aroma and their potential microbial and metabolic drivers. Sensory data showed rising fruity, cocoa-chocolate and nutty notes. In total, 47 volatiles were identified by GC-MS and 40 by GC-IMS. Screening of odorants based on relative odor activity value (rOAV) consistently highlighted seven odorants, with a shift from hexanal-dominated raw profiles to linalool-dominated processed profiles, indicating suppression of aldehyde-derived off-notes and enrichment of terpene/ester notes. Metabolomics detected 2467 metabolites, dominated by lipids and organic acids, and short-peptide enrichment suggested intensified proteolysis supplying aroma precursors. Bacterial succession exceeded fungal variation, with Latilactobacillus and Staphylococcus as core taxa. The integrated dataset provides practical markers and microbial/process cues to enhance flavor quality of sustainable hybrid fermented meats.}, }
@article {pmid42169344, year = {2026}, author = {Song, H and Xue, S and Zhao, W and Yu, Z}, title = {Food-derived bioactive peptides in gut-muscle Axis regulation: Potential and challenges from microbiota homeostasis to muscle metabolism remodeling.}, journal = {Food research international (Ottawa, Ont.)}, volume = {237}, number = {}, pages = {119392}, doi = {10.1016/j.foodres.2026.119392}, pmid = {42169344}, issn = {1873-7145}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Peptides/metabolism ; Animals ; *Muscle, Skeletal/metabolism ; *Sarcopenia/metabolism ; Homeostasis ; Bioactive Peptides, Dietary ; }, abstract = {The global population is aging at an accelerating pace, and sarcopenia has emerged as a central challenge to elderly health. Food-derived bioactive peptides, as natural functional compounds, can interact significantly with the gut microbiota, thereby indirectly influencing muscle metabolism and function. This review systematically summarizes the pathological mechanisms of sarcopenia and its associated complications. Moreover, it reveals the complex interactions between food-derived bioactive peptides and the gut microbiome, and innovatively summarizes the multi-level mechanisms by which these peptides regulate the gut-muscle axis. Furthermore, we discuss current research limitations, including the limited translational potential of animal models, insufficient precision of detection techniques, and lack of clinical validation. Future research directions are proposed, including leveraging multi-omics and artificial intelligence approaches for peptide-microbiota-metabolite functional prediction, employing organoid and organ-on-a-chip platforms for mechanistic validation, and advancing systematic translation through high-quality clinical trials. This review aims to provide a comprehensive theoretical framework and offer direction for the application of food-derived bioactive peptides based on gut-muscle axis interventions.}, }
@article {pmid42169943, year = {2026}, author = {Chittilla, M and Nagdev, P}, title = {A systematic review of artificial intelligence and machine learning for gut microbiome-based CRC screening.}, journal = {Journal of gastrointestinal oncology}, volume = {17}, number = {2}, pages = {95}, pmid = {42169943}, issn = {2078-6891}, abstract = {BACKGROUND: Over the last decade, ample evidence has shown that gut microbiome dysbiosis is significantly associated with colorectal cancer (CRC). More recently, studies have shown that artificial intelligence (AI) and machine learning (ML) models paired with gut microbiome data can detect CRC. The objectives for this systematic review are: (I) to systematically evaluate the diagnostic performance of AI/ML models using gut microbiome data for CRC detection; (II) to compare AI/ML-based microbiome screening approaches; (III) to identify microbial genera consistently associated with CRC across included studies; (IV) to assess study quality and risk of bias using QUADAS-2 and use the GRADE approach to assess certainty.<br><br>METHODS: A systematic review was conducted across PubMed, MEDLINE, Scopus, Embase, and The Cochrane Library including studies from January 1, 2023 to November 1, 2025. Studies applying AI/ML models to human gut microbiome data for CRC screening and reporting diagnostic performance metrics and significant genera were included. Risk of bias was assessed with QUADAS-2 and used the GRADE approach to assess certainty. Primary outcomes included area under the receiver operating characteristic curve (AUC). Secondary outcomes include balanced accuracy, sensitivity, specificity, examine AI/ML approaches used, and identify significant microbial genera associated with CRC detected by AI/ML models. No meta-analysis was done due to the heterogeneity, which came from various microbiome methods, AI/ML/microbiome models used, and validation strategies applied. Thereby the data was synthesized narratively.<br><br>RESULTS: Twelve studies met inclusion criteria. AI/ML models demonstrated moderate diagnostic performance, with internal validation sets AUC values ranging from 0.61 to 0.98 and external validation sets AUC ranging from 0.70-0.87. Random forest and XGBoost models showed consistent performance, with multi-omics approaches achieving the highest AUC of 0.98. Porphyromonas (e.g., P. asaccharolytica), Peptostreptococcus (e.g., P. stomatis), Fusobacterium (particularly F. nucleatum subspecies: animalis, vincentii, polymorphum, sensu stricto), Parvimonas micra, Gemella morbillorum, Bacteroides (B. fragilis), and Streptococcus species were significantly enriched in CRC as predicted the selected AI/ML/microbiome models.<br><br>CONCLUSIONS: AI/ML-based gut microbiome models demonstrate moderate AUC for CRC detection and may enhance noninvasive screening strategies pending prospective validation. Limitations include heterogeneity in AI/ML/microbiome models, microbiome methodologies, and model validation, with predominantly retrospective case-control studies and limited external validation.}, }
@article {pmid42170025, year = {2026}, author = {Higashi, K and Ishikawa, H and Kurokawa, K and Mori, H}, title = {PZLAST-MAG: full length protein sequence similarity search server of large-scale MAG proteins.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbag129}, pmid = {42170025}, issn = {2635-0041}, abstract = {MOTIVATION: Metagenome-assembled genomes (MAGs) provide access to novel protein sequences from uncultured microbes, offering invaluable resources for studying protein diversity, structure prediction, and evolutionary analysis. However, despite the explosive growth of MAG-derived protein data, tools enabling fast and accurate similarity searches against large-scale MAG protein datasets remain limited.<br><br>RESULTS: We present PZLAST-MAG, a web server for ultra-fast sequence similarity searches against 0.4 billion MAG-derived protein sequences (0.1 trillion amino acids) from over 210&#xa0;000 MAGs indexed in Microbiome Datahub. Implemented on PEZY-SC3 MIMD many-core processors, PZLAST-MAG achieves high accuracy and speed, with performance comparable to widely used tools such as DIAMOND and MMseqs2 based on our benchmark analyses. In addition to tabular alignments, PZLAST-MAG provides interactive visualizations of phylogenetic and environmental distributions and co-occurrence patterns of homologous proteins across MAGs. This combination enables rapid homolog mining of functionally important genes across diverse microbial lineages while simultaneously revealing their taxonomic and ecological contexts. Two use case analyses indicate its utility for homolog mining of metabolic enzyme genes and plasmid-derived genes.<br><br>PZLAST-MAG is provided as a web-based service and is freely available at https://pzlast.nig.ac.jp/pzlast/mag without requiring registration.}, }
@article {pmid42170578, year = {2026}, author = {Brodsky, M and Lalla, M and Oh, S and Anampa, JD}, title = {Chemotherapy-induced peripheral neuropathy in breast cancer: a narrative review.}, journal = {Translational breast cancer research : a journal focusing on translational research in breast cancer}, volume = {7}, number = {}, pages = {18}, pmid = {42170578}, issn = {2218-6778}, abstract = {BACKGROUND AND OBJECTIVE: Chemotherapy-induced peripheral neuropathy (CIPN) remains a major, unresolved complication of breast cancer therapy, often leading to treatment modifications and enduring functional impairment. This review addresses the complex pathogenesis of CIPN, as well as the clinical presentation and impact of CIPN on patient quality of life. The primary objective of this review is to highlight the pathophysiology and pathogenesis of CIPN, as well as detail current strategies and future targets to prevent and treat CIPN in breast cancer patients.<br><br>METHODS: We conducted a narrative review using the PubMed/Medline, Cochrane, and Embase databases from database inception to July 2025. We used keyword searches including 'breast cancer', 'chemotherapy-induced peripheral neuropathy/CIPN', 'taxane', 'taxane induced peripheral neuropathy/TIPN', 'platinum', 'alkaloids', 'antibody drug conjugates', 'CIPN prevention', 'CIPN treatment', 'biomarkers', 'microbiome', 'racial disparities', 'genetics', 'quality of life', 'inflammation'. Inclusion criteria included clinical and translational English-language studies addressing CIPN in breast cancer, CIPN biomarkers, and the microbiome in oncology research. Exclusion criteria included non-English language studies and clinical studies unrelated to breast cancer.<br><br>KEY CONTENT AND FINDINGS: In this paper, we synthesize the pathophysiology of CIPN and the growing body of research implicating systemic inflammation and gut microbiome composition in modulating CIPN pathogenesis, suggesting a biological basis for interindividual variability in susceptibility. We also summarize emerging evidence on the role of racial disparities in CIPN. Finally, we explore commonly studied biomarkers that have shown promise as potential predictive markers of CIPN onset as well as potential therapeutic strategies.<br><br>CONCLUSIONS: CIPN remains a common, dose-limiting toxicity in breast cancer care. Preventive strategies and symptomatic management with consistent clinical benefits are lacking. Duloxetine has strongest scientific evidence for pain reduction; other pharmacologic and non-pharmacologic approaches are promising but heterogeneous and should be framed as adjunctive. Biomarker driven trial designs that test anti-inflammatory strategies, as well as microbiome-targeted interventions, may accelerate treatment breakthroughs. Finally, attention to race as a factor in CIPN susceptibility can help to identify high-risk patients and reduce disparities in CIPN burden.}, }
@article {pmid42170678, year = {2026}, author = {Yadav, S and Sharma, N and Yadav, M and Sharma, N and Tripathi, G and Bhat, SH and Pandey, S and Mathew, B and Bindal, V and Saifi, R and Sharma, V and Falari, S and Pamecha, V and Maras, JS}, title = {Distinct bile mycobiome signature identifies fungal peptide panel predictive for gallbladder carcinoma.}, journal = {Molecular therapy. Oncology}, volume = {34}, number = {2}, pages = {201220}, pmid = {42170678}, issn = {2950-3299}, abstract = {Carcinoma of the gallbladder (CAGB) carries a poor prognosis. While alterations in the bile microbiome and lipidome have been linked to CAGB development, the contribution of the fungal microbiome remains unexplored. We investigated fungal microbiome alterations and identified key fungal peptides capable of segregating CAGB patients. Bile samples from gallstone (GS) patients (n = 10), CAGB patients (n = 16), and healthy controls (n = 16) underwent fungal peptide-based diversity analysis and metabolomic profiling. Findings were cross-validated in plasma, correlated with clinical parameters and analyzed using machine learning. Six phyla and 24 fungal species were differentially regulated (p < 0.05). Alpha/beta diversity was higher in CAGB compared to GS and controls (p < 0.05). Ninety-three fungal peptides were upregulated and 63 downregulated in CAGB (p < 0.05, fold change [FC] > 1.5). CAGB patients showed significant enrichment of Aspergillus wentii (log2FC > 12.21), Nosema bombycis (FC > 11.25), Saccharomyces (FC > 10.89), Saccharomyces cerevisiae (FC > 10.68), and Schizosaccharomyces pombe (FC > 10.38). Fungal-metabolite correlations (r[2] > 0.5, p < 0.05) linked these taxa to lysine biosynthesis, taurine and hypotaurine metabolism, fatty acid metabolism in bile, and cysteine/methionine, ascorbate, and purine metabolism in plasma. Fungal peptide panel achieved 96% diagnostic efficiency for mortality prediction with>90% accuracy, sensitivity, and specificity. Bile fungal diversity correlates with CAGB development and identifies fungal peptide panel capable of segregation of CAGB patients.}, }
@article {pmid42170832, year = {2026}, author = {Shorr, AF and Zilberberg, MD}, title = {Ventilator-associated pneumonia: newer insights that can drive improved outcomes.}, journal = {Current opinion in critical care}, volume = {}, number = {}, pages = {}, doi = {10.1097/MCC.0000000000001390}, pmid = {42170832}, issn = {1531-7072}, abstract = {PURPOSE OF REVIEW: Ventilator-associated pneumonia (VAP) results in substantial morbidity and results in high crude mortality rates. Many recent studies address multiple aspects of VAP ranging from its evolving epidemiology and microbiology to novel means for prevention and treatment.<br><br>RECENT FINDINGS: The true incidence of VAP remains difficult to assess given definitional issues, which confound accurate diagnostic conclusions. The lack of a clear gold standard for identifying VAP makes comparisons across different studies difficult, as it remains unclear if like syndromes are actually being described. Nonetheless, VAP remains a clinical and costly challenge. Earlier discussion of achieving 'zero' VAP were clearly misplaced. Furthermore, the microbiology of VAP continues to evolve with the spread of antimicrobial resistance. New attention on the microbiome, though, may prove helpful and enhance our understanding of the pathogenesis of VAP. Simple interventions such a toothbrushing appear to successfully reduce rates of VAP and should be more broadly adopted. Rapid diagnostic tools, which are increasingly utilized to identify the causative pathogen in VAP, appear to have more limitations than previously thought. Several novel antibiotics are now available for treating multidrug-resistant organisms (MDROs) often encountered in VAP. With respect to antibiotic treatment more generally, it appears that shorter durations of therapy are well tolerated and effective, even in cases of VAP caused by MDROs.<br><br>SUMMARY: Although our knowledge and understanding of VAP continues to advance, many of the general questions of the last decade remain unresolved. We continue to lack a clear and simple means for defining VAP and have yet to identify the optimal approach for prevention. Likewise, despite the availability of newer antimicrobials, we continue to lack rapid diagnostics that can clearly be shown to improve patient-centered endpoints. The availability of newer antibiotics may allow us to more easily and safely treat MDROs, but they have not revolutionized outcomes or been shown to reduce mortality.}, }
@article {pmid42170966, year = {2026}, author = {Luo, Y and Xu, H and Ye, X}, title = {Effects of nifuratel-based therapy combined with vaginal lactobacillus probiotics on microecological restoration in pregnant women with abnormal vaginal flora: A retrospective cohort study.}, journal = {Pakistan journal of pharmaceutical sciences}, volume = {39}, number = {7}, pages = {1993-2002}, doi = {10.36721/PJPS.2026.39.7.REG.189.1}, pmid = {42170966}, issn = {1011-601X}, mesh = {Female ; Humans ; Pregnancy ; *Probiotics/administration &amp; dosage/therapeutic use/adverse effects ; Retrospective Studies ; Adult ; *Lactobacillus ; *Vagina/microbiology/drug effects ; Treatment Outcome ; *Microbiota/drug effects ; Young Adult ; Hydrogen-Ion Concentration ; }, abstract = {BACKGROUND: Imbalances in the vaginal flora during pregnancy elevate risks for adverse outcomes. While nifuratel targets pathogens, probiotics restore acidity, and robust cohort evidence supporting their combined safety and efficacy in restoring the microbiome remains limited.<br><br>OBJECTIVES: This retrospective cohort study assessed nifuratel-nystatin therapy plus Lactobacillus probiotics for restoring vaginal flora in pregnancy.<br><br>METHODS: Employing a retrospective cohort design, this study enrolled pregnant women diagnosed with vaginal microecological abnormalities between March 2023 and 2024. Participants were allocated via 1:1 propensity score matching (PSM) into two groups (n=58 each): a combination group receiving nifuratel-nystatin therapy combined with vaginal Lactobacillus probiotics and a monotherapy group receiving nifuratel-nystatin alone. All received a 7-day treatment. The primary endpoint was clinical effectiveness assessed one week post-treatment. Secondary outcomes included vaginal pH, Lactobacillus and bacterial diversity normalization rates, recurrence, adverse pregnancy outcomes and drug-related adverse events, monitored until delivery. Multivariate logistic regression identified independent predictors of treatment efficacy.<br><br>RESULTS: After PSM, baseline characteristics were balanced (P>0.05). The comparative analysis indicated a superior overall efficacy for the combination therapy (93.1%) over monotherapy (77.6%), with statistical significance (P<0.01) Both groups exhibited reduced vaginal pH and increased rates of normalized Lactobacillus and bacterial diversity, with greater improvements observed in the combination group (P<0.01). The recurrence rate was significantly lower in the combination group (8.6% vs. 22.4%; P<0.05), as was the total incidence of adverse pregnancy outcomes (6.9% vs. 20.7%; P<0.01). No significant difference in adverse drug reactions was found. Multivariate analysis identified combination therapy as an independent protective factor for clinical efficacy (aOR=4.25, 95% CI: 1.42-12.71, P<0.05).<br><br>CONCLUSIONS: In pregnant women with vaginal dysbiosis, combining nifuratel-nystatin with Lactobacillus probiotics safely enhances clinical efficacy, normalizes pH and flora and reduces adverse pregnancy outcomes.}, }
@article {pmid42171003, year = {2026}, author = {Pashaki, PA and Niepokny, TD and Khalilzadehsabet, T and Dumais, E and Flamand, N and Di Marzo, V and Mintz, EM and Silvestri, C}, title = {Circadian disruption elicits sex-specific gut microbiota, endocannabinoidome, and lipid mediator responses.}, journal = {The FEBS journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/febs.70592}, pmid = {42171003}, issn = {1742-4658}, support = {R15GM134528/GF/NIH HHS/United States ; //Canadian Tri-Agency/ ; }, abstract = {Circadian disruption is a pervasive environmental stressor associated with increased risk of metabolic and inflammatory disease, yet sex-specific physiological responses remain poorly defined. Here, we investigated how constant light (LL) exposure, used as a circadian stressor, is associated with changes in the fecal microbiome and short-chain fatty acids (SCFAs), tissue-specific bioactive lipid mediator and systemic cytokine levels in female and male mice. Mice were kept under standard light/dark (LD; 12 : 12) or LL (24 : 0) conditions for 10 days before feces collection and for 5 more days before tissue collection. Females exhibited broader microbiota restructuring along with decreases in oxylipins within the jejunum. In the brain pronounced increases of N-acylethanolamine levels in the cerebellum and hypothalamus were observed when male and female mice were analyzed together, though these changes were largely driven by increased levels in the hypothalamus of females. Changes in muscle lipids were associated with the predominant muscle fiber type, with the soleus showing increases in a broad variety of lipid classes in both females and males. Adipose tissues also showed divergent responses to LL, with subcutaneous white adipose tissue having significantly decreased oxylipin levels specifically in males. Within plasma, females generally showed a more inflammatory profile than males. Together, these findings suggest that sex strongly shapes microbial, lipidomic, and immune pathways changes under circadian stress, highlighting divergent physiological strategies in response to light-cycle perturbation, which may contribute to sex-specific vulnerability at the level of metabolic and inflammatory dysregulation.}, }
@article {pmid42171373, year = {2026}, author = {Schroer, HW and Beghini, F and Raygoza Garay, JA and Christakis, NA and Bosch, DE}, title = {Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0030526}, doi = {10.1128/msystems.00305-26}, pmid = {42171373}, issn = {2379-5077}, abstract = {Bacteria use antagonistic interbacterial weapons, such as polymorphic toxin secretion systems (TSS), to compete for niches in the human gut microbiome. We hypothesized that TSS influence gut microbiome development and disease-related dysbiosis. We developed a bioinformatic marker gene approach (PolyProf) to quantify TSS including ~200 effector and immunity genes and applied it to ~15,000 publicly available human metagenomes. PolyProf alpha and beta diversity readily distinguished 12 different human disease states and enabled the construction of highly accurate linear regression classifier machine learning models. Elastic net machine learning models integrating bacterial taxonomy with PolyProf had strong predictive value for 12 disease states, outperforming models utilizing taxonomy alone. During microbiome development in the first year of life, PolyProf alpha diversity increases, and beta diversity becomes increasingly like the maternal microbiome, influenced by vertical transfer, delivery mode, and breastfeeding. PolyProf is related to strain sharing among adults through social interactions. In summary, TSS genes strongly correlate with microbiome development and interpersonal strain sharing, suggesting roles for interbacterial antagonism. Since PolyProf distinguishes diverse adult disease statuses, these dynamics may contribute to non-genetic inheritance.IMPORTANCEPrevious research has demonstrated that bacteria compete within the gut microbiome using toxin secretion systems (TSS). How TSS contribute to human microbiome development and the microbiome alterations observed in human diseases is not known. This study develops a new bioinformatic tool for profiling TSS-related genes in metagenomic data. Application of this approach to large-scale human fecal metagenomic data demonstrates the dynamic association of TSS during microbiome development, including the exchange of strains among social contacts. TSS gene abundance patterns are highly predictive of 12 disease states. This study advances the field by enabling TSS profiling in metagenomes and by identifying disease and microbiome development biomarkers that provide hypotheses for future mechanistic studies and may be useful for disease diagnosis.}, }
@article {pmid42171627, year = {2026}, author = {Ribas, MP and Tort, C and Jasso, MV and Migura-Garcia, L and Cabezón, O}, title = {Skin Microbiome Variation Among Hosts and Batrachochytrium dendrobatidis Infection in Hyla meridionalis and Pelophylax perezi.}, journal = {Molecular ecology}, volume = {35}, number = {10}, pages = {e70393}, doi = {10.1111/mec.70393}, pmid = {42171627}, issn = {1365-294X}, support = {//Fundaci&#xf3; Barcelona Zoo/ ; FI_B 00171//Departament de Recerca i Universitats, Generalitat de Catalunya, Spain/ ; //CERCA Program/ ; }, mesh = {Animals ; *Microbiota/genetics ; *Skin/microbiology ; *Batrachochytrium/pathogenicity ; RNA, Ribosomal, 16S/genetics ; *Ranidae/microbiology ; *Anura/microbiology ; Bacteria/genetics/classification ; *Mycoses/microbiology/veterinary ; Spain ; Chytridiomycota ; Skin Microbiome ; Animal Diseases ; }, abstract = {Chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), is a key driver of global amphibian declines. The amphibian skin microbiome, which may include Bd-inhibitory bacteria, plays a crucial role in defence against infection, influencing host susceptibility and disease outcome. In this study, we investigated the skin microbiota and Bd infection in two frog species, Hyla meridionalis (Hm) and Pelophylax perezi (Pp), from northeastern Spain using full-length 16S rRNA gene sequencing. We found that microbiota composition differed significantly between frog species, with Pp harbouring greater bacterial richness and a community composition more similar to the aquatic environment than Hm. Asymptomatic Bd infection did not significantly alter microbiota diversity or community composition in either species. Nonetheless, differential abundance analyses revealed distinct bacterial taxa associated with host species and, to a lesser extent, with Bd infection. The composition of putative Bd-inhibitory bacteria also differed between frog species but was not influenced by Bd, suggesting that the microbiome's protective role may not be straightforward. Lower pathogen loads in Pp suggest a potential link between microbial richness and disease resistance. Our findings indicate that amphibian skin microbiota do not necessarily shift in response to Bd infection in asymptomatic hosts but may play a role in species-specific mechanisms of tolerance and resistance. Additionally, we detected potentially pathogenic bacteria of public and animal health concern on amphibian skin, highlighting amphibians as potential reservoirs and sentinels of ecosystem and public health. Overall, our findings indicate that amphibian skin microbiomes are shaped primarily by host species identity rather than asymptomatic Bd infection, emphasizing the importance of baseline microbiome variation in understanding host-pathogen dynamics and informing probiotic bioaugmentation strategies.}, }
@article {pmid42171661, year = {2026}, author = {Goodall, T and Busi, SB and Jones, B and Thorpe, A and Griffiths, RI and Redhead, J and Hulmes, L and Hulmes, S and Ridding, L and Peyton, J and Pereira, G and Gweon, HS and Read, DS and Pywell, R}, title = {Taxonomic filtering accompanies functional expansion during long-term soil restoration.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag131}, pmid = {42171661}, issn = {1751-7370}, abstract = {The restoration of species-rich calcareous grasslands is a critical conservation objective, yet the recovery of the invisible below-ground microbiome remains poorly quantified compared to above-ground vegetation. Using a unique 143-year land-use chronosequence on Salisbury Plain, UK, we investigated the trajectory of ecosystem reassembly across arable, regenerating (23 and 67 years), and ancient grasslands. By integrating vegetation surveys with soil physiochemistry, microbial profiling, and shotgun metagenomics, we identified a decoupling between floral and edaphic recovery. While the diversity of vegetation recovered relatively rapidly, approaching ancient grassland levels within 23-67 years, soil properties exhibited persistent legacy effects and slow convergence. Bacterial richness decreased with restoration age; this taxonomic contraction was conversely matched by an expansion in inferred metagenomic functional potential. This was reflected in increased functional gene richness and shifts in the relative abundance of specific SEED-annotated functions toward metabolic pathways associated with complex carbon cycling and stress tolerance. These shifts were congruent with the emergence of specific, unnamed genera belonging to Pseudomonadota and Actinomycetota, and the Bacillota species Pristimantibacillus. The soil ecosystem remained distinct from the 143-year stage even after 67 years of recovery, characterised by persistent legacy phosphorus and a slow accumulation of soil organic matter. These findings suggest that passive regeneration alone may be insufficient for full soil functional recovery, and that strategies targeting microbial assembly and long-term carbon dynamics warrant further evaluation.}, }
@article {pmid42171783, year = {2026}, author = {Rivera, DA and Lara-Guzmán, OJ and Villota-Salazar, NA and Sierra, JA and Muñoz-Durango, K and Escobar, JS}, title = {Analytic attributes of the 16S rRNA gene sequencing methodology for human gut microbiota characterization.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-026-13844-8}, pmid = {42171783}, issn = {1432-0614}, abstract = {Gut microbiota is crucial for human health. While 16S rRNA gene sequencing is most used for characterizing this community, the validation and standardization of the technique are often overlooked. This study analyzes critical factors influencing the repeatability and intermediate precision of 16S rRNA gene sequencing methodology for human gut microbiota characterization, examining the impact of key analytical factors. Our investigation evaluated the effects of the DNA extraction protocol, sample homogenization, thawing, library preparation, and sequencing on measurements of precision. This established a standardized operating procedure (SOP) whose variability was assessed within a single laboratory (intermediate precision) by analyzing DNA extraction kit lot variations and the laboratory analyst handling the samples. We discovered that the DNA extraction protocol and sample thawing were the most significant drivers of variability in gut microbiota profiles. At the same time, the intermediate precision of the method was high. We determined the method's limit of quantification, revealing an impressive sensitivity down to just 11 to 18 rarefied read counts (with coefficients of variation of 30% and 20%, respectively). Beyond technical considerations, we also quantified the variation in gut microbiota profiles among individuals and over time. Our findings confirm substantial inter-individual differences while demonstrating that changes within individuals over a week are relatively small. This research illuminates some critical factors influencing the precision and consistency of 16S rRNA gene sequencing for gut microbiota analysis. By incorporating these insights into standardized protocols, we can significantly improve best practices in DNA sequencing methodologies, strengthening the reliability and comparability of human microbiome studies. KEY POINTS: • DNA extraction and sample thawing critically affect the method's precision. • We established an SOP with high repeatability, intermediate precision, and a specific limit of quantification. • Gut microbiota profiles substantially vary among individuals but remain stable over a week.}, }
@article {pmid42171841, year = {2026}, author = {Gómez-Montañez, E and Rojas-Salazar, YL and Rojas-Salazar, JG}, title = {Microbiome in Gastrointestinal Tumors: Implications in Oncogenesis and Therapeutic Response : Microbiome in Gastrointestinal Tumors.}, journal = {Current oncology reports}, volume = {28}, number = {1}, pages = {}, pmid = {42171841}, issn = {1534-6269}, mesh = {Humans ; *Gastrointestinal Neoplasms/microbiology/therapy/pathology ; *Gastrointestinal Microbiome ; *Carcinogenesis ; *Dysbiosis/microbiology ; Tumor Microenvironment ; *Microbiota ; }, abstract = {PURPOSE OF REVIEW: To provide an updated overview of the role of the human microbiome in the initiation, progression, and therapeutic response of gastrointestinal tumors, emphasizing molecular, immunological, and metabolic mechanisms, as well as its potential as a target for novel therapeutic strategies.<br><br>RECENT FINDINGS: Emerging evidence demonstrates that microbiome dysbiosis contributes to carcinogenesis across gastrointestinal malignancies, including colorectal, gastric, hepatic, and pancreatic cancers. Microbial-derived metabolites, such as short-chain fatty acids and secondary bile acids, modulate key signaling pathways involved in cell proliferation, apoptosis, and genomic stability. In addition, the microbiome influences the tumor microenvironment and immune responses, shaping variability in treatment outcomes. Both preclinical and clinical studies have shown that microbiome composition affects the efficacy and toxicity of chemotherapy and immunotherapy. Notably, specific microbial signatures are being explored as non-invasive biomarkers for early detection and prognostic stratification, while microbiome modulation strategies, such as diet, probiotics, antibiotics, and fecal microbiota transplantation, have demonstrated potential to enhance therapeutic response. The bidirectional interaction between the microbiome and the host plays a central role in gastrointestinal tumorigenesis and treatment response. Although this field holds significant promise for precision oncology, its clinical translation remains limited by interindividual variability, methodological heterogeneity, and insufficient longitudinal evidence. Future efforts should focus on standardization, validation of microbiome-based biomarkers, and integration of multi-omics and artificial intelligence approaches to enable clinically actionable applications.}, }
@article {pmid42172047, year = {2026}, author = {Delgado, LF and Sunyer, JO and Laczny, CC and Hickl, O and May, P and Wilmes, P}, title = {PathoFact 2.0: An Integrative Pipeline for the Prediction of Antimicrobial Resistance Genes, Virulence Factors, Toxins and Toxin-associated Proteins, and Biosynthetic Gene Clusters in Metagenomes.}, journal = {GigaScience}, volume = {}, number = {}, pages = {}, doi = {10.1093/gigascience/giag062}, pmid = {42172047}, issn = {2047-217X}, abstract = {BACKGROUND: Antimicrobial resistance genes (ARG) and virulence factors (VFs) are central contributors to the global health crisis surrounding drug-resistant infections.<br><br>FINDINGS: We introduce PathoFact 2.0, an enhanced pipeline for improved ARG, VF, toxin, and biosynthetic gene clusters (BGC) prediction. Key improvements include an updated machine learning (ML) model for VF identification, expanded hidden Markov model profiles for VFs and toxin-associated proteins, a new ML model for toxin and toxin-associated proteins identification, and the integration of antiSMASH 7.0 for predicting biosynthetic gene clusters.<br><br>CONCLUSIONS: Our upgrades make PathoFact 2.0 a more powerful and user-friendly platform for predicting microbiome-based pathogenicity and resistance, providing a crucial tool for better understanding and addressing the challenges posed by antimicrobial resistance and infectious diseases.PathoFact 2.0 is available at https://gitlab.com/uniluxembourg/lcsb/systems-ecology/pathofact2. It is compatible with Linux operating systems.}, }
@article {pmid42172181, year = {2026}, author = {Gomes, JV and Ribeiro, SPO and Nascimento, GMCD and Santos, DOD and Paula, DJG and Lima, SCS and Simão, TA}, title = {The human microbiome in cancer: Not just a sidekick anymore.}, journal = {Genetics and molecular biology}, volume = {49Suppl 1}, number = {Suppl 1}, pages = {e20250236}, pmid = {42172181}, issn = {1415-4757}, abstract = {The human microbiome is increasingly recognized as a dynamic element in cancer biology. Studies across breast, prostate, lung, colorectal, and cervical tumors reveal that microbial communities influence carcinogenesis, immune regulation, and treatment outcomes. When the balance of these microorganisms is altered, inflammation becomes chronic, metabolism is disrupted, and signaling pathways such as NF-κB, IL6-STAT3, and β-catenin are activated. Bacterial metabolites and genotoxins, including colibactin and bile acids, may damage DNA and reshape the epigenetic landscape. Distinct microbial profiles have been linked to prognosis and to patient responses to chemotherapy and immunotherapy. The presence of beneficial taxa, such as Akkermansia muciniphila and Ruminococcus, has been associated with improved response to immune checkpoint inhibitors. At the same time, antibiotic-induced depletion of gut microbiome can reduce therapeutic efficacy. Strategies that help restore microbial balance, including probiotics, dietary interventions, and fecal microbiota transplantation, are being explored as complementary therapies. Although methodological differences and contamination remain challenges, the growing body of evidence indicates that the microbiome is a measurable and modifiable component of tumor ecosystems with strong potential for diagnostic, prognostic, and therapeutic applications in precision oncology.}, }
@article {pmid42172659, year = {2026}, author = {Liu, C and Yin, X and Yuan, X}, title = {Gut microbiota dysbiosis and osteoporosis: pathogenesis and novel intervention strategies.}, journal = {Future microbiology}, volume = {}, number = {}, pages = {1-12}, doi = {10.1080/17460913.2026.2678122}, pmid = {42172659}, issn = {1746-0921}, abstract = {Osteoporosis represents a major global public health challenge, with current pharmacological treatment often limited by substantial side effects. Recent research identifies the gut-bone axis as a key regulatory pathway linking gut microbiota to bone metabolic homeostasis. This review synthesizes findings from PubMed, Web of Science, and Scopus (up to March 2026) to elucidate how gut microbiota dysbiosis drives osteoporosis pathogenesis through interconnected mechanisms: aberrant immune modulation, altered microbial metabolites, impaired nutrient absorption, endocrine disruption, and systemic inflammation stemming from intestinal barrier failure. Consequently, these pathways disrupt the delicate balance of bone remodeling. Based on these insights, we outline novel microbiota-targeted therapeutic strategies, including probiotics, prebiotics, fecal microbiota transplantation, natural bioactive compounds, traditional Chinese medicine, and nanomaterials. These interventions aim to prevent and manage osteoporosis by reshaping the intestinal microecology via multi-target modulation. Future endeavors should prioritize in-depth mechanistic exploration, personalized precision interventions, and enhanced clinical translation to integrate these strategies into comprehensive osteoporosis care frameworks.}, }
@article {pmid42172767, year = {2026}, author = {Jin, X and Wu, D and Tong, Y and Weng, S and Jiang, Y and Zhang, J}, title = {The mechanism of rumen microorganisms regulating fatty acid and lipid metabolism in brown adipose tissue of sheep analyzed by multi-omics analysis.}, journal = {Food chemistry}, volume = {519}, number = {}, pages = {149670}, doi = {10.1016/j.foodchem.2026.149670}, pmid = {42172767}, issn = {1873-7072}, abstract = {Brown Adipose Tissue (BAT), a thermogenic fat in mammals that consumes energy rather than storing it, possesses unique characteristics. This study sought to clarify the specific mechanism and role of mutton in lipid deposition and nutritional quality. Using gas chromatography, lipidomics, and 16S rRNA gene sequencing, researchers found that BAT exhibited more active lipid metabolism, accompanied by increased abundance of the Firmicutes and Proteobacteria phyla. This activity manifested as a rise in beneficial DHA and EPA levels, along with a significant accumulation of key active lipids, such as cardiolipin and phosphatidylcholine. Further WGCNA and HCA analysis demonstrated that phyla including Verrucomicrobiota, Firmicutes, and Proteobacteria collectively enhanced BAT's nutritional value by regulating the biosynthesis of unsaturated fatty acids. This research successfully constructed a preliminary multi-dimensional interaction network of lipids and fatty acids within the "fat-rumen axis", providing a new theoretical framework for the accurate improvement of mutton's nutritional value.}, }
@article {pmid42172829, year = {2026}, author = {Yang, H and Xie, Y and Wang, H and Sun, H and Li, X and Yao, X and Ding, J and Wang, Q and Lv, H and Turner, BL and Sun, S and Wang, J}, title = {Multi-omics association analysis of the toxicity mechanism differences of typical veterinary antibiotics on tomatoes: From physiological inhibition to metabolic reprogramming.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142457}, doi = {10.1016/j.jhazmat.2026.142457}, pmid = {42172829}, issn = {1873-3336}, abstract = {Widespread application of veterinary antibiotics is contaminating soil via animal feces, leading to uptake by plants and environmental damage. Currently, research on the toxicological mechanisms associated with various classes of antibiotics remains inadequate. Therefore, this study utilized tomato as the test species and selected three representative antibiotics-chlortetracycline (CTC), enrofloxacin (ENR), and tylosin (TYL)-to systematically evaluate their differential toxicity and associated metabolic mechanisms through 14 and 28 days exposure experiments. At the individual level, antibiotics significantly suppressed biomass accumulation and photosynthesis in tomato seedlings, the ENR exhibited maximum inhibition rates of 37.4% for fresh weight and 26.7% for plant height. In contrast, the CTC recorded peak values of 28% for leaf area and 25.1% for SPAD measurements. Furthermore, exposure to antibiotics induced oxidative stress in tomato seedlings, with SOD demonstrating its highest activation rate of 18.3% in the TYL. Within the rhizosphere microenvironment, there was a notable decrease in the abundance of the dominant phylum Bryobacter, which was accompanied by alterations in bacterial community structure, an increase in network complexity, and a reduction in modularity. Under antibiotic stress, microbial communities demonstrated distinct metabolic responses: enhanced lipid metabolism in CTC, elevated carbohydrate metabolism with ENR, and activated nucleotide metabolism associated with TYL. In summary, antibiotics present global ecological risks by inhibiting plant growth and disrupting the rhizosphere microbiome. The class-specific toxicity of these substances necessitates the implementation of targeted risk management strategies.}, }
@article {pmid42172872, year = {2026}, author = {Yu, M and Wang, Z and Han, X and Ge, Y and Geng, Z and Wang, J and Wang, D and Lian, S}, title = {Parvimonas micra is a specifically enriched bacterium in advanced canine periodontal disease and its effects are ameliorated using ADSCs-exosomes.}, journal = {Veterinary microbiology}, volume = {318}, number = {}, pages = {111078}, doi = {10.1016/j.vetmic.2026.111078}, pmid = {42172872}, issn = {1873-2542}, abstract = {Canine periodontitis is a prevalent chronic inflammatory disease, with its pathological progression closely associated with oral microbiome dysbiosis and dysregulated host immune responses. This study aimed to characterize oral microbiome changes across different stages of canine periodontitis, identify bacteria associated with advanced disease and evaluate the immunomodulatory potential of adipose-derived stem cell exosomes (ADSCs-exosomes). We analyzed pooled subgingival and supragingival plaque samples collected from multiple oral sites in 60 dogs with clinical stages S0-S4 using 16S rRNA sequencing, and performed in vitro cell assays, ADSCs-exosomes isolation and characterization. Alpha-diversity analysis showed that, in this cohort and under our pooled oral sampling design, advanced periodontitis was associated with increased community richness and altered evenness at the subject level, while beta-diversity analysis confirmed marked structural differences among study groups (R[2] = 0.161, P = 0.001). P. micra showed significantly higher abundance in severe periodontitis (S4) and was identified by linear discriminant analysis effect-size (LEfSe), random forest, and analysis of variance (ANOVA) analyses (linear discriminant analysis (LDA) > 3.5, P < 0.01), suggesting an association with advanced disease. In vitro, P. micra reduced canine macrophage cell (DH82) (P < 0.05) viability and promoted a pro-inflammatory phenotypes. ADSCs-exosomes were internalized by canine macrophages and significantly downregulated pro-inflammatory cytokines (IL-1β, IL-6, iNOS) and upregulated anti-inflammatory markers (Arg-1, CD163, and IL-10) (P < 0.05), thereby partially reversing the inflammatory imbalance induced by P. micra. Together, these findings identify P. micra as a candidate bacterium associated with advanced canine periodontitis and suggest that ADSCs-exosomes may have potential as a host-modulatory therapeutic strategy in this disease.}, }
@article {pmid42172920, year = {2026}, author = {Maria van Eijk, A and Quinn-Savory, A and Zulaika, G and Skinner, A and Mason, L and Green, SJ and Phillips-Howard, PA and Mehta, SD}, title = {Effect of menstrual cups on vaginal health, reproductive tract and urogenital infections: a systematic review and meta-analysis.}, journal = {EBioMedicine}, volume = {128}, number = {}, pages = {106307}, doi = {10.1016/j.ebiom.2026.106307}, pmid = {42172920}, issn = {2352-3964}, abstract = {BACKGROUND: The menstrual cup is a device inserted into the vagina during menstruation to collect blood. Evidence of its effect on the vaginal microbiome and associations with laboratory-confirmed infections is limited. We compiled existing information to assess associations between menstrual cups and reproductive tract infections (RTIs), sexually transmitted infections (STIs), and the vaginal microbiome.<br><br>METHODS: We searched four databases (PubMed, CINAHL, Global Health, and Scopus, from inception to January 23, 2026) for trials or observational studies reporting on menstrual cup use and laboratory-confirmed RTIs, STIs and the vaginal microbiome. Study quality was assessed using the Cochrane Collaboration tool for trials and the Joanna Briggs Institute Critical Appraisal Checklist for Cohort Studies. Outcomes of interest between cup-users and users of alternative menstrual products (non-cup users) were compared using prevalence ratios (PR). Meta-analyses were conducted using fixed-effects models to generate pooled estimates. PROSPERO registration: CRD42024559595.<br><br>FINDINGS: Eleven studies involving 10,268 participants were included. Only three studies were considered of good quality. In two randomised controlled studies in Kenya, menstrual cups reduced the risk of STIs relative to non-cup users (adjusted PR [aPR] 0.74, 95% CI 0.60-0.91, p = 0.037, n = 695, I[2] = 0.0%). The association with bacterial vaginosis was 0.81 (aPR, 0.63-1.04, p = 0.0963, n = 695, I[2] = 0.0%). When combining observational and randomised studies, a protective effect on bacterial vaginosis persisted (PR 0.79, 95% CI 0.69-0.90, p = 0.0004, five studies, n = 2103, I[2] = 0.0%, 3 continents). One trial showed an association between menstrual cups and HSV-2 of 0.71 (aPR, 95% CI 0.50-1.01, p = 0.057, n = 1451). Optimal vaginal community state type-1 (CST-I) was more likely among cup users compared to non-cup users (PR 1.18, 1.10-1.27, p < 0.0001, n = 2639, 5 studies in Kenya and Europe). No increased infection risks were noted among menstrual cup users across the infections evaluated. Main limitations included the low number and quality of existing studies.<br><br>INTERPRETATION: Menstrual cups reduced the risk of STIs in Kenya. For bacterial vaginosis, the association was consistent with a protective effect and supportive for a healthy vaginal microbiome composition in studies from different geographies. These data strengthen evidence on the value of menstrual cups as a global multipurpose menstrual product solution.<br><br>FUNDING: UK-Medical Research Council, Medical Research Foundation, USA-National Institutes of Health; National Institute of Child Health and Human Development, and the Gates Foundation.}, }
@article {pmid42173308, year = {2026}, author = {Kumar Samanthapudi, VS and Ostos Mendoza, KC and Puvvala, S and Kamma, S and Kotla, S}, title = {Trimethylamine-N-oxide (TMAO) in multiorgan disease: mechanisms, translational insights, and therapeutic opportunities.}, journal = {Drug discovery today}, volume = {}, number = {}, pages = {104703}, doi = {10.1016/j.drudis.2026.104703}, pmid = {42173308}, issn = {1878-5832}, abstract = {Trimethylamine-N-oxide (TMAO), a gut microbe-derived metabolite, acts as a key mediator linking diet, microbial metabolism, and disease across multiple organs. Beyond cardiovascular and metabolic disorders, TMAO has also been implicated in a variety of pathological processes. It influences endothelial, immune, neuronal, and cancer cells, as well as platelets, through mechanisms including oxidative stress, inflammation, and organelle dysfunction. Systemic TMAO levels are influenced by hepatic metabolism, renal clearance, and hormonal factors, offering opportunities for targeted therapies. Approaches to reduce TMAO levels, including pharmacological inhibitors, dietary or microbiome-based interventions, and multiorgan strategies, could slow disease progression. Thus, TMAO shows promise as a diagnostic biomarker and therapeutic target, supporting avenues for drug discovery and precision medicine.}, }
@article {pmid42173442, year = {2026}, author = {Venter, C and Ryczaj, K and Hicks, AG and Mack, DP and O'Mahony, L and Smith, PK and Brough, HA}, title = {Nutritional, Growth, and Microbiome Implications of Oral Immunotherapy: Unintended Consequences and Clinical Considerations.}, journal = {Annals of allergy, asthma &amp; immunology : official publication of the American College of Allergy, Asthma, &amp; Immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.anai.2026.05.024}, pmid = {42173442}, issn = {1534-4436}, abstract = {Food allergy management has changed significantly, with oral immunotherapy (OIT) emerging as a widely adopted strategy to increase reaction thresholds and reduce the risk of severe allergic reactions. Alongside its immunological effects, OIT has important implications for nutrition, growth, and the gut microbiome. Traditional management of food allergy relies on strict allergen avoidance, which may compromise dietary adequacy and growth, particularly in children avoiding nutrient-dense foods such as cow's milk and eggs. OIT offers an opportunity to reintroduce these foods in controlled amounts, potentially improving nutrient intake and supporting growth trajectories. Emerging evidence highlights the role of the gut microbiome in modulating immune tolerance. Microbial diversity, metabolite production, and early-life colonization patterns influence regulatory immune pathways and epithelial barrier integrity. During OIT, microbiome changes appear modest and variable, with some studies suggesting taxon-specific or functional shifts rather than global restructuring. Importantly, dietary factors, particularly the use of ultra-processed foods as dosing vehicles, may confound microbiome outcomes and influence treatment responses. From a nutritional perspective, OIT presents both opportunities and risks. While allergen reintroduction may improve protein and micronutrient intake, reliance on energy-dense masking foods may increase the risk of excessive calorie intake and suboptimal diet quality. Growth outcomes during OIT appear generally favorable, particularly in younger children and those with lower baseline growth. This article summarizes current evidence on OIT, focusing on its interactions with diet, growth, and the gut microbiome, and highlights the need for integrated, multidisciplinary approaches to optimize both clinical and nutritional outcomes.}, }
@article {pmid42173447, year = {2026}, author = {Harvey, HJ and Corrigan, S and Baiocco, D and Zhang, Z and Iqbal, TH and Teughels, W and Chapple, I and Horniblow, RD}, title = {Promicrobial mucoadhesive micro-composites enable delivery of beneficial oral bacteria to restore and modulate oral biofilm communities.}, journal = {Journal of controlled release : official journal of the Controlled Release Society}, volume = {}, number = {}, pages = {115044}, doi = {10.1016/j.jconrel.2026.115044}, pmid = {42173447}, issn = {1873-4995}, abstract = {Imbalances within the oral microbiome, composed of over 700 phylotypes, drive both local diseases, including periodontitis, and systemic conditions, such as rheumatoid arthritis and cardiovascular disease. Given the overuse of conventional antimicrobial agents to manage oral diseases and the relapsing nature associated with current intervention strategies, innovative promicrobial approaches to oral biofilm community restoration are needed. Importantly, there is a critical unmet clinical need for active restoration and sustained delivery of beneficial oral commensals rather than continued disruption of already-imbalanced communities. We have developed a promicrobial formulation encapsulating live, health-associated, oral bacteria within mucoadhesive micro-composites to promote the establishment of beneficial biofilms under simulated oral flow conditions. We encapsulated and characterised a five-species bioactive consortia of oral bacteria in alginate micro-composites, surface modified with poly-l-lysine to enhance their adhesion to artificial saliva-coated surfaces in vitro. Dissemination of the encapsulated bacteria from the micro-composites led to the formation of stable oral biofilms. Notably, biofilm composition could be modulated by altering the encapsulated bioactive composition, enabling a tailored and targeted pathway to biofilm restoration. Under representative saliva flow, delivery of bioactives following their bioencapsulation resulted in strong biofilm-forming capacity, even in the presence of pre-existing oral bacterial communities containing pathobionts, highlighting their potential clinical applications in dental biofilm bioengineering. In experiments designed to simulate periodontal pocket debridement, we observed immunomodulation following treatment with bioactive formulations and pathobiont reduction when Limosilactobacillus reuteri was also incorporated into the consortia. These findings establish a framework for using sustained-release encapsulated probiotics to modulate the oral microbiome, offering a paradigm shift towards biofilm-promoting therapies for oral healthcare and paving the way for oral microbiome transplantation.}, }
@article {pmid42173626, year = {2026}, author = {Sarkar, D}, title = {Artificial intelligence in multi-omics analysis of gastrointestinal diseases.}, journal = {Progress in molecular biology and translational science}, volume = {222}, number = {}, pages = {111-128}, doi = {10.1016/bs.pmbts.2026.02.003}, pmid = {42173626}, issn = {1878-0814}, mesh = {Humans ; *Artificial Intelligence ; *Gastrointestinal Diseases/genetics/microbiology/metabolism ; Precision Medicine ; *Genomics ; Multiomics ; }, abstract = {The assessment and treatment of gastrointestinal diseases face numerous obstacles, including inadequate diagnostic methods, limited therapeutic alternatives, and unequal access to medical services across different regions. However, advancements in technology such as artificial intelligence, personalized medicine, and microbiome analysis offer promising avenues to address these difficulties. An interdisciplinary and patient-centered approach can significantly improve health outcomes and reduce the overall impact of these conditions on both patients and healthcare systems. To effectively utilize AI while safeguarding patient interests, it is essential to establish ethical standards, adopt patient-oriented regulations, and provide strong support structures for spreading awareness among both healthcare providers and recipients.}, }
@article {pmid42173629, year = {2026}, author = {Roy, P and Saha, S}, title = {AI in multi-omics analysis in obstructive lung diseases.}, journal = {Progress in molecular biology and translational science}, volume = {222}, number = {}, pages = {165-206}, doi = {10.1016/bs.pmbts.2026.01.025}, pmid = {42173629}, issn = {1878-0814}, mesh = {Humans ; *Artificial Intelligence ; *Lung Diseases, Obstructive/genetics/microbiology/metabolism ; Pulmonary Disease, Chronic Obstructive/genetics ; *Genomics ; Multiomics ; }, abstract = {The reports of obstructive lung diseases (OLDs) like asthma, chronic obstructive pulmonary disease (COPD), and bronchiectasis show increasing global prevalence. The available treatment options for these diseases are limited to antibiotics and steroids. Different multi-omics integration approaches have been applied in studying host, microbiome, and host-microbiome interactions in these diseases to get better insights. Artificial intelligence (AI)-based, as well as statistical and other approaches, are used for multi-omics analyses, specifically the integration of multi-omics data in OLDs. This chapter discusses various aspects of multi-omics integration studies in asthma, COPD, and bronchiectasis. Overall, these studies focused on disease subtype classification, risk assessment, association with genetic factors, and several other aspects.}, }
@article {pmid42173637, year = {2026}, author = {Rajalakshmi, SG and Sreehari, E and Viswanathan, P}, title = {Artificial intelligence-driven multi-omics analysis of gut-kidney axis in chronic kidney disease.}, journal = {Progress in molecular biology and translational science}, volume = {222}, number = {}, pages = {85-110}, doi = {10.1016/bs.pmbts.2026.01.015}, pmid = {42173637}, issn = {1878-0814}, mesh = {*Renal Insufficiency, Chronic/microbiology/metabolism ; Humans ; *Artificial Intelligence ; *Gastrointestinal Microbiome ; *Kidney/metabolism/pathology ; Animals ; *Metabolomics ; Proteomics ; Multiomics ; }, abstract = {The complex interactions between gut microbiota and kidney function in chronic kidney disease (CKD) present a challenging phenomenon in nephrology research. This comprehensive review explores how artificial intelligence (AI) is utilised for our understanding of the gut-kidney axis through multiomics analysis, offering a new platform for disease management and therapeutic interventions. Recent advances in multi-omics technologies have generated unprecedented volumes of data across microbiomics, metabolomics and proteomics platforms, necessitating sophisticated AI-driven approaches for meaningful interpretation. So, we substantially examined how machine learning methods integrate the omics data to establish the relationship between the gut-kidney axis for a more accurate predictive model and biomarker discovery. In addition, we explained the overview of molecular routes that relate microbiome changes to uremic toxin generation and inflammatory cascades in CKD patients. This timely review offers significant basic insights into using AI to better understand the pathogenesis of CKD progression in early stages via the gut-kidney route.}, }
@article {pmid42173692, year = {2026}, author = {Ambachew, S and Ramezanpour, M and Cooksley, CM and Shaghayegh, G and Burdon, I and Barry, EF and Fenix, KA and Wormald, PJ and Psaltis, AJ and Vreugde, S}, title = {Staphylococcus aureus and Staphylococcus lugdunensis Act in Concert to Disrupt the Nasal Epithelial Barrier.}, journal = {Clinical and translational allergy}, volume = {16}, number = {5}, pages = {e70177}, doi = {10.1002/clt2.70177}, pmid = {42173692}, issn = {2045-7022}, support = {Grant No. 0006008606//Australian National Health and Medical Research Council/ ; }, abstract = {INTRODUCTION: Chronic rhinosinusitis (CRS) pathophysiology and its link to microbiome is an area of ongoing investigation. Certain pathogens, in particular Staphylococcus aureus described to contribute to recalcitrant CRS. In addition, different species of coagulase negative staphylococci (CoNS) are frequently isolated from the sinonasal cavity of CRS patients. However, the influence of Staphylococcal species coexisting in the same niche on the inflammatory process remains unclear. The aim of this study was to explore the impact of exoproteins from various Staphylococcus species isolated from the same patients on the mucosal barrier.<br><br>METHODS: Staphylococcal species isolated from CRS and control patients were cultured from sinus swabs in planktonic and biofilm forms, and their exoproteins extracted. Primary human nasal epithelial cells (HNECs) from CRS patients were cultured at an air-liquid interface (ALI) and exposed to 20&#xa0;&#x3bc;g/mL exoproteins or control. Barrier disruption and cytotoxicity were assessed by measuring the transepithelial electrical resistance (TEER), passage of fluorescein labeled dextrans and lactate dehydrogenase (LDH) levels. IL- 6 concentration was measured employing ELISA. Patient's matched sinonasal tissue samples were analyzed with flow cytometry to detect and quantify immune cells.<br><br>RESULTS: Forty-four Staphylococcal species were isolated from 22 CRS and control patients including: 22 S. aureus, 12 S. epidermidis, and 10 S. lugdunensis. 15 out of 22 S. aureus exoproteins significantly enhanced cytotoxicity, reduced TEER values and increased paracellular permeability compared to control (p&#xa0;<&#xa0;0.05). By contrast, S. epidermidis and S. lugdunensis exoproteins caused either mild or negligible effects on the TEER values, cell viability, and paracellular permeability. However, S. lugdunensis exoproteins induced significantly higher IL-6 compared to control. Correlation analysis indicated S. aureus and S. lugdunensis from the same patient acted in concert to disrupt the nasal epithelial barrier and induce toxicity.<br><br>CONCLUSION: This study shows the significant and detrimental impact of the presence of S. aureus exoproteins on nasal epithelial cell barrier function. S. aureus and S. lugdunensis isolated from the same patients acted in concert to affect the nasal barrier and inducing toxicity.}, }
@article {pmid42173824, year = {2026}, author = {Alanazi, HH}, title = {Immune discrimination between commensals and pathogenic bacteria.}, journal = {Virulence}, volume = {17}, number = {1}, pages = {2677297}, doi = {10.1080/21505594.2026.2677297}, pmid = {42173824}, issn = {2150-5608}, mesh = {Humans ; *Bacteria/immunology/pathogenicity ; *Symbiosis/immunology ; Gastrointestinal Microbiome/immunology ; Animals ; Dysbiosis/immunology/microbiology ; *Bacterial Infections/immunology/microbiology ; *Host-Pathogen Interactions/immunology ; Immune Tolerance ; *Bacterial Physiological Phenomena ; Gastrointestinal Tract/microbiology/immunology ; }, abstract = {Interaction with various bacteria is essential for the development of various components of the immune system. To prevent disease, the immune system must continuously discriminate between commensal and pathogenic bacteria. The immune system employs several mechanisms to discriminate between beneficial and harmful bacteria. This ensures selective immune tolerance toward commensals, especially in the gastrointestinal tract. Both commensal and pathogenic bacteria contain features that provoke immune responses. However, how the immune system reacts to or eliminates bacterial infections while preserving commensals is not fully understood. This review aims to explore the underlying mechanisms used by the immune system to distinguish between commensals and pathogenic bacteria. The review also addresses how commensals interact with immune system components to facilitate immune discrimination and host protection. Finally, dysbiosis and therapeutic interventions used to restore microbial balance are also discussed in this review.}, }
@article {pmid42173935, year = {2026}, author = {Yang, J and Park, Y and Jang, SG and Park, MJ and Moon, SJ and Choi, HK and Kwok, SK}, title = {Clinical significance of gut microbiota-derived metabolite trimethylamine N-oxide in patients with systemic lupus erythematosus.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-53011-7}, pmid = {42173935}, issn = {2045-2322}, support = {RS-2023-00224099//National Research Foundation of Korea/ ; }, abstract = {Trimethylamine N-oxide (TMAO), a gut microbiota-derived metabolite, is associated with cardiovascular disease (CVD) via pro-inflammatory and pro-atherogenic mechanisms. Systemic lupus erythematosus (SLE) is a systemic autoimmune disease with a significantly increased risk of CVD, however, the role of TMAO in SLE remains unclear. This study aimed to assess the clinical significance of TMAO in patients with SLE, including analyses of precursor metabolites and gut microbiome. A total of 207 participants were enrolled, including 157 patients with SLE and 50 healthy controls. Serum TMAO levels were measured using ELISA, fecal precursor metabolites including trimethylamine (TMA) were quantified by [1]H-NMR spectroscopy, and gut microbiota composition was assessed using 16S rRNA sequencing. SLE patients with CVD had significantly higher TMAO levels than HC (P = 0.028) and SLE patients without CVD (P = 0.004). Serum TMAO (P = 0.025) and fecal TMA (P = 0.032) levels were positively correlated with the Systemic Lupus International Collaborating Clinics/American College of Rheumatology (SLICC/ACR) damage index. Serum TMAO was negatively correlated with steroid dose (P = 0.038). Distinct gut microbiota compositions were observed between SLE patients with and without CVD. TMAO is associated with cardiovascular disease and cumulative organ damage in SLE, potentially mediated by gut microbiome alterations and modulated by steroid therapy.}, }
@article {pmid42173975, year = {2026}, author = {Liu, Y and Sun, C and Liu, H and Shu, X and Yu, T and Gong, Y and Li, J}, title = {Gut microbiota dysbiosis and altered fecal metabolome in patients with age-related cataract.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-53261-5}, pmid = {42173975}, issn = {2045-2322}, support = {CSTB2022NSCQ-MSX1274//Natural Science Foundation Project of Chongqing, Chongqing Science and Technology Commission/ ; CSTB2023NSCQ-MSX0194//Natural Science Foundation Project of Chongqing, Chongqing Science and Technology Commission/ ; NSFC; 32300778//National Natural Science Foundation of China/ ; W015//CQMU Program for Youth Innovation in Future Medicine/ ; }, abstract = {Age-related cataract (ARC) is a leading cause of vision loss with incompletely understood mechanisms. Emerging evidence suggests the gut microbiota can influence ocular health, yet the gut-eye connection in cataract remains unexplored. We characterized gut microbial communities and fecal metabolic profiles in 30 ARC patients and 30 healthy controls using 16S rDNA gene sequencing, untargeted LC-MS metabolomics, and targeted GC-MS for short-chain fatty acids (SCFAs). While alpha- and beta-diversity were comparable between groups, ARC patients exhibited significant dysbiosis, including reduced Gut Microbiome Health Index, increased Microbial Dysbiosis Index, higher relative abundance of Bifidobacterium and Klebsiella, and depletion of butyrate-producing taxa (Faecalibacterium, Clostridia). Fecal metabolomic profiles distinctly separated ARC patients from controls, with pathway analysis highlighting disruptions in glycerophospholipid and choline metabolism. Targeted analysis confirmed significant depletion of acetate, propionate, and butyrate in ARC patients (all P< 0.01), which positively correlated with beneficial genera abundance. This integrative study reveals that ARC patients harbor gut microbial dysbiosis and distinct fecal metabolomic signatures, notably a loss of SCFA-producing bacteria and anti-inflammatory SCFAs. These findings support a novel gut-eye axis in cataract pathogenesis and suggest that gut-derived microbial and metabolic biomarkers may aid in non-invasive risk assessment, while microbiome-targeted interventions could offer new preventive or therapeutic avenues.}, }
@article {pmid42174008, year = {2026}, author = {de Mel, R and Al Khafaji, AH and Muthusamy, S and Xu, J and Håkansson, &#xc5;}, title = {Changes in gut microbiota composition following water kefir consumption in healthy adults.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42174008}, issn = {2045-2322}, mesh = {Humans ; *Gastrointestinal Microbiome ; Adult ; Male ; *Kefir/microbiology ; Female ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Young Adult ; Healthy Volunteers ; Middle Aged ; Bacteria/genetics/classification/isolation &amp; purification ; Water ; }, abstract = {Fermented foods have gained increasing scientific interest for their potential to modulate gut microbiota and provide probiotic microorganisms with possible health benefits. This intervention trial examined the impact of daily consumption of water kefir, a sustainable plant-based fermented beverage, on gut microbiota composition in 40 healthy adults. Participants consumed 200 mL of homemade water kefir daily for 14 days, with fecal samples collected before and after the intervention. Some participants reported mild, transient gastrointestinal effects such as flatulence (32%) and bloating (24%), which are common when introducing live microorganisms, while others experienced reduced abdominal pain (28%), and most (66%) reported no noticeable change in symptoms. 16S rRNA sequencing revealed significant shifts in microbial composition, including a 6.5% decrease in Firmicutes and increases in Bacteroidetes (+ 21.6%) and Actinobacteria (+ 14.8%). At the species level, beneficial taxa such as Blautia spp. and Roseburia faecis increased, along with commensals including Bacteroides fragilis, Bacteroides uniformis, Gemmiger formicilis, Prevotella copri, and Parabacteroides distasonis (p < 0.01). Although α-diversity remained unchanged, β-diversity differed significantly between pre- and post-intervention samples (p = 0.025). By comparing the relative abundance of dominant genera in participants' gut microbiota and in water kefir, overlapping genera such as Lactobacillus, Bifidobacterium, Prevotella, Coprococcus, and Faecalibacterium were identified. Among these, Bifidobacterium and Prevotella increased, Coprococcus decreased, and Lactobacillus and Faecalibacterium remained stable. Genera exclusive to the gut microbiota also exhibited differential changes. These findings suggest that water kefir consumption is associated with modulation of the gut microbiota, including increases in saccharolytic and short-chain fatty acid (SCFA)-producing taxa, potentially influenced by its exopolysaccharides and microbial community. Some genera from water kefir may transiently affect the gut microbiome, and the concurrent increase in Bifidobacterium and Prevotella may suggest a potential probiotic-like effect. However, causality cannot be established, and further studies are needed to assess the persistence of these changes and their long-term clinical relevance.}, }
@article {pmid42174021, year = {2026}, author = {Min, U and Kim, J and Kim, J and Jin, H and Oh, H and Ahn, S and Shin, H and Lee, W}, title = {Spicy food intake and dietary factors shape the gut microbiome and metabolism of mucin and short-chain fatty acids in healthy adults.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-53556-7}, pmid = {42174021}, issn = {2045-2322}, abstract = {Whether spicy food intake independently modulates mucin metabolism and short-chain fatty acid (SCFA) production or depends on co-ingested factors such as alcohol remains poorly understood. Herein, shotgun metagenomics characterized gut microbial composition, functional pathways, and their relationship with spicy food intake, alcohol consumption, and intestinal fatty acid-binding protein (I-FABP) and liver fatty acid-binding protein (L-FABP) levels in 229 healthy Korean adults. Alcohol intake was positively correlated with urinary I-FABP levels indicating mild epithelial stress, whereas spicy food intake was not associated with either FABP biomarker. Consumption of highly spicy foods resulted in increased abundance of SCFA-producing and mucin-metabolizing taxa, along with mucin degradation and SCFA production. Individuals with high alcohol intake showed stronger enrichment of mucin-degrading taxa with reduced SCFA flux and increased abundance of Proteobacteria and Fusobacteria. The cross-classified dietary groups exhibited distinct mucin and SCFA activity patterns. The Drink-High-Spicy-High (DHSH) group displayed elevated mucin turnover and SCFA production with dysbiosis. These findings suggest that spicy food may modulate mucus layer metabolism in a context-dependent manner, whereas alcohol more consistently perturbs mucin-SCFA networks and epithelial integrity.}, }
@article {pmid42174097, year = {2026}, author = {Ali, A}, title = {Comment on "Gut microbiome impact on systemic therapy outcomes in metastatic renal cell carcinoma: a systematic review" by Gavi et al.}, journal = {World journal of urology}, volume = {44}, number = {1}, pages = {}, pmid = {42174097}, issn = {1433-8726}, }
@article {pmid42174231, year = {2026}, author = {Schiele, J and Tsai, PL and Schimmele, T and Beck, S and Meyer, M and Mannes, M and Desmond, LW and Noschka, R and Huber-Lang, M and Haffner-Luntzer, M and Jarczok, MN and Lowry, CA and Reif, A and Langgartner, D and Stenger, S and Slattery, DA and Reber, SO}, title = {Microbial Legacy: Mycobacterium vaccae ATCC 15483[T] intergenerationally diversifies the microbiome and enhances stress resilience in male mice.}, journal = {Molecular psychiatry}, volume = {}, number = {}, pages = {}, pmid = {42174231}, issn = {1476-5578}, support = {RE 2911/ 23-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; German Research 251293561//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; German Research 251293561//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SL 141/ 6-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, abstract = {According to the "Old Friends" hypothesis, the increased prevalence of stress-associated disorders in urban concrete landscapes of high-income countries is at least in part due to a reduced exposure to immunoregulatory microorganisms. The latter is particularly impactful when occurring during early prenatal and postnatal life. Accordingly, our own preclinical studies demonstrate that non-pathogenic rapid-growing mycobacteria, including Mycobacterium (M.) vaccae NCTC 11659 and M. vaccae ATCC 15483[T], have immunoregulatory and stress-protective effects when administered repeatedly prior to or during stressor exposure. Here, we advance these findings by showing that repeated intragastric (i.g.) administration of a heat-killed preparation of M. vaccae ATCC 15483[T] to female C57BL/6 N mice provides intergenerational stress protection. Their male offspring, despite never directly receiving administration of rapid-growing mycobacteria, were protected against multiple adverse consequences of chronic stress in adulthood. Moreover, correlational analyses implicate the fecal microbiome as a potential mediator of these effects, with M. vaccae ATCC 15483[T] intergenerationally facilitating α-diversity and increasing the relative abundance of bacterial taxa known to be potent short-chain fatty acid producers. Repeated intragastric (i.g.) administration of a heat-killed preparation of Mycobacterium (M.) vaccae ATCC 15483[T] (MvacATCC)vs. its vehicle borate-buffered saline (BBS) to adult nulliparous female C57BL/6N mice was intergenerationally protective against multiple negative physiological and immunological consequences of chronic subordinate colony housing (CSC; compared with respective single-housed control (SHC) mice), including adrenal hypertrophy, splenomegaly, thymus involution, and tibia growth reduction as well as increased splenic toll-like receptor (TLR) 2 and TLR4 protein concentrations and splenocyte ex vivo (re)activity, but also decreased splenic ex vivo glucocorticoid sensitivity, regulatory T cell (Treg) counts and Treg suppression capacity in their male offspring. In contrast, CSC-induced increase in splenic myeloid cell counts as well as of neutrophilic chemotactic activity was not affected intergenerationally by MvacATCC. Moreover, fecal microbiome analyses before and after CSC showed that MvacATCC intergenerationally facilitated α-diversity and relative abundance of bacterial taxa known to be potent short-chain fatty acid (SCFA) producers. Of note, we abstained from showing respective data of female offspring in the graphical abstract (*), as the intergenerational resilience effects of MvacATCC on female offspring were difficult to interpret. The latter was due to the fact that chronic adult stressor exposure (i.e., social instability paradigm, SIP) per se did not affect any of the physiological and immunological readouts reported in females. The graphical abstract was created with Biorender.com.}, }
@article {pmid42174303, year = {2026}, author = {Kim, CH and Ciloglu, A and Yan, J and Mackay, A and Noel, KR and Cooper, M and Oluoch, A and Canam, T and Stone, CM}, title = {Habitat Type and Locality Structure the Midgut Microbiota of Aedes albopictus.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02792-5}, pmid = {42174303}, issn = {1432-184X}, abstract = {The mosquito midgut microbiome plays a crucial role in nutrition, reproduction, and immunity, yet how locality and urban development shape these communities and their potential relevance to mosquito-pathogen interactions remains poorly understood. Here, we investigated bacterial community composition and diversity in the midguts of adult female Aedes albopictus collected from residential and woodland habitats of Champaign-Urbana and Charleston in Illinois, USA. We sequenced the V4 region of the 16 S rRNA gene from 160 samples and analyzed the data using QIIME 2. After quality and feature filtering, 112 samples were retained, yielding 2,531 unique amplicon sequence variants assigned to 34 bacterial phyla, 246 families, and 404 genera. Because formal contaminant assessment was not possible, findings should be interpreted with appropriate caution. Woodland habitats showed significantly higher Shannon diversity, observed ASV richness, and phylogenetic diversity than residential habitats, with Charleston woodland samples exhibiting the highest richness and phylogenetic diversity. Factorial analyses showed significant associations of both city and habitat type with Shannon diversity, observed richness, and Faith's phylogenetic diversity, with significant interaction terms also detected. Beta diversity analyses revealed distinct clustering of Charleston woodland samples, and factorial PERMANOVA indicated significant associations of both city and habitat type across all four beta diversity metrics, with the strongest interaction effect observed for unweighted UniFrac. In conclusion, these results show that habitat type and locality are strongly associated with the composition and diversity of the Ae. albopictus midgut microbiota, underscoring the importance of habitat-specific microbial patterns in mosquito biology.}, }
@article {pmid42174322, year = {2026}, author = {Tan, Y and Peng, G and Abudouwanli, A and Zhao, W and Sun, Q and Yang, M and Ogawa, H and Okumura, K and Niyonsaba, F}, title = {Tryptophan Metabolism at the Crossroads of Immunity, Barrier Function, and the Microbiome in Atopic Dermatitis.}, journal = {Clinical reviews in allergy &amp; immunology}, volume = {69}, number = {1}, pages = {}, pmid = {42174322}, issn = {1559-0267}, support = {24K23469//Japan Society for the Promotion of Science/ ; 24K11459//Japan Society for the Promotion of Science/ ; }, mesh = {Humans ; *Tryptophan/metabolism ; *Dermatitis, Atopic/metabolism/immunology/therapy/microbiology/etiology ; *Microbiota/immunology ; Animals ; *Skin/immunology/metabolism/microbiology ; Melatonin/metabolism ; Kynurenine/metabolism ; Immunity ; Probiotics/therapeutic use ; Serotonin/metabolism ; }, abstract = {Atopic dermatitis (AD) is a chronic inflammatory skin disease characterized by complex interplay among immune imbalance, impaired barrier function, and alterations in host‒microbiome interactions. Accumulating evidence indicates that tryptophan (TRP) metabolism is associated with these core pathological processes. This review summarizes the major TRP metabolic pathways, including the kynurenine pathway, microbial indole production, and the serotonin-melatonin axis, and outlines how their respective metabolites influence cutaneous inflammation, immune regulation, and barrier integrity in the context of AD. We integrate findings from preclinical and clinical studies to describe disease-associated alterations in TRP metabolism in AD and their potential relevance to disease activity. In addition, we examine both existing and emerging therapeutic strategies aimed at correcting TRP metabolic imbalance, including pharmacological agents, dietary interventions, and probiotic supplementation. Overall, elucidating the multifaceted role of TRP metabolism in AD pathophysiology provides a rational foundation for developing more precise diagnostic tools and targeted therapeutic approaches.}, }
@article {pmid42174554, year = {2026}, author = {Xing, X and Meng, W and Chen, W and Shi, X and Wei, D and Lu, Q}, title = {Causal effects of oral microbiome traits on female reproductive diseases: a two-sample Mendelian randomization study.}, journal = {BMC women's health}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12905-026-04547-3}, pmid = {42174554}, issn = {1472-6874}, support = {CYDXK202203//Multidisciplinary Clinical Research Innovation Team Project of Beijing Chao-Yang Hospital/ ; }, abstract = {OBJECTIVE: Female reproductive diseases (FRDs) impose a substantial health burden. Observational studies suggest links between oral dysbiosis and systemic conditions, but whether oral microbial traits causally influence FRDs remains unclear. We used two-sample Mendelian randomization (MR) to evaluate potential causal effects of genetically predicted oral microbiome traits on FRDs.<br><br>METHODS: Genome-wide association study (GWAS) summary statistics for 44 salivary microbial traits were obtained from a publicly available oral microbiome GWAS based on the Danish ADDITION-PRO cohort (16&#xa0;S rRNA profiling; European ancestry; n&#x2009;=&#x2009;610). Outcome GWAS summary statistics for six FRDs were obtained from FinnGen (R12). The inverse-variance weighted (IVW) method was the primary analysis, complemented by MR-Egger, weighted median, and weighted mode. Sensitivity analyses included Cochran's Q, MR-Egger intercept, MR-PRESSO, leave-one-out, and Steiger directionality tests. Multiple testing for primary IVW analyses was addressed using Benjamini-Hochberg false discovery rate (FDR) correction.<br><br>RESULTS: In primary IVW analyses, several oral taxa showed nominal associations (P&#x2009;<&#x2009;0.05) with uterine leiomyoma (class Bacilli: OR&#x2009;=&#x2009;1.0303, 95% CI 1.0012-1.0602; genus Veillonella: OR&#x2009;=&#x2009;1.0291, 95% CI 1.0075-1.0512) and tubal infertility (family Veillonellaceae: OR&#x2009;=&#x2009;0.8640, 95% CI 0.7824-0.9541; genus Veillonella: OR&#x2009;=&#x2009;0.8900, 95% CI 0.8167-0.9699). However, none of these associations remained statistically significant after Benjamini-Hochberg FDR correction for the primary IVW analyses (all q&#x2009;>&#x2009;0.05). In sensitivity analyses, MR-PRESSO outlier correction suggested a nominal association between Rothia mucilaginosa and uterine leiomyoma (OR&#x2009;=&#x2009;1.0228, 95% CI 1.0069-1.0391; P&#x2009;=&#x2009;0.0202). Overall, sensitivity analyses and Steiger directionality tests did not indicate that the main signals were driven by strong directional pleiotropy or reverse causation.<br><br>CONCLUSION: This two-sample MR study provides suggestive, exploratory genetic evidence that specific oral microbiome traits may be linked to uterine leiomyoma and tubal infertility, but the evidence did not remain statistically significant after multiple-testing correction. Larger oral microbiome GWAS, independent outcome datasets, and functional studies are needed to validate these signals and clarify biological mechanisms.}, }
@article {pmid42174615, year = {2026}, author = {Buddhasiri, S and Muangplod, T and Panathiwat, P and Chandrasrimuang, P and Jitjumnong, J and Boonyayatra, S and Singhla, T}, title = {Seasonal particulate matter exposure is associated with upper respiratory microbiota restructuring in dairy heifers.}, journal = {BMC veterinary research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12917-026-05580-y}, pmid = {42174615}, issn = {1746-6148}, support = {R66IN00536, 2023//CMU Mid-Career Research Fellowship program, Chiang Mai University/ ; }, abstract = {BACKGROUND: Particulate matter (PM), particularly PM2.5 and PM10, is a major environmental health concern linked to respiratory diseases in humans and animals. Northern Thailand, especially Chiang Mai, experiences recurrent seasonal air pollution from biomass burning, exposing outdoor-housed livestock to elevated ambient PM levels. The bovine upper respiratory tract (URT) harbors both commensal and opportunistic microorganisms, and disruption of this microbiota may influence susceptibility to bovine respiratory disease (BRD). However, the impact of natural PM exposure on the bovine URT microbiota remains poorly understood.<br><br>RESULTS: Nasopharyngeal swabs from 25 clinically healthy dairy heifers were analyzed during low-PM and high-PM periods. During the high-PM period, peak PM2.5 levels exceeded 30 times the WHO 24-hour guideline. Alpha diversity, including observed features, Shannon diversity, and Simpson index, was significantly higher during the high-PM period than during the low-PM period. Beta diversity analysis showed significant differences in Bray-Curtis dissimilarity and Jaccard distance, indicating changes in both relative abundance-based community structure and presence-absence-based community membership. The high-PM period was characterized by altered taxonomic profiles, including higher proportions of Proteobacteria, Firmicutes, Gammaproteobacteria, and Bacilli, and lower proportions of Actinobacteriota, Bacteroidota, Actinobacteria, and Bacteroidia. Among selected dominant genera, Moraxella and Fusobacterium were significantly reduced during the high-PM period. BRD-associated genera, including Mycoplasma, Pasteurella, Mannheimia, and Histophilus, showed higher average relative abundances during the high-PM period; however, paired comparisons were not statistically significant.<br><br>CONCLUSIONS: Seasonal high-PM exposure in Chiang Mai was associated with measurable changes in the nasopharyngeal microbiota of clinically healthy dairy heifers, including increased alpha diversity, altered beta diversity, changes in taxonomic profiles, and reductions in selected dominant genera. These findings suggest that ambient air pollution may contribute to respiratory microbiota restructuring in dairy heifers. Further longitudinal studies integrating microbiota composition, host immune responses, farm-level environmental monitoring, and clinical respiratory outcomes are needed to clarify whether PM-associated microbiota changes contribute to BRD susceptibility.}, }
@article {pmid42174668, year = {2026}, author = {Zhang, Z and Ma, X and Zhang, J and Wu, S and Zhang, X and Yang, C}, title = {Intratumoral microbiota exhibiting varied responses to neoadjuvant chemotherapy in triple-negative breast cancer revealed by 2bRAD-M.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-08187-x}, pmid = {42174668}, issn = {1479-5876}, abstract = {BACKGROUND: Neoadjuvant chemotherapy (NACT) is the conventional therapy for early-stage and locally advanced triple-negative breast cancer (TNBC). Pathological complete response (pCR) serves as an essential indicator for predicting the effectiveness of NACT; however, a limited percentage of patients benefit from NACT. This research examined variations in the tumor microbiota between the pCR and non-pCR groups via 2BRAD sequencing for microbiome (2bRAD-M) technology and assessed the potential of the microbiota as a biomarker for predicting the NACT response.<br><br>METHODS: A total of 44 TNBC patients were enrolled, of whom 25 achieved pCR and 19 were classified as non-pCR patients. Clinical data were collected, tumor tissue was biopsied as sample, and DNA was extracted. The 2bRAD-M sequencing method was used to analyse the microbial communities and community structures of tumor tissues in both groups, conduct microbial diversity and differential analyses, and perform qualitative and quantitative studies on the microbes inside the tissues.<br><br>RESULTS: A total of 1,896 microbial species were identified. The microbial diversity in non-pCR tissue exceeded that in pCR patient tissue. The microbial composition of the tumor tissues in both groups was comparable. In the non-pCR group, there were significantly more gram-negative bacteria, such as Klebsiella, Escherichia, Acinetobacter, Vibrio, and Meiothermus, than in the pCR group. Calidithermus chliarophilus, Meiothermus sp.003226535, and Escherichia coli were identified as the three principal species distinguishing the two groups. Seven species were identified as markers to distinguish between non-pCRs and pCRs, with an AUC value of 90.3%. Validation in an independent cohort via qPCR indicated the potential predictive value of this seven-species model, yielding an AUC of 84%. Functional annotation analysis revealed 3,207 differentially expressed COGs and 230 differentially enriched signalling pathways across the non-pCR and pCR microbiomes. In vitro experiments suggested that lipopolysaccharide may contribute to doxorubicin and paclitaxel resistance in MDA-MB-231 cells, a process potentially linked to the reactivation of the PI3K/AKT signaling pathway.<br><br>CONCLUSION: This exploratory 2bRAD-M microbiome study of pCR and non-pCR tissues from TNBC patients receiving NACT identified significant differences in microbial environments between the two groups. Based on these findings, we developed a predictive model for chemotherapy effectiveness and highlighted the microbiome's potential as a biomarker for the efficacy of NACT in TNBC patients, offering novel insights that may inform future clinical diagnostic strategies.}, }
@article {pmid42174754, year = {2026}, author = {Chen, Y and Zhao, J and Zhao, J and Chen, Q and Dong, S and Jia, S and Zhao, Y and Hao, D and Yin, Y and Lin, S and Chen, Y and Zhuang, Y and Peng, H}, title = {Effects of fecal microbiota transplantation and probiotics on the gut microbiome in antibiotic-treated septic patients: A pilot randomized controlled trial.}, journal = {Virulence}, volume = {17}, number = {1}, pages = {2668764}, doi = {10.1080/21505594.2026.2668764}, pmid = {42174754}, issn = {2150-5608}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Probiotics/administration &amp; dosage/therapeutic use ; *Fecal Microbiota Transplantation ; Pilot Projects ; Male ; Middle Aged ; Female ; *Sepsis/therapy/microbiology/drug therapy ; *Anti-Bacterial Agents/therapeutic use/adverse effects ; Aged ; Prospective Studies ; Critical Illness ; Dysbiosis/therapy ; Treatment Outcome ; Feces/microbiology ; Adult ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Broad-spectrum antibiotics, essential for sepsis management in critically ill patients, cause significant gut dysbiosis. Restoring gut microbiota may improve outcomes, but the efficacy of interventions like fecal microbiota transplantation (FMT) and probiotics in this setting remains underexplored. This study aims to evaluate the feasibility and potential efficacy of FMT versus probiotics on gut microbiome restoration and inflammatory markers in critically ill, antibiotic-treated sepsis patients. In this single-center, prospective, exploratory pilot RCT, 40 sepsis patients were were randomized 2:1:1 to: Control (n = 20, antibiotics treatment), Probiotics (n = 10, antibiotics treatment combined one week of probiotics), and FMT (n = 10, antibiotics treatment combined one week of FMT) groups. Gut microbiota composition was analyzed using 16S rDNA sequencing, and clinical inflammatory markers were assessed at baseline, one week, and two weeks post-treatment. FMT significantly mitigated antibiotic-induced reductions in microbial diversity. At 2 weeks, the FMT group exhibited higher alpha-diversity (Chao1 index, p = 0.0125; Shannon/Simpson trends p = 0.06) compared to Control and Probiotics groups. FMT increased beneficial Bacteroides abundance and reduced Enterobacteriaceae. BugBase analysis revealed FMT significantly lowered pathogenic potential of gut microbiota (p = 0.021). Donor-recipient analysis showed FMT shifted recipient microbiomes toward donor enterotype. This study provides preliminary evidence that FMT, but not the probiotic regimen, effectively restores gut microbiome diversity and composition, reduces pathogenic potential, and may improve clinical outcomes in critically ill sepsis patients after broad-spectrum antibiotics. This study was registered on ClinicalTrials.gov (NCT05578196).}, }
@article {pmid42175400, year = {2026}, author = {Wang, D and Zhang, F}, title = {Associations of bowel movements and stool types with risk of chronic kidney disease.}, journal = {Medicine}, volume = {105}, number = {21}, pages = {e48888}, doi = {10.1097/MD.0000000000048888}, pmid = {42175400}, issn = {1536-5964}, mesh = {Humans ; *Renal Insufficiency, Chronic/epidemiology/etiology/physiopathology ; Female ; Male ; Cross-Sectional Studies ; Middle Aged ; Glomerular Filtration Rate ; Adult ; Aged ; Risk Factors ; Nutrition Surveys ; *Feces ; *Defecation/physiology ; *Diarrhea/complications/epidemiology ; }, abstract = {The gut-kidney axis is increasingly recognized in chronic kidney disease (CKD) pathophysiology. Although stool frequency and consistency reflect gut microbiome status, their association with CKD remains underexplored. This study aimed to examine the relationship between bowel habits and CKD risk. In this cross-sectional analysis of 11,760 adults from National Health and Nutrition Examination Survey 2005 to 2010, stool frequency (weekly) and consistency (Bristol Stool Form Scale) were assessed. CKD was defined as estimated glomerular filtration rate (eGFR) < 60 mL/min/1.73m2 and/or urine albumin-to-creatinine ratio (uACR) ≥ 30 mg/g. Weighted logistic regression adjusted for multiple confounders was used; subgroup and mediation analyses were performed. Diarrhea-like stool (Bristol Stool Form Scale types 6/7) was independently associated with higher CKD risk (odds ratio [OR] = 1.57, 95% confidence interval [CI]: 1.14-2.27), consistent across eGFR < 60 (OR = 1.42, 95% CI: 1.01-1.99) and uACR ≥ 30 mg/g (OR = 1.55, 95% CI: 1.03-2.23). Mediation analysis indicated that systemic inflammation (C-reactive protein) explained 10.1%, 8.5%, and 15.3% of these associations for eGFR decline, elevated uACR, and overall CKD, respectively. Subgroup analyses supported robustness across demographic and clinical strata. Bowel movement frequency was not significantly associated with CKD. Diarrhea-like stool consistency, partly mediated by systemic inflammation, is associated with increased CKD risk.}, }
@article {pmid42175487, year = {2026}, author = {Liu, D and Wu, L and Liu, X and Liu, Z and Kuang, L and Wu, S}, title = {The causal role of skin microbiota in rheumatoid arthritis via gut microbiota and immune cell mediation: A Mendelian randomization study.}, journal = {Medicine}, volume = {105}, number = {21}, pages = {e48847}, doi = {10.1097/MD.0000000000048847}, pmid = {42175487}, issn = {1536-5964}, support = {20231A010042, 20251A010040//Science and Technology Project of Guangzhou Municipal Health Commission/ ; 2023A03J0976, 2023A03J0492,2024A03J0499, 2025A03J3440//Science and Technology Program of Guangzhou City/ ; }, mesh = {Humans ; *Arthritis, Rheumatoid/immunology/microbiology/genetics ; Mendelian Randomization Analysis ; *Gastrointestinal Microbiome/immunology ; *Skin/microbiology/immunology ; *Microbiota/immunology ; Genome-Wide Association Study ; Skin Microbiome ; }, abstract = {Emerging evidence suggests that disturbances in skin microbiota homeostasis may contribute to rheumatoid arthritis (RA) development through systemic immunomodulatory pathways. However, the causal relationships and underlying intermediary mechanisms remain to be clarified. We utilized summary-level data from large-scale genome-wide association studies and the FinnGen database, including 150 skin microbiota taxa, 731 immune cell phenotypes, 473 gut microbiota taxa, and RA cases. Two-sample Mendelian randomization (TSMR) was applied to evaluate potential causal associations with RA. Mediation analysis was further performed to identify the intermediary roles of immune cells and gut microbiota. Multiple sensitivity analyses were conducted to ensure the robustness of the findings. We identified significant causal associations between 6 skin microbiota, 25 immune cell phenotypes, and 19 gut microbiotas with RA. Mediation analysis indicated that certain immune cell traits and gut microbes may act as intermediaries in these relationships. Specifically, 20.3% of the protective effect of phylum Proteobacteria_Dry on RA risk was mediated by species Eubacterium F sp000434115. In contrast, genus Photobacterium accounted for 21.1% of the risk effect mediated by family Micrococcaceae_Dry. Additionally, immune phenotypes such as CD3+ Tregs and CX3CR1+ monocytes partially offset microbial risks, underscoring a novel "skin-gut-immune" axis in RA etiology. This Mendelian randomization study provides robust genetic evidence supporting the causal role of skin microbiota in rheumatoid arthritis pathogenesis via dual mediation pathways involving gut microbiota and immune cells. Our results suggest that targeting the skin and gut microbiota could represent a novel preventive or adjunctive therapeutic strategy for RA. For instance, probiotics or prebiotics aimed at enriching protective taxa (e.g., Proteobacteria, Fournierella massiliensis) or suppressing risk-associated microbes (e.g., Photobacterium, Brachyspira) might help restore immune homeostasis. Additionally, immunomodulatory approaches focusing on Treg enhancement or CX3CR1+ monocyte regulation could be informed by the identified immune phenotypes. Future studies should validate these mechanisms in longitudinal cohorts and explore microbiome-based precision medicine for RA.}, }
@article {pmid42175520, year = {2026}, author = {Zeng, J and Ding, Z and Dai, Z}, title = {Dietary patterns supportive of gut microbiota and bacterial vaginosis: A cross-sectional analysis from NHANES 2001 to 2004.}, journal = {Medicine}, volume = {105}, number = {21}, pages = {e48863}, doi = {10.1097/MD.0000000000048863}, pmid = {42175520}, issn = {1536-5964}, mesh = {Humans ; Female ; Cross-Sectional Studies ; Adult ; *Vaginosis, Bacterial/epidemiology/microbiology ; Middle Aged ; Nutrition Surveys ; *Gastrointestinal Microbiome/physiology ; Young Adult ; Prevalence ; United States/epidemiology ; *Diet/statistics &amp; numerical data ; }, abstract = {Bacterial vaginosis (BV) is the leading form of vaginal microbiome imbalance in women of reproductive age and has been associated with dietary patterns and gut microbial profiles. This study investigated the association between a literature-based dietary index for gut microbiota (DI-GM) and BV prevalence in US women. We conducted a cross-sectional analysis of 1169 nonpregnant women aged 20 to 49 years from the National Health and Nutrition Examination Survey 2001 to 2004 with Nugent score measurements and complete dietary data. BV was defined as a Nugent score ≥ 7. Dietary intake was assessed via two 24-hour recalls, and DI-GM was computed based on 14 food groups classified as beneficial or unbeneficial for gut microbial health. Multivariable survey-weighted logistic regression models were used to estimate odds ratios and 95% confidence intervals. BV prevalence was 31.2%. Higher DI-GM scores were associated with lower odds of BV; women with scores ≥6 had reduced odds compared with those with scores of 0 to 3 (adjusted odds ratio = 0.75; 95% confidence interval: 0.60-0.94; P = .015; P-trend = .013). In conclusion, higher DI-GM scores were inversely associated with BV prevalence in this cross-sectional study. These findings should be interpreted cautiously, and prospective studies are needed to confirm causality.}, }
@article {pmid42175662, year = {2026}, author = {Irie, K and Azuma, T and Minoshima, R and Mochida, Y and Yamada, R and Nanashima, K and Fuchida, S and Kubota, N and Tsukinoki, K and Sato, Y and Tomofuji, T and Yamamoto, T}, title = {Salivary Microbiota From a Periodontitis Donor Is Associated With Altered IgA-Related Immune Features in Germ-Free Mice.}, journal = {Journal of clinical periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jcpe.70146}, pmid = {42175662}, issn = {1600-051X}, support = {JP22K10316//JSPS KAKENHI/ ; JP25K13327//JSPS KAKENHI/ ; //Takeda Science Foundation/ ; }, abstract = {AIM: The oral microbiota has been implicated in mucosal immune regulation; however, its causal impact on salivary gland-associated immune features remains incompletely understood. In this proof-of-concept study, germ-free (GF) mice were colonised with salivary microbiota derived from either a periodontitis donor or a periodontally healthy donor, and IgA-associated immune readouts were evaluated across multiple compartments.<br><br>METHODS: GF mice were orally colonised with saliva-derived microbiota from a periodontitis patient or a periodontally healthy donor (or PBS). Total IgA in saliva, serum and faeces were quantified by ELISA. Cervical lymph nodes and blood were analysed by flow cytometry. Submandibular glands underwent histology and bulk RNA-seq.<br><br>RESULTS: Mice receiving microbiota from a periodontitis donor exhibited altered IgA levels in saliva, serum and faeces, increased faecal lipocalin-2, changes in innate immune cell distributions and increased CD138[+] cell signals and IgA immunoreactivity in the submandibular glands. Transcriptomic analysis revealed heterogeneous expression of individual IgA-related genes, with coordinated patterns observed at the level of IgA/mucosal defence-related gene sets.<br><br>CONCLUSIONS: These findings indicate that salivary microbiota from a periodontitis donor are associated with altered IgA-related immune features under GF conditions. While limited by the use of a single donor per group, this study provides proof-of-concept evidence supporting a potential role of oral microbiota in shaping salivary gland-associated immune characteristics.}, }
@article {pmid42175702, year = {2026}, author = {Meadows, NML and Delahay, RJ and McDonald, RA and Powell, S and Hopkins, K and Arnold, L and Harrison, XA}, title = {Fecal Microbiome Varies With Social Group, Age and Bovine Tuberculosis Infection in the European Badger (Meles meles).}, journal = {Molecular ecology}, volume = {35}, number = {10}, pages = {e70369}, doi = {10.1111/mec.70369}, pmid = {42175702}, issn = {1365-294X}, support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Mustelidae/microbiology ; *Feces/microbiology ; *Tuberculosis, Bovine/microbiology ; Cattle ; *Gastrointestinal Microbiome/genetics ; Age Factors ; Mycobacterium bovis/pathogenicity ; RNA, Ribosomal, 16S/genetics ; Social Behavior ; Social Group ; }, abstract = {Host-associated microbes are key components of animal health and physiology, with particular importance for determining responses to pathogen infection. The gut microbiota is highly variable at the individual level, being shaped by a multitude of factors including diet, social behaviour, and age. Yet the relative influence of these traits on microbiota composition, and the consequences of this variation for host responses to pathogens remain unresolved. Here we investigate factors that shape the faecal microbiome in European badgers (Meles meles). Badgers act as a wildlife reservoir of Mycobacterium bovis, a zoonotic pathogen and the causative agent of bovine TB (bTB) in cattle, but the potential role of the microbiome in shaping patterns of infection and severity of disease is not known. Analysing 165 samples from 72 badgers over 3 years, we found that social group and age were key determinants of faecal microbiota composition and identified several bacterial genera associated with bTB infection. Investigation of microbiome dynamics at the individual level using longitudinally sampled badgers revealed marked heterogeneity in age-dependent microbiome trajectories that were not detectable from population level trends in chronological age. These data provide novel insights into the factors associated with microbial community dynamics in complex wild systems and highlight the need for individual-level and longitudinal approaches to studying host-microbiome associations.}, }
@article {pmid42175861, year = {2026}, author = {Tomlinson, CWE and Bergers, MD and Bolam, DN and Luis, AS and Cartmell, A and Armstrong, Z}, title = {Fluorogenic Coupled Assays Reveal Catalytic Properties, Inhibition Constants and Cellular Location of Mucin-Active Carbohydrate Sulfatases.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {}, number = {}, pages = {e2991471}, doi = {10.1002/anie.2991471}, pmid = {42175861}, issn = {1521-3773}, support = {BB/T017805/1//BBSRC/ ; OCENW.M.24.135//NWO/ ; VI.Veni.212.173//NWO/ ; SBF005&#x2216;1065 163470//Academy of Medical Sciences/Wellcome Trust/ ; RGS&#x2216;R2&#x2216;212050//Royal Society/ ; 225897/Z/22/Z//Wellcome Trust CDA/ ; }, abstract = {Sulfated glycans play a central role in human health and influence cell signaling, cancer progression, pathogen invasion, and host-microbiome interactions. Metabolism of these glycans requires a specialized class of enzymes termed carbohydrate sulfatases. These enzymes are particularly important in the human gut where sulfated colonic mucin is produced and subsequently degraded by colonic bacteria. Despite the biological importance of carbohydrate sulfatases, there is currently a lack of chemical tools to study their activity, substrate selectivity, inhibition, and the discovery of novel enzymes. To address this, we have synthesized new chemical tools to rapidly and quantitatively determine the activity and selectivity of carbohydrate sulfatases in plate-based coupled assays. We have synthesized 3-O-sulfated fluorogenic glycosides using efficient synthetic routes and combined these fluorogenic substrates with a glycosidase that selectively cleaves unsulfated glycosides, allowing sensitive detection of sulfatase activity on both purified protein and cell lysate from the S1_20 subfamily sulfatases. Furthermore, we show that the assay enables differentiation and quantification of substrate specificity, identification of sulfatase inhibitors, and determination of sulfatase (sub-)cellular location for two S1_20 subfamily sulfatases. Collectively, we anticipate that these tools will further our understanding of the interplay between carbohydrate sulfatases, sulfated glycans, and human health.}, }
@article {pmid42176025, year = {2026}, author = {Muhammad, N and Ansar, W and Bashir, T and Khan, HR}, title = {Bacillus-derived antimicrobial peptides as alternatives to antibiotics in poultry: mechanisms, applications, and future prospects- a review.}, journal = {Archives of microbiology}, volume = {208}, number = {8}, pages = {}, pmid = {42176025}, issn = {1432-072X}, mesh = {Animals ; *Antimicrobial Peptides/pharmacology/chemistry ; *Poultry/microbiology ; *Bacillus/chemistry/metabolism ; *Anti-Bacterial Agents/pharmacology ; Biofilms/drug effects ; *Poultry Diseases/microbiology/drug therapy ; }, abstract = {Bacterial enteric pathogens, antimicrobial resistance, and mycotoxin-associated intestinal injury remain important challenges in poultry-associated systems. In this context, Bacillus-derived antimicrobial peptides (AMPs) have attracted attention as potential alternatives to conventional antibiotics due to their structural diversity and multifunctional properties. These peptides include ribosomally synthesized bacteriocins and non-ribosomally synthesized lipopeptides, such as surfactin, iturin, and fengycin. Their amphipathic structures enable interaction with microbial membranes, leading to permeabilization and disruption of cellular homeostasis. In addition to direct antimicrobial activity, these AMPs may interfere with biofilm-associated processes, modulate host immune responses, and help protect against toxin-induced epithelial injury. This review summarizes current knowledge on the diversity, structural characteristics, biosynthesis, mechanisms of action, and microbiological relevance of Bacillus AMPs in poultry-associated environments. Emphasis is placed on membrane targeting, biofilm regulation, immunomodulation, and mycotoxin-related gut protection, as well as limitations associated with antimicrobial resistance. Available evidence indicates that these peptides have diverse mechanisms of action; however, their activity is influenced by peptide class, formulation, microbial ecology, and host physiological factors. In addition, the potential for adaptive or genetically encoded resistance should be considered. Key translational challenges include peptide instability, variability in in vivo efficacy, strain-specific differences, safety considerations, and the lack of standardized comparative models. Future progress will depend on improved delivery systems, microbiome-resolved in vivo studies, and the integration of genomic mining, synthetic biology, and computational peptide design. These approaches may support the development of AMPs with improved stability, specificity, and functional performance in poultry-associated microbial systems.}, }
@article {pmid42176051, year = {2026}, author = {Humphrey, JR and Mathai, P and Moran, TP and Kulis, MD and Smeekens, JM}, title = {The Role of the Indoor Exposome in Food Allergy Development.}, journal = {Current allergy and asthma reports}, volume = {26}, number = {1}, pages = {}, pmid = {42176051}, issn = {1534-6315}, mesh = {Humans ; *Food Hypersensitivity/epidemiology/immunology/etiology ; *Allergens/immunology ; *Exposome ; *Environmental Exposure/adverse effects ; *Air Pollution, Indoor/adverse effects ; Animals ; }, abstract = {PURPOSE OF REVIEW: Due to the rapid rise in the prevalence of food allergy, environmental exposures, in addition to genetic susceptibility, are likely contributors to allergic disease. In developed countries, individuals spend a substantial proportion of time indoors. Therefore, the indoor exposome provides a unique framework to examine factors driving the increase in the rates of food allergy. This review summarizes epidemiological and mechanistic evidence of the indoor exposome, consisting of the combined exposures to food antigens, microbes, and chemicals encountered in indoor environments during early life, and their influence on food allergy development.<br><br>RECENT FINDINGS: Indoor house dust contains detectable food allergens, which remain biologically active and may be linked to non-oral exposure, leading to allergic sensitization. In contrast, early-life exposures to diverse microbes and their products are associated with protection from allergic disease. Emerging evidence further demonstrates that indoor chemicals, including detergents, plasticizers, and pollutants, can disrupt epithelial barrier integrity or function as immune adjuvants, thus increasing susceptibility to food sensitization. Collectively, these findings highlight the indoor exposome as a complex and important determinant of food allergy risk. Improved understanding of how the indoor exposome influences food allergy development may inform future primary prevention or intervention strategies.}, }
@article {pmid42176073, year = {2026}, author = {Liu, C and Chang, L and Yan, Y and Ji, H and Ma, J and Sun, H and Wang, L}, title = {Breakthroughs in HBV-related HCC Therapy: The Unmatched Potential of Immune Checkpoint Inhibitors.}, journal = {Current treatment options in oncology}, volume = {27}, number = {1}, pages = {}, pmid = {42176073}, issn = {1534-6277}, support = {2024ZD0523703//National Major Science and Technology Projects of China/ ; 2021-I2M-1-060//Chinese Academy of Medical Sciences/ ; BJ-2025-169//National High Level Hospital Clinical Research Funding/ ; }, mesh = {Humans ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Carcinoma, Hepatocellular/etiology/drug therapy/therapy/virology/pathology ; *Liver Neoplasms/etiology/drug therapy/therapy/virology ; *Hepatitis B virus/immunology ; Tumor Microenvironment/immunology/drug effects ; Immunotherapy/methods ; Combined Modality Therapy ; *Hepatitis B/complications/virology ; Treatment Outcome ; Disease Management ; }, abstract = {Immune checkpoint inhibitors have reshaped the therapeutic landscape of hepatocellular carcinoma by restoring T cell-mediated antitumor immunity. However, the clinical benefit of monotherapy remains limited, highlighting the need for improved patient stratification and more effective treatment strategies. HBV-related hepatocellular carcinoma (HBV-HCC) is a major etiological subtype characterized by a chronically immunosuppressive tumor microenvironment driven by persistent viral antigen exposure and immune exhaustion. We believe that patients with HBV-HCC may be more suitable for immunotherapy, especially treatment with immune checkpoint inhibitors. A deeper understanding of the expression patterns of inhibitory checkpoint and costimulatory molecules, along with the identification of predictive biomarkers and the development of effective combination immunotherapies is essential for improving clinical outcomes. From a safety perspective, hepatitis B virus reactivation is generally manageable when appropriate antiviral therapy is administered concurrently with immunotherapy. Consequently, patients with HBV-HCC should not be excluded from treatment with immune checkpoint inhibitors. We anticipate that combination strategies, including multi-target immune checkpoint blockade, combinations with other immunotherapeutic approaches, and microbiome-based therapy, will further enhance therapeutic efficacy in HBV-HCC. Combination immune checkpoint therapy may enhance antitumor responses and potentially contribute to better control of viral activity.}, }
@article {pmid42176089, year = {2026}, author = {Žukauskaitė, K and Horvath, A and Tripolt, S and Habisch, H and Madl, T and Pacher-Deutsch, C and Nepel, M and Balazs, I and Stadlbauer, V}, title = {MyBioScope: a new frontier in gut microbiome and health research.}, journal = {Bioresources and bioprocessing}, volume = {13}, number = {1}, pages = {}, pmid = {42176089}, issn = {2197-4365}, abstract = {UNLABELLED: Disruptions in the gut microbiome are linked to various diseases, but their roles in conditions such as age-related muscle loss (sarcopenia) and drug-induced microbial changes remain poorly understood. To address this gap, MyBioScope, a novel in vitro model using the DASbox[®] mini bioreactor system and human stool samples, was developed to simulate the anaerobic environment of the gastrointestinal (GI) tract. Bioreactors containing 120–200 mL of cultivation media were inoculated with stool slurry, stabilized over 24 h, and maintained with a customizable feeding protocol for multi-day experiments. Samples were analyzed using 16S rRNA gene sequencing, quantitative PCR, and metabolomics. Four pilot studies were conducted to validate the platform and model specific disease states, including proton pump inhibitor-induced GI tract oralization and microbiome alterations associated with sarcopenia. The workflow incorporated an anaerobic stool collection kit for user-friendly, room-temperature sample transport and storage. Our results demonstrated consistent microbial community structure and metabolic activity within disease-mimicking conditions. MyBioScope enabled reproducible, controlled studies of gut microbial dynamics and provided a scalable tool for investigating disease-specific microbiome changes. This platform may support translational efforts to integrate microbiome insights into clinical research, therapeutic development, and personalized medicine. In conclusion, this novel bioreactor-based in vitro model, MyBioScope, shows strong potential for in-depth exploration of disease-specific microbiomes and can facilitate new ways for integrating the knowledge of the microbiome’s impact on human health and disease into clinical practice.<br><br>GRAPHICAL ABSTRACT: [Image: see text]<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40643-026-01044-1.}, }
@article {pmid42176172, year = {2026}, author = {Liu, C and Zhang, S and Yue, Q and Sun, X and Zheng, K and Li, K and Su, L and Zhao, L}, title = {Gut microbiome-mediated bioactive ingredients and health benefits of medicinal and edible fermented products: A comprehensive review.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {42176172}, issn = {1874-9356}, abstract = {Fermented foods and beverages represent dynamic biological ecosystems that integrate microbial communities, bioactive metabolites, and host interactions to promote health across nutritional, functional, and therapeutic domains. This comprehensive narrative review synthesizes current evidence on medicinal and edible fermented products, focusing on their bioactive generation, molecular mechanisms, and systemic health outcomes mediated by the gut microbiome. Fermentation processes, driven by lactic acid bacteria, yeasts, and mixed consortia, transform substrates into 31 key bioactives, including short-chain fatty acids (SCFAs), bioactive peptides, exopolysaccharides (EPS), and modified polyphenols. These compounds arise through microbial proteolysis, glycolysis, and biotransformation, enhancing bioavailability and functionality compared to unfermented counterparts. Mechanistically, bioactives strengthen gut barrier integrity via tight-junction upregulation and mucin production; modulate immunity through Toll-like receptor activation and T-cell differentiation; regulate metabolism by improving glucose/lipid profiles; and mitigate inflammation via NF-κB inhibition and Nrf2 activation. Gut microbiota-host crosstalk extends these effects systemically, influencing the gut-brain axis and extra-intestinal organs. Epidemiological and clinical data link regular consumption particularly of yogurt, kimchi, and kefir-to reduced risks of colorectal cancer (dose-response patterns), type 2 diabetes (8-15% HbA1c reductions), cardiovascular disease (5-10% cholesterol lowering), and enhanced immune resilience (20-35% fewer infections). Benefits also encompass gastrointestinal health (IBS symptom relief), neuroprotection (cognitive improvements), and cancer prevention. Despite promising findings, challenges persist in standardization, microbial viability during processing, and long-term human trials. Future directions emphasize multi-omics integration, AI-driven precision fermentation, and personalized interventions to validate fermented products as evidence-based therapeutics, bridging traditional practices with modern nutrition science.}, }
@article {pmid42176375, year = {2026}, author = {Zhang, Y and Wang, R and Su, X and Lang, T and Li, D}, title = {Freeze-thaw specifically regulates microbiome patterns and phosphorus acquisition strategies in the lake-groundwater interaction zone.}, journal = {Water research}, volume = {302}, number = {}, pages = {126129}, doi = {10.1016/j.watres.2026.126129}, pmid = {42176375}, issn = {1879-2448}, abstract = {Freeze-thaw regulates phosphorus cycling in lake-groundwater interaction zones (LIZ) of seasonally frozen regions, where microorganisms and their functional traits play indispensable roles. However, the spatiotemporal dynamics of phosphorus pools and their driving mechanisms in the LIZ remain poorly understood, especially with insufficient quantitative evidence. Using absolute quantitative metagenomics, this study investigated the LIZ of Lake Chagan, a typical eutrophic lake in the seasonally frozen region. Results showed that Losses of Fe-P (44.69%) and Res-P (35.47%) dominated sediment phosphorus dynamics. Freeze-thaw induced opposing trends in diversity and similarity of PCGs-microbial communities between sediment and the lake-groundwater. The assembly of PCGs-microbial communities shifted from stochastic to deterministic processes in lake-groundwater, while stochastic processes persisted in sediments. DIP and DOP in lake-groundwater were driven by genes involved in P-uptake and transport (r = 0.65 and 0.40, respectively, P<0.05), while phosphorus release from sediments was co-regulated by inorganic P-solubilization and organic P-mineralization genes (r = 0.89 and -0.36, respectively, P<0.05). Microbial taxa harboring complete phosphorus cycling pathways (42.2%) and organic P-mineralization genes (48.1%) were relatively rare, with Pseudomonadota as the dominant phylum (65.2% and 57.0%, respectively). This study reveals medium-specific adaptive strategies of microorganisms and PCGs-mediated phosphorus cycling mechanisms, providing scientific support for predicting eutrophication risks and managing lake ecosystems in seasonally frozen regions.}, }
@article {pmid42176539, year = {2026}, author = {Cheng, H and Sun, H and Gu, J and Yang, W and Gao, M and Xu, H}, title = {Valorization of vitamin C industrial byproduct as a soil amendment: Environmental benefits and enhancement of maize productivity.}, journal = {Journal of environmental management}, volume = {409}, number = {}, pages = {129982}, doi = {10.1016/j.jenvman.2026.129982}, pmid = {42176539}, issn = {1095-8630}, abstract = {The mechanisms by which vitamin C residue after evaporation (RAE) regulates soil microbial processes and maize productivity remain unclear. A randomized complete block field trial was conducted in 2023. The trial evaluated the effects of RAE on soil nutrient availability, microbial functional potential, and maize productivity, with three treatments: (1) untreated control (CK), (2) low RAE rate (LR: 150 L/ha), and (3) high RAE rate (HR: 300 L/ha), each with four replicates. RAE was applied through drip irrigation at the six-leaf and fourteen-leaf stages of maize. RAE application increased soil dissolved organic carbon (5.75-16.73%) and mineral nitrogen availability, with ammonium and nitrate increasing by 24.79-51.04% and 23.24-69.25%, respectively, whereas soil organic carbon and total nitrogen, phosphorus, and potassium were unchanged. RAE also increased soil microbial biomass, soil respiration, and key enzymes involved in carbon, nitrogen, and phosphorus cycling, whereas HR shifted bacterial community composition and increased copy numbers of functional genes involved in these processes. RAE further enhanced maize physiological performance: photosynthetic rate increased by 12.88-33.41%, relative chlorophyll content (SPAD) by 9.73-25.10%, and dry matter translocation by 18.79-31.93%, resulting in a grain yield increase of 8.26-13.46% in 2023. Grain yield was recorded during 2023-2025, confirming the stability of this yield response. RAE application enhanced soil nutrient availability and microbial functional potential, thereby improving maize physiological performance and grain yield, likely through the regulation of nutrient cycling and microbial processes. These findings provide a value-added management strategy for utilizing RAE in agroecosystems.}, }
@article {pmid42176589, year = {2026}, author = {Kuerban, Z and Shao, Y and Jiang, R and Shi, Y and Ma, Y and Li, H and Mei, X and Xu, Y and Dong, C and Shen, Q}, title = {Trichoderma modulates Pseudomonas metabolism: Co-inoculation enhances phosphorus acquisition of Pyrus betulifolia in calcareous soil.}, journal = {Microbiological research}, volume = {310}, number = {}, pages = {128552}, doi = {10.1016/j.micres.2026.128552}, pmid = {42176589}, issn = {1618-0623}, abstract = {Phosphorus (P) is poorly available in calcareous soils, limiting pear growth. We evaluated whether Trichoderma brevicompactum TB2 improves P availability and the rhizosphere microbiome. This study used Trichoderma brevicompactum TB2 to investigate the regulatory mechanisms influencing rhizosphere phosphorus transformation and microbiome structure in pear seedlings. Four treatments were analyzed: sterilized soil control (SSC), sterilized soil with TB2 (SST), natural soil control (NSC), and natural soil with TB2 (NST). SST and NST treatments significantly increased plant height, biomass, and soil available phosphorus (AP) while reducing soil pH compared to SSC and NSC. Notably, only the NST treatment significantly enhanced plant phosphorus content and accumulation. Compared to NSC, NST led to significant restructuring of the rhizosphere microbial community (via 16S rRNA) and functional differentiation in phosphorus cycling (as shown by metagenomics), including increased abundances of key phosphorus-metabolism genes (phnN, phnL, phnP, gcd) and improved organic phosphoester hydrolysis and transport pathways. Metagenome-assembled genomes (MAGs) identified five high-quality gcd-containing MAGs, including those from Bacteroidota (bin43, bin16) and Pseudomonas (bin53, bin72, bin13), with a bin13-match strain isolated from the NST rhizosphere. Pot trials confirmed that inoculation with TB2 or PSE significantly improved plant biomass and phosphorus nutrition indices compared to CK. Co-inoculation with TB2 and PSE elicited synergistic effects that exceeded those of the individual inoculants. In natural calcareous soil, TB2 enhances pear growth by recruiting P-solubilizing Pseudomonas and activating rhizosphere P cycling. This offers a practical route to improve P-fertilizer efficiency in orchards.}, }
@article {pmid42176620, year = {2026}, author = {Li, Z and Wang, L and Tuo, D and Huang, F and Shi, Y and Zhang, Y}, title = {Cross-scale mechanisms and molecular-ecological thresholds of phthalate stress in the cucumber-soil system.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142398}, doi = {10.1016/j.jhazmat.2026.142398}, pmid = {42176620}, issn = {1873-3336}, abstract = {Phthalates (PAEs) are widespread soil contaminants that threaten the sustainability of agricultural lands, yet the threshold mechanism by which they trigger collapse of the cucumber-soil system remains unclear. Integrating physiological, ultrastructural, proteomic, and microbiome analyses, this study tracked the dose-response of the cucumber-soil system to PAEs (0, 5, and 15 mg/kg). A biphasic response was identified: 5 mg/kg induced "reversible compensation," where upregulated antioxidant enzymes and proline preserved physiological function and high rhizosphere bacterial diversity. Conversely, 15 mg/kg triggered "irreversible collapse." Proteomics and pathway modeling revealed the core mechanism: despite a burst in GST synthesis, the failure of the ASA-GSH regeneration cycle caused a redox collapse (GSH/GSSG ≈ 0.02) and subsequent organelle disintegration. Concurrently, the rhizosphere microbiome underwent structural simplification, shifting from a complex cooperative network to one dominated by tolerant taxa (Bacillus, Sphingomonas). By identifying the topological flip from protective to destructive regulation, this study establishes a cross-scale "molecular-ecological" threshold framework, providing a quantifiable scientific basis for hierarchical risk management in PAEs-contaminated farmland.}, }
@article {pmid42176735, year = {2026}, author = {Nguyen, N and Ackerman, SJ and Shoda, T and Katzka, D}, title = {Beyond Endoscopy, Toward Innovative Diagnosis and Monitoring of Eosinophilic Gastrointestinal Diseases.}, journal = {The journal of allergy and clinical immunology. In practice}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jaip.2026.05.017}, pmid = {42176735}, issn = {2213-2201}, abstract = {Currently, esophagogastroduodenoscopy (EGD) with biopsy is essential to the diagnosis and management of eosinophilic gastrointestinal diseases (EGIDs) to visually evaluate the gastrointestinal mucosa, obtain mucosal biopsies and assess treatment response as symptoms do not necessarily correlate with histology. To assess mucosal inflammation after initiating or modifying treatment, multiple repeat EGDs are commonly needed and are burdensome due to post-procedure recovery, costs and impact on quality-of-life. For these reasons, there is increasing interest in novel less invasive modalities in the management of EGIDs, particularly eosinophilic esophagitis (EoE). Here in, we review innovative modalities that may be used in lieu of EGD for EoE including unsedated transnasal endoscopy, esophageal string test, and sponge based devices; innovative modalities complementary to endoscopy such as impedance planimetry; we discuss the role of pH impendence monitoring and radiologic imaging in EoE and explore the future of non-invasive modalities including biomarkers and the microbiome.}, }
@article {pmid42176766, year = {2026}, author = {Avolio, E and Olivito, I and Minervini, D and Soda, T and De Bartolo, A and Rocca, C and Alò, R and Facciolo, RM}, title = {Neuronutrition in ASD: Involvement of gut microbiota, oxidative stress and inflammatory markers.}, journal = {Neuroscience and biobehavioral reviews}, volume = {187}, number = {}, pages = {106775}, doi = {10.1016/j.neubiorev.2026.106775}, pmid = {42176766}, issn = {1873-7528}, abstract = {Autism spectrum disorder (ASD) is a neurodevelopmental disorder displaying altered human behaviors, such as social interaction impairments, stereotypical/repetitive activities and emotional dysregulation. Children with ASD are often affected by gastrointestinal problems and gut microbiota dysbiosis. Inflammation and immune dysfunction are key contributors to ASD, as shown by high proinflammatory cytokines and oxidative stress. Indeed, notable implication of the nuclear factor kappa B in the severity of ASD derives from its ability to amplify neuroinflammation. This narrative review focused attention on neuronutrition and gut microbiota manipulation for mitigation of ASD symptoms, including neuroinflammation and oxidative stress. Studies in both rodents and humans with ASD have revealed that both pure and mixed Lactobacillus and Bifidobacterium were effective in ameliorating behavioral symptoms and GABA/glutamate imbalance. Often, the combined use of probiotics and prebiotics can have greater health benefits in ASD. Additionally, dietary interventions and microbiota transfer therapies along with low-to-moderate-intensity exercise have been proposed to improve gastrointestinal and behavioral symptoms. However, despite some encouraging results, biases in the neuronutrition/microbiota literature still exist. Indeed, many studies rely on small sample sizes, cross-sectional designs, and heterogeneous populations that differ in diet, medications, and comorbidities. In this context, the development of a precision diet tailored to individual gut microbiome profiles will allow for a broader understanding of the microbial ecosystem and relative therapeutical applications. Hence, by integrating metagenomics, metabolomics, epigenomics, with evaluation of environmental and nutritional factors, it will be possible to significantly improve the quality of life for people with ASD and their families.}, }
@article {pmid42176777, year = {2026}, author = {Shen, X and Shu, C and Dong, Y and Li, J and Li, R and Zan, J and Xie, X and Jin, J and Zhang, H and Lv, J}, title = {Therapeutic Efficacy and Antigenicity of a Novel PEGylated IgA Protease in Preclinical Models of IgA Nephropathy.}, journal = {Kidney international}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.kint.2026.04.020}, pmid = {42176777}, issn = {1523-1755}, abstract = {INTRODUCTION: IgA nephropathy is the most common primary glomerulonephritis worldwide, characterized by IgA deposition and a high risk of progression to kidney failure. While emerging therapies target IgA production or downstream inflammation, strategies to directly clear established IgA deposits from the kidney remain underexplored. Here, we evaluate a novel therapeutic IgA protease for its ability to clear glomerular IgA deposits and restore normal histology.<br><br>METHODS: The recombinant IgA protease was derived from Thomasclavelia ramosa (strain AK183), a human commensal bacterium presumed to have evolved for mutual tolerance within the microbiome with the host. The enzyme was PEGylated to reduce immunogenicity and prolong its half-life, producing the drug product PEG-AK183. We characterized its ex vivo potency and pharmacokinetic-pharmacodynamic profile in mice, then assessed therapeutic efficacy over eight weeks.<br><br>RESULTS: In vitro, a single molecule of PEG-AK183 cleaved between 500 and 1000 hIgA1 molecules in 60 minutes, demonstrating high catalytic efficiency. A single injection into human IgA1 (hIgA1) transgenic mice induced complete clearance of serum hIgA1 for up to eight days. Following eight-week weekly treatments, PEG-AK183 reduced circulating IgA and immune complex levels by approximately 80% and completely cleared glomerular IgA and associated complement C3 deposits. This was accompanied by a 45.5% reduction in proteinuria and significant improvements in histopathological indices, including mesangial proliferation and endocapillary hypercellularity. No treatment-related adverse effects were observed, including abnormalities in intestinal plasma B cells, hepatotoxicity, or the anti-drug antibody development, supporting a favorable safety profile for long-term, repeated administration.<br><br>CONCLUSIONS: Our preclinical study demonstrated that the engineered IgA degrader PEGAK183 is a potent, effective, and safe therapeutic in a humanized IgA nephropathy mouse model. By achieving sustained clearance of pathogenic IgA from both circulation and glomerular deposits, this IgA-protease-based therapy represents a promising candidate for the future treatment of IgA nephropathy.}, }
@article {pmid42177038, year = {2026}, author = {Strobel, KM and Leibel, SL and Bhute, S and Aja, E and Jacobs, JP and Calkins, K}, title = {Gut microbial differences and function in infants with gastroschisis: a pilot prospective cohort study.}, journal = {Beneficial microbes}, volume = {}, number = {}, pages = {1-14}, doi = {10.1163/18762891-bja00121}, pmid = {42177038}, issn = {1876-2891}, abstract = {Newborns with gastroschisis hospitalised in the neonatal intensive care unit (NICU) are at risk for a disrupted gut microbiome. Infants with gastroschisis are particularly vulnerable to a dysbiotic microbiome; they require prolonged parenteral nutrition (PN) due to intestinal dysmotility, which often leads to growth faltering (GF). This pilot study's goals were to (1) compare the gut microbiome in infants with gastroschisis to infants admitted to the NICU without congenital anomalies, (2) identify differences in the gut microbiome between infants with gastroschisis requiring prolonged PN and those who do not, and (3) compare the microbiome in infants with gastroschisis with GF to those without GF. This was a multi-site prospective cohort study including 17 infants born with gastroschisis and 16 infants with a gestational age greater than 34 weeks admitted to the NICU without congenital anomalies (controls). Prolonged PN was defined as more than 28 days. GF was defined as a decline in weight or length z-score from birth to discharge of ≤-0.8. Stool samples were collected weekly during hospitalisation and analysed by shotgun metagenomics to assess bacterial composition, diversity, and function. Gestational age and birth weight were similar in the gastroschisis group and the control group. Infants with gastroschisis showed increased Staphylococcus aureus and decreased Bifidobacterium longum. Those requiring prolonged PN had a reduced abundance of genes in the glucosidase pathway compared to those who did not. Infants with GF showed a lower abundance of genes involved in the NAD-diphosphatase pathway compared to those without GF. Infants with gastroschisis display a distinct microbial composition and function compared to NICU infants without this condition. Among infants with gastroschisis, differences in bacterial functional capacity were observed in those who required prolonged PN and developed GF.}, }
@article {pmid42177066, year = {2026}, author = {Yendreddy, SR and Patchigolla, D and Singh, S and Baghel, K and Ojha, R and Prajapati, VK}, title = {Microbiome and microbial products as immunomodulators: Implications for gastrointestinal cancers.}, journal = {Advances in protein chemistry and structural biology}, volume = {152}, number = {}, pages = {1-35}, doi = {10.1016/bs.apcsb.2025.10.008}, pmid = {42177066}, issn = {1876-1631}, mesh = {Humans ; *Gastrointestinal Neoplasms/immunology/microbiology/therapy/diagnosis ; *Gastrointestinal Microbiome/immunology ; }, abstract = {The Hippocratic adage "all disease starts in the gut" remains pertinent as research uncovers how the gut microbiome and its products influence immunity and gastrointestinal cancers. The immune system's remarkable paradox lies in its ability to distinguish and tolerate trillions of beneficial microbes while defending against harmful pathogens to maintain health. Disruptions to this delicate balance, known as dysbiosis, contribute to chronic inflammation and create a favourable tumour development and progression environment. Microbial metabolites, such as- short-chain fatty acids and secondary bile acids further modulate inflammation, gut barrier integrity, and immune checkpoint pathways. Emerging microbial biomarkers show promise in diagnosis and prognosis and compete with traditional clinical factors. Innovative therapeutic strategies are being explored to harness the microbiome's immunomodulatory potential. Integrating microbiome profiling into personalised medicine offers new opportunities to prevent, detect, and treat gastrointestinal cancers, shifting the microbiome from a passive disease marker to an active agent that modulates and influences the disease. This chapter discusses the emerging understanding of microbiomes and microbial products in gastrointestinal cancers, highlighting diagnostic advances and novel therapeutic approaches that leverage microbial interactions to improve patient outcomes.}, }
@article {pmid42177172, year = {2026}, author = {Peters, BA and Qi, Q and Xue, X and Moon, JY and Yu, B and Thomas, SN and Cordero, C and Daviglus, ML and Burk, RD and Kaplan, RC and Isasi, CR}, title = {Association of gut microbiome with mobility impairment in the Hispanic Community Health Study/Study of Latinos.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01019-2}, pmid = {42177172}, issn = {2055-5008}, support = {R03HL182350/HL/NHLBI NIH HHS/United States ; R01DK134672/DK/NIDDK NIH HHS/United States ; R01AG085320/AG/NIA NIH HHS/United States ; }, abstract = {Aging-related declines in mobility are more common in women than men. The gut microbiome may play a role in physical function, but sex-specific roles are unknown. In adults ≥50 years old (n = 1187 women, 585 men), we examined associations of self-reported mobility impairment with gut microbiome assessed by stool shotgun sequencing, and examined heterogeneity by sex. Gut microbiome α-diversity was lower and overall composition (β-diversity) altered in women with mobility impairment compared to without, but this was not the case in men. Fifteen microbiome species were associated with mobility impairment in both women and men, including enrichment of Streptococcus and Lactobacillus and depletion of Eubacterium species. An additional 84 species were associated with mobility impairment in women only, including enrichment of Gammaproteobacteria species, but none were associated with mobility impairment in men only. Correlations of impaired mobility-related microbiome scores, derived from universal and women-specific microbiome species, with serum metabolites (n = 385) suggested that impaired mobility-related species may be involved in synthesis of imidazole propionate and deoxycholic acid metabolites, while species depleted with mobility impairment may be involved in sex hormone metabolism and guanidinoacetate production, the latter in women only. Gut microbiota may play a role in physical function and sex differences therein.}, }
@article {pmid42177348, year = {2026}, author = {Kelly, SA and Zhao, L and Nzakizwanayo, J and Rodgers, AM and Thompson, TP and Lee, AJ and McCarthy, HO and McGrath, JW and Ingram, RJ and Jones, BV and Gilmore, BF and Donnelly, RF}, title = {Preserving the gut microbiome: hydrogel-forming microneedle delivery of tetracycline reduces gut microbiome disruption compared to oral administration.}, journal = {Drug delivery and translational research}, volume = {}, number = {}, pages = {}, pmid = {42177348}, issn = {2190-3948}, support = {UNS39792/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Antibiotics cause significant gut microbiome dysbiosis, particularly when administered orally. This contributes to antimicrobial resistance (AMR) and is associated with myriad health conditions. Novel drug delivery strategies that minimize gut exposure while maintaining therapeutic efficacy are urgently needed. This study aimed to evaluate whether a novel transdermal system could reduce gut microbiome disruption compared to oral delivery. Sprague-Dawley rats received a single tetracycline dose via oral gavage, IV injection, or hydrogel-forming microneedle patch. Faecal samples were collected longitudinally and analysed using 16 S rRNA gene sequencing. Oral tetracycline caused the greatest disruption to gut microbiota. Compared to the timepoint immediately prior to treatment (Day 5a), peak dysbiosis was observed at Day 7. The Firmicutes: Bacteroidetes ratio was significantly reduced following oral and IV tetracycline therapy, but not following microneedle administration. The most significant reductions in alpha and beta diversity at Day 7 were observed in the oral group. Differential abundance analysis showed oral treatment resulted in the highest number of depleted and enriched taxa. The microbiome-sparing effect of microneedle delivery was consistent across all analytical measures, offering a promising strategy to preserve host microbiome health. This minimally invasive approach represents a clinically viable alternative to oral and IV antibiotic administration.}, }
@article {pmid42177350, year = {2026}, author = {Gæde, J and Fan, Y and Lyu, L and Gasbjerg, LS and Rossing, P and Hartmann, B and Holst, JJ and Lund, AB and Knop, FK and Pedersen, O}, title = {A randomised clinical trial testing the safety of and metabolic responses to short-term duodenal infusion of recombinant RORDEP1 in healthy men.}, journal = {Diabetologia}, volume = {}, number = {}, pages = {}, pmid = {42177350}, issn = {1432-0428}, support = {NNF21SA0070428//Novo Nordisk Fonden/ ; NNF23SA0084103//Novo Nordisk Fonden/ ; }, abstract = {AIMS/HYPOTHESIS: RUMTOR-derived peptides (RORDEPs) 1 and 2 are polypeptides synthesised by specific strains of the human gut commensal Ruminococcus torques. Preclinical studies have shown that RORDEPs lower blood glucose via an impact on plasma incretins and an improvement of hepatic insulin sensitivity. In a randomised, placebo-controlled, crossover trial, we here explore the safety and tolerability of, as well as any metabolic responses to, a duodenal infusion of recombinant RORDEP1 (r-RORDEP1) given to healthy men after oral intake of a liquid mixed meal.<br><br>METHODS: Seventeen healthy, normal-weight men between 18 and 35 years of age were randomised through block randomisation to receive either r-RORDEP1 or placebo as the initial intervention at Gentofte Hospital, Denmark. Exclusion criteria were use of any form of medication, use of antibiotics during the 3 months before intervention, lactose intolerance, smoking, alcohol or drug abuse, or the use of probiotics or creatine as dietary supplements during the study period. Blocks were created prior to trial initiation. Both participants and investigators were blinded to treatment. Following intake of a standardised liquid meal, r-RORDEP1 was given via a naso-duodenal tube as an initial bolus of 0.0108 mg/kg body weight followed by a continuous infusion of 0.25 &#xb5;g kg[-1] min[-1] for 170 min. Primary outcomes were changes in plasma concentrations of incretins and peptide YY, while secondary endpoints were safety and tolerability, and changes in plasma insulin, C-peptide and glucose.<br><br>RESULTS: All 17 participants completed the trial. Duodenal infusion of r-RORDEP1 was well tolerated and without changes in biochemical measures of haematological, liver or renal functions. Compared with placebo, the bolus of r-RORDEP1 induced an early (at 15 or 30 min) rise in plasma glucagon-like peptide-1, insulin and C-peptide (q=0.001, q=0.001 and q=0.003, respectively) and a decline in plasma gastric inhibitory polypeptide and glucose (q=0.02 and q=0.006, respectively), while also increasing whole-body insulin sensitivity as measured with the Matsuda index of insulin sensitivity (p=0.049).<br><br>CONCLUSIONS/INTERPRETATION: Short-term duodenal infusion of r-RORDEP1 is safe and well tolerated and elicits changes in plasma incretins, insulin and glucose, and a measure of whole-body insulin sensitivity, aligning with findings in rodents, supporting the hypothesis that RORDEPs hold a role in impacting host metabolism.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov NCT06923839 FUNDING: EFSD/Lilly European Diabetes Research Programme 2021, RUCILP F-19235-01-64 - NNF21SA0070428 grant and NNF23SA0084103 grant, the latter two from the Novo Nordisk Foundation.}, }
@article {pmid42177352, year = {2026}, author = {Matsuda, K and Yuda, J and Yoshimaru, R and Harima, I and Sakuma, H and Uehara, A and Oto, M and Fukatsu, M and Ikezoe, T and Araie, H and Hosono, N and Ohwada, C and Nakaseko, C and Kakiuchi, S and Fujisawa, T and Hashimoto, T and Shibuki, T and Imai, M and Nagamine, M and Sakashita, S and Yamashita, R and Dodo, A and Horasawa, S and Nakamura, Y and Bando, H and Yoshino, T}, title = {SCRUM-Japan MONSTAR3 hematology cohort: a nationwide multi-omics integrated platform for next-generation precision medicine in hematologic malignancies.}, journal = {International journal of clinical oncology}, volume = {}, number = {}, pages = {}, pmid = {42177352}, issn = {1437-7772}, abstract = {BACKGROUND: Hematologic malignancies exhibit marked biological heterogeneity that is often insufficiently characterized by genomic profiling alone. Integrated multi-omics approaches are required to enable more accurate prognostic stratification, elucidate resistance mechanisms, and identify therapeutic vulnerabilities across lymphoma, leukemia, and plasma cell neoplasms.<br><br>METHODS: SCRUM-Japan MONSTAR3 is a nationwide, prospective, integrated multi-omics platform. The hematology cohort aims to enroll 400 patients with newly diagnosed or relapsed/refractory hematologic malignancies. Tumor specimens-including bone marrow aspirates/biopsies or lymph node tissues-are collected at diagnosis and at relapse. The multi-omics workflow encompasses whole-exome sequencing, whole-transcriptome sequencing, spatial transcriptomics, plasma proteomics, metabolomics, microbiome analysis, and tumor-informed measurable residual disease (MRD) monitoring. MRD is assessed using next-generation sequencing-based immunoglobulin heavy (IgH) and T-cell receptor (TCR) rearrangement analysis for lymphoid malignancies and whole-genome sequencing-based variant tracking for myeloid malignancies.<br><br>RESULTS: Patient enrollment began in December 2024, followed by nationwide multicenter activation in November 2025. Multi-omics analyses have been implemented in a stepwise manner. Early operational indicators, including biospecimen acquisition, data quality control, and initiation of molecular assays, demonstrate the feasibility of coordinated nationwide deployment of this complex platform.<br><br>CONCLUSION: The MONSTAR3 hematology cohort represents the first nationwide integrated multi-omics initiative dedicated to hematologic malignancies. Its large scale, standardized biospecimen framework, and capacity to incorporate emerging technologies provide a robust infrastructure for molecular stratification, longitudinal disease monitoring, and hypothesis-driven interventional research, thereby advancing clinically actionable precision hematology.}, }
@article {pmid42177354, year = {2026}, author = {Hashemian, N and Hamedi, J and Haghighat, S}, title = {Scorpion gut microbiomes as a source of bioactive and rare actinobacteria with nonribosomal peptide potential.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {6}, pages = {}, pmid = {42177354}, issn = {1572-9699}, mesh = {*Actinobacteria/genetics/isolation &amp; purification/classification/metabolism ; *Scorpions/microbiology ; Animals ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; DNA, Bacterial/genetics/chemistry ; Iran ; *Peptide Biosynthesis, Nucleic Acid-Independent ; *Peptides/metabolism ; }, abstract = {Actinobacteria are well-known for their ability to produce bioactive secondary metabolites, including nonribosomal peptides (NRPs); however, many host-associated reservoirs remain underexplored. In this study, cultivable actinobacteria were isolated from scorpion gut, including both the intestinal tissue and its luminal contents, and evaluated their antimicrobial activity and presence of NRPs genes. Fifty scorpions (Odontobuthus doriae and Mesobuthus eupeus) were collected from Qom Province, Iran. Dissected gut homogenates were plated on selective media, yielding 120 pure isolates. Taxonomic identification was performed by 16S rRNA gene sequencing, antimicrobial activity was assessed using agar diffusion assays against a broad panel of bacteria and fungi, and isolates were screened for NRPS gene biosynthetic markers by PCR (using A3F/A7R primers). The collection was dominated by Streptomyces, with additional recovery of rarer genera such as Amycolatopsis and Nonomuraea. Overall, 57% of the isolates inhibited at least one test microorganisms, and some strains exhibited specific bioactivity, making them candidates for further investigation. NRPS amplicons (~ 700 bp) were detected in 33.3% of the isolates and were enriched among the 42.6% of bioactive isolates, suggesting a partial association between antimicrobial phenotypes and putative NRP biosynthetic capacity. Five isolates showed < 98.5% 16S rRNA similarity to described species, indicating potential taxonomic novelty. Collectively, these findings support scorpion guts as promising, niche-derived sources of diverse actinobacteria with antimicrobial activity and biosynthetic potential for natural product discovery.}, }
@article {pmid42177592, year = {2026}, author = {Turjeman, S and Zgairy, S and Koren, O}, title = {The effects of parity on the maternal microbiome - challenges associated with mouse models.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00582-5}, pmid = {42177592}, issn = {2524-4671}, abstract = {Understanding how parity shapes the maternal microbiota is critical for advancing maternal and offspring health. We investigated the effects of parity and spacing between births on the maternal microbiota in mice. While maternal age strongly influenced microbiota diversity and composition, parity and lengths of gaps between births showed minimal impact. These findings highlight key model constraints that must be considered when designing longitudinal microbiome studies within and beyond the context of reproduction.}, }
@article {pmid42177600, year = {2026}, author = {Wagner, L and Springer, A and Koehler, S and Brüggemann, DA and Strube, C}, title = {[1]H NMR-based metabolomics reveals metabolic changes in porcine ingesta and serum during Ascaris suum infection.}, journal = {Parasites &amp; vectors}, volume = {19}, number = {1}, pages = {}, pmid = {42177600}, issn = {1756-3305}, support = {STR 1171/16-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; *Ascariasis/veterinary/parasitology/metabolism/blood ; *Ascaris suum/physiology ; Swine ; *Metabolomics ; *Swine Diseases/parasitology/metabolism/blood ; *Serum/chemistry ; Magnetic Resonance Spectroscopy ; Proton Magnetic Resonance Spectroscopy ; Colon/metabolism/parasitology ; Amino Acids/metabolism ; Fatty Acids, Volatile/metabolism ; Metabolome ; }, abstract = {BACKGROUND: Roundworm infections are of major importance both for humans and livestock. The porcine roundworm Ascaris suum, the most economically important nematode in pig production worldwide, serves as a valuable model for human ascariosis, yet knowledge of its metabolic impact remains limited.<br><br>METHODS: Metabolic changes were investigated in pigs infected once with 10,000 A.&#xa0;suum eggs versus trickle-infected pigs (1000 eggs/day over 10&#xa0;days) compared with uninfected controls. Ingesta and serum samples of six pigs each were collected on days 21, 35, and 49 post&#xa0;infection (pi) for nuclear magnetic resonance (NMR)-based metabolomics analyses.<br><br>RESULTS: Trickle-infected pigs showed more pronounced metabolic changes than single-infected pigs, following a triphasic temporal pattern with initial changes at day 21 pi, maximal disruption at day 35 pi, and partial recovery by day 49 pi. The colon exhibited the most significant changes in short-chain fatty acids (SCFAs) and amino acids. On day 21 pi, trickle-infected pigs showed increased acetate, butyrate, valerate, and amino acids in the colon, with reversed patterns on day 35 pi. Serum changes mirrored colonic alterations, suggesting the colon as primary driver of systemic responses. Single-infected pigs showed less pronounced changes, with increased lactate and acetate in the ileum and elevated amino acids in the cecum on day 35 pi.<br><br>CONCLUSIONS: These findings reveal complex, compartment-specific host-parasite-microbiome interactions, with SCFAs as important mediators. Enhanced growth performance in trickle-infected pigs corresponding with metabolic recovery challenges exclusively antagonistic host-parasite relationships. This study deepens the understanding of A.&#xa0;suum pathophysiology and provides crucial insights for human ascariosis, supporting targeted interventions for animal and human health.}, }
@article {pmid42177729, year = {2026}, author = {Li, G and Ye, X and Zhou, T and Zhou, Z and Min, Y and Song, H and Liu, X}, title = {Exploratory gut microbiota-host interaction in parkinson's disease: integrative multi-omics analysis of metabolic and epigenetic pathways.}, journal = {AMB Express}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13568-026-02078-6}, pmid = {42177729}, issn = {2191-0855}, support = {PWZxq2022-08//the Key Disciplines Group Construction Project of Pudong Health Bureau of Shanghai/ ; }, abstract = {Mounting evidence has associated gut microbial composition and systemic metabolic profiles with Parkinson's disease (PD), yet causal pathways and molecular mechanisms remain unclear. We employed a systematic two-stage analytical framework integrating multiple Mendelian randomization (MR) approaches, transcriptome and epigenome-wide regulatory analyses, and colocalization analysis to genetically dissect the microbiota-host regulatory network implicated in PD susceptibility. Initially, two-sample MR was performed using gut microbiota data from the MiBioGen consortium, followed by an independent replication MR analysis using mbQTL data from the Dutch Microbiome Project (DMP). The two-step MR approach was employed to identify potential mediation of blood metabolites. Summary data-based MR (SMR) methods were also used to pinpoint key blood metabolic genes and regulatory regions associated with PD risk, with the combination of PD GWAS data, blood expression quantitative trait loci (eQTLs), and DNA methylation quantitative trait loci (mQTLs). Colocalization analyses were performed to explore interactions between host metabolic gene expression and the gut microbiota using blood expression quantitative trait loci (eQTLs) and fecal microbial quantitative trait loci (mbQTLs). Our multi-stage analyses identified five microbial taxa with nominal positive associations with Parkinson's disease (PD), including class Clostridia, order Bacillales, and genera Clostridium sensu stricto 1, Dorea, and Lachnospiraceae UCG001. By contrast, three additional microbial genera (Butyricimonas, Defluviitaleaceae UCG011 and Marvinbryantia) exhibited nominal protective correlations with PD. Cross-cohort analyses further indicated a shared correlation pattern along the Clostridia-Clostridiales-Clostridiaceae/Lachnospiraceae taxonomics potentially linking to PD risk across both discovery and validation cohorts. Mediation analyses indicated that betaine may mediate the Lachnospiraceae UCG001-PD associations, while androstenediol monosulfate may serve as a mediator linking Clostridium sensu stricto 1 to PD. SMR analysis highlights genes like SH2B1, JUP, as key host metabolic genes with potential causal relevance to PD, with colocalization indicating genetic overlaps supporting their potential involvement in gene-microbiota interactions. These findings deepen our understanding of gut-brain axis dysregulation in PD and may provide novel insights for future mechanistic validation and targeted preventive or therapeutic investigations.}, }
@article {pmid42177806, year = {2026}, author = {Faraji, J and Metz, GAS}, title = {The epigenetic archaeology of human-dog companionship.}, journal = {Epigenetics}, volume = {21}, number = {1}, pages = {2676911}, doi = {10.1080/15592294.2026.2676911}, pmid = {42177806}, issn = {1559-2308}, mesh = {Humans ; Animals ; *Epigenesis, Genetic ; Dogs ; DNA Methylation ; Archaeology ; *Human-Animal Bond ; }, abstract = {Humans have coexisted with dogs for at least 20,000 years, yet the biological consequences of long-term human-dog co-residence remain poorly understood. We propose that sustained exposure to dogs may have contributed to context-dependent variation in human stress regulation, immune function, and socio-emotional neurobiology through environmentally responsive epigenetic mechanisms. Here, we define an epigenetic imprint as detectable differences in gene-regulatory marks, including DNA methylation at environmentally sensitive loci, consistent with developmental plasticity and early-life environmental calibration rather than germline inheritance. In this Commentary, we integrate evidence from genomics, neuroscience, microbiome research, evolutionary anthropology, and palaeoepigenetics to examine whether multispecies living environments may represent an under-recognised biological exposure shaping human regulatory biology. We further outline a framework to test whether archaeologically inferred dog co-residence is associated with epigenetic and regulatory signatures in ancient human populations while accounting for major ecological and demographic confounds. Overall, we argue that human-dog cohabitation provides a plausible and testable model for investigating how long-term social and ecological relationships may influence stress and immune regulation across populations.}, }
@article {pmid42177863, year = {2026}, author = {Ye, Y and Jiang, Y and Azeem, S and Zhao, L and Dong, Y and Zhu, J and Fang, S and Wu, Y and Gu, S}, title = {Information gain-based molecular ecological network reveals core microbial taxa involved in gastrointestinal recovery following H. pylori infection and intervention with Weizmannia coagulans BC99 in mice.}, journal = {Microbial pathogenesis}, volume = {217}, number = {}, pages = {108581}, doi = {10.1016/j.micpath.2026.108581}, pmid = {42177863}, issn = {1096-1208}, abstract = {Helicobacter pylori infection is closely linked to gastric diseases such as ulcers and cancer. Recent studies have suggested that probiotics may help regulate H. pylori-induced dysbiosis. In this study, 25 female C57BL/6 mice were randomly assigned to five groups (n = 5 per group), including a control group, an H. pylori model group, and three BC99 intervention groups receiving low, medium, and high doses, after a 1-week acclimation period. The mice were infected for 1 week and then received BC99 intervention for 4 weeks, examines gastrointestinal microbiome dynamics from infection through recovery following probiotic intervention. A specificity-enhanced, information gain-based molecular ecological network approach was utilized to identify the core microbial taxa in H. pylori-infected mice. We evaluated microbiota restoration, serum inflammatory markers, and digestive enzyme activity utilizing network similarity, linear discriminant analysis, and Euclidean distance metrics for evaluation, followed by causal inference to elucidate microbial interactions. Among the tested groups, high-dose Weizmannia coagulans BC99 exhibited the most pronounced effects. H. pylori primarily disrupted nodes in microbial community 1, while BC99 restored this network structure and promoted microbial balance. Network similarity in the intestine increased from 0.39 to 0.60, and in the stomach it increased from 0.53 to 0.62. Serum indices improved from 0.41 to 0.58, and digestive enzyme activity increased from 0.612 to 0.682. Notably, Lachnospiraceae and Lactobacillaceae exhibited strong causal relationships with H. pylori and Escherichia-Shigella, while Lachnospiraceae and Muribaculaceae were associated with several microbial taxa and physiological indices in the stomach and intestine, respectively. These findings highlight the potential of BC99 in alleviating H. pylori-induced dysbiosis and improving host systemic health, thereby providing a theoretical basis for probiotic-based interventions in gastrointestinal disorders.}, }
@article {pmid42178033, year = {2026}, author = {Fiod Riccioa, BV and Debiasi, BW and de Jesus da Silva, I and Tonani, L and Dos Santos Cunha Chellegatti, MA and Jacometti Cardoso Furtado, NA and von Zeska Kress, MR and Badra Lopes Bentley, MV and Gaspar, LR}, title = {Cupuaçu (Theobroma grandiflorum) butter nanoparticles associated with oligosaccharides as cosmetic carriers for prebiotic effect: development, physicochemical characterization, and preclinical evaluation.}, journal = {European journal of pharmaceutics and biopharmaceutics : official journal of Arbeitsgemeinschaft fur Pharmazeutische Verfahrenstechnik e.V}, volume = {}, number = {}, pages = {115119}, doi = {10.1016/j.ejpb.2026.115119}, pmid = {42178033}, issn = {1873-3441}, abstract = {The skin microbiota is essential for cutaneous homeostasis, and prebiotics may support it. Nanostructured systems, such as cupuaçu-derived nanoparticles, enhance the delivery and stability of cosmetic active substances, but their role in modulating the skin microbiota remains unclear and requires targeted evaluation. In this study, lipid-polymeric nanoparticles based on cupuaçu (Theobroma grandiflorum) butter were developed as potential carriers for oligosaccharides. Three formulations were developed: cupuaçu butter (CB-NP), α-glucan oligosaccharide (AGO-CB-NP), and polydextrose nanoparticles (PD-CB-NP). They showed mean diameters of approximately 110 nm, low polydispersity (PdI < 0.30), and moderately negative zeta potentials (around -16 mV). Rheology demonstrated pseudoplastic behavior. Structural characterization by X-ray diffraction (XRD), differential scanning calorimetry (DSC), Fourier-transform infrared spectroscopy (FTIR), transmission electron microscopy (TEM), and small-angle X-ray scattering (SAXS) indicated reduced crystallinity, chemical compatibility among the ingredients, and a hybrid core-shell organization, with a lipid-rich inner region and an outer layer likely associated with oligosaccharides. The formulations exhibited neither eye irritation nor phototoxicity potential in toxicological screening, conducted in accordance with OECD TG 491 and TG 432. In vitro prebiotic potential showed species-dependent responses: AGO-CB-NP stimulated the mutualist Staphylococcus epidermidis while inhibiting Malassezia furfur, whereas CB-NP inhibited Candida albicans growth. Moderate antioxidant activity (around 20% DPPH scavenging) was observed, and cupuaçu butter contained low levels of phenolic compounds (around 0.12 mg GAE g[-1]) and intermediate protection against UVA-induced reactive oxygen species. Among the tested formulations, AGO-CB-NP showed the most favorable overall profile. Overall, the results suggest a promising strategy for developing carriers for microbiome-oriented cosmetic formulations, encouraging further investigation in more complex biological systems, such as in clinical trials.}, }
@article {pmid42178099, year = {2026}, author = {Wu, M and Chen, S and Guo, W and Gu, S and Li, K and Shi, Y and Qian, Y and Sun, Y and Liu, Y and Zhu, H}, title = {Pre-existing liver dysfunction modulates di-(2-ethylhexyl) phthalate (DEHP)-associated biological responses through host-microbiome networks.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128417}, doi = {10.1016/j.envpol.2026.128417}, pmid = {42178099}, issn = {1873-6424}, abstract = {Pre-existing metabolic conditions may profoundly alter biological responses to environmental pollutants, yet this dimension remains underexplored in environmental health. This study examined whether pre-existing metabolic dysfunction-associated steatotic liver disease (MASLD) is associated with altered biological responses to di-(2-ethylhexyl) phthalate (DEHP), a ubiquitous plasticizer. In a human cohort, fatty liver status was associated with altered urinary DEHP metabolite profiles, characterized by a higher proportion of the bioactive mono-(2-ethylhexyl) phthalate, suggesting disease-associated differences in DEHP biotransformation. Using a rat model and multi-omics approaches, we observed that hepatic lipid accumulation was associated with higher systemic DEHP burden and altered tissue distribution, with increased accumulation in the liver and intestine. Under this dual stress, DEHP exposure was associated with perturbations in key metabolic pathways, including amino acid, lipid, and drug metabolism. Transcriptomic analysis revealed upregulation of genes involved in fatty acid synthesis and cholesterol metabolism, consistent with enhanced hepatic lipogenesis. Concurrently, gut microbiota dysbiosis intensified, characterized by shifts in microbial community composition, including reduced Firmicutes and Bacteroidota and altered genus-level taxa linked to host metabolic and inflammatory responses. Integrative multi-omics analysis indicated possible coordinated alterations across the microbiome, metabolome, and hepatic transcriptome, potentially involving lipid metabolism and inflammatory signaling pathways. Taken together, these findings suggest that pre-existing MASLD may exacerbate DEHP-associated biological responses through pathways involving the gut-liver axis, highlighting host metabolic status as an important consideration in interpreting chemical-associated biological responses.}, }
@article {pmid42178430, year = {2026}, author = {Chen, Z and Bao, W and Su, J and Wu, X and Tan, X and Yang, X}, title = {Research on gut microbiota and metabolic characteristics in patients with sleep disorders after ischemic stroke.}, journal = {Metabolic brain disease}, volume = {41}, number = {1}, pages = {}, pmid = {42178430}, issn = {1573-7365}, support = {82302852//National Natural Science Foundation of China/ ; 2021YFA1301102//National Key Research and Development Program of China/ ; 2024E10108//Zhejiang Key Laboratory of Intelligent Rehabilitation and Translational Neuroelectronics/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Middle Aged ; *Ischemic Stroke/complications/metabolism/microbiology ; Aged ; *Sleep Wake Disorders/metabolism/etiology/microbiology ; Metabolomics/methods ; }, abstract = {Post-stroke sleep disorder (PSSD) is a common but underrecognized complication of ischemic stroke, affecting neurological recovery and quality of life. Emerging evidence suggests a role for the gut-brain axis (GBA) in regulating sleep and post-stroke inflammation, yet the microbiome and metabolomic signatures of PSSD remain poorly defined. This study aimed to characterize the gut microbiota and metabolic profiles of PSSD patients, identify potential biomarkers, and explore potential microbial-metabolite-clinical associations. A total of 42 ischemic stroke patients (17 with PSSD, 25 without) and 23 healthy controls were enrolled. Sleep quality was assessed using the Pittsburgh Sleep Quality Index (PSQI). Fecal samples were analyzed by 16 S rDNA sequencing and untargeted metabolomics, and KEGG pathway enrichment were used to integrate multi-omic data and clinical parameters. Age and serum lymphocyte levels were independent risk factors for PSSD. PSSD patients exhibited enriched pro-inflammatory genera such as Veillonella and Citrobacter. Metabolomic profiling demonstrated elevated histamine and hesperetin in PSSD, along with decreased 6-Dimethylaminopurine and LysoPE(0:0/18:3). Integrated microbiota-metabolite-host analyses revealed correlations between differential taxa, metabolites, and clinical indices, including PSQI scores, HDL-C, and inflammatory markers. Our findings indicate that PSSD is associated with a distinct gut microbial and metabolic signature, highlighting potential mechanistic links through neuroinflammation, neurotransmitter imbalance, and disrupted energy metabolism. These results provide a foundation for developing gut-targeted biomarkers and therapeutic strategies for post-stroke sleep disorders.}, }
@article {pmid42178487, year = {2026}, author = {McPolin-Hall, E and Stephen, AS and Pardieu, C and Georgeu, G and Allaker, RP and Bhogal, RK and Pople, JE and Philpott, MP and Hannen, RF}, title = {Engineering microbial symbiosis and dysbiosis reveals a new AhR-mediated mechanism underlying dandruff pathogenesis.}, journal = {The British journal of dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1093/bjd/ljag210}, pmid = {42178487}, issn = {1365-2133}, abstract = {BACKGROUND: The skin microbiome plays a pivotal role in regulating epidermal barrier integrity and immune homeostasis. However, the molecular mechanisms through which microbial dysbiosis drives dermatological disease and in particular, the pathways by which alterations in the scalp microbiome give rise to the pathological features of dandruff are not fully understood.<br><br>OBJECTIVES: This study aimed to establish and validate microbially colonised, full-thickness human skin equivalents (HSEs) that incorporate scalp-relevant bacterial and fungal microbiome species, to dissect the molecular pathways linking microbiome composition to epidermal morphology, barrier function and skin homeostasis.<br><br>METHODS: We engineered HSEs colonised with microbial consortia representing healthy (5M) and dandruff-associated (5MP) scalp microbiomes. Morphological and histological analyses were used to assess epidermal architecture and barrier integrity. Expression of key barrier proteins and enzymes involved in corneodesmosome hydrolysis was quantified. Bulk RNA-sequencing was performed to identify differentially regulated signalling pathways, followed by protein validation using immunofluorescence analysis. Key findings were further corroborated with human scalp biopsy specimens from individuals with and without dandruff.<br><br>RESULTS: HSEs colonised with the 5M microbiome maintained normal epidermal morphology and expression of barrier-associated proteins. In contrast, HSEs colonised with the 5MP microbiome developed hallmark dandruff-like phenotypes, including altered epidermal morphology, reduced barrier protein expression, and abnormal corneodesmosome degradation. Transcriptomic analysis and protein validation revealed significant attenuation of the aryl hydrocarbon receptor (AhR) signalling pathway in 5MP-colonised HSEs. Consistent downregulation of AhR and associated proteins was observed in dandruff patient samples, confirming the clinical relevance.<br><br>CONCLUSIONS: Microbial dysbiosis on the scalp can compromise AhR signalling. This study provides mechanistic evidence linking microbiome composition to pathological epidermal changes. The developed microbially colonised HSE model provides a versatile and clinically relevant tool for advancing our understanding of microbiome-driven skin pathology and translating mechanistic insights into precision interventions.}, }
@article {pmid42178569, year = {2026}, author = {Garritano, AN and J Hill, L and Ribeiro, B and Damasceno, T and Medeiros, L and Duarte, G and L S Vilela, C and Majzoub, ME and Allen, MA and Nappi, J and S Peixoto, R and Thomas, T}, title = {Ammonia oxidation and recalcitrant carbon degradation fuel mixotrophic growth in the symbiont community of a deep-sea sponge.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42178569}, issn = {2049-2618}, support = {BAS/1/1095-01-01//KAUST/ ; ANP 21005-4//ANP, Brazil/ ; }, mesh = {Animals ; *Porifera/microbiology ; *Ammonia/metabolism ; *Symbiosis ; Oxidation-Reduction ; *Archaea/metabolism/genetics/classification/isolation &amp; purification ; *Microbiota ; *Carbon/metabolism ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Metagenomics/methods ; Autotrophic Processes ; Carbon Cycle ; Seawater/microbiology ; }, abstract = {BACKGROUND: Sponges are important members of shallow-water, benthic ecosystems, where they often rely on their microbial symbionts to acquire organic or inorganic carbon. Sponges are also found in the deep sea, however, how they metabolically interact there with their symbionts remains underexplored. Here, we combined metagenomic, metatranscriptomic and stable-isotope labelling approaches to investigate the metabolic activities of the microbial community of the deep-sea sponge Calyx sp.<br><br>RESULTS: Approximately 84% of the total estimated microbial abundance was composed of nine heterotrophic phyla, whilst the remaining 16% consisted of two autotrophic ammonia-oxidising archaea. Metatranscriptomic analysis revealed the high expression of genes involved in the degradation of recalcitrant polysaccharides of algal origin, suggesting that an undegraded fraction of marine snow plays a role in the nutrition of this deep-sea holobiont. Additionally, we detected active ammonia oxidation and carbon fixation pathways in the autotrophic community members and, through ex situ incubations with labelled carbonate show a potential to fix 13.67&#xa0;mg CO2 per g dry weight in a year.<br><br>CONCLUSIONS: This study highlights the mixotrophic lifestyle of a deep-sea sponge microbiome, expanding our knowledge of the sponge-microbe symbiosis in the oligotrophic environment of the deep ocean. Video Abstract.}, }
@article {pmid42178591, year = {2026}, author = {Wu, X and Li, J and Zhang, X and Huang, H and Li, T and Kong, M and Dai, Z and Yang, Y and Chen, X}, title = {The crosslink between autophagy and ferroptosis in polycystic ovary syndrome: from synergistic pathogenesis to targeted therapy.}, journal = {Journal of ovarian research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13048-026-02146-2}, pmid = {42178591}, issn = {1757-2215}, support = {YDZJ202401150ZYTS//Department of Science and Technology of Jilin Province/ ; }, abstract = {Polycystic ovary syndrome (PCOS) is a highly heterogeneous endocrine-metabolic disorder whose core pathological features-follicular atresia and ovulatory dysfunction-are attributed to functional failure of ovarian granulosa cells (GCs). Although autophagy (a cellular quality-control mechanism) and ferroptosis (iron-dependent lipid peroxidation-driven cell death) have been shown to independently contribute to the pathophysiology of PCOS, their interactive networks and regulatory mechanisms within specific pathological microenvironments remain to be systematically elucidated. This review aims to systematically unravel this overlooked micro-pathogenic network. The dysfunction of GCs in PCOS is not an isolated event involving a single mode of cell death, but rather a pathological crosstalk arising from the disruption of the dynamic equilibrium between autophagy and ferroptosis. This paper elucidates the pathological mechanisms driving this cascade of disturbances through four distinct pathways: the intracellular stress hub formed by the synergistic action of oxidative stress (OS) and endoplasmic reticulum stress (ERS) serves as the initiating factor. This is compounded by the gut-ovarian axis's long-range amplification effect, mediated by gut microbiome (GM) dysregulation and low-grade chronic inflammation (LGI), collectively disrupting cellular homeostasis. while circadian rhythm disruption and epigenetic reprogramming, respectively, cement this imbalance at the temporal and molecular memory levels. Moreover, we have elucidated the specific execution pathways of autophagy-dependent ferroptosis, namely how selective autophagy (e.g., ferritinophagy and mitophagy) acts as a key amplifier of ferroptosis by exacerbating iron overload and energy collapse. On this basis, this paper explores therapeutic strategies ranging from upstream restoration of signal homeostasis to downstream precise inhibition of autophagy-ferroptosis interaction nodes. This review aims to provide novel theoretical perspectives for fundamentally reversing follicular atresia in PCOS and improving patients' reproductive outcomes by re-examining these lethal interactions at the microscopic level.}, }
@article {pmid42178691, year = {2026}, author = {Kang, Z and Huang, H and Lin, J and Niu, Y and Chen, J and Tang, J and Hu, Z and Liu, P and Qu, J}, title = {Unraveling Oral Dysbiosis: Microbial Complexity in Common Oral Diseases.}, journal = {MicrobiologyOpen}, volume = {15}, number = {3}, pages = {e70305}, doi = {10.1002/mbo3.70305}, pmid = {42178691}, issn = {2045-8827}, support = {S202510555045//Hunan Provincial College Students' Innovation and Entrepreneurship Training Program/ ; S202410555239//Hunan Provincial College Students' Innovation and Entrepreneurship Training Program/ ; S202310555226//Hunan Provincial College Students' Innovation and Entrepreneurship Training Program/ ; }, mesh = {*Dysbiosis/microbiology ; Humans ; *Microbiota ; *Mouth/microbiology ; *Mouth Diseases/microbiology ; Periodontal Diseases/microbiology ; Dental Caries/microbiology ; Biofilms/growth &amp; development ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {The oral microbiome is highly intricate, hosting billions of bacteria and other microorganisms that form biofilms on various oral surfaces. An imbalanced ecological relationship between the microbial community and the host can lead to various oral diseases. This narrative review explores the current understanding of the correlation between the microbiome and oral diseases. The main body of this manuscript is divided into seven parts, including a review of current research on oral microbial colonization and early life development, an introduction to five common oral diseases related to microorganisms, and a discussion on the relationship between dental caries and periodontal disease at the microbial level. Our aim in presenting this review is to offer a valuable resource for further research on the role of oral microorganisms in diagnosing and treating oral diseases. The oral microbiome's significant impact and diversity characteristics on health and disease have been recognized; however, there remains a severe lack of systematic understanding of its functions, host interactions, and environmental factors. Comprehensive research is urgently needed to elucidate the mechanisms that maintain its ecological balance, providing a scientific foundation for the precise prevention and control of oral diseases. This review comprehensively synthesizes current knowledge regarding oral microbial dysbiosis in the context of the major oral diseases mentioned and proposes a conceptual framework grounded in microbial ecology to elucidate disease progression and guide therapeutic strategies.}, }
@article {pmid42178714, year = {2026}, author = {Zeamer, AL and Lai, Y and Loew, E and Sanborn, V and Tracy, M and Jo, C and Ferdinand, D and Ward, DV and Bhattarai, SK and Drake, J and McCormick, BA and Bucci, V and Haran, JP}, title = {Microbiome functional gene pathways are indicative of cognitive performance in older adults at risk for Alzheimer's disease.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2676162}, doi = {10.1080/19490976.2026.2676162}, pmid = {42178714}, issn = {1949-0984}, mesh = {Humans ; *Alzheimer Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; Aged ; Female ; Male ; *Cognition ; Middle Aged ; *Cognitive Dysfunction/microbiology ; Aged, 80 and over ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Cohort Studies ; Metagenomics ; Metabolic Networks and Pathways/genetics ; }, abstract = {Disturbances in the gut microbiome are increasingly correlated with neurodegenerative disorders, including Alzheimer's disease. Multiple lines of emerging evidence are consistent with the microbiome's involvement in disease pathology in AD by triggering or potentiating systemic and neuroinflammation, thereby influencing disease pathology through the "microbiota-gut-brain axis." Currently, the copathologies contributing to cognitive decline and symptomatic progression in AD remain unknown and understudied. Changes in the gut microbiome composition may offer clues to potential systemic physiologic and neuropathologic changes that contribute to cognitive decline. Here, we recruited a cohort of 260 older adults (aged 60 y or older) living in the community and followed them over time, tracking objective measures of cognition, clinical information, and gut microbiome samples. Subjects were classified as healthy controls, exhibiting mild cognitive impairment, or having dementia based on clinical assessments. Using metagenomic sequencing and gene pathway analyses, we found that certain microbial-encoded metabolic pathways correlated with worse cognitive performance. Specifically, genes involved in the urea cycle, polyamine synthesis, or the metabolism of methionine and cysteine predicted worse cognitive performance. Our study suggests that the gut microbiome composition may be linked to cognitive impairment along the AD continuum and points to microbial metabolic pathways that may potentiate disease.}, }
@article {pmid42178752, year = {2026}, author = {Ding, M and de Farias, FM and O'Connor, PM and Huang, X and Ross, FC and Kennedy, EC and Hawkes, CP and Hill, C and Stanton, C and Ross, RP}, title = {Production of Multiple Variants of the Antimicrobial Sactipeptide Gnavucin D by the Human Gut Isolate Mediterraneibacter gnavus HB038.}, journal = {MicrobiologyOpen}, volume = {15}, number = {3}, pages = {e70315}, doi = {10.1002/mbo3.70315}, pmid = {42178752}, issn = {2045-8827}, support = {SFI/12/RC/2273//Science Foundation Ireland (SFI)/ ; 101054719//European Union/ ; }, mesh = {Humans ; *Bacteriocins/pharmacology/chemistry/genetics/biosynthesis/metabolism/isolation &amp; purification ; *Eubacteriales/metabolism/isolation &amp; purification/genetics ; Child, Preschool ; *Anti-Bacterial Agents/pharmacology/chemistry/metabolism ; Clostridium perfringens/drug effects ; Bacillus cereus/drug effects ; Multigene Family ; Streptococcus agalactiae/drug effects ; Microbial Sensitivity Tests ; Enterococcus/drug effects ; Gastrointestinal Microbiome ; Amino Acid Sequence ; }, abstract = {While several bacteriocins have been identified from gut-isolated cultures, there remains a need for the discovery of bacteriocins with varying inhibition spectra for strain applications such as microbiome editing, pathogen elimination and colonization resistance. With this in mind, here we describe a new antibacterial sactipeptide gnavucin D, produced by Mediterraneibacter gnavus HB038 isolated from a healthy 2-year-old child. Gnavucin D has activity against the pathogens Clostridium perfringens, Streptococcus agalactiae, Bacillus cereus, and vancomycin-resistant Enterococcus. The gene cluster includes five structural genes in tandem that encode for three different core peptides (29 amino acids each) with molecular masses of 2704.21 (D1), 2734.23 (D2/D3), and 2732.21 (D4/D5) Da. The nearest relative to these bacteriocins was found to be another sactipeptide thurincin H produced by Bacillus thuringiensis with which it shares 30% identity. Although the amino acids encoding the gnavucin and thurincin are similar with regard to putative functions, their homology to each other is low, varying from 30% to 55%. Interestingly, all these bacteriocins had short leader peptides of only 9 amino acids. Gnavucin D was found to be extremely stable to temperature, pH and proteolysis which is possibly a reflection of the sulfur to carbon post-translational modifications. The observed molecular masses of the 3 different peptides correspond to four modifications, yielding a structurally restricted, most likely double-hairpin conformation which is characteristic of such sactipeptides. Consequently, gnavucin D can be a promising candidate for selective antibacterial activity against human pathogens.}, }
@article {pmid42178807, year = {2026}, author = {Singh, S and Nalli, Y and Krishan,  and Gajjar, A and Shinde, UP and Shinde, PB}, title = {Shared Secondary Metabolites Between Salicornia brachiata and Its Bacillus Endophytes Reveal a Cooperative Chemical Defense.}, journal = {Chemistry &amp; biodiversity}, volume = {23}, number = {5}, pages = {e71352}, doi = {10.1002/cbdv.71352}, pmid = {42178807}, issn = {1612-1880}, support = {ECRA/2016/000788//Department of Science and Technology/ ; //Scientific and Engineering Research Board (SERB)/ ; MLP/0027//Council of Scientific and Industrial Research/ ; MLP/0027//Council of Scientific and Industrial Research/ ; }, mesh = {*Chenopodiaceae/metabolism/chemistry/microbiology ; *Endophytes/metabolism/chemistry ; *Bacillus/metabolism/chemistry ; *Anti-Bacterial Agents/pharmacology/chemistry/isolation &amp; purification/metabolism ; Microbial Sensitivity Tests ; Mycobacterium smegmatis/drug effects ; Secondary Metabolism ; *Lipopeptides/pharmacology/chemistry/isolation &amp; purification/metabolism ; }, abstract = {This study explores the chemical ecology of the halophytic plant Salicornia brachiata and its associated Bacillus endophytes using LC-MS-based metabolomics. A total of 43 Bacillus strains were isolated and screened for the production of bioactive lipopeptides, with 26 strains showing both lipopeptide production and antimicrobial activity, particularly against Mycobacterium smegmatis MTCC6. Fermentation of a potent endophyte, Bacillus subtilis NPRoot-3, yielded purified surfactins and fengycins, which displayed significant inhibitory activity with low IC50 values against Mycobacterium smegmatis. LC-MS analysis of aqueous and methanolic extracts of S. brachiata revealed molecular features putatively corresponding to surfactins, fengycins, and bacillibactins, indicating the presence of similar bioactive compounds in both the host plant and its endophytic microbiome. These findings suggest that the antimycobacterial properties of S. brachiata may be partly attributed to metabolites produced by its endophytes. Overall, this study highlights cooperative defense mechanisms between the plant and its endophytes, confirms the role of endophyte-derived secondary metabolites in shaping plant bioactivity and offers promising leads for the discovery of novel antimycobacterial agents.}, }
@article {pmid42178844, year = {2026}, author = {Peterson, RD and van der Made, J and Donovan, SM and Wang, M and Dilger, RN and Kaplan, N and Clark, AJ}, title = {Effects of Human Lactoferrin (Effera[®]) at Two Doses Versus Bovine Lactoferrin on the Adult Gut Microbiome and Fecal Short-Chain Fatty Acids: a Randomized, Double-Blind Trial.}, journal = {Journal of dietary supplements}, volume = {}, number = {}, pages = {1-25}, doi = {10.1080/19390211.2026.2673021}, pmid = {42178844}, issn = {1939-022X}, abstract = {Human lactoferrin (hLF) is a glycoprotein of commercial interest as a food ingredient for gut health. We conducted an exploratory analysis comparing the effects of Helaina hLF (effera[®]), produced by Komagataella phaffii, and bovine LF (bLF) on the adult gut microbiome and fecal metabolites. In a randomized, double-blind, parallel-arm, controlled trial, 66 healthy adults received either high-dose (HD) effera[®] (3.4 g/day), low-dose (LD) effera[®] (0.34 g/day), or bLF (3.4 g/day) supplementation for 28 days. Fecal samples collected at Days 0 (baseline), 28, 56, and 84 were analyzed for microbial diversity, taxonomic shifts, and volatile fatty acids (VFA). Alpha-diversity remained stable across all groups. Beta-diversity showed no main effect of treatment; however, bLF was associated with significant visit-related shifts, as assessed by weighted UniFrac. At the phylum level, significant changes associated with effera[®] were observed, including decreases in Bacillota (LD) and Verrucomicrobiota (HD), and notable genus-level increases in Lachnospira, Paraprevotella, and Faecalibacterium (HD), while bLF was associated with an increase Bacteroidota at the phylum level and with an increase in the genus Roseburia. Both effera[®] and bLF were associated with decreases in Blautia and Dorea. VFA analysis revealed that bLF increased absolute concentrations of total short-chain fatty acids (SCFAs) and branched-chain fatty acids (BCFAs); both effera[®] treatments produced proportional changes in SCFAs as a percent of total VFA, acetate, and individual BCFAs. In healthy adults, effera[®] supplementation promoted a proportional increase in acetate and supported potentially beneficial taxa while maintaining microbial diversity, without disrupting community structure. As a pre-specified exploratory outcome, microbiome and VFA findings should be interpreted as hypothesis-generating. (clinicaltrials.gov: NCT06012669).}, }
@article {pmid42178901, year = {2026}, author = {Ganamurali, N and Sabarathinam, S}, title = {Oxysterol Signaling Within the Microbiome-Regulated Gut-Liver-Brain Axis: Implications for Metabolic Homeostasis and Neurodegeneration.}, journal = {Comprehensive Physiology}, volume = {16}, number = {3}, pages = {e70181}, doi = {10.1002/cph4.70181}, pmid = {42178901}, issn = {2040-4603}, mesh = {Humans ; *Oxysterols/metabolism ; Animals ; *Gastrointestinal Microbiome/physiology ; *Brain/metabolism ; Homeostasis/physiology ; *Liver/metabolism ; Signal Transduction/physiology ; *Neurodegenerative Diseases/metabolism ; }, abstract = {The gut-liver-brain axis integrates metabolic and inflammatory signals that influence systemic homeostasis and cognitive function. While current models emphasize short-chain fatty acids and bile acids, they do not fully explain lipid-driven neurodegenerative processes. Oxysterols, oxidized derivatives of cholesterol, are emerging as key signaling molecules that bridge peripheral metabolism and brain function. Generated at the gut-liver interface through enzymatic and oxidative pathways, oxysterols regulate lipid and glucose metabolism via nuclear receptors, including liver X receptors and farnesoid X receptor. Importantly, specific oxysterols cross the blood brain barrier, enabling bidirectional communication between the periphery and central nervous system. By modulating neuroinflammation and synaptic function, oxysterols provide a mechanistic link between metabolic dysfunction and cognitive decline.}, }
@article {pmid42178903, year = {2026}, author = {Xu, M and Peng, S and Sun, T and Liang, H and Hu, Q and Feng, G and Luo, J and Tan, L and Zhang, J and Fang, J}, title = {Chitosan-Loaded Melatonin Carbon Dots-Copper Nanocomposite Improves Rice Seedling Salt Tolerance via Scavenging-Regulation-Repair Trilevel Synergistic Mechanisms.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c11334}, pmid = {42178903}, issn = {1520-5118}, abstract = {Soil salinity severely limits rice growth, necessitating effective and safe mitigation strategies. Here, a chitosan-encapsulated melatonin carbon dots-copper nanocomposite (MT-CDs@Cs-Cu) was developed to enhance rice salt tolerance via a trilevel "scavenging-regulation-repair" mechanism. The nanocomposite effectively scavenges reactive oxygen and nitrogen species, activates antioxidant enzymes, and reduces oxidative damage. It suppresses ABA accumulation while upregulating aquaporin genes, improving stomatal conductance and water transport. Under salt stress, MT-CDs@Cs-Cu increases the germination rate, fresh weight, and chlorophyll content, while reducing Na[+] accumulation and elevating the K[+]/Na[+] ratio. Furthermore, it reconstructs the rhizosphere microbiome, enriching beneficial taxa such as Sphingomonas and Actinobacteria, and reverses salt-induced metabolic disturbances. This integrated strategy provides an effective framework for developing nanoagricultural technologies to mitigate soil salinization and enhance sustainable crop production.}, }
@article {pmid42179053, year = {2026}, author = {Rodríguez-Perálvarez, ML}, title = {Proton pump inhibitors in acute-on-chronic liver failure: a sheep in a sheep's clothing.}, journal = {Revista espanola de enfermedades digestivas}, volume = {}, number = {}, pages = {}, doi = {10.17235/reed.2026.12005/2026}, pmid = {42179053}, issn = {1130-0108}, abstract = {Proton pump inhibitors (PPIs) are one of the safest drugs available which are largely overprescribed in clinical practice. Preclinical studies have suggested that chronic use of PPIs may alter gut microbiome and could promote gastrointestinal infections. Although the number-to-treat for a single infection event is high, the risk in patients with end-stage liver disease could be increased due to inherent immune-suppression, altered gastroenteric barrier and opportunity for bacterial translocation resulting in spontaneous bacterial peritonitis. In the present issue of the Spanish Journal of Gastroenterology, García Gavilán et al. published a prospective multicenter Andalusian study including 59 patients with acute-on-chronic liver failure (ACLF), among whom 26 patients were chronically exposed to PPI. Patients with and without PPIs showed a comparable grade of ACLF, rate of complications, and mortality. The rates of infection and length of hospitalization were also evenly distributed in patients exposed and not exposed to PPIs. These results add to the existing evidence and discourage deprescription of PPIs in patients with ACLF if otherwise indicated.}, }
@article {pmid42179443, year = {2026}, author = {Bautista, J and López-Cortés, A}, title = {The microbiome-gerogene axis: a new frontier in precision geromedicine.}, journal = {Frontiers in aging}, volume = {7}, number = {}, pages = {1794192}, pmid = {42179443}, issn = {2673-6217}, abstract = {Aging is increasingly recognized as a biologically heterogeneous process arising from dynamic interactions among genetic programs, environmental exposures, and adaptive physiological responses. Within the geroscience framework, conserved hallmarks, including genomic instability, epigenetic alterations, mitochondrial dysfunction, chronic inflammation, cellular senescence, and dysbiosis, capture the systems-level nature of age-related decline. Parallel to this framework, the concept of gerogenes defines coordinated molecular programs that actively drive biological aging when persistently engaged, counterbalanced by gerosuppressive pathways that preserve resilience. Here, we synthesize evidence supporting a unifying microbiome-gerogene axis in which the gut microbiome functions as an upstream, modifiable regulator of molecular aging trajectories. Age-associated microbial remodeling leads to loss of beneficial metabolic functions, including short-chain fatty acid production, bile acid transformation, and mitochondrial-supportive co-metabolism, with downstream effects on epithelial barrier integrity, immune homeostasis, and tissue repair. Integrated multi-omics studies link these microbial changes to host transcriptional, epigenomic, proteomic, and metabolomic signatures of biological aging, enabling mechanistic insights beyond taxonomic associations. Immune aging represents a major convergence point of microbiome-gerogene crosstalk, as dysbiosis driven barrier dysfunction and microbial translocation reinforce inflammaging, immunosenescence, and senescence-associated signaling networks. In parallel, microbial metabolites interface with epigenetic regulation, mitochondrial quality control, circadian biology, and gut-brain-immune communication, extending microbial influence to systemic and neurodegenerative aging processes. Building on this mechanistic foundation, we propose the microbiome-gerogene axis as an integrative framework for precision geromedicine, linking lifestyle exposures to intracellular aging programs and informing biomarker discovery and personalized interventions aimed at extending healthspan rather than treating late-stage disease.}, }
@article {pmid42166641, year = {2026}, author = {Nodehi, M and Veisi Malekshahi, Z and Rahimnia, R and Verdi, J and Vousooghi, N and Seyhoun, I}, title = {Immunometabolism crosstalk between regulatory T cells and glucose homeostasis of type 1 diabetes.}, journal = {Clinical and experimental immunology}, volume = {220}, number = {1}, pages = {}, pmid = {42166641}, issn = {1365-2249}, mesh = {*Diabetes Mellitus, Type 1/immunology/metabolism/therapy ; Humans ; *T-Lymphocytes, Regulatory/immunology/metabolism ; Homeostasis/immunology ; Animals ; Hyperglycemia/immunology ; Immune Tolerance ; *Glucose/metabolism ; Forkhead Transcription Factors/genetics ; }, abstract = {Type 1 diabetes mellitus (T1D) is an autoimmune disease that is associated with the loss of pancreatic β cells. Regulatory T cells (Tregs) play a critical role in the maintenance of immune tolerance; however, the number and function of Tregs have been found to be compromised in T1D. Genetic changes in FOXP3, as well as the role of hyperglycaemia and the accumulation of advanced glycation end products, have been proposed as potential mechanisms for the dysfunction of Tregs. However, the current understanding suggests that the role of the metabolic reprogramming associated with hyperglycaemia is more likely to be a potential mechanism for the instability of Tregs rather than a well-established primary mechanism for the development of T1D. Several therapeutic strategies have been explored in experimental models for the management of autoimmune diseases associated with Tregs dysfunction. These include the administration of low-dose interleukin-2, metformin, and dietary or microbiome-based therapies. These therapies have been found to modulate the immune system; however, the efficacy of these therapies for the management of T1D is to be established. In the present review article, the current understanding of the role of the interrelationship between hyperglycaemia, metabolic reprogramming, and Tregs-mediated immune tolerance in the pathogenesis of type 1 diabetes is reviewed.}, }
@article {pmid42166933, year = {2026}, author = {Penalba-Iglesias, D and Robas-Mora, M and González-Reguero, D and Fernández-Pastrana, VM and Lobo, AP and Jiménez-Gómez, PA}, title = {A novel Bacillaceae bacterium enhances phytoprotection and mercury detoxification in contaminated soils.}, journal = {Ecotoxicology and environmental safety}, volume = {319}, number = {}, pages = {120261}, doi = {10.1016/j.ecoenv.2026.120261}, pmid = {42166933}, issn = {1090-2414}, abstract = {Environmental pollution due to heavy metals has become a global issue over the latest decades, affecting environmental, animal, and human health. This research conducted a phenotypic, genomic, and functional characterization of Methalobacillus radiculiexplorans C204, a bacterial strain isolated from highly mercury-contaminated soils in the Almadén mining district (Ciudad Real, Spain). The main objective was to evaluate its potential as a bioremediation agent and plant growth-promoting bacterium (PGPB) for application in the recovery of heavy metal-degraded soils. Morphological and biochemical analyses revealed typical adaptations of bacteria resistant to abiotic stress. Genomic analysis identified a broad repertoire of genes associated with PGPB functions, as well as key operons conferring resistance to mercury (merA, merB), copper (copA, copB), and zinc/cadmium (czc), along with multiple antibiotic resistance mechanisms. Additionally, species-level genomic divergence from the closest validated relatives (ANI = 83%, dDDH = 28.8%), together with AAI-based differentiation, phylogenomic placement and the partial absence of conserved signature indels characteristic of Neobacillus, support the recognition of this strain as a distinct genus-level lineage within the Bacillaceae family. In plant assays using Lupinus albus grown in soils with varying Hg concentrations, the bacterial inoculation significantly enhanced plant growth, stabilized nutritional profiles, improved physiological indicators, and reduced mercury accumulation in plant tissues by up to 93%. Positive effects were also observed on the soil microbiome, with the strain contributing to the recovery of microbial metabolic activity and the maintenance of functional diversity under toxic conditions. Overall, the results position M. radiculiexplorans C204 as a native, multifunctional bacterial strain of high biotechnological interest and a promising candidate for assisted phytoremediation strategies aimed at restoration of mercury-contaminated soils.}, }
@article {pmid42166940, year = {2026}, author = {Ali, S and Chaudhary, AA and Sheikh, WM and Ali, MAM and Chopra, C and Dar, MA and Wani, AK and Bashir, SM}, title = {Genome-resolved metagenomics of the tumour microbiome: From strain diversity to functional cancer ecology.}, journal = {Pathology, research and practice}, volume = {285}, number = {}, pages = {156543}, doi = {10.1016/j.prp.2026.156543}, pmid = {42166940}, issn = {1618-0631}, abstract = {Advances in genome-resolved metagenomics, spatial transcriptomics, and single-cell sequencing have revealed that tumour-associated microbes are not random contaminants but structured, functionally heterogeneous components of the tumour microenvironment. Strain-level genomic reconstruction uncovers substantial intra-species diversity, encompassing accessory genes, mobile elements, and metabolic modules that collectively influence genotoxicity, immune modulation, drug metabolism, redox regulation, and biofilm formation. These microbial traits often assemble into convergent functional guilds that drive DNA damage, immune polarization, therapeutic resistance, and metastatic potential across tumour types. Integrative multi-omics analyses demonstrate that only a subset of detected microbial taxa is transcriptionally and metabolically active within tumours, underscoring the importance of combining metatranscriptomics, proteomics, metabolomics, and spatial profiling to delineate biologically meaningful host-microbe interactions. Spatial and single-cell mapping further reveal that intratumoural microbes occupy defined intracellular and extracellular microniches often aligned with hypoxic regions, myeloid-rich aggregates, T-cell exclusion zones, and metabolically reprogrammed epithelial states, reinforcing their role as active participants in tumour physiology rather than passive passengers. Mechanistic evidence now indicates that tumour-resident microbial ecosystems modulate responses to chemotherapy, immune checkpoint blockade, and radiotherapy, while contributing to premetastatic niche conditioning. Low-abundance but high-impact keystone microbial genomes can exert a disproportionate influence on tumour progression and therapeutic outcomes, providing new opportunities for biomarker discovery and microbiome-targeted interventions. This review integrates genome-resolved, spatial, and functional perspectives to propose an onco-metagenome framework that links tumour microbial ecology to cancer evolution, immune regulation, and translational intervention.}, }
@article {pmid42167019, year = {2026}, author = {Abdullaeva, Y and Rochau, S and Löwe, M and Holert, J and Philipp, B}, title = {Occurrence and metabolic properties of bacteria from the genus Novosphingobium indicate their use as model organisms for studying biodegradation processes in activated carbon filters in advanced wastewater purification.}, journal = {Water research}, volume = {302}, number = {}, pages = {126123}, doi = {10.1016/j.watres.2026.126123}, pmid = {42167019}, issn = {1879-2448}, abstract = {Activated carbon filters are increasingly being installed in sewage treatment plants to adsorb organic micropollutants from purified wastewater. Biodegradation also contributes to micropollutant removal in the filters, but the respective microorganisms and underlying processes are largely unexplored. Particularly, it is unknown to which extent active desorption of micropollutants takes place and which molecular mechanisms are involved. For addressing these questions microbial model organisms are required. In this study, the prokaryotic microbiome of a newly installed activated carbon filter in a fourth clarification stage of a municipal wastewater treatment plant was analyzed over 12 months by 16S rRNA gene amplicon sequencing. Bacterial families with relative abundancies above 1% stabilized after 2 months and included the potential micropollutant degraders Hyphomonadaceae and Sphingomonadaceae. Among the latter, members of the genus Novosphingobium were frequently found and closely related to the type strain N. aromaticivorans DSM 12444, which is known to degrade synthetic chemicals. Strain DSM 12444 and the Pseudomonadaceae strains Teo15 and Salic, which were isolated from enrichment cultures with filter material but not detected in the microbiome, were selected as model organisms for laboratory growth experiments with granulated activated carbon loaded with benzoate and salicylate. Strain DSM 12444 reached a significantly higher final optical density when grown on granular activated carbon pre-loaded with either benzoate or salicylate compared to strains Teo15 and Salic, respectively. Extraction of residual benzoate and salicylate from activated carbon granules indicated that >95% of the aromatic compounds had been depleted by strain DSM 12444 compared to about 70% and 50% by strains Teo15 and Salic, respectively. Transcriptomic analysis indicated differential gene expression of strain DSM 12444 during growth with benzoate in the presence and absence of GAC. These results qualify N. aromaticivorans as a feasible model organism to study the mechanisms of bacterial growth with organic substrates adsorbed to activated carbon which could support the design of bioaugmentation strategies for enhancing micropollutant removal.}, }
@article {pmid42167245, year = {2026}, author = {Sun, H and Noya-Alarcon, O and Wang, J and Daniel, SG and Bittinger, K and Mohamed, W and Scanlan, PD and Shah, C and Kundu, T and Blaser, MJ and Mueller, NT and Lander, O and Bevilaqua, M and Robles, DV and Contreras, M and Dominguez-Bello, MG}, title = {Rapid microbiome restructuring associated with medical exposure in remote Amazonian Indigenous communities.}, journal = {Cell reports}, volume = {}, number = {}, pages = {117343}, doi = {10.1016/j.celrep.2026.117343}, pmid = {42167245}, issn = {2211-1247}, abstract = {Many factors contribute to reduced microbial diversity associated with Westernization, complicating efforts to identify early drivers of microbiome change. Here, we examine microbiome variation during the introduction of a sustained medical program into previously low-exposure remote Indigenous villages. We analyze fecal samples and body-site swabs from 335 Amerindians across multiple villages before and during repeated program visits, prior to major dietary or lifestyle transitions. Low-exposure villages show higher baseline gut microbiota diversity than the medium-exposure village, and microbiota diversity declines over time in association with repeated exposure, particularly in children. Changes include loss of specific gut taxa, reduced bacterial network connectivity, and shifts in functional gene profiles toward those reported in urban populations. Oral microbiota diversity decreases, while skin and nasal diversity show modest changes. These findings indicate that repeated exposure to basic medical interventions coincides with rapid microbiome restructuring during early stages of ecological transition.}, }
@article {pmid42167251, year = {2026}, author = {Zheng, X and Wang, J and Sun, Y and Zhang, H and Tang, Y and Kuang, J and Jiao, F and Zhou, C and Xia, M and Ren, J and Cai, Y and Yao, C and Zhao, A and Qu, C and Liu, L and Yang, Y and Guan, Q and Jiang, R and Ren, Z and Chen, T and Li, M and Xia, X and Xia, L and Zhao, M and Li, Y and Ding, K and Zhou, Z and Shi, Y and Wan, X and Sun, B and Xie, G and Gao, F and Zhou, J and Hu, C and He, Y and Jia, W and Xie, RH and Jia, W}, title = {Hyocholic acids shape neonatal immune tolerance and microbiota assembly.}, journal = {Cell metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmet.2026.04.016}, pmid = {42167251}, issn = {1932-7420}, abstract = {Bile acids (BAs) are essential for regulating metabolism, immune responses, and host immunity-gut microbiome interactions. Here, we report that in human newborns, hyocholic acid (HCA) species constitute 51.03% of total BAs in meconium and 13.74% in infant serum, declining to <5% in adults. HCAs drive CD4[+] T cell differentiation toward regulatory T cells while suppressing pro-inflammatory T helper (Th)17 cells, facilitating healthy microbiome colonization. Neonates with high HCA levels show a reduced incidence of infections and gastrointestinal disorders during the first year of life. Mechanistically, HCAs are produced by the fetal-specific enzyme CYP3A7, creating a transient metabolic window that coordinates the gut-immune axis during early development. These findings reveal HCAs as primary BAs and critical mediators of immune programming, with implications for preventing early-life inflammatory diseases.}, }
@article {pmid42167294, year = {2027}, author = {Zeng, S and Almeida, A and Mu, D and Wang, S}, title = {Temporal variations of the gut microbiome in human health.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {101388}, doi = {10.1016/j.lanmic.2026.101388}, pmid = {42167294}, issn = {2666-5247}, abstract = {The colonisation of the human gut microbiome commences at birth and continues to evolve throughout the lifespan. A balanced symbiotic relationship between the host and gut microbiome is essential for maintaining overall health. This two-part Series presents a comprehensive overview of the gut microbiome across temporal and spatial dimensions, considering diurnal, seasonal, and lifespan variations while covering the entire gastrointestinal tract. We also discuss the extrinsic and intrinsic factors that shape the microbial ecosystem and affect host homoeostasis, health, and disease susceptibility. In this first Series paper, we summarise current knowledge on the microbial succession and evolutionary trajectory of the gut microbiome from neonates to adults aged 100 years and older, subsequently focusing on diurnal rhythms and seasonal patterns. We then discuss how these temporal variations in the gut microbiome are determined and how they contribute to beneficial or detrimental health outcomes in the host. Overall, elucidating the multiscale temporal dynamics of the human gut microbiome will open crucial opportunities to expand knowledge of host-microbiome interactions and their biological and clinical implications.}, }
@article {pmid42167295, year = {2027}, author = {Wang, S and Almeida, A and Mu, D and Zeng, S}, title = {Spatially resolved architecture of the human gut microbiome and its health implications.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {101389}, doi = {10.1016/j.lanmic.2026.101389}, pmid = {42167295}, issn = {2666-5247}, abstract = {The human gut microbiome shows dynamic variation throughout the lifespan and remarkable spatial organisation within the gastrointestinal tract. Complementing the focus of the first paper of this Series on the human microbiome dynamics and health, which focused on the temporal dynamics of the human gut microbiome, this second Series paper explores its biogeographical signatures, which often reflect distinct physiological niches in gastrointestinal tract regions. The spatial architecture of the gut microbiome is shaped by various factors and has important clinical implications for host homoeostasis, health, and disease. In this Series paper, we discuss current knowledge on the microbial biogeography along the gastrointestinal tract, the factors governing these spatial patterns, and their functional consequences for the host. We further focus on host-microbe interactions mediated by microbial metabolites and their impact on host health. Finally, we summarise the methodological advances that are enabling in-situ high-resolution spatial mapping of the gut microbiome as crucial tools for unravelling the detailed mechanisms of host-microbiome crosstalk. Overall, understanding the principles that govern the spatial ecology of the gut microbiome can inform the development of novel therapies designed to precisely manipulate microbial niches and restore homoeostasis along the gastrointestinal tract, thereby improving human health.}, }
@article {pmid42167365, year = {2026}, author = {Hu, X and Huang, J and Dong, S and Xu, K and Zheng, M and Cai, J and Chen, Y and Wang, T and Zhang, Y}, title = {Functionalized nanoparticles for the precise treatment and prevention of bacterial infections.}, journal = {Journal of controlled release : official journal of the Controlled Release Society}, volume = {}, number = {}, pages = {115035}, doi = {10.1016/j.jconrel.2026.115035}, pmid = {42167365}, issn = {1873-4995}, abstract = {Multidrug-resistant (MDR) bacterial infections are an escalating health issue, and their rise poses a major threat worldwide. Inappropriate antibiotic use, including unnecessary prophylaxis, and nonpathogen-directed therapy, accelerates resistance, diminishing the effectiveness of conventional antibiotics. Consequently, novel antimicrobial strategies are urgently required to achieve precise prevention and treatment of bacterial infections while minimizing selective pressure for resistance. Nanotechnology-based antimicrobials are promising candidates because of their unique advantages: payload concentration at infection sites, biofilm penetration and disruption, synergism with conventional antibiotics, and modulation of host immunity via innate/adaptive immune activation (e.g., macrophage polarization, dendritic cell maturation, and immunogenic cell death induction). This review describes the current classifications and antibacterial mechanisms of nanoantibacterial agents and summarizes strategies for targeted antibacterial and immunoregulatory nanoparticle therapies. We also identify key translational challenges, including safety and immunotoxicity, biodistribution and clearance, microbiome and environmental impacts, scalable manufacturing, assay standardization, regulatory issues, and clinical validation. Finally, we outline future directions, such as rational design of stimulus-responsive nanocarriers, data-driven optimization, theranostics, and clinically aligned evaluation. These efforts aim to advance nanoantibacterials that complement antibiotics, enabling precise MDR infection management, thereby bridging the gap between prevention and treatment to address the global antimicrobial resistance crisis.}, }
@article {pmid42167424, year = {2026}, author = {Fan, J and Li, Y and Jin, H and Yu, X and Wang, D and Lin, Y and Wang, Y and Wei, F}, title = {Comprehensive review on Cistanche polysaccharides: Structure, gut microbiota and processing characteristics.}, journal = {International journal of biological macromolecules}, volume = {367}, number = {}, pages = {152634}, doi = {10.1016/j.ijbiomac.2026.152634}, pmid = {42167424}, issn = {1879-0003}, abstract = {Cistanche deserticolaY.C.Ma and Cistanche tubulosa (Schenk) Wight are Cistanche Hoffmg. Et Link medicinal plants with a long traditional medicine history. Polysaccharides, the primary bioactive components, exhibit diverse pharmacological effects. Recently, research on the interaction between herbal polysaccharides and the gut microbiota has gained significant attention. Cistanche polysaccharides modulate the intestinal microbiome, and processing techniques significantly affect the content, structure, and function of these polysaccharides. Systematic reviews on structural characterization, bioactivities, gut microbiota interactions, and processing effects of Cistanche polysaccharides remain scarce. This review examines Cistanche polysaccharide research advances, including extraction, structural characterization, bioactivities and quality control. It emphasizes the link between bioactivities and gut microbiota, and how processing techniques influence them. Key findings show Cistanche polysaccharides have multiple bioactivities, including regulating gut microbiota and intestinal barrier. By modulating gut microbiota and metabolites, they confer health benefits such as relieving constipation and treating alcoholic fatty liver. Processing techniques alter their properties via physical-chemical changes, affecting herbal quality. Integration with advanced disciplines expands their biomedical applications. This review provides insights for deepening Cistanche polysaccharide research, improving herbal quality, promoting standardized production, and facilitating their development.}, }
@article {pmid42167440, year = {2026}, author = {Kuttiappan, A and Vanangamudi, M and Ashique, S and Mishra, N}, title = {Pharmacomicrobiomics and the gut-brain axis: microbial modulation of drug response in brain disorders.}, journal = {Drug discovery today}, volume = {}, number = {}, pages = {104700}, doi = {10.1016/j.drudis.2026.104700}, pmid = {42167440}, issn = {1878-5832}, abstract = {Pharmacomicrobiomics is the study of how the gut microbiota affects the metabolism, efficacy, and safety of drugs. Gut microbes play a key role in neurochemical communication along the gut-brain axis and can alter responses to neuroactive medications. Dysbiosis alters pharmacodynamics by modulating the synthesis of neurotransmitters, immune function and neuroinflammation. Concurrently, it alters pharmacokinetics through microbial biotransformation, which directly changes drug bioavailability, activation, and clearance {AuQ: Edit OK?}. Increasing evidence shown an association between variations in microbiome and differences in response to treatment in brain disorders. By integrating pharmacomicrobiomics into neuropharmacology, there are opportunities to achieve precision medicine by optimising therapy selection. This review emphasizes the importance of the gut microbiome in controlling drug response and highlights emerging microbiome-targeted approaches aiming to improve therapeutic efficacy and reduce adverse effects in neuropsychiatric and neurodegenerative disorders.}, }
@article {pmid42167558, year = {2026}, author = {Shafiq, M and Ali, S and Zeb, L}, title = {Antimicrobial Peptides in Shrimp Aquaculture: Mechanisms, Translational Applications, and Future Perspectives.}, journal = {Fish &amp; shellfish immunology}, volume = {}, number = {}, pages = {111428}, doi = {10.1016/j.fsi.2026.111428}, pmid = {42167558}, issn = {1095-9947}, abstract = {Shrimp aquaculture is a cornerstone of global seafood production but continues to face recurrent disease outbreaks and increasing restrictions on antibiotic use. The declining efficacy of conventional antibiotics and rising antimicrobial resistance (AMR) underscore the urgent need for novel, immune-based strategies. Antimicrobial peptides (AMPs) are small, bioactive molecules integral to the shrimp innate immune system that exhibit broad-spectrum antimicrobial activity and immunomodulatory potential. This review highlights recent mechanistic and applied advances in AMPs as sustainable, antibiotic-sparing alternatives for disease management. This review synthesizes current knowledge on endogenous shrimp AMPs and evaluates exogenous AMPs applications, delivery technologies, and regulatory considerations. Particular attention is given to limitations related to peptide stability, production scalability, delivery efficiency, and potential resistance development. A structured translational framework is proposed to guide the development of AMP-based disease management strategies for shrimp aquaculture, linking peptide discovery and engineering with formulation, farm validation, environmental assessment, and regulatory implementation. This framework leverages AI-assisted peptide discovery, host immune priming, microbiome-informed formulations, and scalable biomanufacturing to achieve farm-ready solutions that enhance shrimp health and sustainability.}, }
@article {pmid42167664, year = {2026}, author = {Getange, D and Mukaratirwa, S and Khogali, R and Yuko, E and Kabii, J and Bargul, JL and Villinger, J}, title = {Tissue-specific and sex-dependent microbiome structure in east African cattle ticks (Amblyomma gemma and Rhipicephalus pulchellus) and their bovine hosts.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {105961}, doi = {10.1016/j.meegid.2026.105961}, pmid = {42167664}, issn = {1567-7257}, abstract = {Ticks and their vertebrate hosts share intimate ecological interactions that shape microbial community composition, with implications for tick fitness and pathogen transmission. However, the extent and specificity of tick-host microbial interactions remain poorly understood, particularly in East African tick species. Here, we characterised microbial communities across multiple tissue types from two economically important tick species (Amblyomma gemma and Rhipicephalus pulchellus) and their shared bovine host using 16S rRNA V1-V2 gene sequencing. We profiled haemolymph, midgut, salivary glands, and gonads from individual ticks (25 Am. gemma and 8 Rh. pulchellus), alongside 12 bovine blood samples. Microbiota were dominated by Proteobacteria, Firmicutes, Actinobacteriota, and Bacteroidota, with Coxiella, Rickettsia, and Acinetobacter as the most abundant genera. Despite substantial taxonomic overlap, Am. gemma harboured more unique bacterial genera than Rh. pulchellus, suggesting species-specific microbial associations. Alpha and beta diversity analyses indicated distinct community structures between tick species and host blood. Tissue-level analyses revealed striking sexual dimorphism in both species: males exhibited stable microbial communities across tissues, whereas females showed strong tissue-dependent variation in richness, diversity, and composition. Co-occurrence network analyses, restricted to Am. gemma due to limited Rh. pulchellus sample size, identified sex- and tissue-specific putative keystone taxa, including Georgenia in male midguts, Serratia in female salivary glands, Enhydrobacter in ovaries, and Gemmatimonas in testes, suggesting roles in community stability. These findings highlight tissue-specific and sex-dependent factors as key determinants of tick microbial community composition, with implications for pathogen maintenance and transmission in East African livestock systems.}, }
@article {pmid42167755, year = {2026}, author = {Goerlich, K and Solis, NV and Filler, SG and Mitchell, AP}, title = {Shared anti-biofilm targets of biofilm regulators Wor3 and Bcr1 in Candida albicans.}, journal = {Genetics}, volume = {}, number = {}, pages = {}, doi = {10.1093/genetics/iyag129}, pmid = {42167755}, issn = {1943-2631}, abstract = {Candida albicans is an opportunistic fungal pathogen and a component of the human microbiome. C. albicans virulence traits include biofilm production, which is governed by a large transcriptional network. Mutations of some biofilm regulators cause the same severe biofilm-defective phenotype in multiple clinical isolates. Mutations of others, such as Wor3, Bcr1, Ndt80, and Ume6, have mild or variable phenotypes among clinical isolates. We hypothesized that Wor3 may share functions with another variable-phenotype biofilm regulator. This hypothesis predicts that a double mutant lacking Wor3 and the shared-function regulator will have a severe biofilm defect in all clinical isolates. We observed that a wor3Δ/Δ bcr1Δ/Δ double mutant has a severe biofilm defect in vitro in 5 strain backgrounds tested. It also has a severe oral biofilm defect in a mouse oropharyngeal candidiasis model in the SC5314 strain background. RNA-seq data indicate that 5 genes encoding cell surface/secreted proteins are upregulated in wor3Δ/Δ, bcr1Δ/Δ, and wor3Δ/Δ bcr1Δ/Δ strains: CWH8, DAG7, JEN2, PGA6, and YWP1. Deletion mutations of CWH8, DAG7, PGA6, or YWP1 enable biofilm formation in vitro in an SC5314-derived wor3Δ/Δ bcr1Δ/Δ strain, and deletion of YWP1 enables biofilm formation in vitro in wor3Δ/Δ bcr1Δ/Δ strains from 4 other genetic backgrounds. YWP1 has been shown to have anti-biofilm activity previously, but CWH8, DAG7, and PGA6 are newly described anti-biofilm genes. Our study illustrates the value of strain variation considerations for gene function analysis and the importance of repression targets of biofilm regulators. In addition, our results expand the number of anti-biofilm genes.}, }
@article {pmid42167838, year = {2026}, author = {Opatoyinbo, JO and Akanbi, CA and Ojo, AB and Ogunlakin, AD and Molehin, OR and Ojo, OA}, title = {Emerging trends in cancer biomarkers and their clinical effect on personalized treatment.}, journal = {Advances in cancer research}, volume = {170}, number = {}, pages = {139-173}, doi = {10.1016/bs.acr.2025.12.002}, pmid = {42167838}, issn = {2162-5557}, mesh = {Humans ; *Precision Medicine/methods/trends ; *Biomarkers, Tumor/genetics/metabolism ; *Neoplasms/therapy/diagnosis/genetics/metabolism ; }, abstract = {One of the most difficult global health issues is cancer, whose incidence and mortality rates are expected to rise significantly over the next several decades. This increasing burden highlights the need for early diagnosis, accurate prognostic tools, and predictive markers for individualized treatment plans. Biomarkers, which are measurable indicators of disease states or therapeutic responses, have become essential to modern oncology and are driving the precision medicine revolution by improving patient stratification, directing therapy choices, and facilitating disease monitoring. This review explores the development of cancer biomarkers, tracing their progression from early histopathological and serum markers to advanced molecular and immunological tools. The key biomarker categories discussed include genomic alterations such as somatic mutations, gene fusions, and copy number variations, all of which offer actionable insights for targeted therapies. Epigenetic markers, which include noncoding RNAs, histone modifications, and DNA methylation, are notable for their regulatory functions and hold promise as noninvasive diagnostic instruments. Proteomic and metabolomic methods offer useful insights into tumor biology, while circulating biomarkers, including circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), and exosomes, allow real-time, noninvasive monitoring of disease progression and minimal residual disease. Immunological biomarkers such as the tumor mutational burden (TMB) and programmed cell death ligand-1 (PD-L1) expression are becoming increasingly important in guiding immunotherapy choices. This study also highlights how emerging technologies, including next-generation sequencing, liquid biopsy platforms, and artificial intelligence-based analytics, have accelerated biomarker discovery and integration into clinical workflows. The observable advantages of biomarker-driven care are demonstrated by case studies and real-world applications in a variety of cancer types. Despite tremendous advancements, obstacles such as tumor heterogeneity, intertest variability, high costs, inconsistent regulations, and differences in healthcare infrastructure prevent widespread adoption, particularly in low- and middle-income nations where access to biomarker technologies is still unequal and could exacerbate global disparities in cancer outcomes. Future directions include the use of multiplex biomarker panels, the integration of digital pathology, and the exploration of novel biomarker domains such as the tumor microenvironment and microbiome. Personalized neoantigen-based vaccines and immunotherapies also represent promising frontiers. Overall, this review underscores the transformative potential of biomarkers in reshaping cancer diagnostics and therapeutics and calls for sustained collaborative research, technological advancements, and equitable policy frameworks to realize their full global impact.}, }
@article {pmid42167887, year = {2026}, author = {Cui, D and Zhou, Y and Zhou, Y and Ge, R and Mao, H and Mathesh, M and Han, L and Yang, W and Yan, F}, title = {Gut microbiota dysbiosis and metabolic alterations in rheumatoid arthritis: a barrier to periodontal repair.}, journal = {RMD open}, volume = {12}, number = {2}, pages = {}, doi = {10.1136/rmdopen-2026-006931}, pmid = {42167887}, issn = {2056-5933}, mesh = {Animals ; *Dysbiosis/metabolism/etiology ; *Arthritis, Rheumatoid/metabolism/etiology/microbiology/pathology ; *Gastrointestinal Microbiome ; Rats ; Male ; Disease Models, Animal ; Fecal Microbiota Transplantation ; Arthritis, Experimental/metabolism ; Rats, Sprague-Dawley ; Metabolomics/methods ; X-Ray Microtomography ; RNA, Ribosomal, 16S/genetics ; Bone Regeneration ; Biomarkers ; }, abstract = {OBJECTIVE: To investigate the impact of rheumatoid arthritis (RA) on periodontal healing and the underlying mechanisms.<br><br>METHODS: Mandibular periodontal bone defect (PBD) and collagen-induced arthritis (CIA) models were established in male Sprague-Dawley rats aged 6 weeks, assigned to four groups: control (CON), CIA, PBD and CIA+PBD. Periodontal repair was evaluated at 1, 3 and 6 weeks. To examine the contribution of gut microbiota, pseudo-germ-free rats with PBD received 3-week faecal microbiota transplantation (FMT) from either healthy or CIA donors. Arthritis severity was assessed by paw thickness and arthritis index, while bone microarchitecture was examined by micro-CT and histology. Gut microbiota and metabolites were analysed using 16S ribosomal RNA high-throughput sequencing and untargeted metabolomics.<br><br>RESULTS: CIA was found to significantly impair periodontal bone healing and suppress osteogenesis-related markers, including runt-related transcription factor 2 and alkaline phosphatase. Compared with CON rats, CIA and PBD, CIA+PBD groups exhibited gut microbial dysbiosis and metabolic alterations, particularly in arachidonic acid and tryptophan pathways. FMT from CIA donors further increased osteoclast numbers and delayed bone regeneration. Furthermore, gut-derived factors from CIA animals were associated with increased macrophage expression of pro-inflammatory cytokines, including tumour necrosis factor-alpha and interleukin-1 beta.<br><br>CONCLUSION: Overall, RA-related gut microbiota dysbiosis and metabolic disturbances are linked to impaired periodontal healing, potentially through enhanced inflammatory responses. This study highlights a microbiome-immune-metabolic axis that may influence periodontal regeneration in RA.}, }
@article {pmid42167986, year = {2026}, author = {Thomas, J and Ananthanarayanan, V and Padmanabhan, S}, title = {Metagenomic analysis of oral microbiome around zinc oxide nanoparticle-coated mini-implants: A split-mouth trial.}, journal = {Journal of the World federation of orthodontists}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ejwf.2026.03.003}, pmid = {42167986}, issn = {2212-4438}, abstract = {BACKGROUND: This study aimed to evaluate the changes in the oral microbiome surrounding zinc oxide nanoparticle (NP)-coated orthodontic mini-implants using whole-genome metagenomic sequencing and to compare the microbial colonization and clinical stability with uncoated orthodontic mini-implants.<br><br>METHODS: A randomized split-mouth trial was conducted on 12 orthodontic patients requiring bilateral skeletal anchorage in the maxillary arch. Each patient received one zinc oxide NP-coated mini-implant and one uncoated implant. The implants were coated using radiofrequency magnetron sputtering. Peri mini-implant crevicular fluid samples were collected at 1 week (T1), 4 weeks (T2), and 3 months (T3) postinsertion, and the pooled sample at each time point was subjected to whole-genome shotgun metagenomic sequencing. Taxonomic and functional profiles were analyzed using Kraken and MEGAN6, with diversity indices calculated via the VEGAN R package. Stability was assessed using a 4-point semiquantitative mobility scoring.<br><br>RESULTS: Alpha diversity indices (Shannon and Chao1) showed no comparable differences between coated and uncoated mini-implants at any time point. Descriptive analysis of pooled metagenomic samples showed lower relative abundance or absence of peri&#x2011;implant pathogens, including Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, and Parvimonas micra, around coated implants. Functional gene analysis revealed reduced expression of bacterial motility, chemotaxis, and ribosomal pathways in the coated group. All mini-implants remained clinically successful during follow-up. Mobility scores were significantly lower at 1 month (P = 0.04), but not at 3 months (P = 0.102).<br><br>CONCLUSIONS: Within the constraints of pooled metagenomic analysis, zinc oxide NP-coated mini-implants were associated with a lower relative abundance of selected peri&#x2011;implant pathogens and differences in functional pathway profiles compared with uncoated implants. Overall microbial diversity did not differ significantly between groups. Both implant types remained clinically stable, although coated implants showed reduced early mobility at 1 month. These findings should be interpreted as exploratory, and further validation through patient-level metagenomic studies is warranted.}, }
@article {pmid42168143, year = {2026}, author = {Verma, AK and Narwal, A and Kamboj, M and Devi, A and Tewari, S and Bhardwaj, R}, title = {Oral microbiome dysbiosis of Porphyromonas gingivalis in oral leukoplakia, oral squamous cell carcinoma and radiation-induced oral mucositis: a qPCR-based cross-sectional study.}, journal = {Future microbiology}, volume = {}, number = {}, pages = {1-10}, doi = {10.1080/17460913.2026.2678151}, pmid = {42168143}, issn = {1746-0921}, abstract = {BACKGROUND: Porphyromonas gingivalis is a key periodontal pathogen increasingly implicated in periodontitis and oral carcinogenesis. Among its virulence determinants, fimbriae encoded by the fimA gene exhibit pathogenic potential. While previous studies have mainly focused on fimA II and IV genotypes in periodontitis, limited data exist on the role of fimA I in oral squamous cell carcinoma (OSCC), and radiation-induced oral mucositis (RIOM). The present study aimed to evaluate the relative abundance of the fimA I genotype across different oral disease conditions and to assess its potential role as a biomarker of disease associated microbial dysbiosis.<br><br>METHODS: In total, 96 oral swab samples were collected from six groups: healthy nonsmokers, healthy smokers, periodontitis, OL, OSCC, and RIOM. Quantitative real-time PCR was performed to assess the relative abundance of the genotype using genotype-specific primers.<br><br>RESULTS: FimA I expression was highest in RIOM, followed by OSCC and periodontitis, and lowest in OL and healthy groups. A statistically significant increase was observed in RIOM and OSCC compared to controls (p&#x2009;<&#x2009;0.05).<br><br>CONCLUSION: The fimA I genotype shows higher abundance in OSCC and RIOM, suggesting its potential role as a microbial biomarker in disease monitoring and therapeutic targeting.}, }
@article {pmid42168337, year = {2026}, author = {Tao, M and Liu, Y and Guo, H and Gao, S and Wang, Y and Yan, X and Zhu, Y}, title = {The role of the gut microbiota in radiation enteritis: from mechanistic insights to therapeutic applications.}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {}, pmid = {42168337}, issn = {2399-3642}, support = {BK20250559//Natural Science Foundation of Jiangsu Province (Jiangsu Provincial Natural Science Foundation)/ ; 82403008//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024M762749//China Postdoctoral Science Foundation/ ; }, mesh = {*Gastrointestinal Microbiome/radiation effects ; Humans ; *Enteritis/microbiology/therapy/etiology ; *Radiation Injuries/microbiology/therapy ; Dysbiosis/microbiology ; Animals ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; Radiotherapy/adverse effects ; }, abstract = {Radiation enteritis (RE) is a severe adverse reaction after abdominal and pelvic radiotherapy, with a complicated pathogenesis and no effective treatment. Although gut microbiota dysbiosis was reported to play a critical role in RE, related molecular characteristics and intervention strategies have not been extensively summarized. In this review, the mechanisms of RE, including injury to intestinal stem cells, damage to the vascular endothelium, reshaped immune microenvironment, and mucosal barrier dysfunction, are discussed. In addition, radiation-induced gut microbiota dysbiosis is characterized by decreased abundance of beneficial bacteria such as Faecalibacterium prausnitzii and Bifidobacterium bifidum, and increased abundance of detrimental bacteria such as Escherichia-Shigella and Enterococcus. Beneficial and detrimental bacteria affect the development of RE by regulating inflammatory signaling pathways such as NF-κB and JAK/STAT3, and through their metabolites such as bile acids and short-chain fatty acids. Accordingly, several microbiome-targeted therapeutic strategies, including antibiotic administration, dietary interventions, fecal microbiota transplantation, probiotic administration and engineered bacteria, have been developed to mitigate RE. However, some challenges still remain for these therapeutic strategies. The goal of this review is to highlight the crucial role of gut microbiota dysbiosis in the pathogenesis of RE, thereby accelerating the development of individualized microbial therapies against this disease.}, }
@article {pmid42168404, year = {2026}, author = {Huang, L and Liu, X and Huang, F and Chen, L and Yue, J}, title = {Berberine reshapes gut microbiota and attenuates bone loss in estrogen-deficient osteoporosis via the gut-bone axis.}, journal = {Naunyn-Schmiedeberg's archives of pharmacology}, volume = {}, number = {}, pages = {}, pmid = {42168404}, issn = {1432-1912}, support = {LGF22H060014//the Basic Public Welfare Research Project of Zhejiang Natural Science Foundation of China/ ; }, abstract = {Postmenopausal osteoporosis (PMO) is a metabolic bone disorder characterized by estrogen deficiency-induced bone loss, deterioration of bone microstructure, and increased fracture risk. Current therapeutic agents are limited in efficacy and may have adverse effects. Berberine, a traditional Chinese medicinal compound, exhibits multitarget regulatory potential. However, its mechanism of action in alleviating PMO through modulation of the gut microbiota remains unclear. The objectives of this study are to assess the potential of berberine in mitigating estrogen deficiency-induced osteoporosis through modulation of the gut microbiota and to elucidate its underlying mechanisms. An ovariectomy (OVX)-induced PMO mouse model was established and divided into control, model, and berberine-treated (100 mg/kg/day) groups. Bone microstructure was examined using micro-CT, gut microbiota composition was analyzed through 16S rRNA sequencing; inflammatory factors and bone metabolism markers were evaluated using immunofluorescence; western blotting, qRT-PCR, and serum cytokine levels were quantified using ELISA. Berberine effectively reversed the OVX-induced gut dysbiosis by restoring the diminished levels of norank_f_Muribaculaceae and mitigating the elevated abundance of Lachnospiraceae_NK4A136_group, norank_f_Lachnospiraceae, and Roseburia. This modulation led to the suppression of intestinal inflammation, evidenced by decreased expression of IL-1β, IL-6, IL-8, and TNF-α, and an enhancement in gut barrier integrity, as indicated by increased levels of occludin and ZO-1. These changes collectively reduced the translocation of LPS into circulation. Consequently, berberine attenuated systemic and local release of pro-inflammatory cytokines and the activation of osteoclasts, resulting in the amelioration of PMO. Berberine mitigates PMO by reshaping the gut microbiota, improving intestinal barrier function, and suppressing systemic inflammation, thereby inhibiting bone resorption and restoring bone metabolic balance. This study offers a novel microbiome-targeted therapeutic approach for PMO.}, }
@article {pmid42168503, year = {2026}, author = {Yang, X and Huang, B and Ren, J and Fang, L and He, W and Mei, Y}, title = {Synergistic Consortia with Bacillus megaterium A14 Enhance Cadmium Immobilization in the Arachis hypogaea Rhizosphere.}, journal = {Current microbiology}, volume = {83}, number = {7}, pages = {}, pmid = {42168503}, issn = {1432-0991}, mesh = {*Cadmium/metabolism ; *Rhizosphere ; *Arachis/microbiology/metabolism ; *Bacillus megaterium/metabolism/physiology ; Soil Microbiology ; *Microbial Consortia ; *Soil Pollutants/metabolism ; Plant Roots/microbiology/metabolism ; Soil/chemistry ; }, abstract = {The microbial immobilization of cadmium bioavailability in peanut-growing soils is crucial for food safety. This study investigated the effects of exogenously applied Bacillus megaterium A14 on the indigenous rhizosphere microbiome of peanut plants and its role in modulating cadmium uptake and bioavailability. Shake-flask experiments revealed that co-culture of A14 with two native rhizosphere strains, Microbacterium S3 and Paenibacillus S22, synergistically enhanced cadmium immobilization. Non-invasive micro-test technology (NMT) further demonstrated that A14 promoted the Cd[2+] uptake capacity of S22 in co-inoculation. Pot experiments showed that inoculation with the three-strain consortium SD6 (A14, S3, and S22) reduced cadmium (Cd) content in peanut stems and roots by 51.34% and 29.14%, respectively. Additionally, the consortium altered Cd speciation in rhizosphere soil, decreasing the exchangeable fraction from 41% to 23% while increasing the residual fraction from 10% to 30%. B. megaterium A14 attracted cooperative strains S3 and S22 via metabolic secretions, and their close biofilm-based association facilitated metabolite exchange and functional synergy. The consortium immobilized Cd[2+] through intracellular uptake and extracellular adsorption, thereby reducing soil Cd bioavailability and alleviating Cd-induced oxidative stress in plants. This study proposes an ecological strategy using synergistic microbial consortia to mitigate cadmium bioavailability and uptake in crops, providing new insights into rhizosphere microbial interactions and a theoretical basis for developing composite microbial inoculants in sustainable agriculture.}, }
@article {pmid42168524, year = {2026}, author = {Akagi, S and Sato, Y and Sakamoto, T and Minamisawa, M}, title = {Sequential co-extraction of gut microbial DNA and fecal polyamines enables integrated microbiome-metabolite profiling in an Alzheimer's disease mouse model.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-54312-7}, pmid = {42168524}, issn = {2045-2322}, support = {FTR-156//Translational Research Grant from Fujita Health University/ ; FTR-156//Translational Research Grant from Fujita Health University/ ; }, abstract = {Early, non-invasive biomarkers for Alzheimer's disease (AD) are urgently needed. Impaired polyamine metabolism, regulated by intracellular pathways and the gut microbiota, has been reported in postmortem brains of AD patients. Here, we developed a sequential co-extraction workflow (Method 10) that enables recovery of gut bacterial DNA and fecal free polyamines-putrescine, spermidine, and spermine-from the same small mouse fecal sample, allowing paired microbiome and metabolite profiling. Applying this workflow to an AD knock-in mouse model and age-matched controls at 8, 32, and 56 weeks revealed an early decrease in Lactobacillus abundance at 8 weeks accompanied by elevated spermidine levels (p < 0.05), while total fecal polyamine concentrations increased further in AD mice at 56 weeks. These findings suggest that integrated fecal microbiome-polyamine profiling may provide exploratory microbiota-polyamine signatures associated with AD progression.}, }
@article {pmid42168567, year = {2026}, author = {Yakabe, K and Inoue, Y and Yanagisawa, Y and Imai, S and Suwa, S and Ando, M and Wu, Y and Kurokawa, R and Srirat, T and Haneda, T and Miki, T and Ito, M and Hirayama, A and Kurashima, Y and Fukuda, S and Hase, K and Suda, W and Takeyama, H and Hori, S and Kim, YG}, title = {Author Correction: Acarbose redirects gut microbiome utilization of dietary carbohydrates to suppress anaphylaxis in mice.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41564-026-02393-5}, pmid = {42168567}, issn = {2058-5276}, }
@article {pmid42168582, year = {2026}, author = {Ferriz-Jordán, M and Hervás, D and Bagan, L and Gimeno, C and Herreros-Pomares, A and Bagán, J}, title = {Oral squamous cell carcinoma is associated with altered salivary microbiome structure and reduced community evenness.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-54192-x}, pmid = {42168582}, issn = {2045-2322}, support = {PID2022-138398OB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, abstract = {Oral squamous cell carcinoma (OSCC) remains a major global health burden, highlighting the need for improved non-invasive tools for early detection and disease monitoring. Because saliva is easily accessible and reflects the oral microenvironment, the salivary microbiome has emerged as a promising source of candidate biomarkers. In this study, we characterized the salivary microbiota of 113 individuals, including 52 patients with OSCC and 61 healthy controls, using 16S rRNA gene sequencing targeting the V3-V4 region. Microbial diversity and composition were analyzed using complementary bioinformatic and statistical approaches, including four differential abundance methods (MaAsLin2, ANCOM-BC2, LinDA, and ALDEx2). OSCC was associated with significant differences in overall microbial community structure, as shown by beta diversity analyses, together with reduced community evenness but no major loss of richness. Differential abundance analyses identified several taxa overrepresented in OSCC, including the genera Tannerella, Solobacterium, Dialister, and Bergeyella, as well as species such as Solobacterium moorei, Tannerella forsythia, and Prevotella nigrescens. In contrast, Leptotrichia was underrepresented in OSCC. These findings support the existence of an OSCC-associated salivary dysbiosis characterized by ecological restructuring rather than global diversity loss. The identified taxa represent exploratory candidate microbial signatures associated with OSCC that require validation in larger, independent, and longitudinal cohorts before any potential clinical application can be considered.}, }
@article {pmid42168603, year = {2026}, author = {Li, R and Zhang, J and Mao, K and Meng, D and Han, JJ}, title = {Skin aging: mechanisms, evaluation, and rejuvenation.}, journal = {The EMBO journal}, volume = {}, number = {}, pages = {}, pmid = {42168603}, issn = {1460-2075}, support = {32088101//MOST | National Natural Science Foundation of China (NSFC)/ ; 92374207//MOST | National Natural Science Foundation of China (NSFC)/ ; 32330017//MOST | National Natural Science Foundation of China (NSFC)/ ; 82361148130//MOST | National Natural Science Foundation of China (NSFC)/ ; 92049302//MOST | National Natural Science Foundation of China (NSFC)/ ; IS23077//| Natural Science Foundation of Beijing Municipality ()/ ; L254002//| Natural Science Foundation of Beijing Municipality ()/ ; 2020YFA0804000//Ministry of Science and Technology of the People's Republic of China (MOST)/ ; }, abstract = {Skin aging, the most visible and accessible manifestation of organismal aging, reflects systemic physiological decline, compromising barrier integrity, immune defense, and regenerative capacity-functions essential for overall tissue homeostasis and longevity. Understanding why and how the skin ages offers crucial insights into tissue homeostasis and systemic aging. Here, we dissect the multi-layered mechanisms of skin aging across the epidermis, dermis, and appendages, highlighting how intrinsic cellular senescence, disrupted inter-compartmental communication, and dysregulation of the skin microbiome and hormonal signaling collectively undermine epithelial structure and function. We also summarize advances in quantitative evaluation of skin aging, from molecular signatures to morphological, microbial, and phenotypic indices, enabling objective assessment of biological age and intervention efficacy. Finally, we highlight rejuvenation strategies, encompassing rewiring of gene expression programs, metabolic modulation, microenvironmental remodeling, microbiome modulation, and hormone regulation, offering a framework for precision interventions and next-generation regenerative therapies.}, }
@article {pmid42168694, year = {2026}, author = {Sahu, P and Satapathy, T}, title = {The Gut-Liver Axis in Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD): Mechanisms, Microbiome Interactions and Therapeutic Targets.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {42168694}, issn = {1867-1314}, abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is increasingly recognized as a multifactorial condition in which the gut-liver axis plays a central pathogenic role. While a large body of literature has described associations between gut microbiota alterations and MASLD, a critical synthesis of the mechanistic pathways linking microbial activity to liver injury remains lacking. This review specifically focuses on gut-derived microbial metabolites as key mediators of disease progression. We examine how short-chain fatty acids, bile acids, lipopolysaccharide (LPS), trimethylamine-N-oxide (TMAO) and microbially derived ethanol influence hepatic lipid metabolism, inflammation and fibrogenesis through defined molecular pathways, including FXR signaling, TLR4 activation and immune-metabolic crosstalk. Importantly, we highlight inconsistencies in human microbiome studies, limitations in establishing causality and the challenges in translating preclinical findings into effective therapies. Although microbiome-targeted interventions such as probiotics, bile acid modulators and fecal microbiota transplantation show promise, their clinical efficacy remains variable due to interindividual heterogeneity and lack of mechanistic precision.By integrating current mechanistic evidence with translational insights, this review identifies critical knowledge gaps and proposes future directions for metabolite-focused therapeutic strategies. A more precise understanding of gut-derived signaling pathways will be essential to move from associative microbiome research toward targeted and personalized interventions in MASLD.}, }
@article {pmid42168704, year = {2026}, author = {Zhang, X and Mallick, H and Rahnavard, A}, title = {Meta-analytic microbiome target discovery for immune checkpoint inhibitor response in advanced melanoma.}, journal = {Communications medicine}, volume = {6}, number = {1}, pages = {}, pmid = {42168704}, issn = {2730-664X}, support = {2109688//National Science Foundation (NSF)/ ; 2109688//National Science Foundation (NSF)/ ; }, abstract = {BACKGROUND: Immune checkpoint inhibitors have transformed melanoma therapy, yet only a subset of patients achieve durable responses. Gut microbes have been linked to response, but reported biomarkers vary across studies. We aim to identify reproducible microbial features and test their generalizability across cohorts and treatment settings.<br><br>METHODS: We reprocessed stool metagenomic sequencing data from 15 melanoma cohorts (763 samples from 484 individuals), including 12 cohorts treated with immune checkpoint inhibitors alone and 3 trials combining immune checkpoint inhibitors with fecal microbiota transplantation. Using a unified analysis pipeline, we profiled microbial species, metabolic pathways, and biosynthetic gene clusters, and analyzed their associations with treatment response using Tweedie regression, random-effects meta-analysis, and multimodal integration with leave-one-dataset-out validation.<br><br>RESULTS: Here, we show that responders in immune checkpoint inhibitor-only cohorts are enriched for several short-chain fatty acid-producing commensals, whereas non-responders show higher abundance of taxa associated with disrupted gut communities. In fecal microbiota transplantation plus immune checkpoint inhibitor trials, response associates with distinct communities and shifts in amino-acid, nucleotide and cofactor metabolism. Across cohorts, multiview prediction models repeatedly select gene clusters linked to antimicrobial peptides and surface polysaccharides, but cross-study discrimination remains modest.<br><br>CONCLUSIONS: Microbiome signatures of response are treatment-context dependent and are not captured by a single universal species. These harmonized findings prioritize microbial taxa and functions for mechanistic studies and future microbiome-informed interventions.}, }
@article {pmid42168723, year = {2026}, author = {Min, J and Vishnyakova, O and Brooks-Wilson, A and Elliott, LT}, title = {A new sparse Bayesian quantile neural network-based approach and its application to discover physiological sweet spots in the Canadian Longitudinal Study on Aging.}, journal = {GeroScience}, volume = {}, number = {}, pages = {}, pmid = {42168723}, issn = {2509-2723}, support = {PAD 179760/CAPMC/CIHR/Canada ; }, abstract = {Identifying physiological sweet spots (optimal ranges for homeostasis) is essential for precision medicine. However, traditional statistical methods often rely on globally linear or locally jagged models that struggle to capture the smooth, non-linear nature of biological regulation in high-dimensional data. We present the Quantile Feature Selection Network (Q‑FSNet), a neural network-based framework that integrates quantile regression, feature selection, and uncertainty estimation to identify biomarkers with sweet spots. Unlike traditional methods, Q-FSNet learns continuous response curves without requiring a pre-specified number of change points. We further introduce Quantile Dirichlet Network (Q-DirichNet), a fully Bayesian extension that utilizes Dirichlet priors to automate feature shrinkage. Using data from the Canadian Longitudinal Study on Aging, we identified 25 metabolites with distinct homeostatic ranges for which biological age acceleration is minimized. The metabolites with sweet spots for biological aging include some derived from diet or produced by the gut microbiome; this highlights their potential for knowledge translation and public health impact. Our results, corroborated by existing literature, demonstrate that these sparse neural network-based methods offer a scalable and interpretable tool for discovering metabolic signatures of healthy aging vs. dysregulation in large-scale omics research.}, }
@article {pmid42168724, year = {2026}, author = {Schrenk, SJ and Bang, C and Best, L and Dost, T and Flor, S and Frahm, C and Gaser, C and Hamdan, RA and Herbsleb, M and Kaleta, C and Kattlun, F and Müller, HJ and Puta, C and Radscheidt, M and Ruiz-Rizzo, AL and Scherag, A and Steidten, T and Witte, OW and Brodoehl, S and Finke, K}, title = {Impact of an online-guided physical activity intervention on cognition, resting-state brain connectivity, and the gut microbiome in healthy older adults-a randomized controlled trial.}, journal = {GeroScience}, volume = {}, number = {}, pages = {}, pmid = {42168724}, issn = {2509-2723}, support = {859890//Horizon 2020 Framework Programme/ ; FI 1424/2-2//Deutsche Forschungsgemeinschaft/ ; P2019-01-006//Carl-Zeiss-Stiftung/ ; }, abstract = {INTRODUCTION: Physical activity may enhance cognition in older adults, yet evidence from randomized controlled trials (RCTs) on mechanistic pathways remains inconclusive.<br><br>METHODS: This single-blinded RCT examined the effects of an 8-week, online-guided, multicomponent physical activity intervention on cognitive function, resting-state functional brain connectivity (rsFC), and the gut microbiome in 92 healthy older adults (M age&#x2009;=&#x2009;66.35). Participants were randomized to a physical activity group performing moderate-to-vigorous-intensity aerobic, coordination, and balance exercises, or to an active control group engaging in progressive muscle relaxation and listening to aging-related podcasts. The primary outcome was change in visual processing speed (items/s) from pre- to post-assessment. Secondary outcomes included changes in additional cognitive measures, rsFC, cardiorespiratory fitness (CRF), and the gut microbiome.<br><br>RESULTS: The primary outcome showed no significant between-group differences. However, exploratory analyses revealed potential improvements in inhibition (&#x3b7;2&#x2009;=&#x2009;0.061; p&#x2009;=&#x2009;0.025) and visual memory (&#x3b7;2&#x2009;=&#x2009;0.047; p&#x2009;=&#x2009;0.040) in the physical activity group. This group also showed a potential increase in rsFC between visual and dorsal attention networks (&#x3b7;2&#x2009;=&#x2009;0.101; p&#x2009;=&#x2009;0.009). Visual memory gains correlated with improvements in rsFC (p&#x2009;=&#x2009;0.013). No between-group differences were observed in CRF or gut microbiome composition.<br><br>DISCUSSION: While the primary outcome (visual processing speed) and predefined mechanistic pathways (e.g., gut microbiome composition) remained unaffected, this may partly reflect the sample's high baseline fitness, which likely limited observable improvements. Exploratory findings suggest potential cognitive and associated rsFC benefits in memory and attention-related networks. The online format enabled a structured, scalable intervention while minimizing potential confounding from social interaction.<br><br>TRIAL REGISTRATION: https://drks.de/search/de/trial/DRKS00028022 (date of registration: 14.02.2022).}, }
@article {pmid42168837, year = {2026}, author = {Tong, L and Liu, Y and Han, F and Jiang, Y and Ying, S and Zhang, B and Cheng, Y and Liu, Z and Shi, Y and Xu, M and Tang, C and Sui, S and Chen, T}, title = {Exploring microbial ecology in public swimming pools: a metagenomic investigation of community structure and environmental correlates.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05157-7}, pmid = {42168837}, issn = {1471-2180}, support = {GWVI-4//The Key Projects in the Three-year Plan of Shanghai Municipal Public Health System (2023-2025)/ ; }, abstract = {Epidemiological studies have identified correlations between swimming and outbreaks of various infectious diseases. However, a comprehensive understanding of the pathogens present in public swimming pool water has yet to be systematically established. Swimming pool water samples were collected from 20 indoor public swimming pools in Shanghai, China during the summer of 2023. After quality inspection of the extracted nucleic acid, the qualified samples were subjected to metagenomic sequencing to profile the microbial communities of swimming pool water. A total of 24,035 microbial species were identified with the abundance of bacteria (99.46%), followed by archaea (0.29%), viruses (0.20%), and fungi (0.05%), including 441 pathogenic species, 23 of which were classified as biosafety level 3 (BSL-3) microorganisms. Environmental sources constituted the dominant origin (86.00%) of the pool water microbiome. Additionally, suburban pools demonstrated greater microbial diversity than urban pools (P < 0.05). The abundance of viruses exhibited a positive correlation with the concentration of urea in pool water (r = 0.31, P < 0.05). This study demonstrated that swimming pool water serves as a potent reservoir and mixing vessel for various highly pathogenic microorganisms. Effective water quality management strategies are essential to mitigating the potential public health threats of public swimming pools.}, }
@article {pmid42168845, year = {2026}, author = {Zhao, Q and Zuo, S and Liu, S and Wang, J and Tang, J and Zou, X and Leng, Y and Li, X and Zhou, M and Tian, J and Wang, P}, title = {Integrative multi-omics analysis reveals host-microbiome metabolic alterations and candidate biomarkers in Parkinson's disease.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05168-4}, pmid = {42168845}, issn = {1471-2180}, support = {2023AFD045//Hubei Provincial Natural Science Foundation / Joint Fund Project Cultivation Project/ ; 2023BCB140//Hubei Provincial plan of science and technology key research project/ ; 2023XKQT1//The Advantages Dicipline Group (Medicine) Project in Higher Education of Hubei Province (2021-2025)/ ; }, abstract = {Alterations in the gut microbiome have been increasingly implicated in Parkinson's disease (PD), but the associated metabolic changes remain incompletely understood. Here, we applied an integrative multi-omics approach combining shotgun metagenomic sequencing and untargeted LC-MS-based plasma metabolomics to investigate host-microbiome alterations in PD. Fecal and plasma samples were collected from 30 PD patients and 30 healthy spouse controls. Significant differences in microbial diversity and taxonomic composition were observed between the two groups. Taxonomic profiling revealed marked gut microbial dysbiosis in PD, including altered abundances of Phocea massiliensis, Bacteroides sp900766005, and Alistipes_A indistinctus. Metabolomic analysis identified 86 significantly altered plasma metabolites, including glycerophospholipids, indoleacetic acid, and kynurenic acid. Integrative pathway analysis suggested links between microbial functional alterations and host metabolic changes. Machine-learning analyses identified three biomarker panels that distinguished PD patients from controls in validation datasets, with the highest area under the curve (AUC) reaching 0.92. In silico molecular docking further suggested potential interactions between several metabolite biomarkers and alpha-2-macroglobulin (A2M) or the human B[act] spliceosome. Overall, these findings provide an integrative view of host-microbiome metabolic alterations associated with PD and highlight candidate biomarkers and exploratory host-metabolite associations for further investigation.}, }
@article {pmid42103282, year = {2026}, author = {Cissé, M and Moullé, V and Brossaud, R and Oullier, T and Neunlist, M}, title = {Microbiota-Gut-Brain Axis in Neurodegenerative Diseases: The Role of Bacterial Amyloids.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {}, number = {}, pages = {101802}, doi = {10.1016/j.jcmgh.2026.101802}, pmid = {42103282}, issn = {2352-345X}, abstract = {Neurodegenerative diseases are proteinopathies, characterized by misfolded protein aggregation in the brain that drives neuronal dysfunctions. Neurodegenerative diseases are also increasingly recognized as multi-organ disorders in which the gut plays a pivotal role. Indeed, recent advances in the research field of neurodegenerative diseases suggest that the gut is not merely a passive bystander, given the high prevalence of gastrointestinal symptoms, but a critical contributor to disease etiology, with evidence supporting a direct role in initiating and driving disease progression. Among environmental factors increasingly recognized as modulators of neurodegenerative disease progression, the gut microbiota has gained prominence. Beyond the impact of altered bacterial metabolites, growing evidence indicate a potential role of gut microbiota-derived amyloids in neurodegenerative diseases. For instance, gut microbial amyloids such as curli can cross-seed host proteins like α-synuclein and β-amyloid promoting aggregation, gut-to-brain propagation, and exacerbating neurodegeneration, revealing a novel mechanism linking the microbiome to neurodegenerative diseases. This conceptual shift opens promising avenues for strategies targeting the gut microbiota, including therapeutic and preventive interventions aimed at reshaping microbial communities or limiting exposure to pathogenic amyloids to reduce risk of neurodegenerative diseases. Here, we review recent discoveries to elucidate the complex interplay between gut microbiota and host amyloids, offering insights for enhancing gut and brain health and potentially preventing or reversing neurodegenerative disease progression.}, }
@article {pmid42164666, year = {2026}, author = {Wu, X and Li, M and Xu, Y and Liu, X and Gao, Z and Jiang, X and He, J and Wu, Y and Wu, C}, title = {Axillary and gut microbiota characteristics in axillary bromhidrosis patients and the effect of microwave therapy: a case-control study.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1769465}, pmid = {42164666}, issn = {1664-302X}, abstract = {INTRODUCTION: Axillary bromhidrosis is characterized by excessive sweat gland activity and foul body odor, significantly affecting patients' psychological well-being and social interactions.<br><br>METHODS: This study recruited 30 axillary bromhidrosis patients and 30 healthy controls, collecting sweat and stool samples for microbiome analysis. Among the patients, 8 patients received microwave therapy, collecting pre- and post-treatment samples for microbiome analysis.<br><br>RESULTS: The axillary microbiota of patients showed significant differences compared to healthy controls, particularly with increased abundance of odor-causing bacteria such as Staphylococcus and related species (Staphylococcus hominis, Staphylococcus haemolyticus) (LDA&#x202f;>&#x202f;3, p&#x202f;<&#x202f;0.05). While the gut microbiota composition showed no significant changes, but LEfSe analysis revealed that SCFAs-producing bacteria (Bacteroides stercoris, Phocaeicola massiliensis, and Phocaeicola vulgatus) was significantly elevated (LDA&#x202f;>&#x202f;3, p&#x202f;<&#x202f;0.05), indicating that the abundance changes of SCFAs-producing bacteria may be associated with axillary odor production through the regulation of metabolic processes. Correlation analysis revealed positive correlations between axillary odor-producing genera (Staphylococcus, Peptoniphilus, Anaerococcus) and gut SCFAs-producing genera (Roseburia, Blautia, Clostridium), suggesting a bidirectional microbiota network through gut-derived butyrate production and immune modulation (p&#x202f;<&#x202f;0.05). However, further experimentals are required to confirm the causal relationship. Furthermore, microwave therapy significantly altered axillary microbiota diversity, potentially alleviating axillary odor by inhibiting odor-producing bacteria (Staphylococcus) (LDA&#x202f;>&#x202f;3, p&#x202f;<&#x202f;0.05), while exerting minimal impact on the gut microbiota. KEGG pathway enrichment analysis revealed significant metabolic activity changes in lipid, carbohydrate, sulfur, and amino acid metabolism pathways.<br><br>CONCLUSION: This study is the first to demonstrate the interrelationship between the axillary and gut microbiota in axillary bromhidrosis patients, showing a link between gut-derived butyrate production and axillary odor. These findings offer new insights into the microbiological mechanisms underlying axillary bromhidrosis and identify potential microbial targets for future gut-based systemic treatments.}, }
@article {pmid42164667, year = {2026}, author = {Ma, H and Li, J and BanMa, C and Yuan, F and Chen, Y and Yang, X and Yang, X and Wang, T and Zhou, G}, title = {Analysis of microbial diversity in Lagotis brevituba Maxim. from different production areas on the Qinghai-Xizang Plateau and its correlation with secondary metabolic products.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1797784}, pmid = {42164667}, issn = {1664-302X}, abstract = {Lagotis brevituba Maxim. (Lagotis brevituba), belonging to the genus Lagotis within the family Scrophulariaceae. The content of its secondary metabolites exhibits significant variation across different provenances, yet the underlying mechanisms linking these variations to microbial associations remain unclear. In this study, 12 samples of rhizosphere soil, root systems, and plant specimens of Lagotis brevituba were collected from various locations on the Qinghai-Xizang Plateau, and the physicochemical properties of the soil were systematically determined. Using high-throughput 16S and ITS rRNA sequencing technologies, the diversity and composition of bacterial and fungal communities were analyzed; simultaneously, the concentrations of 10 key secondary metabolites were quantitatively determined using high-performance liquid chromatography (HPLC). Furthermore, correlation network analysis and redundancy analysis were used to investigate the relationships among soil physicochemical factors, microbial communities, and secondary metabolites. The results indicate that an elevation of 4500 m serves as a critical threshold, marked by significant changes in soil physicochemical properties. Specifically, compared to the HA group (3500-4500 m), the EA group (elevation > 4500 m) exhibited significantly lower soil organic matter and available phosphorus content, while pH and total nitrogen content were significantly higher. These soil changes indicate the presence of nutrient-poor and alkaline stress conditions, which in turn led to the differentiation of rhizosphere bacterial communities and stimulated the synthesis of more antioxidant metabolites (e.g., significantly elevated β-Sitosterol, Quercetin, and Plantamajoside) in the EA group. Microbial community analysis revealed that bacterial community structure exhibited a significant response to changes in elevation, whereas fungal communities showed no significant differences. Soil physicochemical properties (particularly pH, SOM, and AP) are key mediating factors driving microbial community differentiation and the accumulation of secondary metabolites. A combined analysis of correlation networks and Zi-Pi values identified 19 key OTUs (Operational Taxonomic Units) mediating the relationships between microorganisms and metabolites. Notably, Aquabacterium exhibited significant negative correlations with Luteolin and Acteoside, while Streptomyces showed significant positive correlations with Hyperoside (P < 0.05). This study demonstrates that soil environmental factors structure microbial communities, which in turn play a crucial role in regulating the secondary metabolites of medicinal plants. These findings provide theoretical foundations for elucidating the environment-microbiome-metabolite nexus in Lagotis brevituba.}, }
@article {pmid42164668, year = {2026}, author = {Moro, MS and Ludwig, TD and Scaketti, M and Francisconi, AF and Mendes, LW and Pinheiro, JB and Zucchi, MI}, title = {Host genetics and environment shape the gut microbiome of Euschistus heros and Piezodorus guildinii and potentially influencing their adaptation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1782301}, pmid = {42164668}, issn = {1664-302X}, abstract = {BACKGROUND: Euschistus heros and Piezodorus guildinii are major soybean pests across the Americas. Gut-associated bacteria influence insect nutrition, detoxification, and stress tolerance, potentially enhancing adaptation to diverse hosts and management regimes. We investigated how host genetics and environment shape gut microbiome structure and functional potential in these species.<br><br>RESULTS: We sequenced the 16S rRNA V4 region from 189 insects collected across Brazil and the United States. Microbiomes were dominated by Proteobacteria and Firmicutes, exhibiting high intra- and interpopulation variability. Diversity and community structure varied significantly among lineages and locations; while environment explained a larger share of overall variance, host genetics provided a more distinct statistical signal for group differentiation. In E. heros, genera linked to nutrient acquisition and detoxification (e.g., Pantoea, Wolbachia) were more prevalent. In P. guildinii, Candidatus Benitsuchiphilus-associated with diapause and uric-acid metabolism-predominated. Predicted functions included chemoheterotrophy, nitrogen fixation, and degradation of aromatic compounds, with distinct patterns across species and geographic lineages.<br><br>CONCLUSION: Both genetic and environmental factors shape the composition and functional capacity of stink bug gut microbiomes, potentially contributing to host adaptation across different agricultural landscapes. These insights open avenues for microbiome-informed strategies to improve the sustainability and efficacy of soybean pest management.}, }
@article {pmid42164669, year = {2026}, author = {Yuan, B and Li, C and Wang, Q and Yao, Q and Guo, X and Wang, Z}, title = {Maize stover mulching combined with an optimized fertilization strategy reshapes rhizosphere microbial communities and functions in greenhouse potato.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1670904}, pmid = {42164669}, issn = {1664-302X}, abstract = {Protected cultivation systems offer opportunities for improving potato productivity but are often constrained by inefficient maize stover utilization and suboptimal fertilization practices. In this study, a 4 × 4 factorial experiment was conducted using the potato cultivar 'Jishu No. 1' to decode the rhizosphere microbial mechanisms underpinning plant growth and yield enhancement under greenhouse conditions. We hypothesized that integrated management (the synergy between stover mulching and fertilization) would modify the soil microenvironment, thereby reshaping microbial community assembly patterns and functional gene distributions. The results showed that while split fertilization combined with moderate stover mulching (F2S2, 8,500 kg·hm[-2] stover mulching) was most effective in enhancing plant physiological status, full topdressing combined with the same mulching level (F3S2) achieved the highest agronomic productivity, increasing total yield to 42.33 t·hm[-2]. Metagenomic analysis revealed that the F3S2 strategy significantly reshaped the rhizosphere microbiome, characterized by higher α-diversity and the enrichment of pathways related to carbon metabolism and carbohydrate processing. Notably, F3S2 promoted the recruitment of copiotrophic taxa, particularly Actinobacteriota, whose relative abundance was significantly and positively correlated with soil organic phosphorus (r = 0.623, p < 0.05). In contrast, oligotrophic groups like Acidobacteriota were relatively less abundant in nutrient-rich treatments. These findings demonstrate that moderate stover mulching combined with dynamic fertilization provides a high-resource niche that favors functional microbial groups, thereby driving rhizosphere nutrient cycling to support potato performance. This study underscores the importance of optimized stover and fertilizer management strategies in protected cultivation.}, }
@article {pmid42164770, year = {2026}, author = {Botia Carreño, EO and Elghandour, MMMY and De Palo, P and Maggiolino, A and De Angelis, M and Salem, AZM}, title = {Nano/microencapsulation of feed additives for ruminal microbiome modulation and enteric methane mitigation in ruminants: a critical review.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1798669}, pmid = {42164770}, issn = {2297-1769}, abstract = {The latest advances in nutrition, microbiology, and omics sciences are redefining strategies to improve health indices and productivity in livestock. A novel strategy focuses on the deliberate modulation of rumen and intestinal microbiome ecosystems, which, besides being complex, are crucial for animal performance. The use of feed additives, such as bioactive compounds derived from plants and probiotics, has a long tradition supported by their known antioxidant, anti-inflammatory, and antimicrobial properties, among others. However, their practical efficacy is often compromised by their high susceptibility to degradation. Environmental factors such as light, temperature, and harsh conditions like extreme pH and enzymatic and microbiota activity in the gastrointestinal tract of livestock can inactivate these compounds before they reach their site of action to exert the beneficial effects mentioned above. To solve this challenge, nanotechnology, specifically micro- and nanoencapsulation techniques, presents an innovative solution. These strategies can protect bioactive compounds, providing controlled release and targeted delivery to specific absorption sites. This design not only optimizes probiotic survival and bioavailability of bioactive compounds but also facilitates more effective modulation of ruminal and intestinal microbial communities. Recent evidence indicates that this modulation translates into tangible productive benefits, such as better nutrient absorption and higher energy efficiency, positively impacting parameters like milk production. Additionally, these encapsulation techniques improve the efficiency of these bioactive compounds to mitigate enteric methane emissions by altering ruminal fermentation patterns. This review critically analyzes the mechanisms, applications, and potential of encapsulation technologies in ruminant production. Special emphasis is placed on how these delivery systems represent a significant advance toward precision nutrition. Indeed, the efficacy of encapsulation for microbiota manipulation and toxicological challenges for safe and sustainable implementation is discussed. This critical review addresses the following questions: (1) Under what conditions could encapsulation offer real advantages over traditional additives in ruminant livestock? (2) Are there biologically significant differences between nano- and microencapsulation in the ruminal environment? (3) How are changes in the ruminal microbiota translated into productive performance and environmental impact? (4) What is the balance between productive and environmental sustainability benefits versus the toxicological risks of nanomaterials?}, }
@article {pmid42164832, year = {2026}, author = {Kumar, A and Krishan, B and Dhiman, S and Sharma, A and Thadiyan, V and Azmi, W}, title = {Beyond antibiotics: innovative and translational strategies to overcome antimicrobial resistance.}, journal = {3 Biotech}, volume = {16}, number = {6}, pages = {201}, pmid = {42164832}, issn = {2190-572X}, abstract = {The rapid rise of antimicrobial resistance demands therapeutic strategies that extend beyond conventional antibiotics. However, most existing reviews describe emerging alternatives without systematically linking their mechanistic advances to translational readiness and clinical implementation barriers. This review addresses this gap by integrating evidence across multiple beyond-antibiotic approaches, including antimicrobial peptides, bacteriophage therapy, CRISPR-based antimicrobials, nanotechnology-enabled delivery systems, anti-virulence agents, host-directed immunotherapies, microbiome modulation (engineered probiotics and fecal microbiota transplantation), and drug-repurposing or combination therapies. The principal contribution of this synthesis is a comparative framework that maps mechanisms of action, engineering innovations, and translational evidence across these diverse strategies. Advances such as peptidomimetics, engineered phages, and nanoparticle carriers that enhance stability, targeting, and therapeutic efficacy are highlighted, along with synergistic strategies including phage-antibiotic and CRISPR-nanocarrier combinations. The review further identifies major barriers limiting clinical translation, including delivery efficiency, toxicity and ecological concerns, large-scale production challenges, cost, inconsistent clinical outcomes, and regulatory fragmentation for biologics and live therapeutics. To facilitate clinical implementation, the study proposes a translational roadmap emphasizing standardized evaluation assays, physiologically relevant infection models, integrated rapid diagnostics, and regulatory frameworks tailored for emerging antimicrobial platforms, thereby supporting the development of sustainable therapies for the post-antibiotic era.}, }
@article {pmid42164875, year = {2026}, author = {Lei, C and Liang, R and Cheng, B and Cao, X and Zhang, J and Wang, C and Wang, Z}, title = {Foodborne Carbon Dots Trigger Appetite Suppression: Mechanistic Insights from the Microbiota-Gut-Brain Axis.}, journal = {Environment &amp; health (Washington, D.C.)}, volume = {4}, number = {5}, pages = {965-977}, pmid = {42164875}, issn = {2833-8278}, abstract = {Foodborne carbon dots (FCDs) are an overlooked ingestible nanoscale food substance, and the potential ingestion risks associated with persistent dietary preferences need to be clearly articulated. In this study, the effects of FCDs and glucose CDs on feeding behavior in mice were elucidated from the perspectives of gut microbiome, metabolic flow monitoring, and metabolomics. The results demonstrated that persistent intake of FCDs (25 mg/kg/day) for 30 days significantly caused diminished appetite. Mechanistic findings suggested that FCDs were involved in the regulation of appetite reduction through the microbiota-gut-brain axis. FCDs induce perturbations in the gut microbiota, leading to increased levels of intestinal inflammation. In addition, the intake of FCDs was directly involved in microbial metabolism to generate SCFAs, activate intestinal GPR-41/43, promote the release of glucagon-like peptide, and further stimulate the hypothalamus to significantly downregulate the expression of AGRP and upregulate the expression of POMC, ultimately leading to the reduction of appetite. Moreover, intake of FCDs regulates intestinal fatty acid metabolism, amino acid metabolism, and other factors affecting the level of health of the organism. The present work highlights the impact of dietary intake of source FCDs on ingestion, providing unique perspectives on the potential health threats of FCDs.}, }
@article {pmid42164883, year = {2026}, author = {Gai, S and Li, G and Xu, W and Nan, X and Qu, G and Peng, G and Jiang, G}, title = {From Microbial Dysbiosis to Host Pathogenesis: Unraveling the Gut Microbiome's Role in Environmental Toxicology.}, journal = {Environment &amp; health (Washington, D.C.)}, volume = {4}, number = {5}, pages = {800-803}, pmid = {42164883}, issn = {2833-8278}, }
@article {pmid42164891, year = {2026}, author = {Zhang, Y and Meng, X and Gong, J and Xu, Y and Hua, Q and Chen, W and Wang, T and He, X and Xu, R and Gao, Y and Ye, C and Wu, C and Fan, Y and Zu, L and Zhu, T}, title = {Short-Term High-Altitude Exposure Alters Pharyngeal and Gut Microbiome.}, journal = {Environment &amp; health (Washington, D.C.)}, volume = {4}, number = {5}, pages = {1002-1011}, pmid = {42164891}, issn = {2833-8278}, abstract = {High-altitude exposure poses significant health challenges, where microbial communities may serve as important contributors to host acclimatization. We conducted a longitudinal study to investigate the dynamic changes in pharyngeal and gut microbiota before, during, and after acclimatization to the Mount Qomolangma region (high-altitude, 4300-5200 m above sea level, m.a.s.l.). Twenty healthy participants underwent four health visits: at baseline level (Beijing, 50 m.a.s.l.), upon arrival at the high altitude, after a week of acclimatization, and upon return to the baseline level. Throat swabs and fecal samples were collected for 16S rRNA amplicon sequencing to assess microbial composition and diversity. Linear mixed-effects models were employed to estimate the altitude-associated variations in pharyngeal and gut microbes compared to the baseline. Pharyngeal microbial diversity showed statistically significant alterations after 1 week at high altitude, with the Shannon index decreasing by 12.0% (95% CI: -21.8 to -2.9%) and the Simpson index increasing by 2.6% (1.3 to 4.0%). In contrast, gut microbial diversity decreased upon initial high-altitude exposure but tended to revert to baseline after 1 week of acclimatization. Beta diversity analyses revealed significant differences in pharyngeal microbiota across visits, while gut microbiota differences were less pronounced. Using the linear discriminant analysis effect size (LEfSe) method, we identified 11 pharyngeal and four gut microbes that were differentially abundant across visits, which could shape the host's resilience to high-altitude challenges. Our study reveals that high-altitude exposure disrupts pharyngeal and gut microbial diversity over time and modulates the abundance of some opportunistic pathogens. These shifts may mediate host responses to hypoxic environments, underscoring the microbiomes' role in physiological acclimatization.}, }
@article {pmid42165017, year = {2026}, author = {Hansson, P and Myhrstad, MCW and Costantini, L}, title = {Editorial: Impact of dietary factors on human gut microbiota and gastrointestinal endocrinology.}, journal = {Frontiers in endocrinology}, volume = {17}, number = {}, pages = {1858858}, doi = {10.3389/fendo.2026.1858858}, pmid = {42165017}, issn = {1664-2392}, }
@article {pmid42165190, year = {2026}, author = {Iqbal, T}, title = {Gut microbiota and disease.}, journal = {Essays in biochemistry}, volume = {69}, number = {6}, pages = {}, doi = {10.1042/EBC20250046}, pmid = {42165190}, issn = {1744-1358}, support = {N/A//NIHR | Birmingham Biomedical Research Centre (Birmingham BRC)/ ; N/A//NIHR | Efficacy and Mechanism Evaluation Programme (EME)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; Neoplasms/microbiology/drug therapy/metabolism ; *Neurodegenerative Diseases/microbiology/metabolism ; }, abstract = {The human gut microbiome-predominantly in the colon-comprises vastly more genetic material than that contained in human cells. Three papers in this journal highlight the functional consequences of imbalance (dysbiosis) of the gut microbiome regarding neurodegenerative conditions, cancer chemotherapy, and the wide-reaching consequences of aberrant metabolism of complex carbohydrates and amino acids in the gut.}, }
@article {pmid42165232, year = {2026}, author = {Nap, B and Thinnes, CC and Thiele, I}, title = {Whole-body metabolic modelling and its prospects in precision nutrition.}, journal = {The Proceedings of the Nutrition Society}, volume = {}, number = {}, pages = {1-19}, doi = {10.1017/S0029665126103061}, pmid = {42165232}, issn = {1475-2719}, abstract = {Nutrition has long been investigated with respect to its influence on human health. With the availability of various omics data, such as metagenomics and metabolomics, novel insights have been obtained into the influence of nutrition, particularly concerning the gut microbiome. The gut microbiome plays an important role in the breakdown of food-derived compounds and in producing essential bioactive metabolites required for human health. However, this wealth of information made the interactions between nutrition and human health increasingly intricate, and unravelling these links is complex. This review covers the concepts of genome-scale metabolic modelling as a tool to understand the links between nutrition, the gut microbiome and human metabolism and its applications. Genome-scale metabolic modelling treats metabolism as a mathematical problem which was used to develop models of human metabolism that incorporate physiology and organ-specific metabolism, known as whole-body metabolic models (WBMs). WBMs can incorporate physiological data, such as sex, weight, and body fat percentage, as well as nutrition in the form of its metabolite constituents. Finally, the gut microbiome can also be incorporated through a mathematical representation of the species present, based on stool metagenomics. WBMs have already been applied to understand gut microbiome-host co-metabolism in various non-communicable diseases. However, challenges remain, as metabolites measured in food items in public databases typically cover only common metabolites, and engagement with end-users such as nutritionists and policymakers is limited. Nevertheless, WBMs represent a promising step towards digital metabolic twins and thus personalised nutrition and medicine.}, }
@article {pmid42165244, year = {2026}, author = {Kouraki, A and McWilliams, D and Valdes, AM}, title = {Interactions between nutrition, GLP-1 secretion, and composition of the gut microbiome.}, journal = {Current opinion in clinical nutrition and metabolic care}, volume = {}, number = {}, pages = {}, pmid = {42165244}, issn = {1473-6519}, abstract = {PURPOSE OF REVIEW: Glucagon-like peptide-1 (GLP-1) is a key incretin hormone regulating insulin secretion, appetite, and energy balance. Recent research highlights complex interactions between dietary composition, gut microbiome metabolism and GLP-1 secretion. Understanding these relationships is increasingly important given the widespread clinical use of GLP-1 receptor agonists for obesity and type 2 diabetes and the growing interest in microbiome-targeted nutritional strategies.<br><br>RECENT FINDINGS: Recent studies demonstrate that microbial metabolites mediate many nutritional effects on GLP-1 secretion. Fermentation of dietary fibres generates short-chain fatty acids (SCFAs) that stimulate GLP-1 secretion through FFAR2/FFAR3 signalling. Additional microbial metabolites can regulate enteroendocrine signalling, including indole derivatives, N-acyl glycines and bile acid metabolites. Human and preclinical studies show that dietary interventions such as &#x3b2;-glucan supplementation, fermentable carbohydrate diets, probiotics, polyphenols and plant polysaccharides can influence GLP-1 secretion through microbiome-dependent mechanisms.<br><br>SUMMARY: Evidence supports an interaction between nutrition, the gut microbiome and GLP-1 signalling. Microbial metabolites link dietary substrates to GLP-1 secretion and diet shapes the microbial communities producing them. Integrating microbiome profiling with dietary interventions may help optimise metabolic therapies and explain variability in responses to GLP-1-based treatments.}, }
@article {pmid42165302, year = {2026}, author = {Tian, L and Ren, W and Li, Y and Ding, L and Yu, Z and Yu, Y and Li, S and Zhang, T and Du, Z}, title = {Nanocarriers enhance oral bioavailability: from absorption mechanisms to design strategies.}, journal = {Critical reviews in food science and nutrition}, volume = {}, number = {}, pages = {1-23}, doi = {10.1080/10408398.2026.2672547}, pmid = {42165302}, issn = {1549-7852}, abstract = {Gastrointestinal barriers (acidic environment, mucus barrier, tight junctions, and microbiota metabolism) have long constrained the oral bioavailability of food-derived bioactives, especially lipophilic constituents. Recent advances in functionalized nanoparticle strategies offer sophisticated techniques to address these challenges. Specifically, precise control of particle size, morphology and surface functionalization enhances mucus penetration and cellular uptake of nanocarriers. Advanced nanocarrier strategies, such as mucosal adhesion, receptor-mediated targeting, and co-delivery with permeation enhancers, facilitate efficient absorption by opening intercellular gaps and activating specific endocytosis pathways. Intelligent designs for pH, enzyme, redox, and microbiome responses resulted in precise protection and targeted release of cargoes in various gastrointestinal segments. This review summarizes critical strategies for absorption-optimized oral nanoplatforms, including absorption mechanisms, mucosal retention, receptor-mediated endocytosis, co-delivery with absorption enhancers, and multi-strategy coupling. We emphasize strategic orientations for maximizing oral absorption efficiency of bioactive ingredients, offering a transformative framework for architecting next-generation oral nanocarrier platforms of food-derived components.}, }
@article {pmid42165387, year = {2026}, author = {Sekiya, S and Masuda, M and Mizuno, Y and Naka, H and Goto, C and Imai, H and Umezaki, M}, title = {Interindividual Variation in Adult Gut Microbiome Composition in Two Rural Communities in Japan: Associations With Energy and Nutrient Intakes.}, journal = {American journal of human biology : the official journal of the Human Biology Council}, volume = {38}, number = {5}, pages = {e70274}, doi = {10.1002/ajhb.70274}, pmid = {42165387}, issn = {1520-6300}, support = {24H00575//JSPS KAKENHI/ ; 19H03315//JSPS KAKENHI/ ; 23K21790//JSPS KAKENHI/ ; 20K21443//JSPS KAKENHI/ ; 23K17525//JSPS KAKENHI/ ; 20H05127//JSPS KAKENHI/ ; 22003//Cooperative Research Program of the Institute of Nature and Environmental Technology, Kanazawa University/ ; 23003//Cooperative Research Program of the Institute of Nature and Environmental Technology, Kanazawa University/ ; JPMJSP2108//JST SPRING/ ; //The Kyoto University Center for Maritime Asian and Pacific Studies (MAPS)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Japan ; Rural Population/statistics &amp; numerical data ; Male ; Female ; Adult ; Cross-Sectional Studies ; Middle Aged ; *Energy Intake ; *Diet/statistics &amp; numerical data ; *Nutrients ; Aged ; Young Adult ; RNA, Ribosomal, 16S/analysis ; }, abstract = {OBJECTIVES: The "Japanese diet" has long been regarded as a key factor contributing to the remarkable life expectancy of the Japanese population. Given that the gut microbiome is thought to mediate the link between diet and health, this study investigated energy and nutrient intake among rural populations in Japan, who are presumed to adhere closely to the traditional "Japanese diet," and examined their association with gut microbiome diversity and composition.<br><br>METHODS: A cross-sectional study of 263 individuals aged &#x2265;&#x2009;20&#x2009;years was conducted in two rural communities in Japan, in July and August 2022. Participants completed a food frequency questionnaire, and we measured weight and height and collected fecal samples. The diversity and composition of the gut microbiome were assessed using 16S ribosomal RNA analysis. The associations between energy and nutrient intakes and alpha diversity metrics, beta diversity metrics, and the relative abundance of bacteria at the genus level were assessed.<br><br>RESULTS: Individuals who consumed more nutrients characteristic of seafood, rice, and vegetables (vitamin D, omega-3 highly unsaturated fatty acids, carbohydrates, total dietary fiber, and insoluble dietary fiber) had significantly higher gut microbiome diversity, while those who consumed more alcohol and fat had significantly lower microbiome diversity. Energy intake from alcohol, as well as intakes of cholesterol, iron, vitamin B1, vitamin C, carbohydrates, soluble dietary fiber, omega-3 highly unsaturated fatty acids, and calcium were significantly associated with beta diversity metrics (p&#x2009;<&#x2009;0.05), indicating that gut microbiome composition varied with these nutrient intakes.<br><br>CONCLUSION: Nutrient intakes may influence the interindividual variation in the gut microbiome seen in two rural populations in Japan. Future research should focus on elucidating the interactive effects between the "Japanese diet" and the gut microbiome.}, }
@article {pmid42165419, year = {2026}, author = {Green, ET and Carbone, I and Mitchell, CE}, title = {Seasonal Assembly of the Phyllosphere Fungal Microbiome of a Perennial Grass is Robust to Nutrient Addition.}, journal = {Molecular ecology}, volume = {35}, number = {10}, pages = {e70384}, doi = {10.1111/mec.70384}, pmid = {42165419}, issn = {1365-294X}, support = {2016-67013-25762//U.S. Department of Agriculture/ ; DEB-2308472//National Science Foundation/ ; }, mesh = {Seasons ; *Plant Leaves/microbiology ; *Fungi/genetics/classification ; Nutrients ; *Mycobiome/genetics ; *Microbiota/genetics ; Phylogeny ; Soil Microbiology ; *Poaceae/microbiology ; Soil/chemistry ; *Lolium/microbiology ; Biodiversity ; }, abstract = {The leaf microbiome plays an important role in plant health and defence. Despite its importance, how the assembly of the leaf microbial community is modified by environmental conditions such as nutrient availability remains relatively uninvestigated. Soil nutrient availability may shift the outcome of microbial interactions within a host individual or influence the pool of microbes across the plant community. We hypothesised that leaf microbial diversity would increase across the season as leaves collect additional taxa, and that this seasonal assembly would be sensitive to nutrient addition. To assess this, we tracked the assembly of the fungal phyllosphere microbiome of the grass tall fescue (Lolium arundinaceum) in old-field vegetation over the growing season and experimentally tested whether the seasonality of the microbiome was modified by experimental addition of soil nutrients. Fungal diversity (Shannon diversity index, richness, and evenness) increased early in the season, with most metrics saturating before the end of the season. Community composition as measured by Bray-Curtis dissimilarity also shifted over the early and mid-growing season. Phylogeny-based machine-learning identified fungal lineages that were abundant in different seasons, linking seasonal community shifts to their evolutionary context. Nutrient addition was less important than time of season, but still significantly altered community composition and interacted with time to influence richness, with lowest richness in the low nutrient addition plots early in the season. The clear seasonality of the microbiome provides support for a dynamic phyllosphere microbiome, suggesting further studies manipulating fungal recruitment over the season. Furthermore, it highlights the robustness of seasonal assembly to variation in nutrient availability.}, }
@article {pmid42165584, year = {2026}, author = {Lee, S and Dobes, P and Mascellani Bergo, A and Killer, J and Marciniak, J and Hurychova, J and Sreibr, S and Kamler, M and Purnoch, V and Hlinakova, L and Titera, D and Cinek, O and Carolan, JC and Hyrsl, P and Havlik, J}, title = {Bacterial supplementation shapes honey bee gut microbiota and host metabolism under controlled and field conditions.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0028326}, doi = {10.1128/msystems.00283-26}, pmid = {42165584}, issn = {2379-5077}, abstract = {Gut bacteria are essential to honey bee (Apis mellifera) health, supporting digestion, immunity, and resilience against stressors. Probiotic-based strategies have been proposed to enhance core gut symbionts, yet the underlying mechanisms and influences of environmental context on these effects are not fully understood. This study examined the influence of gut-derived bacterial supplementation on the honey bee gut microbiome, proteome, and metabolome across three conditions: (i) controlled cages, (ii) semi-controlled cages allowing contact with nestmates, and (iii) field conditions. Treatment groups received a bacterial supplement containing Lactobacillus helsingborgensis, Lactobacillus apis, Bifidobacterium choladohabitans, and Bifidobacterium polysaccharolyticum, while control groups received only a sucrose solution. Gut samples from 10-day-old bees were analyzed. Supplemented bees showed strong gut colonization by Bifidobacterium and Lactobacillus, especially under controlled and semi-controlled conditions. In the field, L. helsingborgensis remained significantly enriched in the treatment group, demonstrating short-term ecological resilience in the natural hive environment. Proteomic changes in supplemented bees included an increased abundance of major royal jelly protein precursors and mitochondrial-associated proteins, together with reduced abundance of several ribosomal and translation-related proteins involved in peptide biosynthesis and cellular protein quality control. Metabolomic analysis revealed reproducible shifts across all three conditions. Treatment groups showed higher concentrations of microbial fermentation products (acetate, succinate) and potential neuromodulatory metabolites (ornithine, γ-aminobutyrate), while sucrose, N-acetylglucosamine, and uridine were constantly lower compared to controls. These findings highlight reproducible, context-dependent effects of bacterial supplementation on honey bee gut physiology and provide a framework for interpreting microbiome-based interventions in pollinator health.IMPORTANCEHoney bees are essential pollinators whose health is influenced by their gut microbiome. Probiotic applications aimed at improving gut health have been proposed, yet outcomes remain inconsistent and vary across settings. Results from laboratory experiments often differ from those observed under field conditions, making it difficult to understand the complex dynamics of eusocial insect colonies. Here, we evaluate honey bee gut-derived bacterial supplementation across controlled, semi-controlled, and field settings using bacterial profiling, proteomic, and metabolomic analyses. We demonstrate that bacterial-supplemented groups consistently reshape gut community composition and modulate host physiological processes, but in a context-dependent manner. These results provide a unified understanding of how microbial interventions function at colony and individual levels, guiding the rational design of probiotic strategies to support honey bee health under realistic conditions.}, }
@article {pmid42165805, year = {2026}, author = {Brown, TL and Ng, DYK and Savva, GM and Elek, CKA and Docherty, JAD and Cook, R and Ansorge, R and Telatin, A and Kutter, E and Adriaenssens, EM}, title = {The effects of bacteriophage cocktail treatment on healthy gut microbiota: an in vitro human colon model study.}, journal = {Microbial genomics}, volume = {12}, number = {5}, pages = {}, pmid = {42165805}, issn = {2057-5858}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteriophages/genetics/physiology ; *Colon/microbiology/virology ; Escherichia coli/virology/genetics ; Bacteria/genetics/virology/classification ; Phage Therapy ; Feces/microbiology ; }, abstract = {The human gut microbiome is a complex community that plays an important role in health, where perturbations can result in dysbiosis and disease. Bacteriophages (phages) can provide treatment for bacterial gastrointestinal disease, and commercial preparations such as the Intesti bacteriophage cocktail can be taken orally to target bacterial pathogens. However, interactions between these phages and the native gut microbiota are understudied. To investigate the impact of phage treatment, we used simulated gut models seeded with healthy donor microbiota from three individuals, sequenced the DNA and analysed the bacterial and viral portions from samples obtained over time. Each donor had a unique bacterial composition that diverged with time. When comparing phage-treated to control samples, we observed that Escherichia coli abundance accounted for the largest portion of bacterial community variance and was more associated with the controls. The lower abundance in phage-treated samples may have resulted from the lytic action of phages from the cocktail. Additionally, our analyses of the viral portion revealed a phage bloom exclusive to phage-treated samples. A highly abundant phage in this bloom was matched with the Intesti bacteriophage cocktail, showed similarity to Enterobacteria phage phi92 and provided evidence of productive infection within the model. While we did observe fluctuations in relative abundance of additional viral sequences in the presence of the phage cocktail, these changes were often transient. Furthermore, we detected only slight differences from typical members of the virome and low numbers of active prophages. Our experiments suggest that the phage cocktail had minimal interruption to the native gut microbiota within the model.}, }
@article {pmid42165911, year = {2026}, author = {Chen, H and Chen, H and Xie, L and Jiang, K and Xia, E and Mao, J and Liu, Z and Li, X and Xiao, Y and Qian, X and Jin, Z}, title = {Novel salivary biomarkers of Alzheimer's disease identified by integrated metabolomics and microbiomics analysis.}, journal = {Clinical oral investigations}, volume = {30}, number = {6}, pages = {}, pmid = {42165911}, issn = {1436-3771}, support = {LGF22H100005 and LTGY24H100005//the Natural Science Foundation of Zhejiang Province/ ; 2023YFF0611002//the National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Alzheimer Disease/metabolism/microbiology/diagnosis ; *Saliva/microbiology/chemistry/metabolism ; Biomarkers/metabolism/analysis ; Male ; *Metabolomics/methods ; Female ; Aged ; *Cognitive Dysfunction/metabolism/microbiology ; Case-Control Studies ; Microbiota ; Aged, 80 and over ; }, abstract = {OBJECTIVES: Alzheimer's disease (AD) and mild cognitive impairment (MCI) represent significant health challenges, with identification of biomarkers from non-invasive biofluid critical for large-scale screening and effective intervention.<br><br>MATERIAL AND METHODS: In this study, we performed a comprehensive analysis integrating non-targeted metabolomics and 16S rDNA sequencing of saliva samples from 3 age and sex-matched groups containing 18 AD patients, 15 MCI individuals and 19 healthy controls (HC).<br><br>RESULTS: Salivary metabolites including histamine (biogenic amine), carveol (monoterpene), and 2-phosphoglycerate (glycolytic intermediate) were significantly altered in AD patients. In addition, L-glutamic acid (excitatory neurotransmitter) levels were notably reduced in MCI patients, suggesting its potential as a biomarker for MCI. Microbial analysis revealed a decrease in the abundance of Actinomyces and Stomatobaculum in AD patients. In contrast, MCI patients exhibited a reduction in Atopobium and Actinomyces, along with an increase in Gemella and Peptostreptococcus compared to HC. An integrated analysis of microbiota and metabolites uncovered significant correlations, such as a positive correlation between Lactobacillus crispatus and GABA in AD patients, and an association between Klebsiella pneumoniae and multiple metabolites in AD patients. Additionally, MCI patients exhibited a higher abundance of "potentially pathogenic" microbiota species, highlighting a distinct microbiome profile.<br><br>CONCLUSIONS: Our findings revealed distinct metabolic and microbiomic alterations across the groups.<br><br>CLINICAL RELEVANCE: These findings suggest that saliva may harbor valuable biomarkers for the early diagnosis of AD and MCI. Moreover, our results underscore the involvement of the "oral-brain axis" in the pathogenesis of neurodegenerative diseases, offering new insights into potential therapeutic targets.}, }
@article {pmid42165922, year = {2026}, author = {Xiao, L and Zhao, F}, title = {Microbiome research beyond description and association.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {42165922}, issn = {1869-1889}, }
@article {pmid42165942, year = {2026}, author = {Tamahane, V and Shah, N and Kajale, N and Khadilkar, A and Khadilkar, V and Gondhalekar, K and Shouche, Y and Mylari, G}, title = {Effect of prebiotic intervention on glycemic control and gut microbiome profile in Indian children with type 1 diabetes mellitus (T1DM): a pilot randomised control trial.}, journal = {Endocrine}, volume = {91}, number = {1}, pages = {}, pmid = {42165942}, issn = {1559-0100}, mesh = {Humans ; *Prebiotics/administration &amp; dosage ; Child ; *Diabetes Mellitus, Type 1/microbiology/blood/diet therapy ; *Gastrointestinal Microbiome/drug effects/physiology ; Pilot Projects ; Male ; Female ; Adolescent ; *Oligosaccharides/administration &amp; dosage/therapeutic use/pharmacology ; Double-Blind Method ; India ; *Glycemic Control ; Inulin/administration &amp; dosage ; Glycated Hemoglobin/analysis ; Blood Glucose ; }, abstract = {BACKGROUND: Type 1 diabetes mellitus (T1DM) is increasingly associated with gut microbial dysbiosis. Emerging evidence suggests that short-chain fatty acids(SCFA) producing bacteria play a role in glucose regulation and immune modulation. However, interventional data in children remain limited.<br><br>OBJECTIVE: To evaluate the effect of an oligofructose-enriched inulin intervention on glycemic control and gut microbiome composition in Indian children with T1DM.<br><br>METHODS: In double-blind, randomised, placebo-controlled pilot trial, 68-children (8-18years) with established T1DM were allocated to receive either 8&#xa0;g/day of oligofructose-enriched inulin or an isocaloric maltodextrin placebo for 12 weeks. Anthropometry, glycated-hemoglobin (HbA1c), and stool-microbiome-profiles (16SrRNA sequencing) were assessed at baseline and endline. Alpha and beta-diversity indices, differential abundance analyses(DESeq2), were compared between groups.<br><br>RESULTS: Sixty-one participants (32 prebiotic, 29 placebo) completed the study with a mean compliance of 80%. Baseline characteristics and HbA1c levels were comparable between groups. No significant difference in HbA1c was observed after intervention (prebiotic 9.8&#x2009;&#xb1;&#x2009;1.4% vs. placebo 10.6&#x2009;&#xb1;&#x2009;2.5%; p&#x2009;>&#x2009;0.05). However, the prebiotic group demonstrated a significant enrichment of SCFA-producing taxa, including Intestinibacter, Lachnospiraceae_UCG004, Megasphaera, Prevotella_2, and Agathobacter(p&#x2009;<&#x2009;0.05). Families such as Lachnospiraceae, Bifidobacteriaceae, Ruminococcaceae, Atopobiaceae and Akkermensiaceae were increased significantly, while alpha- and beta-diversity indices remained stable. No significant adverse events were reported apart from isolated mild hypoglycemic episodes.<br><br>CONCLUSIONS: Prebiotics intervention modulated beneficial gut bacteria(SCFA-producing) without any change in glycemic control, suggesting possible long-term metabolic and anti-inflammatory benefits in T1DM. Larger studies are needed. Adding natural prebiotic-rich foods to daily diets of children with T1DM could be a simple, affordable.}, }
@article {pmid42165961, year = {2026}, author = {Sammad, A and Khan, S and Zhang, YY and Bai, XL and Zhu, X and Yin, K}, title = {Gut Microbial Dysbiosis in Type 2 Diabetes Patients with Concurrent Atherosclerosis.}, journal = {Current atherosclerosis reports}, volume = {28}, number = {1}, pages = {}, pmid = {42165961}, issn = {1534-6242}, support = {2022GXNSFBA035664//the Regional Science Fund project grants/ ; }, mesh = {Humans ; *Dysbiosis/microbiology/complications ; *Gastrointestinal Microbiome ; *Atherosclerosis/microbiology/complications/epidemiology ; *Diabetes Mellitus, Type 2/complications/microbiology ; }, abstract = {PURPOSE OF REVIEW: The association of the gut microbiome with T2DM has been conflicting due to the disease's inherent complexity-a challenge that is further exacerbated in T2DM-related atherosclerotic cardiovascular diseases (ASCVD). Even when individual microbial species are associated with T2DM or ASCVD, mechanisms remain elusive-highlighting a pressing need for gut microbiota profiling in T2DM-related ASCVD. This perspective review examines gut microbial dysbiosis in T2DM with atherosclerosis (T2DM-AS), focusing on population-specific profiles from southern China and microbial biomarkers to predict disease progression.<br><br>RECENT FINDINGS: T2DM-AS patients exhibit reduced Firmicutes-to-Bacteriodota ratio, with reduced Clostridia, Oscillospirales, Ruminococcaceae, and Faecalibacterium. Dysbiosis includes increased pro-inflammatory Enterobacteriaceae, Enterococcaceae, and Streptococcaceae, with higher abundances of Escherichia-Shigella, Klebsiella, Streptococcus, and Alloprevotella. Beneficial butyrate-producing genera Faecalibacterium, Dialister, and Butyricicoccus are markedly depleted. Enterobacteriaceae/Escherichia-Shigella abundance strongly correlates with the Gensini score, serum zonulin (a gut permeability marker), cholesterol, triglyceride, and alanine aminotransferase. Mechanistically, the bacterial type III secretion system primarily drives a pathogenic cascade involving: (1) ferroptosis-mediated intestinal damage, (2) gut barrier disruption, (3) abnormal glycerophospholipid metabolism with phosphatidylcholine upregulation, and (4) macrophage activation and systemic inflammation that aggravates atherosclerosis. Pathogenic gut microbial signatures-enrichment of type III secretion system-harboring Enterobacteriaceae and depletion of butyrate-producing taxa-represent potential biomarkers for T2DM-AS progression. The type III secretion system-ferroptosis-lipid metabolism axis critically links gut dysbiosis to accelerated atherosclerosis, suggesting interventions targeting gut barrier integrity or lipid metabolism as therapeutic avenues. Population-specific profiling is essential for microbiome-based approaches to T2DM-AS management.}, }
@article {pmid42165973, year = {2026}, author = {Shaffer, M and North, D and Bibby, K}, title = {Correction: Evaluating Nanotrap Microbiome Particles as A Wastewater Viral Concentration Method.}, journal = {Food and environmental virology}, volume = {18}, number = {2}, pages = {}, doi = {10.1007/s12560-026-09697-z}, pmid = {42165973}, issn = {1867-0342}, }
@article {pmid42166037, year = {2026}, author = {Sasse, R and Mejias-Beck, J}, title = {Nitric Oxide in the Intestinal Stem Cell Niche: A Spatial Model of Nitrosative Stress and Clonal Evolution in Colitis-Associated Colorectal Cancer.}, journal = {Digestive diseases and sciences}, volume = {}, number = {}, pages = {}, pmid = {42166037}, issn = {1573-2568}, abstract = {PURPOSE: Chronic colitis is a major risk factor for colitis-associated colorectal cancer (CAC), but the mechanisms linking recurrent inflammation to crypt-level dysplasia remain incompletely defined. This review examines whether spatially heterogeneous nitric oxide (NO) and reactive nitrogen species (RNS) exposure within the intestinal stem cell (ISC) niche may connect inflammation, DNA damage, stemness, and clonal evolution in CAC.<br><br>METHODS: This narrative, mechanistic review synthesized peer-reviewed English-language studies identified through PubMed/MEDLINE, Web of Science, and Google Scholar through 1 May 2026. Included literature addressed NO/NOS biology, ISC and crypt niche regulation, colitis-associated carcinogenesis, nitrosative DNA damage, cancer stem-like traits, and epithelial, stromal, immune, vascular, lymphatic, microbial, neural, and glial NO sources.<br><br>RESULTS: Constitutive NOS-derived NO supports mucosal perfusion, barrier integrity, and homeostasis, whereas colitis-associated NOS upregulation can generate high-flux NO, peroxynitrite, epithelial injury, and mutagenic nitrosative stress. The reviewed evidence supports a spatial NO/RNS-field model in which recurrent crypt-level nitrosative microdomains influence DNA damage, repair stress, Wnt/stemness signaling, immune selection, microbiome-redox interactions, and cancer stem-like programs. However, direct causal evidence in human colitic ISCs remains limited.<br><br>CONCLUSION: Chronic colitis may create recurring NO/RNS-rich crypt microenvironments that favor survival and expansion of damaged or NO-tolerant stem/progenitor clones. This model may guide crypt-resolved biomarker development and locally restricted prevention strategies, but prospective validation is required.}, }
@article {pmid42166056, year = {2026}, author = {Jayaneththi, U and Sneddon, NW and Burkitt, LL and Jeyakumar, P and Anderson, CWN and Fermin, LM and Donaghy, DJ}, title = {Host Filtering Shapes the Soil-gut Microbiome Linkages in Pastoral Systems.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02791-6}, pmid = {42166056}, issn = {1432-184X}, abstract = {Soil and ruminant gut microbiomes are linked within grazing pastoral systems, yet the strength and direction of these connections under different pasture management systems remain poorly understood. This study characterised bacterial communities in soil and faeces from cattle and sheep grazing standard and diverse pastures managed under contemporary and regenerative practices using 16 S rRNA gene sequencing. Shared bacterial taxa between soil and gut were identified, and their dominance patterns and soil-gut diversity relationships were evaluated using Spearman correlations and Procrustes analyses. Several taxa, including Prevotella copri, Faecalibacterium prausnitzii, Akkermansia muciniphila, Bacteroides uniformis, Clostridium perfringens and Fibrobacter succinogenes were commonly shared between soil and gut but were usually more prevalent in the gut, indicating predominant host‑associated dominance. Soil exhibited significantly greater bacterial alpha diversity than the gut across all treatments, and neither pasture diversity nor management significantly affected soil-gut alpha diversity differences or the contributions of shared taxa. Correlations between soil and gut alpha diversity were weak and non-significant, and correlations for beta diversity between soil and gut varied through time and among treatments without reaching significance. These findings indicate that, although soil-gut microbial connectivity exists, gut communities are primarily shaped by host-related ecological processes and internal filtering, with soil acting mainly as a diverse reservoir and sink for gut-derived taxa. This highlights that host-driven gut microbiomes primarily shape the soil-gut microbiome link, limiting the strong direct influence of pasture diversity or management.}, }
@article {pmid42166181, year = {2026}, author = {Hijri, M and Aliyat, FZ and Legeay, J and Lee, SJ and Idbella, M and Anwar, AF and Errafii, K and Marasco, R and Biswas, MK and Venturi, V and Zézé, A and Gemeda, M and Eziuzor, SC and Makhalanyane, T and Ahmed, B}, title = {Advancing microbial ecology, microbiomes, and One Health in Africa: From regional initiatives to pan-African flagship programs.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag132}, pmid = {42166181}, issn = {1751-7370}, abstract = {Microbial ecology and microbiome science are increasingly central to global "One Health" efforts, a framework that recognizes the interconnected health of humans, animals, and the environment. In Africa, these fields are particularly important for addressing interconnected challenges in public health, agriculture, and ecosystem resilience. Discussions at the ISME-Africa Morocco 2025 regional meeting highlighted both progress and persistent gaps in African microbiome research. Initiatives such as the African BioGenome Project and Human Heredity and Health in Africa demonstrate the feasibility of population-representative studies, regional training, networking, and open-science frameworks; however, the research landscape remains fragmented, with limited intra-African collaboration and continued reliance on external funding and leadership. The development of Africa-specific reference genomes, population-based microbiome datasets, is essential to address these gaps and ensure global representation. This perspective synthesizes current evidence and outlines strategic priorities to transition from toward coordinated pan-African research networks and flagship programs. Key recommendations include developing Africa-specific genome reference datasets, establishing pan-continental consortia, fostering equitable African-non-African partnerships, integrating microbiome science into policy frameworks, and adopting FAIR open-science practices. Strengthening bioinformatics and computational capacity will be essential to transform fragmented data into high-impact, coordinated insights. Advancing these priorities will accelerate translation into One Health outcomes, including antimicrobial resistance surveillance, food security, climate-resilient agriculture, and precision medicine. Africa's rich microbial diversity offers significant potential for antibiotic discovery, improved crop productivity, and sustainable agricultural systems. Collectively, strengthening Africa-led, collaborative microbiome research will enable the continent's microbial diversity to drive impactful solutions with regional and global relevance.}, }
@article {pmid42166227, year = {2026}, author = {Kaushik, K and Sharma, M and Sharma, R and Reza, A and Sharma, G and Panwar, S and Nagraik, R and Negi, P and Sharma, A}, title = {Gut microbiota: The hidden hallmark of aging.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {}, number = {}, pages = {}, doi = {10.1556/030.2026.02808}, pmid = {42166227}, issn = {1588-2640}, abstract = {Aging is the natural process of changes that are accumulated over time and are responsible for the ever-increasing susceptibility to diseases and death. Extensive research has been done to understand the role of gut microbiota in aging, however, limited progress has been made. Thus, considering the need of the hour we have tried to give a new perspective to this body of research by delving deep into all major factors that are associated with gut microbiome and aging. This review presents a holistic view of the relation between gut microbiome and aging starting from hallmarks of aging and evolution of gut microbiome over lifespan to intricate mechanisms like inflammaging, immunosenescence, gut-brain axis, mitochondrial dysfunction, nutrient imbalance and cardiac implications. In addition, it highlights different therapies like fecal microbiota transplantation, omics and metabolomics studies, and gut modulation therapies that show a promising future towards regulation of gut microbiota for aging interventions. More importantly, this review is an addition to the existing literature which advocates gut microbiome as an additional hallmark of aging, summarising the known status of the research in this field, contributing to developing gut microbiota targeted healthy aging.}, }
@article {pmid42166232, year = {2026}, author = {Rettschlag, S and Barrantes, I and Hahn, A and Bull, J and Raschke, U and Mlynski, R and Kreikemeyer, B and Warnke, P and Skusa, R}, title = {Microbiome of the Eustachian tube in patients with chronic obstructive Eustachian tube dysfunction and healthy individuals.}, journal = {European journal of microbiology &amp; immunology}, volume = {}, number = {}, pages = {}, doi = {10.1556/1886.2026.00015}, pmid = {42166232}, issn = {2062-509X}, abstract = {OBJECTIVE: The Eustachian tube (ET) is essential for middle ear ventilation. Chronic obstructive ET dysfunction may lead to chronic otitis media and cholesteatoma, but its pathophysiology remains unclear. Commensal bacterial colonization of the ET has not previously been studied in healthy individuals or affected patients.<br><br>STUDY DESIGN AND PATIENTS: Prospective cohort study was conducted at a tertiary academic referral center including 13 patients with chronic obstructive ET dysfunction and 37&#xa0;controls. Between 2017 and 2020, intraoperative tissue samples and swabs were collected using a&#xa0;contamination-minimized Yankauer suction technique. Samples underwent conventional culture&#xa0;diagnostics, microbiome analysis via 16S rDNA sequencing, and histopathological examination.<br><br>RESULTS: Culture identified 552 bacterial strains, with greater diversity in controls (34 genera) than in patients (19&#xa0;genera). Microbiome analysis confirmed a larger core microbiome in controls. Rothia was more abundant in patients, whereas Veillonella predominated in controls. Genera such as Rothia and Gemella may be linked to microbial alterations in chronic ET dysfunction.<br><br>CONCLUSION: This first combined culture-based and molecular analysis using a novel sampling-technique demonstrated reduced bacterial diversity in chronic ET dysfunction patients, resembling patterns seen in other chronic respiratory morbidities. Future studies should incorporate complementary sampling approaches&#xa0;and cutting-edge sequencing technologies, additionally assessing viral etiologies.}, }
@article {pmid42166336, year = {2026}, author = {Lv, C and Xia, Q and Yan, S}, title = {Symbiont-mediated mechanisms of insecticide resistance in insects.}, journal = {Journal of insect science (Online)}, volume = {26}, number = {3}, pages = {}, pmid = {42166336}, issn = {1536-2442}, mesh = {Animals ; *Insecticide Resistance/genetics ; *Symbiosis ; *Insecta/microbiology/genetics/drug effects ; *Insecticides/pharmacology ; }, abstract = {Insecticide resistance threatens sustainable agricultural intensification worldwide. Once regarded solely as a host-encoded evolutionary response, resistance is now known to be strongly influenced by microbial symbionts. Here, we synthesize recent advances showing that vertically and horizontally transmitted bacteria, fungi, and viruses modulate insect-toxicant interactions through 3 intertwined mechanisms: (i) direct enzymatic degradation of the active ingredient inside the gut lumen or hemocoel, (ii) transcriptional or posttranscriptional up-regulation of host detoxification gene networks (cytochrome P450s, carboxylesterases, and glutathione S-transferases), and (iii) epigenetic or immune-mediated priming that accelerates metabolic clearance while dampening insecticide-induced oxidative stress. Symbiont-mediated shifts in toxicity thresholds are context-dependent, varying with host genotype, symbiont strain, insecticide chemistry, and route of exposure. Symbionts may synergize with classical resistance mutations to produce super-resistant phenotypes, or conversely sensitize insects through pro-toxicant bioactivation. We propose an integrative "symbiont-insecticide-host" triangulation framework combining gnotobiotic manipulation, spatial metabolomics, and CRISPR-based microbial genetics to identify causal loci. Microbiome engineering through symbiont replacement, phage therapy or engineered plasmids offers a green resistance-management tool that lowers selection pressure on synthetic chemistries while preserving biocontrol compatibility. Clarifying these microbe-centered pathways is essential for predicting resistance trajectories and for designing durable, next-generation pest-control strategies aligned with food-security and environmental-quality goals.}, }
@article {pmid42166504, year = {2026}, author = {Seo, SH and Lee, JW and Oh, S and Hong, JS and Lee, BS and Kwon, SJ and Kim, KS and Park, JS and Heo, JS and Ahn, KH and Lee, HJ and Park, KU}, title = {Machine learning reveals microbiome differences by periodontitis severity.}, journal = {PloS one}, volume = {21}, number = {5}, pages = {e0349686}, pmid = {42166504}, issn = {1932-6203}, mesh = {Humans ; *Machine Learning ; *Periodontitis/microbiology/pathology ; *Microbiota/genetics ; Male ; Female ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Adult ; Severity of Illness Index ; Dysbiosis/microbiology ; Aged ; }, abstract = {Periodontitis is a chronic inflammatory disease driven by microbial dysbiosis, yet the microbial signatures associated with severity remain incompletely understood. This study investigated changes in subgingival microbial composition across clinically defined severity groups and evaluated the performance of microbiome-based machine-learning models for classifying periodontitis severity. Subgingival plaque samples from 84 patients were analyzed using 16S rRNA gene sequencing. Microbial diversity showed a modest decreasing trend with increasing severity, although differences were not statistically significant. Five machine learning models were applied to classify periodontitis. Random Forest and XGBoost achieved AUC values of 0.98, indicating statistically significant classification performance (p < 0.05) after feature selection. Validation using three external cohorts demonstrated substantial performance variability across populations, reflecting differences in oral microbiome composition, sample type, and periodontal status definitions. Feature importance analysis identified Fusobacterium, Campylobacter, Stomatobaculum, Leptotrichia and Segatella as key contributors to periodontitis severity classification, consistent with their established roles in periodontal dysbiosis. These findings highlight the potential of microbiome-based models for classifying periodontitis severity while underscoring the need to incorporate diverse populations and robust feature-selection strategies to enhance generalizability.}, }
@article {pmid42163620, year = {2026}, author = {Lu, D and Lu, J and Yang, P and Lou, L and Li, W and Zhou, Y}, title = {Microbiome and Lipidomics Reveal the Mechanism of Eight Zhes Decoction on MAFLD.}, journal = {Combinatorial chemistry &amp; high throughput screening}, volume = {}, number = {}, pages = {}, doi = {10.2174/0113862073460107260407065758}, pmid = {42163620}, issn = {1875-5402}, abstract = {INTRODUCTION: The therapeutic potential of Eight Zhes Decoction (EZD) against metabolic dysfunction-associated fatty liver disease (MAFLD) is well-recognized; however, the underlying biological pathways are not well understood. To address this gap, an integrated investigation using both lipidomics and metagenomics was conducted to reveal the mechanistic rationale behind the effects of EZD.<br><br>METHODS: A MAFLD mouse model was established using a Methionine-Choline-Deficient (MCD) diet combined with CCl&#x2081;. The mice were treated with EZD for four weeks. Hepatic injury was assessed via H&amp;E, Oil Red O, and Masson staining. Untargeted hepatic lipidomics and shotgun metagenomics were employed to profile lipid species and the gut microbiota composition, respectively.<br><br>RESULTS: Histopathological analysis confirmed that EZD significantly alleviated hepatic steatosis, ballooning degeneration, and fibrosis. Lipidomics identified 277 differential lipids; EZD treatment notably downregulated 24 TGs and modulated pathways related to arachidonic acid metabolism and bile secretion. Metagenomics revealed that EZD reshaped the gut microbiota, significantly increasing the abundance of Alistipes sp. while reducing the abundance of Faecalibaculum rodentium.<br><br>DISCUSSION: Correlation analysis demonstrated that the restored Alistipes sp. was negatively correlated with multiple hepatic TGs, whereas Faecalibaculum rodentium was positively correlated with lipid accumulation.<br><br>CONCLUSION: EZD mitigates MAFLD in mice by synergistically regulating hepatic lipid metabolism and gut microbiota. Specifically, the therapeutic effect involves restoring Alistipes sp. and modulating the gut-liver axis, providing experimental evidence for the clinical application of EZD.}, }
@article {pmid42163680, year = {2026}, author = {Yan, Q and Liu, Y and Liu, X and Zhou, S and Zhang, Y}, title = {From the Gut to the Mind: Elucidating the Microbiome-chronobiology Axis in the Context of Depressive Illness.}, journal = {Current neuropharmacology}, volume = {}, number = {}, pages = {}, doi = {10.2174/011570159X433342260331161438}, pmid = {42163680}, issn = {1875-6190}, abstract = {INTRODUCTION: Depression is a highly prevalent mood disorder and is often comorbid with gastrointestinal dysfunction and circadian disturbances. Many studies suggest that gut microbiota (GM) dysbiosis and circadian rhythm disruption may contribute to depressive pathophysiology; however, the mechanistic interactions between these systems remain incompletely defined. Deciphering these interactions may provide insights into prospective therapeutic targets or biomarkers for depression, although further mechanistic studies are needed to validate these findings.<br><br>METHODS: The PubMed, Web of Science, Embase, and the Cochrane Library for articles published between January 2000 and December 2024 served as the basis of this review for analyzing, which covers original research, meta-analyses, high-impact reviews published in English, and excluding conference abstracts, case reports, and studies focusing solely on animal models without potential translational implications. After independently screening all retrieved articles and resolving discrepancies, a narrative synthesis approach was adopted to integrate data on mechanistic pathways, clinical associations, and translational potential.<br><br>RESULTS: In this review, we focused on the dynamic interaction network between the GM and circadian rhythms, considering a new pathway by which they participate in the occurrence and development of depressive symptoms through bidirectional regulation: significant abnormalities in the GM structure of depressed patients are specifically associated with disruption of the circadian rhythm, and this association is dysbiosis-misalignment.<br><br>DISCUSSION: Deciphering the molecular mechanisms of the regulatory loop may provide valuable information that can help screen specific therapeutic targets and biomarkers for depression, which may promote the transformation of depression diagnosis and treatment models from symptomatic treatment to precision-targeted intervention.<br><br>CONCLUSION: Studies have confirmed dysbiosis-misalignment between the GM and circadian rhythms: dysbiosis can reshape the regulatory system underlying circadian rhythm, and disruption of the circadian rhythm in turn exacerbates dysbiosis. This interaction imbalance may drive the pathophysiological processes of depression. In this review, we highlighted that a comprehensive assessment of the interaction mechanism of the microbiome-chronobiology axis may help overcome the current bottleneck in treating depression and may provide a theoretical basis for developing novel intervention strategies with both timeliness and targeting.}, }
@article {pmid42163696, year = {2026}, author = {Seneff, S and Nigh, G and Kyriakopoulos, AM}, title = {Melatonin in Health and Disease and its Metabolism by the Gut Microbes: Implications for Deuterium Homeostasis?.}, journal = {Current medicinal chemistry}, volume = {}, number = {}, pages = {}, doi = {10.2174/0109298673468554260508041733}, pmid = {42163696}, issn = {1875-533X}, abstract = {Deuterium (2H), a heavy isotope of protium (1H), is a naturally occurring element with a significant impact on human metabolism. Despite its natural presence, deuterium can impair mitochondrial function by damaging ATPase pumps; consequently, biological organisms have evolved sophisticated strategies to mitigate the risks of deuterium overload and protect mitochondrial integrity. Multiple enzymes have evolved to prefer hydrogen over deuterium in their reactions to protect these pumps. One class of enzymes is the cytochrome P450 (CYP) enzymes, which oxidize many substrates, mainly in the Endoplasmic Reticulum (ER), often producing water as a by-product. Furthermore, hydrogen peroxide (H2O2), produced in the ER by ERO1, can travel via the cytoplasm to the mitochondria, where it is reduced to two molecules of water via glutathione peroxidase. Melatonin is an ancient antioxidant molecule that first appeared in photosynthetic bacteria billions of years ago to protect against oxygen produced by respiration. In this paper, we present a hypothesis that melatonin metabolism in the gut provides deuterium- depleted protons to the enterocyte mitochondria. Few are aware that melatonin, known mainly as the hormone produced by the pineal gland to regulate circadian rhythms, is produced in the gut at 400 times the amount produced by the pineal gland. In the gut lining, melatonin is synthesized from N-acetylserotonin through the addition of a methyl group from S-adenosylmethionine. This methyl group, which we argue is severely deuterium-depleted due to its gut microbial source, is then fully metabolized by CYP2C19 in the ER of enterocytes in the small intestine, producing four molecules of water, which we argue would also be depleted in deuterium. Melatonin is recycled from the gut to the liver multiple times via the bile acids, and it is repeatedly converted back to N-acetylserotonin and regenerated, each time producing four water molecules derived from its methyl group. Butyrate, another nutrient supplied by gut microbes, stimulates the synthesis of serotonin and melatonin from tryptophan in the gut. Melatonin is a powerful antioxidant in mitochondria and promotes a healthy microbiome. Melatonin deficiency is associated with the severity of long COVID, and melatonin supplementation can help minimize side effects.}, }
@article {pmid42163722, year = {2026}, author = {Hackmann, TJ and Parris, JP and Seshadri, R and Lingga, C}, title = {Microbe Decoder uncovers functional traits of microbes in microbiome datasets.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkag515}, pmid = {42163722}, issn = {1362-4962}, support = {2018-67015-27495//National Institute of Food and Agriculture/ ; 1019985//National Institute of Food and Agriculture/ ; //University of California, Davis Small Grant in Aid of Research/ ; }, abstract = {Microbe Decoder is a web server that predicts functional traits of microbes in microbiome sequencing datasets. Sequencing has revealed thousands of organisms in most ecosystems, but the functional traits of many organisms remain unclear. Existing tools can predict names of organisms or their genes, but they rarely predict concrete biological functions (e.g. fermentation or anaerobic growth). Microbe Decoder fills this gap using three complementary tools relying on taxonomy, metabolic networks, or machine learning. These tools accept either names or gene functions as inputs and are integrated into an easy-to-use web app. When tested against data for microbial isolates, Microbe Decoder showed good predictive performance (e.g. balanced accuracy of 0.85). When applied to datasets from the gut, sediment, and sea, it predicted shifts in functional traits over space and time. Microbe Decoder is designed for use with prokaryotes, with the goal of including eukaryotes in the future. By revealing functional traits of microbes in biological systems, Microbe Decoder will advance biology, medicine, and environmental science. Microbe Decoder is available at https://www.microbe-decoder.org/.}, }
@article {pmid42163806, year = {2026}, author = {Devi, S and Debnath, N and Yadav, P and Satyavolu, S and Yadav, AK and Tyagi, N}, title = {Dynamic Modulation of the Gut Microbiome in Neurodegenerative Diseases: Mechanisms, Therapeutic Potential, and Clinical Perspective.}, journal = {Comprehensive Physiology}, volume = {16}, number = {3}, pages = {e70165}, doi = {10.1002/cph4.70165}, pmid = {42163806}, issn = {2040-4603}, support = {TPA-971566//American Heart Association/ ; 24TPA1304527//American Heart Association/ ; 25TPA1481771//American Heart Association/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Neurodegenerative Diseases/microbiology/metabolism/therapy ; Animals ; Brain-Gut Axis/physiology ; Brain/metabolism ; }, abstract = {The gut and brain communicate bidirectionally through the gut microbiota, forming a complex network often referred to as the "microbiota-gut-brain axis." The gastrointestinal microbiome produces various metabolites, including short-chain fatty acids (SCFAs), tryptophan-derived compounds, and secondary bile acids. Research indicates that disruptions in the intestinal microbiota (dysbiosis) and impaired gut-brain axis are associated with various neurological conditions. The central nervous system (CNS) influences digestive processes via the hypothalamic-pituitary-adrenal (HPA) axis and autonomic nervous system (ANS). On the other hand, the gut reciprocally affects brain function through microbial metabolites, neuroactive substances, and intestinal hormones via multiple pathways, including neural (vagal), immune, and endocrine signaling; however, only a subset of metabolites can directly access the CNS due to blood-brain barrier (BBB) selectivity. These microbial metabolites can directly or indirectly influence the CNS and modulate neuro-immune signaling by activating receptors, such as the aryl hydrocarbon receptor (AhR) and G protein-coupled receptors (GPCRs). By acting as ligands for these receptors, metabolites modulate neural signaling and exert neuroprotective effects. This review discusses how probiotic-derived metabolites modulate the gut-brain axis and provide neuroprotective effects, focusing on the receptors they activate and their downstream signaling pathways involved in neuroprotection.}, }
@article {pmid42164043, year = {2026}, author = {Ng, MK and Jacofsky, D and Barsoum, W and Mont, MA}, title = {Calcium montmorillonite clay: a clinically oriented narrative review of emerging perioperative and supportive applications.}, journal = {Annals of translational medicine}, volume = {14}, number = {2}, pages = {18}, pmid = {42164043}, issn = {2305-5839}, abstract = {Calcium montmorillonite (CMM) clay, a naturally occurring mineral-rich volcanic clay has garnered scientific attention for its detoxification properties, gastrointestinal (GI) support, skin benefits, and potential metabolic modulation. Recent advances in pharmaceutical-grade formulation and mechanistic understanding have renewed clinical interest in CMM as a low-risk, non-systemic adjunct in modern medical practice. General practitioners and surgeons may find it particularly useful as a safe adjunct in gut health, topical recovery, and inflammatory modulation. With supporting data from preclinical and clinical research, including studies on aflatoxin binding, microbiome modulation, and treatment of radiation enteritis and pediatric diarrhea, CMM represents a promising natural therapeutic mineral for integration into modern health protocols. This narrative review summarizes the biological properties, clinical safety, indications, and emerging efficacy data surrounding CMM, with a focus on potential perioperative and wellness applications.}, }
@article {pmid42164238, year = {2026}, author = {Garrido-Martín, EM and Kontic, M and Rooney, C and Mansouri, N}, title = {Immune checkpoints in lung cancer.}, journal = {Breathe (Sheffield, England)}, volume = {22}, number = {2}, pages = {250244}, pmid = {42164238}, issn = {1810-6838}, abstract = {The advent of immune checkpoint inhibitors (ICIs) has revolutionised the management of lung cancer, transforming it from a historically immune-resistant malignancy into a paradigm for durable immunotherapy response. This review provides a comprehensive overview of the biological and clinical foundations of checkpoint regulation in the lung and their implications for patient care. We first explore the unique pulmonary immune environment, where continuous exposure to environmental antigens necessitates a delicate balance between tolerance and defence. Within this context, immune checkpoints, such as programmed cell death protein 1 (PD-1) and its ligand PD-L1 as well as cytotoxic T-lymphocyte-associated protein 4, maintain physiological self-tolerance but can be subverted by tumour cells to evade immune surveillance. Emerging inhibitory receptors, including LAG-3, TIGIT and TIM-3, contribute additional layers of immune regulation and resistance, highlighting opportunities for combinatorial therapeutic strategies. The clinical section summarises pivotal trials establishing ICIs as the standard of care across metastatic, locally advanced and early-stage lung cancer. These agents now span the full disease continuum, from neoadjuvant and adjuvant to perioperative and consolidation settings. We also address the management of immune-related adverse events and the need for precision in patient selection through biomarkers, such as PD-L1 expression, tumour mutational burden and circulating immune signatures. Finally, we discuss ongoing challenges, including mechanisms of primary and acquired resistance, and emerging approaches integrating spatial multi-omics, dynamic immune monitoring and microbiome profiling. Together, these advances are reshaping lung cancer immunotherapy towards a more precise, adaptive and durable model of care.}, }
@article {pmid42164255, year = {2026}, author = {Ma, D and Xu, Y and Liang, R and Meng, Q and Liu, Y and Hu, D and Zhu, B and Zheng, Y and Luo, Q}, title = {Chlorogenic acid modulates gut microbiota and metabolites to alleviate intrahepatic cholestasis of pregnancy: Insights from 16S rRNA sequencing and metabolomics.}, journal = {Biochemistry and biophysics reports}, volume = {46}, number = {}, pages = {102619}, pmid = {42164255}, issn = {2405-5808}, abstract = {Intrahepatic cholestasis of pregnancy (ICP) is a liver disorder marked by impaired bile flow, elevated serum bile acids, and pruritus, posing significant risks to maternal and fetal health. Current treatments, including ursodeoxycholic acid, have shown limited efficacy, underscoring the need for more effective therapies. Chlorogenic acid (CGA), a polyphenolic compound with antioxidant, anti-inflammatory, and hepatoprotective properties, has shown promise in managing liver diseases, but its role in ICP remains poorly understood. This study investigated the therapeutic effects of CGA in a rat model of ICP induced by 17α-ethinylestradiol. CGA treatment significantly reduced liver enzyme levels, total bile acids, and bilirubin, while improving histopathological liver damage. CGA also modulated key proteins involved in bile acid synthesis and transport, including FXR, CYP7A1, NTCP, and BSEP. Additionally, CGA treatment improved intestinal barrier function by upregulating tight junction proteins, including ZO-1. Metabolomics and 16S rRNA gene sequencing revealed that CGA treatment restored gut microbiota balance in ICP rats. CGA demonstrated a dose-dependent response, with higher doses providing more pronounced therapeutic effects. These findings suggest that CGA alleviates ICP by regulating bile acid metabolism, improving liver function, and modulating the gut microbiome, highlighting its potential as an effective therapeutic option for managing ICP.}, }
@article {pmid42164260, year = {2026}, author = {Shi, H and Jiang, L and Cai, Y and Chen, Z and Hu, Y and Zhou, Y and Li, J and Zhang, D and Cao, Z and Wang, S}, title = {Regulatory Effects of a Lipid-Lowering Strain Lactobacillus plantarum 58 Isolated From Dregs Vinegar on Metabolism-Related Gene Expression, Gut Microbiota, and Metabolic Biomarkers of Hybrid Grouper Under High-Fat Diets.}, journal = {Aquaculture nutrition}, volume = {2026}, number = {}, pages = {4888310}, pmid = {42164260}, issn = {1365-2095}, abstract = {Lactobacillus plantarum 58 (lactic acid bacteria [LAB] 58), isolated from vinegar dregs, was incorporated at 1 × 10[8] CFU/g diet into the feeds of hybrid groupers to assess its lipid-lowering efficacy under normal (7.52 % lipid) or high-fat (14.83 % lipid) regimens. A 2 × 2 factorial design generated four diets: C (normal), H (high-fat), C58 (normal + LAB 58), and H58 (high-fat + LAB 58). Serum biochemical parameters tests, histological section, and Oil Red O staining results indicated that in both LAB 58-supplemented groups (C58 and H58), serum triglycerides and total cholesterol (T-CHO) declined regardless of basal lipid content, and hepatic fat vacuolation and lipid-droplet accumulation were markedly curtailed. The qPCR data revealed that LAB 58 elevated the levels of hepatic lipolysis genes (adipose triglyceride lipase [ATGL], carnitine palmitoyltransferase 1 [CPT-1], farnesoid X receptor [FXR], and lipoprotein lipase [LPL]) while simultaneously suppressing lipid synthesis gene expressions (fatty acid synthase [FAS] and stearoyl-CoA desaturase 1 [SCD-1]) in the H58 group compared with the H group. Gut-microbiota profiling showed a pronounced Firmicutes-to-Bacteroidetes shift, driven by increased Bacteroides, Faecalibacterium, and Lachnospiraceae-UCG-004; the relative abundance of Lactobacillus spp. surged, especially in the H58 group. Metabolomic analysis of intestinal contents further disclosed elevated levels of beneficial fatty acids-linoleic and α-linolenic acids in H58 group. In conclusion, these findings demonstrate that LAB 58 alleviates lipid metabolic disorders by modulating hepatic gene expression, restructuring the gut microbiota, and enhancing beneficial metabolites.}, }
@article {pmid42164266, year = {2026}, author = {Lin, SH and Lin, RJ and Chang, RY and Huang, YF and Hsu, YY and Chu, CL and Chen, YL and Lin, CY and Fu, SC}, title = {Heterogeneity in the association between gut microbiota and insomnia moderated by Parkinson's disease status.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1691665}, pmid = {42164266}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Parkinson Disease/complications/microbiology ; *Sleep Initiation and Maintenance Disorders/microbiology/etiology/complications ; Male ; RNA, Ribosomal, 16S/genetics ; Female ; Aged ; Middle Aged ; *Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; DNA, Bacterial/genetics/chemistry ; }, abstract = {INTRODUCTION: Parkinson's disease (PD) is frequently accompanied by insomnia, and emerging evidence suggests the gut microbiome may play a role. This study investigates gut microbiome differences associated with insomnia in PD patients compared to non-PD individuals.<br><br>METHODS: We analyzed 310 participants (185 PD patients, 125 controls) categorized by insomnia status. Gut microbiome profiles were obtained using 16S rRNA sequencing and processed with DADA2 using the SILVA database for taxonomic assignment. Alpha and beta diversity analyses and differential abundance analysis were conducted, and functional prediction was performed using PICRUSt2, adjusting for relevant confounders.<br><br>RESULTS: Insomnia was linked to higher alpha diversity in non-PD individuals but lower alpha diversity in PD patients. Interaction analysis confirmed distinct associations between insomnia and microbial diversity in the two groups. Differential abundance analysis identified unique insomnia-associated bacterial genera, with differing insomnia-risk-reducing and insomnia-risk-increasing taxa. Functional analysis showed six enriched pathways in controls but only two in PD patients, with no overlap.<br><br>DISCUSSION: These findings suggest that insomnia in PD is associated with distinct gut microbiome profiles compared with non-PD individuals. The results highlight the importance of considering disease context when examining microbiome-sleep relationships and may inform future research on microbiome-based approaches for sleep disturbances in PD.}, }
@article {pmid42164272, year = {2026}, author = {Yaghi, M and Gonzalez, T and Vecin, N and Pastar, I and Lev-Tov, H}, title = {A bioelectric dressing improves postderoofing outcomes in hidradenitis suppurativa by microbiome modulation: A split-body, randomized clinical trial.}, journal = {JID innovations : skin science from molecules to population health}, volume = {6}, number = {4}, pages = {100461}, pmid = {42164272}, issn = {2667-0267}, abstract = {UNLABELLED: Hidradenitis suppurativa tunnels represent treatment-resistant disease compartment that perpetuates inflammation, microbial dysbiosis, and relapse. Surgical deroofing remains the standard intervention, yet optimal postoperative wound management strategies are lacking.<br><br>OBJECTIVES: We aimed to evaluate the efficacy of a wireless bioelectric wound dressing compared with that of standard of care in modulating tunnel-associated microbiota and preventing surgical site recurrence after hidradenitis suppurativa deroofing.<br><br>METHODS: In this randomized, single-center, split-body trial, patients with bilateral Hurley stages II-III axillary disease underwent tunnel deroofing, with 1 side randomized to bioelectric wound dressing or standard of care (petrolatum and gauze dressing). Subjects (n = 12) were followed for 8 weeks to assess primary outcomes: healing rates. Secondary outcomes included disease recurrence at week 8, change in bacterial load, microbiome composition, and QOL.<br><br>RESULTS: Bioelectric wound dressing-treated sites showed a significant reduction in bacterial load at weeks 2 and 4 after excision, with enrichment of commensals and a shift away from anaerobic taxa, which were not observed in standard of care-treated sites. Minimal recurrences were observed on bioelectric wound dressing-treated sides alone compared with multiple recurrences on standard of care-treated sites, with trends of improved healing trajectories.<br><br>CONCLUSIONS: Optimized wound care holds a potential to reduce surgical site recurrence and reverse hidradenitis suppurativa dysbiosis. Our data emphasize the importance of postsurgical care to improve outcomes in patients with hidradenitis suppurativa. This trial was registered at ClinicalTrials.gov with NCT05057429. Study registration was submitted on September 15, 2021.}, }
@article {pmid42164318, year = {2026}, author = {Aizpurua, O and Brenner, E and Martin-Bideguren, G and Garin-Barrio, I and Cabido, C and Alberdi, A}, title = {Beyond the core microbiome: endemic bacteria drive functional and microdiversity differences across salamander populations.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag106}, pmid = {42164318}, issn = {2730-6151}, abstract = {Population-specific variation in animal microbiomes is well documented, yet the functional consequences and underlying mechanisms remain poorly understood. To address this, we conducted genome-resolved metagenomic analyses on gut and skin microbiomes from four populations of Pyrenean brook salamanders (Calotriton asper) inhabiting two distinct environments: Pyrenean subalpine brooks and Atlantic montane streams. From paired faecal and skin swab samples, we reconstructed 539 and 43 metagenome-assembled genomes, respectively, and examined taxonomic composition, metabolic capacity, and microdiversity across environments. Although alpha diversity remained similar across environments, both gut and skin microbiomes exhibited significant differences in community composition and functional potential between environments. Partitioning the gut microbiome into core, endemic, and marginal fractions revealed a dominant core community-shared across environments and accounting for over 85% of reads-that did not drive functional divergence. Instead, functional differences were primarily shaped by low-abundance, population-specific endemic bacteria. Atlantic salamanders hosted endemic taxa with significantly greater metabolic potential and higher strain-level microdiversity than those at the Pyrenees. These patterns were not associated with broad-scale dietary differences and may reflect environmental influences such as temperature and nutrient availability. Our findings highlight the relevance of rare, endemic bacteria in driving microbiome function and underscore the power of genome-resolved metagenomics to uncover functional and evolutionary dynamics in wild host-microbe systems.}, }
@article {pmid42164491, year = {2026}, author = {Green, M and Cleary, S and Kwiecien-Delaney, B and Foster, JA}, title = {Compositional maturation of the microbiome and adaptive immunity in the postnatal period.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1772425}, pmid = {42164491}, issn = {1664-3224}, mesh = {Animals ; *Adaptive Immunity ; *Gastrointestinal Microbiome/immunology ; Mice ; Mice, Inbred C57BL ; T-Lymphocyte Subsets/immunology ; T-Lymphocytes/immunology ; }, abstract = {INTRODUCTION: Recent research has highlighted the role of the gut microbiome in shaping the development and function of the mammalian immune system. Interactions between these complex networks of microbes and host cells serve not only to train major aspects of adaptive and innate immunity but also to establish commensal host-microbe relationships and symbiosis throughout the lifespan. T-cells are a critical aspect of this paradigm, acting as intermediates between the microbiome and many aspects of host health and disease. Despite a large body of literature examining these interactions, we have yet to completely understand how the ontogeny of these systems co-evolves across the lifespan and how the emergence of specific T-cell-microbe signals relates to key developmental milestones.<br><br>METHODS: To answer this question, this work conducted a compositional integrative analysis on deep immune and microbiome profiling of wild-type C57Bl/6 mice across the first two weeks of life, post-weaning, and young adulthood.<br><br>RESULTS: The results show that T-cell ontogeny follows different developmental trends in mucosal and peripheral immune compartments and that temporal trends in microbial community abundance creates a modular network of associations between specific taxa and functional T-cell subsets.<br><br>DISCUSSION: These results provide insight into the longitudinal development of microbiota-immune system interactions throughout the lifespan, as well as the mechanistic relevance of microbiota-derived signals at key developmental milestones.}, }
@article {pmid42164500, year = {2026}, author = {Mao, Q and Lin, B and Xia, W and Zhang, Y and Lei, Y and Cao, Q and Xu, M}, title = {Melatonin-induced restoration of the intestinal mucosal barrier in inflammatory bowel disease via activation of the SIRT1-LKB1-pAMPK axis.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1811583}, pmid = {42164500}, issn = {1664-3224}, mesh = {Animals ; *Sirtuin 1/metabolism ; *Melatonin/pharmacology/metabolism ; *Intestinal Mucosa/drug effects/metabolism/pathology/microbiology ; *AMP-Activated Protein Kinases/metabolism ; Mice ; *Inflammatory Bowel Diseases/metabolism/drug therapy/pathology ; Humans ; Male ; AMP-Activated Protein Kinase Kinases ; *Protein Serine-Threonine Kinases/metabolism ; Disease Models, Animal ; Signal Transduction/drug effects ; Gastrointestinal Microbiome/drug effects ; Female ; Mice, Inbred C57BL ; Colitis ; }, abstract = {BACKGROUND: Numerous studies indicated inflammatory bowel disease (IBD) patients suffered from sleep disturbances. Although melatonin (MT) exerts positive effects on maintaining circadian rhythms and anti-inflammation, its impact on the gut microbiome and its function in mediating gut health remain largely unexplored. To evaluate the efficacy and investigate the mechanisms of MT in repairing the intestinal mucosal barrier in IBD.<br><br>METHODS: Fecal MT and its metabolites in IBD patients were detected. A DSS-induced colitis mice model and a LPS-stimulated NCM460 cell inflammation model were used to explore the mechanism of melatonin in IBD.<br><br>RESULTS: IBD patients had lower levels of serum MT and fecal 2-oxomelatonin. Furthermore, MT enhances intestinal antimicrobial peptides and effectively alleviates colitis. Mechanistically, MT restored the abundance of the probiotic Akkermansia and decreased the conditional pathogen Desulfovibrio. MT upregulates the SIRT1 (Sirtuin 1) and pAMPK (phosphorylated AMP-Activated Protein Kinase) in mouse colonic tissues. Whereas Ex-527 (the SIRT1 inhibitor) and Compound C (the pAMPK inhibitor) abolished the protective effects of MT in DSS mice. In LPS-stimulated cells, the inhibitor blocked the regulation of MT on proinflammatory factors, antimicrobial peptides and tight junctions. Mechanistically, MT was associated with activation of the SIRT1-LKB1-pAMPK pathway, suggesting its potential involvement in regulating the above changes.<br><br>CONCLUSION: Our findings suggest that MT may ameliorate colitis by regulating gut microbiota, modulating antimicrobial peptide secretion, and reinforcing intestinal epithelial barrier integrity potentially via activation of the SIRT1-LKB1-pAMPK axis.}, }
@article {pmid42164501, year = {2026}, author = {Yu, J and Li, Q and Zou, S and Rong, Y and Zhang, Y and Chen, C}, title = {Antibiotic use and immune-related adverse events in patients treated with immune checkpoint inhibitors: analysis of the FAERS database.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1733373}, pmid = {42164501}, issn = {1664-3224}, mesh = {Humans ; *Immune Checkpoint Inhibitors/adverse effects/therapeutic use ; *Anti-Bacterial Agents/adverse effects/therapeutic use ; Male ; Female ; Middle Aged ; Aged ; Databases, Factual ; *Neoplasms/drug therapy/immunology ; *Drug-Related Side Effects and Adverse Reactions/etiology/epidemiology ; Gastrointestinal Microbiome/drug effects ; Aged, 80 and over ; Adult ; Adverse Drug Reaction Reporting Systems ; Risk Factors ; }, abstract = {BACKGROUND: The use of antibiotics may influence the efficacy and toxicity of immune checkpoint inhibitors (ICIs) by altering the gut microbiota. However, current evidence on the link between antibiotic use and immune-related adverse events (irAEs) is limited. This study aims to evaluate whether antibiotics increase the risk of irAEs in ICI-treated patients and to examine their relationship to the timing of irAEs onset.<br><br>METHODS: We analyzed data from the FAERS database from 2014 to the fourth quarter of 2024. Using multivariable logistic regression and descriptive statistical analyses, we evaluated the association between antibiotic co-reporting and irAE reporting frequency and the timing across different antibiotic categories and ICIs regimens.<br><br>RESULTS: Our study included 155,157 patients treated with ICIs, of whom 9,518 (6.1%) received antibiotic therapy. Patients who used antibiotics had a significantly higher reported frequency risk of irAEs (OR&#xa0;=&#xa0;1.17; 95%CI: 1.12-1.23; FDR<0.001) compared to those who did not. The strongest associations were observed in patients receiving fluoroquinolones, sulfonamides, penicillin, macrolides, cephalosporins, and monobactams. Co-reporting was associated with a higher reported frequency of irAEs in patients receiving PD-L1 inhibitors (OR&#xa0;=&#xa0;1.51; 95% CI: 1.39-1.65; FDR<0.001). In exploratory descriptive analysis restricted to patients who reported irAEs, the median time to first reported irAE was shorter in the antibiotic co-reporting group than in the non-co-reporting group (31 days (IQR: 9-105) vs. 42 days (IQR: 14-122), Wilcoxon rank-sum test P < 0.001). Stratified analysis by ICI type showed that this pattern was most evident in patients receiving PD-1 inhibitors.<br><br>CONCLUSIONS: Analysis of the FAERS database suggests that antibiotic co-reporting during ICIs therapy is associated with a higher reported frequency of irAEs and a shorter median time to first reported irAE among patients who experienced irAEs. These findings are subject to the inherent limitations of the FAERS database, including the inability to determine the temporal sequence of antibiotic and ICI exposure, unmeasured confounding, reporting artifacts, and the unsuitability of spontaneous reporting data for formal time-to-event analysis. Prospective cohort studies with detailed medication timing, clinical phenotyping, and microbiome profiling are needed to validate these signals.}, }
@article {pmid42164510, year = {2026}, author = {Yin, X and Peng, H and Li, Y and Song, Y and Yao, N and Shen, Z and Chen, H and Huang, L and Li, P and He, Z and Chen, Q}, title = {Ankylosing spondylitis and the gut microbiome: future research hotspots and trends.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1784757}, pmid = {42164510}, issn = {1664-3224}, mesh = {*Spondylitis, Ankylosing/microbiology/immunology/etiology ; Humans ; *Gastrointestinal Microbiome/immunology ; Bibliometrics ; *Biomedical Research/trends ; }, abstract = {BACKGROUND: Ankylosing spondylitis (AS) is an autoimmune disease. Its exact cause remains unclear. It is generally believed to result from a combination of genetic and environmental factors, as well as immune disorders. However, growing evidence suggests that the gut microbiota plays a key role in the pathogenesis of AS. Therefore, this study aims to systematically analyze the current state of research on AS and the gut microbiome. It also explores future research hotspots.<br><br>METHODS: We searched the Web of Science Core Collection (WoSCC) and PubMed databases, including relevant literature on AS and the gut microbiome published up to January 1, 2026. We then performed a visualized bibliometric analysis using CiteSpace, VOSviewer, and Bibliometrix software.<br><br>RESULTS: The WoSCC dataset included 165 articles. Both the annual publication volume and citation counts showed an upward trend. Brown, Ma, and Liu B were the most productive authors. Regarding country output, China ranked first with 60 articles, followed by the USA with 36. Major contributing institutions were also primarily located in China and the USA. Current research hotspots focus on inflammation, Mendelian randomization, HLA-B27, probiotics, and short-chain fatty acids. A validation analysis using the PubMed database (115 articles) yielded results consistent with the WoSCC findings.<br><br>CONCLUSION: Our study provides key insights into the relationship between the gut microbiota and AS. It clarifies current research hotspots and development trends. Future researchers should conduct prospective studies to confirm causality and combine multi-omics analysis to reveal underlying molecular mechanisms.}, }
@article {pmid42164524, year = {2026}, author = {Hu, S and He, C and Sun, K and Zhou, H and Liu, X and Wang, H and Li, S and Yu, H and Xu, K and Li, W}, title = {The gut-liver/bile axis: Gut microbiota and bacterial extracellular vesicles remodeling hepatobiliary pathogenesis.}, journal = {iScience}, volume = {29}, number = {5}, pages = {115623}, pmid = {42164524}, issn = {2589-0042}, abstract = {Global hepatobiliary disease burden is increasing, prompting gut-liver axis research. Gut microbiota-secreted bacterial extracellular vesicles (BEVs) carry bioactive molecules affecting host immunity, inflammation, and metabolism. Whether BEVs actively or passively cause liver damage is unclear. This review suggests gut-derived BEVs trigger hepatic innate immunity and sterile inflammation. By combining current findings on how gut microbes, their BEVs, and hepatobiliary diseases interact, we improve the "gut-liver/bile axis" idea. Acknowledging BEVs' active part in disease offers new ways to use them as diagnostic markers and treatment targets, likely better managing hepatobiliary disorders.}, }
@article {pmid42164586, year = {2026}, author = {Unuvar, GK and Mese, EA and Rello, J}, title = {Strategies to prevent cross-transmission of multidrug-resistant microorganisms in intensive care units: A narrative review.}, journal = {Journal of intensive medicine}, volume = {6}, number = {3}, pages = {221-228}, pmid = {42164586}, issn = {2667-100X}, abstract = {Organisms' transmission in intensive care units (ICUs) should be addressed by modulation of the skin and gut microbiome (endogenous) or by acquisition of the environment (exogenous). The microbiome has recently been reported as a reservoir of organisms, modulating the immune host response. Interventions on the gut microbiome are a promising way to prevent the development of hospital-acquired infections in the ICU and reduce the risk of cross-transmission of multidrug-resistant microorganisms. Maintaining the cleanliness of patient care areas is a safety strategy for preventing healthcare-associated infections and recent insights on microbiome modulation to reduce the risk for cross-infection. Evidence indicates that regular cleanliness monitoring can positively influence patient outcomes. The development of standardized cleaning checklists is strongly recommended. Key procedural strategies include preliminary site evaluations to determine the extent of contamination or surface damage, cleaning from low-touch to high-touch areas, and progressing from clean to contaminated regions. Chemical agents such as quaternary ammonium compounds, sodium hypochlorite, and hydrogen peroxide are effective for decontamination. Studies demonstrate a positive correlation between the number of touches a surface receives and its bacterial load, emphasizing the importance of assessing contamination levels and cleaning quality. Such evaluations inform the development of environmental cleaning protocols, guide facility policies, and improve program effectiveness. Cleanliness evaluation monitoring should measure the assessment of cleaning practices and cleanliness levels. Using probiotics, prebiotics, and synbiotics is an innovative strategy to reduce dysbiosis and improve host immunity. Lastly, strengthening staff education is essential to enhancing environmental infection control.}, }
@article {pmid42164663, year = {2026}, author = {Glapa-Nowak, A and Nowak, JK and Kurek, S and Walkowiak, J}, title = {What a pickle-a metagenomic perspective on the cucumber fermentation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1809866}, pmid = {42164663}, issn = {1664-302X}, abstract = {Food fermentation involves an interplay between multiple strains and species. This delicate composition during fermentation has been investigated so far using both classical and molecular methods; however, the results remain difficult to interpret. In this perspective article, we discuss the spontaneous fermentation of cucumber from organic and commercial cultivation (from 1st day to 90th day) based on our preliminary data from a nanopore sequencing study. The present study is the first to report the occurrence of coagulase-negative cocci in cucumber fermentation [Staphylococcus saprophyticus (0.01%) and Staphylococcus schleiferi (0.03%)]. Furthermore, we conclude that own-cultivation cucumbers may exhibit a lower incidence and diversity of phages, which have practical implications for designing future studies as well as for direct consumers. Our data also show that, even in the absence of phages (own-cultivation cucumbers <1%), lactic acid bacteria dominance occurs, which contrasts with previous conclusions and contributes to the discussion on the role of phages in maintaining the balance between Enterobacteriaceae and lactic acid bacteria in plant fermentation. The powerful metagenomic approach provides a broader understanding of the day-to-day and sample-to-sample diversity within microbiome communities. The maturity of the fermentation product may play a significant role in exerting specific biological actions. This should be accounted for before planning an intervention study.}, }
@article {pmid42153004, year = {2026}, author = {Bogatyrenko, E and Dunkai, T and Kim, A}, title = {Core Bacterial Microbiome in Wild Sea Cucumbers (Apostichopus japonicus) from the Sea of Japan.}, journal = {Indian journal of microbiology}, volume = {66}, number = {2}, pages = {441-451}, pmid = {42153004}, issn = {0046-8991}, abstract = {UNLABELLED: The taxonomic composition of gut bacterial communities in wild Japanese sea cucumbers, Apostichopus japonicus, from coastal waters of the Russian part of the Sea of Japan was identified by high-throughput sequencing. The bacterial communities were comprised mainly of the phyla Proteobacteria (38.33-57.22%), Actinobacteriota (24.24-29.93%), Firmicutes (12.01-25.12%), and Bacteroidota (1.6-2.17%) that made up a total of 94.5% of the samples studied. As the results showed, the region and habitat have a significant effect on the bacterial structure of the gut microbiome in A. japonicus. The invertebrates from each of the water bodies under study were characterized by their unique sets of symbiotic microorganisms. However, 32 bacterial genera were found in the animals from all of the water bodies. Of these, nine bacterial genera were the dominant taxa in terms of percentage of their representation in the samples: Stappia (15.89-34.68%), Stenotrophomonas (3.45-11.44%), Bacillus (1.05-7.71%), Staphylococcus (4.64-11.76%), Rhodococcus (3.07-11.08%), Corynebacterium (2.55-7.77%), Cutibacterium (15.89-34.68%), Pseudomonas (1.2-1.7%), and Streptococcus (1.09-1.57%). The discovery of bacterial genera common across all samples indicates the existence of a core microbiome potentially essential for the host's health and functions.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-025-01493-w.}, }
@article {pmid42153502, year = {2026}, author = {Kumar, S and Jindal, A and Mainuddin,  and Rastogi, H and Kumar, A}, title = {Unraveling the Multifunctional and Translational Paradigm of Nanoparticulate Systems against Colorectal Cancer.}, journal = {ACS applied bio materials}, volume = {}, number = {}, pages = {}, doi = {10.1021/acsabm.5c02297}, pmid = {42153502}, issn = {2576-6422}, abstract = {Colorectal cancer (CRC) is a health burden due to its high mortality rate, recurrence rate, and drug resistance. The limitations of traditional methodologies (such as radiotherapy, chemotherapy, surgery, and targeted active ingredients) include inefficient delivery to tumor tissue, systemic toxicity, drug resistance, and poor specificity. Hence, drug delivery through micro- and nanoparticulate systems offers innovations and can address these obstacles successfully. The design, functionality, and translational potential of particulate systems specifically designed for CRC treatment are reviewed in this study. Next, this review discusses various primary aspects, including the types of carriers (polymeric, solid lipid, inorganic, and hybrid nanoparticles/NP), their particulate physical attributes (size, shape, surface charge, composition), and factors affecting drug encapsulation and release kinetics that affect the basic design principles. Additionally, this review unfolds a discussion over targeting approaches, such as active ligand-mediated targeting, passive EPR-based accumulation, and stimulus-responsive systems activated by external stimuli, pH, enzymes, redox, or even the microbiome. Furthermore, conventional chemotherapeutics, phytochemicals and nutraceuticals, gene-based therapies (siRNA, miRNA), and combinatorial modalities (chemo and immunotherapy, photothermal, photodynamic) are included in the therapeutic payloads. Moreover, in vitro, in vivo, and clinical-stage nanoparticulate systems are highlighted with translational advancements. Specifically, this review emphasizes the benefits offered, including enhanced solubility, stability, targeted distribution, and multifunctionality (imaging, triggered release). In addition, primary challenges to translation, such as regulatory, scalability, reproducibility, biological processes, and long-term safety issues, are also discussed. Conclusively, innovative approaches like regulatory frameworks, microbiome-driven delivery designs, aspects of artificial intelligence/machine learning (AI/ML)-guided optimization, and stealth and biomimetic hybrid particulates can be beneficial from futuristic aspects. Suggestively, to expedite the transition from NP invention to effective CRC therapeutics, a translational roadmap is required that encourages the combination of modern materials science, computational design, and clinical validation.}, }
@article {pmid42153538, year = {2026}, author = {Julanon, N and Unhapipatpong, C and Wongjirattikarn, R and Anutraungkool, T and Chaowattanapanit, S and Choonhakarn, C and Sawanyawisuth, K and Shantavasinkul, PC and Zouboulis, CC and Piguet, V}, title = {Role of Probiotics in Managing Acne Vulgaris: A Systematic Review and Meta-Analysis of Clinical Trials.}, journal = {Journal of cutaneous medicine and surgery}, volume = {}, number = {}, pages = {12034754261445880}, doi = {10.1177/12034754261445880}, pmid = {42153538}, issn = {1615-7109}, abstract = {BACKGROUND: Dysregulation of the skin microbiome is implicated in acne pathogenesis.<br><br>OBJECTIVE: To evaluate the efficacy of probiotics in the management of acne.<br><br>METHODS: Searches were conducted in 3 databases through June 30, 2024. Clinical trials that compared probiotics with controls and investigated their efficacy in acne were included. Primary outcomes were standardized mean differences (SMDs) for the change from baseline to posttreatment in total lesion count (TLC), noninflammatory lesion count (NILC), and inflammatory lesion count (ILC). Secondary outcomes included Global Acne Grading System (GAGS) scores, Investigator's Global Assessment, erythema, and sebum levels.<br><br>RESULTS: Thirteen studies comprising 18 study arms and 1453 participants were included. There were no significant reductions in TLC (SMD, -0.22; 95% confidence interval [CI]: -0.50 to 0.07; I[2]&#x2009;=&#x2009;75%), NILC (SMD, -0.20; 95% CI: -0.48 to 0.08; I[2]&#x2009;=&#x2009;72%), or ILC (SMD, -0.13; 95% CI: -0.34 to 0.09; I[2]&#x2009;=&#x2009;52%) with probiotics compared with controls. However, oral probiotics were associated with a significant reduction in GAGS scores (SMD, -0.47; 95% CI: -0.81 to -0.13; I[2]&#x2009;=&#x2009;67%) versus controls. Subgroup analyses indicated that this effect was most prominent in mild-to-moderate acne patients who received oral probiotics containing Lactobacillus species combined with other strains for a minimum of 12&#x2009;weeks.<br><br>CONCLUSIONS: Probiotics did not demonstrate a significant reduction in acne lesion counts. However, they were associated with improvements in acne severity as measured by GAGS scores. These findings should be interpreted with caution given the heterogeneity across studies and the fluctuating natural course of acne.}, }
@article {pmid42153569, year = {2026}, author = {Zhang, Q and Li, Y and Han, Y and Zhou, W and Li, X and Sun, J and Bai, W}, title = {Correction to "Lactiplantibacillus plantarum FEED8 Biosynthesis of Pyranoanthocyanin (Cyanidin-3-glucoside-4-vinylcatechol) Improves Oxidative Stress and Inflammation of the Gut Microbiome in Cadmium-Exposed Mice".}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.6c06010}, pmid = {42153569}, issn = {1520-5118}, }
@article {pmid42153643, year = {2026}, author = {Jeilu, O and Simachew, A and Hartmann, EM and Alexandersson, E and Johansson, E}, title = {CAZyme fold architecture is conserved between disparate environments despite extreme sequence divergence.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0048526}, doi = {10.1128/msystems.00485-26}, pmid = {42153643}, issn = {2379-5077}, abstract = {Microbial carbohydrate-active enzymes (CAZymes) underpin carbon cycling across Earth's ecosystems; however, how contrasting environments shape CAZyme diversity and structural conservation remains poorly understood. Here, we applied shotgun metagenomics to compare the carbohydrate-degradation potential of two functionally prolific but physicochemically opposed ecosystems: the alkaline-saline soda lakes of the East African Rift Valley and the anaerobic ruminant gut. From 34 metagenomes (12 soda lake and 22 rumen), we recovered 371 quality-filtered metagenome-assembled genomes, of which 84% of soda lake and 52% of rumen MAGs represented novel species. Rumen communities, dominated by Bacteroidota, Fibrobacterota, and Bacillota, exhibited significantly higher taxonomic diversity and were enriched in carbohydrate catabolism and fermentation pathways. Soda lake communities, dominated by Pseudomonadota, displayed greater evolutionary divergence (lower RED scores) and were enriched in pH homeostasis, oxidative and osmotic stress, sulfur cycling, and carbon fixation pathways. To assess whether structural conservation persists despite extreme sequence divergence, we predicted three-dimensional structures for 12 representative enzymes from six glycoside hydrolase families (GH1, GH3, GH5_11, GH9, GH10, and GH28) using AlphaFold 3. All 12 structures adopted canonical GH family folds with high confidence (pTM 0.75-0.97). These results demonstrate that environmental selection drives distinct taxonomic and functional strategies for carbon processing while preserving three-dimensional CAZyme architecture, positioning soda lake and rumen metagenomes as complementary reservoirs for bioprospecting industrially relevant enzymes.IMPORTANCECarbohydrate-active enzymes, or CAZymes, are the molecular machines that microorganisms use to break down plant material and other complex sugars, and they underpin both the global carbon cycle and many industrial processes, from biofuel production to food, feed, and textile manufacturing. In this study, we compared the CAZyme repertoires of two microbial worlds that could hardly be more different: the alkaline, salty soda lakes of the East African Rift Valley, and the anaerobic stomachs of cattle, sheep, and goats. We show that although these communities are taxonomically distinct and their enzyme sequences have diverged dramatically, the three-dimensional shapes of their key carbohydrate-degrading enzymes remain remarkably well preserved. Soda lakes, in particular, hold a large pool of previously uncharacterised enzymes, identifying them as a promising, largely untapped source of robust biocatalysts for sustainable biotechnology and industrial applications.}, }
@article {pmid42153646, year = {2026}, author = {Revel-Muroz, AZ and Sonets, IV and Chistyakov, AS and Vasiluev, PA and Surovoy, YA and Ivanova, VA and Kozlovskaya, LI and Khokhlova, OE and Fursov, MV and Fursova, NK and Ulianov, SV and Tyakht, AV}, title = {Gut Hi-C metagenomes of severe COVID-19 patients: bacteria and yeast involved in gut-lung axis.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0013926}, doi = {10.1128/msphere.00139-26}, pmid = {42153646}, issn = {2379-5042}, abstract = {Antimicrobial resistance (AMR) poses a critical threat to global health, particularly in intensive care units, where vulnerable patients are frequently exposed to multidrug-resistant microorganisms. The human gut microbiome serves as a key reservoir for AMR genes, which can disseminate to other body sites, including the lungs, especially during severe illness. We applied Hi-C metagenomics to stool samples from 11 critically ill COVID-19 patients and analyzed microbial isolates from their lungs to investigate intra-host transmission of AMR genes. Plasmid-resolved microbial interaction networks revealed AMR gene sharing across 13 bacterial genera, primarily from Firmicutes and Proteobacteria, with evidence of plasmid-mediated transfer across phylum boundaries and between gut and lung compartments. Notably, we identified genetically identical Klebsiella pneumoniae strains colonizing both the gut and lungs of a single patient, as well as shared plasmids carrying qnrS-1 and blaCTX-M-231 resistance genes between gut Escherichia coli and lung K. pneumoniae. In addition to bacterial pathogens, Candida yeast species isolated from both niches harbored resistance genes to multiple antifungal classes, including azoles. These findings underscore the dynamic, cross-compartmental nature of AMR dissemination within the human body and highlight the importance of integrative surveillance strategies to control resistance in clinical settings.IMPORTANCEWhile COVID-19 itself caused severe illness, many deaths were ultimately due to secondary microbial infections-often worsened by antibiotic resistance. Plasmids, which shuttle resistance genes between bacterial species, are key players in their spread, yet their roles in transmission, especially across body sites such as the gut and lungs, are to be elucidated. The use of Hi-C metagenomics allowed us to map bacterium-plasmid links in the guts of severe COVID-19 patients and reconstruct high-quality genomes of opportunistic fungi. Comparing these with lung-derived isolate genomes, we gained insight into possible intra-host dissemination routes of resistance genes. Preparing for future pandemics will require not only rapid pathogen detection but also tools to monitor microbiome health and resistance dynamics, and understanding how treatments and microbial imbalances shape infection risks.}, }
@article {pmid42153658, year = {2026}, author = {Chen, X and Chen, GG and Gong, Z and Zhu, H and Liang, Z and Chan, JYK and Tong, MCF and Chen, Z and Chang, WT}, title = {The middle ear-nasopharyngeal microbiome axis associated with obstructive Eustachian tube dysfunction in chronic otitis media.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0000726}, doi = {10.1128/msystems.00007-26}, pmid = {42153658}, issn = {2379-5077}, abstract = {Obstructive Eustachian tube dysfunction (ETD) commonly complicates chronic otitis media (COM), yet microbial factors at the Eustachian tube (ET) openings remain poorly understood. In this prospective cohort study, we characterized the microbiota at both the middle ear (ME) and nasopharyngeal (NP) ET openings in COM patients undergoing ear surgery and examined associations with obstructive ETD over one year of follow-up. Using 16S rRNA gene sequencing and functional inference, we profiled microbial communities from the ME-side ET opening and the torus tubarius on both surgical-side and contralateral nasopharynx. Among 37 patients (18 with ETD, 19 without), ME and NP microbiota differed significantly in composition. Ears with ETD showed increased ME microbial diversity and enrichment of Neobacillus, Agrobacterium, and Sphingomonas. Paired NP-ME analyses indicated an altered NP-ME microbial relationship in ETD, with Neobacillus showing a nasopharyngeal source signal. Functional prediction revealed increased porphyrin metabolism and decreased pyruvate metabolism in ME microbiota with ETD, suggesting a shift toward biofilm formation and altered redox states. Anaerococcus was increased in the nasopharynx of patients with bilateral COM. These findings identify distinct microbial and metabolic features of COM with obstructive ETD, supporting a role for nasopharyngeal-microbial influence on ME pathology.IMPORTANCEChronic otitis media (COM) is a common and often persistent ear disease, especially when complicated by Eustachian tube dysfunction (ETD). By profiling microbiota at both Eustachian tube openings, this study links upper-airway microbial ecology with middle-ear microbial states in COM and helps clarify where clinically relevant signals may arise along the Eustachian tube pathway. The paired nasopharyngeal-middle ear design revealed that nasopharyngeal microbes may be linked to middle-ear community shifts in COM with obstructive ETD, consistent with a potential upper airway contribution to the middle-ear microbiota, generating testable hypotheses about microbial exchange and persistence. These findings highlight the upper airway microbiome as a potential target for developing new preventive and therapeutic strategies in COM.}, }
@article {pmid42153706, year = {2026}, author = {Borren, NZ and Paulides, E and Klaassen, MAY and Alm, E and Xavier, RJ and Janneke van der Woude, C and Ananthakrishnan, AN}, title = {Microbiome-Directed Therapy for Fatigue in Quiescent Inflammatory Bowel Disease: A Randomized Placebo-Controlled Trial of Multi-Strain Probiotic Supplementation.}, journal = {The American journal of gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.14309/ajg.0000000000004056}, pmid = {42153706}, issn = {1572-0241}, abstract = {INTRODUCTION: Fatigue is a challenging symptom for patients with inflammatory bowel diseases (IBD). Emerging evidence links alterations in the gut microbiome with fatigue in IBD, highlighting the potential of microbiome-targeted treatments. Our aim was to evaluate the clinical efficacy and biological effects of a multi-strain probiotic supplementation on fatigue in patients with quiescent IBD.<br><br>METHODS: This multi-center, placebo-controlled, randomized controlled trial included patients with quiescent IBD, defined as being in clinical remission and a colonoscopy within 1 year which demonstrated no active disease, and with significant fatigue (FACIT-F score < 43). Patients were randomized to receive either probiotics (Ecologic&#xae; BARRIER, containing 9 different bacterial strains) or placebo for 12 weeks. Gut microbiome and serum metabolome were analyzed at baseline and at the end of the study.<br><br>RESULTS: Our study enrolled 100 patients (52 Crohn's disease (CD), 44 ulcerative colitis (UC), 4 IBD-unspecified) with quiescent IBD and with a mean age of 41 years; 61% were women. After 12 weeks, 29.4% of the probiotic group and 40.0% of the placebo group met criteria for no fatigue (p=0.34). However, all participants reported an improvement in fatigue (p<0.001) with the most striking change noted at 4 weeks in both groups. Probiotic treatment led to beneficial shifts in gut microbiome and serum metabolome composition, particularly an increase in Bifidobacterium animalis after 12 weeks.<br><br>DISCUSSION: While 12 weeks of probiotic administration was not associated with relief of fatigue in patients with quiescent IBD, we observed beneficial alterations in the gut microbiome and serum metabolome. ClincialTrials.gov number, NCT03266484.}, }
@article {pmid42153723, year = {2026}, author = {O'Sullivan, B and Herbst, KW and Hogan, AH and Maltz-Matyschsyk, M and Radolf, JD and Lawrence, D and Lynes, MA and Salazar, JC and Graf, J and , }, title = {Comparison of a long-read amplicon sequencing approach to short-read amplicons for microbiome analysis.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0277625}, doi = {10.1128/spectrum.02776-25}, pmid = {42153723}, issn = {2165-0497}, abstract = {UNLABELLED: Most microbiome studies to date rely on sequencing short amplicons of the 16S rRNA gene on Illumina's platforms. Because of the short read length, sequences often can be identified reliably only to the family or genus levels. Long-read sequencing with whole-length 16S rRNA sequencing can improve taxonomic resolution but often only to the species level. StrainID is an alternative approach that amplifies a large segment of the ribosomal operon, including the entire 16S rRNA gene, internal transcribed spacer, and a portion of the 23S rRNA gene. This longer amplicon is designed to allow ribotype-level classification. Although studies have demonstrated the utility of StrainID for several sample types, a direct comparison of StrainID to alternative approaches has not been done for saliva. Here, we compared the performance of StrainID to short-read amplicons with saliva samples as well as a synthetic mock DNA community. Short reads were amplified with primer pairs targeting the V1-V3 region of the 16S rRNA gene and were classified with several different taxonomic databases. We found that StrainID outperformed short reads not only in identifying amplicon sequence variants to the species level but also in demonstrating a key benefit with phylogenetic-based beta-diversity tests. Our results further build on establishing StrainID as a powerful method and specifically for its use with saliva samples.<br><br>IMPORTANCE: The interpretation of microbiome composition studies is highly dependent on the methodologies chosen during experimental design, which affects factors such as resolution, throughput, cost, and accuracy. StrainID is an approach that can improve resolution while maintaining high-throughput and similar costs to short-read sequencing. The salivary microbiome represents a diverse community of microbes with links to a variety of health conditions and disease states. Closely related strains of bacteria can have drastically different effects on their host. Establishing StrainID as a valid approach for studying the salivary microbiome opens avenues for research that improve upon alternative methods by increasing sensitivity and accuracy compared to traditional short-read approaches.}, }
@article {pmid42153897, year = {2026}, author = {Jain, M and Babu, R and Jain, A}, title = {Phosphate binders and the gut microbiota in chronic kidney disease: mechanisms, mixed evidence, and clinical considerations.}, journal = {Journal of nephrology}, volume = {}, number = {}, pages = {}, doi = {10.1093/joneph/aajag023}, pmid = {42153897}, issn = {1724-6059}, abstract = {Chronic kidney disease (CKD) disrupts the gut microbiome through dietary restrictions, uraemia, and polypharmacy, including phosphate binders. This dysbiosis contributes to systemic inflammation, accumulation of uremic toxins, and reduced short-chain fatty acid (SCFA)-producing bacteria. Hyperphosphatemia, a key CKD complication, typically emerges in advanced stages. This review examines the impact of phosphate binders on gut microbiota and explores emerging biological therapies. Phosphate binders are standard treatment for hyperphosphatemia but may influence gut microbiota by altering luminal pH, intestinal transit, and availability of metabolites such as SCFAs and vitamin K. These changes can impair gut barrier integrity and promote inflammation. Evidence on their microbiome effects is mixed: some studies show minimal compositional changes with calcium acetate or sucroferric oxyhydroxide, while others report individual variability and subtle taxon-specific shifts, particularly with iron-based binders. Even when compositional changes are limited, certain binders may modulate uremic toxin levels. Given the limitations of conventional therapies, biological approaches such as probiotics, synbiotics, and phosphate-accumulating organisms (PAOs) are gaining interest. These strategies may reduce intestinal phosphate availability by lowering pH, enhancing calcium-phosphate binding, and promoting microbial phosphate uptake and storage, while supporting gut barrier function. Overall, current evidence remains heterogeneous and limited by small cohorts and preclinical designs. Although microbiota-targeted therapies show mechanistic promise, robust clinical trials are needed before they can be recommended beyond adjunctive use.}, }
@article {pmid42153961, year = {2026}, author = {Zhu, B and Chen, S and Diao, Y and Wang, W and Huang, Y and Liang, L and Lu, X and Han, R and Guo, M and Li, Z and Wang, S and Li, H and Liu, C and Zhou, J and Xiong, D and Li, X and Ning, Y and Shi, X and Wu, F and Wu, K}, title = {Dissecting the Ecological Structure of Health and Disease in the Global Gut Microbiome.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e17087}, doi = {10.1002/advs.202517087}, pmid = {42153961}, issn = {2198-3844}, support = {2023YFC2414500//National Key Research and Development Program of China/ ; 2023YFC2414504//National Key Research and Development Program of China/ ; 2025YFC3410000//National Key Research and Development Program of China/ ; 2025YFC3410005//National Key Research and Development Program of China/ ; 82271953//National Natural Science Foundation of China/ ; 82301688//National Natural Science Foundation of China/ ; 2023B0303020001//Key Research and Development Program of Guangdong/ ; 2023B0303010003//Key Research and Development Program of Guangdong/ ; 2024A1515013058//Natural Science Foundation of Guangdong Province/ ; 2025A1515010507//Natural Science Foundation of Guangdong Province/ ; 2023A1515011383//Natural Science Foundation of Guangdong Province/ ; 2019B121203008-KJ-2024-040/KJ-2024-041//Guangdong Key Laboratory of Battery Safety at Guangzhou Institute of Energy Testing/ ; 2025A03J3357//Science and Technology Program of Guangzhou/ ; ZDYN-2024-A-121//Clinical Collaboration Project on Integrated Traditional Chinese and Western Medicine for Major and Difficult Diseases/ ; 2024SRP200//Research Capacity Improvement Project of Guangzhou Medical University/ ; GCAAL2022001//Guangzhou Key Clinical Specialty (Clinical Medical Research Institute), the Announcement and Leading Science and Technical Foundation of Guangzhou Civil Affairs/ ; 2023B04J0106//Guangzhou Planned Project of Science and Technology/ ; 2025B04J0011//Guangzhou Planned Project of Science and Technology/ ; }, abstract = {The gut microbiota plays a crucial role in human health, but its coordinated ecological dynamics remain largely unclear. We present Wiredancer, a novel scalable framework based on similarity-constrained non-negative matrix factorization (NMF), which extracts continuous and overlapping microbial ecological factors (MEFs). By integrating 20,178 metagenomes spanning 36 countries and over 50 disease states, Wiredancer identified three robust and interpretable MEFs delineating the health-disease continuum. MEF1, the dysbiotic factor dominated by Bacteroides uniformis, was elevated in disease populations; MEF2, the protective factor characterized by Prevotella copri, was reduced compared with the healthy group; and MEF3, the intermediate factor represented by Bifidobacterium adolescentis, reflected a mixed ecological configuration between MEF1 and MEF2. MEFs exhibited high reproducibility across individuals and longitudinal cohorts, but showed significantly increased variability in disease, consistent with the Anna Karenina principle and highlighting disrupted ecological stability. These findings were validated in the largest Chinese metagenomic cohort of major psychiatric disorders, where MEFs were associated with clinical symptoms, peripheral biomarkers, and disease subtypes, and remained essentially stable under short-term treatment. Together, Wiredancer provides a generalizable strategy to define microbiome states and decode ecological transitions, offering new opportunities for precision diagnostics and stratified medicine in complex disorders.}, }
@article {pmid42154316, year = {2026}, author = {Ulrich, JF and Redlich, SB and Mohr, A and Vollmers, J and Petersen, J and Wichard, T}, title = {Marine Rhodobacterales as Drivers of Ulva Growth: From Macroalgal-Bacterial Interactions to Bioactive Factor Enrichment.}, journal = {Journal of chemical ecology}, volume = {52}, number = {3}, pages = {}, pmid = {42154316}, issn = {1573-1561}, mesh = {*Ulva/growth &amp; development/microbiology ; *Seaweed/growth &amp; development/microbiology ; }, abstract = {Marine bacteria significantly influence the development and productivity of algal communities. The green seaweed Ulva (Chlorophyta) relies on bacteria that secrete algal growth and morphogenesis-promoting factors (AGMPF). In a reductionist model system of Ulva compressa (cultivar U. mutabilis), the diverse microbiome can be substituted by two key bacteria, Roseovarius sp. MS2 and Maribacter sp. MS6, both of which release AGMPFs, thereby inducing cell division and cell differentiation. Our study examined various algal growth-promoting substances produced by marine Rhodobacterales (Alphaproteobacteria). The exploration survey indicated that 74 of the 97 examined strains demonstrated growth-promoting, cytokine-like action. These findings underscore the extensive impact of marine Rhodobacterales on Ulva growth. Bioactive fractions containing AGMPF activity were enriched from the culture supernatant of Roseovarius sp. strain MS2. Bioactive raw extracts were obtained through bioassay-guided fractionation and semi-preparative high-performance liquid chromatography; cell division-promoting properties were observed, but did not reach the activity level of the harvested supernatant. This study provides new insights that underscore the importance of bacterial-macroalgal interactions for marine ecosystems. Replacing bacteria with AGMPFs, including thallusin, enables the complete thallus formation of axenic Ulva cultures, facilitating various applications in biotechnology and aquaculture.}, }
@article {pmid42154337, year = {2026}, author = {Sain, M and Rani, S and Singh, SP and Pothal, P and Yadav, S and Suttee, A and Kumar, A and Kumar, S and Ranawat, P and Singh, G and Barnwal, RP}, title = {The Influence of Gut Microbiome on Alpha-Synuclein Aggregation: Implications for Parkinson's Disease Pathogenesis.}, journal = {Molecular neurobiology}, volume = {63}, number = {1}, pages = {}, pmid = {42154337}, issn = {1559-1182}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Parkinson Disease/metabolism/pathology/microbiology ; *alpha-Synuclein/metabolism ; Animals ; Dysbiosis ; *Protein Aggregates ; }, abstract = {Parkinson's disease (PD) is a progressive neurodegenerative disorder traditionally characterized by dopaminergic neuronal loss in the substantia nigra and the accumulation of misfolded α-synuclein (α-syn) aggregates. While genetic susceptibility and environmental exposures are well-recognized contributors to PD, growing evidence indicates that disease initiation and progression may also involve peripheral mechanisms originating in the gastrointestinal (GI) tract. Early non-motor symptoms such as constipation, along with the presence of α-syn pathology in the enteric nervous system, have led to increasing interest in the gut-brain axis as a critical modulator of PD pathogenesis. Recent literatures reveal that gut microbiota dysbiosis can influence neurodegeneration through immune activation, intestinal barrier dysfunction, and altered production of microbial metabolites, including short-chain fatty acids, bile acids, lipopolysaccharides, and tryptophan-derived compounds. However, the precise molecular mechanisms by which these microbial factors modulate α-syn aggregation, propagation, and clearance remain incompletely understood. In this article, we review current clinical and experimental literature linking gut microbiota alterations to α-syn pathology, with particular emphasis on inflammatory signaling, microbial metabolites, and impaired proteostatic pathways that promote α-syn misfolding. We further integrate emerging concepts of "body-first" and "brain-first" PD subtypes and discuss proposed routes of α-syn transmission from the enteric to the central nervous system, including vagal, hematogenous, and immune-mediated pathways. By highlighting underexplored mechanistic connections between gut dysbiosis and α-syn biology, this review underscores the potential of microbiome-targeted strategies for early diagnosis and disease modification. A deeper understanding of gut-brain communication may ultimately enable personalized therapeutic approaches and reshape current paradigms of PD pathogenesis.}, }
@article {pmid42154370, year = {2026}, author = {Benekos, K and Katsanos, A and Laspas, P and Panos, GD and Vagiakis, I and Fousekis, FS and Luca, R and Zhou, B and Kostoulas, C and Georgiou, I and Katsanos, KH and Skondra, D and Konstas, AG}, title = {An Update and Overview of the Ocular and Extraocular Microbiome and Its Impact on Ophthalmic Care.}, journal = {Advances in therapy}, volume = {}, number = {}, pages = {}, pmid = {42154370}, issn = {1865-8652}, abstract = {The microbiome has been described as the last human "organ" and is currently the topic of great research interest worldwide. The application of culture-independent methods, like 16S ribosomal next-generation sequencing, has offered researchers the opportunity to identify bacterial populations that were impossible to detect previously using conventional culture methods. Further standardization of these new approaches to characterizing the microbiome is desirable. The present review discusses the mounting evidence suggesting that alterations in the microbiome and microbial metabolites, such as short-chain fatty acids in the gut, mouth, and ocular surface, may play a key role in the pathogenesis of ocular pathologies such as ocular surface disease, glaucoma, uveitis, age-related macular degeneration, and diabetic retinopathy. Clarifying the probable role of the microbiome in ocular diseases would not only offer valuable insights into pathogenesis but could also enable the development of novel therapeutic approaches. As yet, microbial-based therapeutic applications in ophthalmology are limited. Nevertheless, recently emerging strategies utilizing probiotics and prebiotics, or even fecal transplantation to regulate microbiome composition, offer promising research avenues for developing future innovative therapies for ocular diseases. Further studies employing standardized methodological protocols are needed to ensure the reproducibility of results and to eventually unlock the precise links between the microbiome and the eye.}, }
@article {pmid42154646, year = {2026}, author = {Alciati, A and Cracò, F and Burgio, A and Pezzano, A and Atzeni, F}, title = {Fibromyalgia and metabolic syndrome: prevalence, potential shared pathophysiological mechanisms and non-pharmacological treatment strategies.}, journal = {Clinical and experimental rheumatology}, volume = {}, number = {}, pages = {}, doi = {10.55563/clinexprheumatol/y4a7s4}, pmid = {42154646}, issn = {0392-856X}, abstract = {Fibromyalgia (FM) is a chronic pain syndrome defined by widespread musculoskeletal pain, fatigue and sleep disturbances, frequently accompanied by metabolic disturbances. Among these, metabolic syndrome (MetS), a cluster of abdominal obesity, hypertension, dyslipidaemia and impaired glucose regulation, stands out because of its strong association with cardiovascular disease and type 2 diabetes. Recent studies suggest that MetS and its individual components, particularly obesity, are highly prevalent in FM populations, raising important clinical and pathophysiological questions.Both FM and MetS are associated with chronic low-grade inflammation, autonomic nervous system dysfunction, and dysregulation of the hypothalamic-pituitary-adrenal (HPA) axis. Moreover, environmental factors, particularly early-life stress, may increase vulnerability by triggering persistent neuroendocrine and immune alterations. These overlapping pathways not only predispose to comorbidity but also contribute to increased symptom burden and therapeutic complexity. Systematic screening for MetS in patients with FM may improve cardiovascular risk stratification and inform more comprehensive treatment strategies. This narrative review summarises current evidence on the comorbidity of FM with MetS and its individual components, highlighting their shared pathophysiology. It also explores the therapeutic potential of non-pharmacological strategies, including structured exercise, dietary interventions, and microbiome-targeted approaches, that address common underlying mechanisms and hold promise for improving long-term outcomes.}, }
@article {pmid42155002, year = {2026}, author = {Meng, X and Wu, X and Sun, H and Cong, J and Gu, Y}, title = {Maternal-Infant Gut Microbiota Transmission and the Early Origins of Metabolic Liver Diseases: Mechanisms and Interventional Opportunities.}, journal = {Nutrition reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/nutrit/nuag074}, pmid = {42155002}, issn = {1753-4887}, support = {42307182//National Natural Science Foundation of China/ ; }, abstract = {Metabolic dysfunction-associated steatotic liver disease is associated with a growing global health burden with increasing prevalence in both adult and pediatric populations. Emerging evidence suggests that the origins of steatotic liver disease may trace back to early life, with the gut microbiota serving as a critical mediator in this developmental programming. This review synthesizes current knowledge on maternal-infant gut microbiota transmission and its role in shaping long-term liver health through the gut-liver axis. We examined key maternal factors, including delivery mode, feeding of breast milk, diet, metabolic status, and antibiotic exposure, that profoundly influence infant microbiota assembly. The critical window of microbiota establishment during the first 1000 days shapes intestinal barrier function, immune development, and metabolic pathways that persist into adulthood. Mechanistically, early dysbiosis contributes to metabolic dysfunction-associated steatotic liver disease pathogenesis through multiple interconnected pathways, including compromised intestinal barrier integrity facilitating endotoxemia, altered short-chain fatty acid production affecting energy metabolism and inflammation, disturbed bile acid signaling disrupting metabolic homeostasis, and epigenetic modifications potentially shaping long-term susceptibility. We critically evaluated emerging microbiota-targeted interventional strategies during pregnancy and infancy, including probiotics, human milk oligosaccharide supplementation, and synbiotic approaches, highlighting their potential for disease prevention. This review uniquely integrates concepts of developmental origins with detailed gut-liver axis mechanisms, emphasizing the maternal-infant microbial continuum as an underexplored but promising target for preventing metabolic liver disease. While significant research challenges remain, particularly in establishing causality and developing personalized interventions, modulation of the early gut microbiome offers an innovative preventive strategy against the rising tide of metabolic dysfunction-associated steatotic liver disease, potentially disrupting the intergenerational cycle of metabolic disease.}, }
@article {pmid42155039, year = {2026}, author = {Wang, L and Wang, Q and Wolfe, TM and Pinkham, NV and Erickson, R and Yoshinaga, M and Mcdermott, TR and Walk, ST}, title = {Technical and biological factors driving inter-individual body burden of arsenic species in murine models of human arsenic exposure.}, journal = {Toxicological sciences : an official journal of the Society of Toxicology}, volume = {}, number = {}, pages = {}, doi = {10.1093/toxsci/kfag055}, pmid = {42155039}, issn = {1096-0929}, abstract = {Arsenic is one of the most important environmental toxicants, requiring advanced analytical techniques to resolve individual species. There is little consensus on arsenic speciation methodology for in vivo studies. The objectives of this study were to generate a robust framework for arsenic speciation in murine models of human exposure and evaluate factors influencing the levels of arsenobetaine, inorganic arsenite, dimethylarsinate, monomethylarsonate, and inorganic arsenate resolved by HPLC-ICPMS. Enzyme-assisted digestion by papain vs. pepsin and maceration by bead beating vs. mechanical homogenization were evaluated using chemical standard spiking experiments. Dose-controlled mouse exposures to inorganic arsenite were conducted and species detected in urine and bladder tissue were compared. Species in stool, liver, and bladder were compared between groups of mice eating a standard vs. purified diet; fasted vs. unfasted mice; and conventional vs. germ-free mice. Finally, between-lab differences in HPLC-ICPMS instrumentation/quantification procedures were evaluated. These comparisons led to several important conclusions including: Significant conversion of inorganic arsenate to arsenite by papain, significant inorganic arsenate background in bead-beating lysing matrix, significant arsenobetaine in mice eating standard but not purified chow, significant correlation between species detected in urine and bladder, significant correlation of results between laboratories that differed in absolute quantification, and large inter-individual variability between mice of the same treatment group. Finally, diet type and the presence of a microbiome had the largest effect on arsenic species levels. Our results provide a benchmark for evaluating arsenic species in murine models, including adequate sample sizes for powering studies to avoid erroneous conclusions.}, }
@article {pmid42155496, year = {2026}, author = {Hull, RC and Liu, Y and Cao, Z and Xuan, KTL and de Lima Headley, DA and Richardson, H and Hennayake, C and Lind, H and McIntosh, E and Pollock, J and Hughes, C and Viligorska, K and Choi, H and Gao, Y and Chotirmall, SH and Shoemark, A and Robertson, K and Burgel, PR and Vendrell, M and Xu, X and Qu, JM and Song, Y and Guan, WJ and Chen, R and Singh, S and Talwar, D and Mohan, BVM and Tripathi, SK and Swarnakar, R and Trivedi, S and Goeminne, PC and Shteinberg, M and De Soyza, A and Altenburg, J and Haworth, CS and Sibila, O and Polverino, E and Loebinger, MR and Ringshausen, FC and Mertsch, P and Lorent, N and Dimakou, K and Mendez, R and Mclaughlin, AM and Borrill, Z and Lord, R and Finch, S and Blasi, F and Burr, L and Crisafulli, M and Keating, R and Middleton, PG and Long, MB and Aliberti, S and Morgan, L and Dhar, R and Chalmers, JD and Xu, JF and , }, title = {Comorbid diabetes disease severity and microbial changes in patients with bronchiectasis: a combined analysis of data from the EMBARC, EMBARC-India, Australian, and BE-China registries.}, journal = {The Lancet. Respiratory medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/S2213-2600(26)00057-3}, pmid = {42155496}, issn = {2213-2619}, abstract = {BACKGROUND: Bronchiectasis and diabetes commonly coexist and are associated with immune dysfunction and increased susceptibility to infection. Although diabetes is associated with worse prognosis in cystic fibrosis-related bronchiectasis, data are scarce for its impact on non-cystic fibrosis bronchiectasis. This study aimed to characterise the impact of diabetes on clinical outcomes and microbial and inflammatory profiles in patients with bronchiectasis.<br><br>METHODS: This analysis comprised data from the European Bronchiectasis Registry (EMBARC), Respiratory Research Network of India (EMBARC-India), Chinese Bronchiectasis Registry (BE-China), and Australian Bronchiectasis Registry (ABR); 30&#x2008;263 patients with CT-confirmed bronchiectasis in 33 countries were included in the analysis: 16&#x2008;963 from EMBARC (Jan 12, 2015, to April 12, 2022), 2361 from EMBARC-India plus additional Asian countries (June 1, 2015, to Sept 1, 2017), 10&#x2008;324 from BE-China (Jan 10, 2020, to March 31, 2024), and 615 from the ABR (March 7, 2016, to Sept 11, 2018). Clinical data were compared between patients with and without diabetes. Long-term outcome data were available in EMBARC and EMBARC-India. Microbiome and inflammatory profiles were characterised in a sub-cohort of EMBARC patients by sputum 16S rRNA sequencing (n=433) and serum Olink (n=479).<br><br>FINDINGS: 2487 (8&#xb7;2%) of 30&#x2008;263 patients with bronchiectasis had diabetes. Patients with diabetes had a higher prevalence of comorbidities than those without diabetes, including cardiovascular disorders (53&#xb7;5% vs 21&#xb7;8%, p<0&#xb7;0001), asthma (27&#xb7;5% vs 21&#xb7;0%, p<0&#xb7;0001), and chronic obstructive pulmonary disease (34&#xb7;3% vs 19&#xb7;0%, p<0&#xb7;0001). Patients with diabetes had more severe disease than those without diabetes, with higher Bronchiectasis Severity Index scores (8 [IQR 5-12] vs 7 [4-10], p<0&#xb7;0001) and UK Medical Research Council (MRC) dyspnoea scores (p<0&#xb7;0001) and more hospital admissions in the previous year (p<0&#xb7;0001). After adjustment for confounders, outcomes were significantly worse in patients with diabetes than in those without diabetes, including more frequent exacerbations (incidence rate ratio [IRR] 1&#xb7;18 [95% CI 1&#xb7;09-1&#xb7;28], p<0&#xb7;0001), hospital admissions (IRR 1&#xb7;57 [1&#xb7;40-1&#xb7;76], p<0&#xb7;0001), and higher 5-year mortality (hazard ratio 1&#xb7;80 [1&#xb7;53-2&#xb7;12], p<0&#xb7;0001). The sputum microbiome was significantly altered in patients with diabetes compared to those without diabetes, with increased isolation of Enterobacteriaceae (p<0&#xb7;0001), Moraxella catarrhalis (p=0&#xb7;0035), and Haemophilus influenzae (p=0&#xb7;046). In serum, Gal-4 and GDF-15, established biomarkers of disease severity and cardiovascular risk in diabetes, were significantly increased in patients with diabetes (Gal-4, p<0&#xb7;0001; GDF-15, p=0&#xb7;0019).<br><br>INTERPRETATION: Patients with diabetes and bronchiectasis are a high-risk population with more severe disease, worse outcomes, increased comorbidities, and increased risk of infections compared with patients without diabetes. These findings support inclusion of diabetes as a risk factor in individualised risk assessments for bronchiectasis.<br><br>FUNDING: European Respiratory Society, Armata, AstraZeneca, Boehringer Ingelheim, Chiesi, CSL Behring, GSK, Grifols, Insmed, Janssen, Lifearc, Roche, Verona Pharma, Zambon, National Natural Science Foundation of China, Innovation Program of the Shanghai Municipal Education Commission, Program of the Shanghai Municipal Science and Technology Commission, Program of the Shanghai Shenkang Development Center, EU/European Federation of Pharmaceutical Industries and Associations, Innovative Medicines Initiative, and Inhaled Antibiotics in Bronchiectasis and Cystic Fibrosis Consortium.}, }
@article {pmid42155536, year = {2026}, author = {Shahvali, N and Adibi, M and Mohebi, A and Mousavianfard, SR and Salehi, M and Zamani, S and Sharifianjazi, F and Chegini, L and Bastami, F}, title = {Mesenchymal stem cell therapy for treatment of medication related osteonecrosis of the jaw (MRONJ): A systematic review.}, journal = {Tissue &amp; cell}, volume = {102}, number = {}, pages = {103489}, doi = {10.1016/j.tice.2026.103489}, pmid = {42155536}, issn = {1532-3072}, abstract = {BACKGROUND: Medication-related osteonecrosis of the jaw (MRONJ) is a significant adverse effect associated with antiresorptive and antiangiogenic therapies. Therapies utilizing mesenchymal stem cells (MSCs) represent a promising regenerative strategy; however, conventional management methods have shown limited effectiveness. This systematic review aimed to evaluate the effectiveness of MSC-based interventions in preventing and treating MRONJ.<br><br>METHOD: A comprehensive literature search was conducted using PubMed, Scopus, and Web of Science to identify studies published from 2011 to 2024. Studies examining MSCs therapy in the context of MRONJ were incorporated according to predefined inclusion and exclusion criteria.<br><br>RESULTS: Seventeen studies (6 clinical, 11 preclinical) met inclusion criteria. Preclinical models demonstrated that MSCs enhance angiogenesis and bone regeneration, providing mechanistic support for human application. Clinically, 80-90% of patients achieved complete mucosal healing with radiographic evidence of bone regeneration. However, due to species differences in oral microbiome and immunity, animal findings require confirmation in human trials.<br><br>CONCLUSION: This review integrates human clinical data with mechanistic insights from preclinical studies. Human evidence shows promising mucosal and bone regeneration, while animal studies elucidate underlying mechanisms-particularly angiogenesis and immunomodulation. Given that animal models cannot replicate the human oral immune environment, these findings should be interpreted as hypothesis-generating. MSC therapy represents a biologically sound but experimental strategy, warranting confirmation through randomized controlled trials.}, }
@article {pmid42155708, year = {2026}, author = {Biber, P and Muhammad, AR and Hartinger, T and Reisinger, N and Gressley, T and Zebeli, Q and Castillo-Lopez, E}, title = {Elucidating the separate and synergistic impacts of ruminal and hindgut acidosis on fermentation and microbiome of dairy cows.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2025-27887}, pmid = {42155708}, issn = {1525-3198}, abstract = {The aim of this study was to evaluate the short-term impacts of both subacute ruminal acidosis (SARA) and hindgut acidosis (HGA) on the ruminal and fecal fermentation and microbiome of dairy cows. The study was conducted as a change-over design using 9 rumen-cannulated Holstein cows (724 ± 79 kg body weight and 198 ± 74 d in milk). The SARA was induced by feeding a diet containing 65% concentrate (DM basis), and HGA was induced through daily abomasal infusion of 3 kg of starch (1:1 corn to wheat weight ratio). The evaluated treatments were 1) a control diet containing 40% concentrate (CON), 2) CON+HGA, 3) a diet containing 65% concentrate (SARA), and 4) SARA+HGA. Ruminal pH was measured every 15 min, and the fecal pH was measured 3 times per day (0, 6 and 12 h relative to feeding). Ruminal and fecal samples were collected in the morning before first feeding and were analyzed for microbiome through 16S rRNA gene amplicon sequencing. Additionally, rumen and fecal samples were taken at 0, 6 and 12 h relative to feeding and were analyzed for volatile fatty acids (VFA) and lactate to evaluate postprandial effects of treatments. Results showed that changing from CON to SARA lowered ruminal pH and increased ruminal propionate, without affecting fecal VFA profile or pH. Compared with CON, SARA shifted the ruminal microbiome, decreased α diversity in the rumen and feces, and increased abundance of several taxa such as Succinivibrionaceae UCG-001 (OTU 2994), Lachnospiraceae (OTU 3043), and Acetitomaculum (OTU 80). The HGA decreased fecal pH, increased total fecal VFA at 12 h post-feeding, and increased fecal lactate and butyrate at the expense of acetate and propionate. In addition, HGA shifted the fecal microbiome and increased butyrate producing bacteria such as Lachnospiraceae (OTU 18), Blautia (OTU 508), Acetitomaculum (OTU 622), resulting in positive correlations between fecal butyrate and abundance of these taxa; however, family Ruminococcaceae (OTU 1580), and Christensenellaceae (OTU 550) decreased in feces and correlated negatively with fecal butyrate. Moreover, results showed that SARA in combination with HGA aggravates shifts of the fecal microbiome as revealed by further reductions of microbial α diversity indices and families Ruminococcaceae (OTU 1580) and Christensenellaceae (OTU 550) in cows receiving the SARA diet and abomasal starch infusion. Overall, new findings from this study reveal not only separate effects of SARA and HGA on ruminal and fecal fermentation but also show additive negative impacts particularly on fecal microbial diversity and increase in fecal butyrate and lactate. Such alterations in microbial profile increase the risk of creating niches for pathogens proliferation and fecal shedding.}, }
@article {pmid42155725, year = {2026}, author = {Intze, E and Schaubeck, M and Arendt, BM and Fleddermann, M and Beyer, K and Clavel, T and Lagkouvardos, I and Hitch, TCA and , }, title = {Mixed feeding and mode of birth modulate the effects of a hydrolyzed synbiotic formula on the gut microbiome in infants at risk of atopic disease.}, journal = {Clinical nutrition ESPEN}, volume = {}, number = {}, pages = {103338}, doi = {10.1016/j.clnesp.2026.103338}, pmid = {42155725}, issn = {2405-4577}, abstract = {BACKGROUND AND AIMS: Intestinal colonization by microbial communities is important for infant health. Little knowledge about the effect of infant formula matrix (i.e. form of protein) on the infant microbiome, is available. The main aim of this study was to investigate how mode of birth, cessation of breastfeeding, and the formula matrix i.e. protein matrix of synbiotic infant formulas modulate intestinal colonization in infants.<br><br>METHODS: Stool microbiota profiles of 342 healthy term infants participating in a randomized controlled trial were studied. Infants received synbiotic infant formula manufactured from extensively hydrolyzed (eHF) or intact protein (control formula; CF) as exclusive formula feeding or as mixed feeding (MF) with human milk. Stool samples at 4 and 12 months of age were analyzed by 16S rRNA gene amplicon sequencing.<br><br>RESULTS: Phylogenetic profiles of the stool microbiota showed age-dependent maturation. Protein hydrolyzation had only minor effects on overall community types. However, compared to CF, eHF feeding was linked to a Bifidobacterium-dominated microbiota at 4 months of age in two subgroups: in infants born by Cesarean section and those who had received MF for less than 3 months.<br><br>CONCLUSION: In this comparison of two synbiotic infant formulas, the formula matrix based on hydrolyzed protein was linked to a Bifidobacterium-dominated community, dependent on birth and feeding mode. Because bifidobacteria are positively linked to infant health and allergy-prevention, further studies are needed to confirm these results and to investigate the effects on clinical outcomes.}, }
@article {pmid42155873, year = {2026}, author = {Sun, Q and Li, X and Wu, J and Zhang, J and Zhu, Y and Dong, Y}, title = {Immune Checkpoint Inhibitor Resistance in Non-Small Cell Lung Cancer: An Updated View Through the Cancer-immunity Cycle.}, journal = {Critical reviews in oncology/hematology}, volume = {}, number = {}, pages = {105382}, doi = {10.1016/j.critrevonc.2026.105382}, pmid = {42155873}, issn = {1879-0461}, abstract = {Despite the transformative impact of immune checkpoint blockade (ICB) in non-small cell lung cancer (NSCLC), durable responses remain limited to a subset of patients. Resistance-either intrinsic or acquired-continues to undermine the full therapeutic potential of immunotherapy. The cancer-immunity cycle provides a useful conceptual scaffold to dissect the multistep requirements for effective antitumor immunity. Recent advances in single-cell technologies, spatial profiling, longitudinal immune monitoring, and real-world clinical datasets have uncovered additional layers of complexity, including non-canonical pathways involving tumor metabolism, stromal architecture, vascular remodeling, epigenetic plasticity, microbiome-immune crosstalk, and host-related determinants of response. In this review, we provide an updated and integrated synthesis of both primary and acquired resistance mechanisms across each phase of the cancer-immunity cycle. We emphasize pathways that have gained mechanistic or clinical relevance in recent NSCLC literature and consolidate them in an updated reference figure (Figure 1). To strengthen translational relevance, we additionally include a dedicated section on host-related determinants of ICI efficacy-including immunosenescence, performance status, comorbidity burden, systemic inflammation, body composition, and concomitant medications-and a stepwise summary of representative primary versus acquired mechanisms with NSCLC clinical anchors (Table 1). Our goal is to frame resistance not as a single lesion, but as a dynamic tumor-host system that must be mapped to inform biomarker development and rational combination strategies.}, }
@article {pmid42155931, year = {2026}, author = {Gong, J and Mei, X and Jin, Y and Wang, Y and Liu, Y and Song, W and Wang, Z and Yang, M and Ye, C and Liu, Y and Huang, H and Zhu, S and Deng, W}, title = {Synergistic foliar titanium and soil organic fertilizer drive terpenoid-mediated microbiome assembly to restrict Cd/Pb uptake in Panax notoginseng.}, journal = {Journal of hazardous materials}, volume = {512}, number = {}, pages = {142356}, doi = {10.1016/j.jhazmat.2026.142356}, pmid = {42155931}, issn = {1873-3336}, abstract = {Achieving safe utilization of heavy metal-contaminated soils without compromising crop productivity represents a grand challenge for sustainable agriculture. Although foliar titanium (Ti) and soil organic fertilizers (OF) independently alleviate abiotic stress, it remains unclear whether and how aboveground Ti signaling coordinates with OF mediated rhizosphere processes to enhance crop productivity and restrict heavy metal accumulation through plant-metabolite-microbiome networks. Here, using Panax notoginseng as a model, the results showed that co-application of foliar Ti with soil OF significantly outperformed individual applications. This "top-down" strategy synergistically increased root biomass and saponin content (synergistic index > 1), while reducing root Cd and Pb concentrations by 46.60% and 47.23%, respectively. Mechanistically, soil OF established a functional rhizosphere foundation by enhancing nutrient bioavailability and enriching beneficial microbial taxa. Concurrently foliar Ti acted as a systemic trigger to reprogram plant metabolism, upregulating arginine and proline metabolic pathways in leaves and coinciding with enhanced diterpenoid biosynthesis in roots. Specifically, accumulated diterpenoids (forskolin and ingenol) functioned as selective semiochemicals, recruiting a specialized microbiome consortium with enhanced metal-resistant, growth-promoting, and nutrient-solubilizing bacteria (Sphingomonas, Rhodanobacter, Bacillus) and fungi (Penicillium, Aspergillus), while inhibiting the pathogen Ilyonectria. Consequently, this engineered rhizosphere microbiome may have contributed to rhizosphere-level Cd/Pb exclusion or immobilization, thereby decoupling root metal uptake from bulk soil metal pools. This study supports a novel "aboveground trigger-belowground support" framework in which Ti-induced metabolites promote the assembly of functional microbiomes that are further supported by OF. We propose a targeted biofortification strategy leveraging plant-metabolite-microbiome coordination for safe cultivation of crops.}, }
@article {pmid42155948, year = {2026}, author = {Yang, W and Li, Z and Chen, X and Chen, J and Lu, Z}, title = {Association between a gut microbiota-targeted dietary index and osteoarthritis/rheumatoid arthritis: a cross-sectional study.}, journal = {Clinics (Sao Paulo, Brazil)}, volume = {81}, number = {}, pages = {100995}, doi = {10.1016/j.clinsp.2026.100995}, pmid = {42155948}, issn = {1980-5322}, abstract = {BACKGROUND: Diet plays a key role in regulating the gut microbiota. This study aimed to investigate the association between the Dietary Index of the Gut Microbiome (DI-GM) ‒ a score designed to reflect the potential of a diet to support a healthy gut microbiota ‒ and different types of arthritis, an area where systematic studies remain scarce.<br><br>METHODS: Data from the National Health and Nutrition Examination Survey (NHANES) 2007-2018 were analyzed using multivariable logistic regression, Restricted Cubic Spline (RCS) regression, and subgroup analyses to assess associations between DI-GM and Osteoarthritis (OA) and Rheumatoid Arthritis (RA).<br><br>RESULTS: A total of 6168 participants were included, among whom 506 had Osteoarthritis (OA) and 303 had Rheumatoid Arthritis (RA). Multivariable analyses showed no significant association between DI-GM and OA (p > 0.05), but significant inverse associations with RA across models (ORs 0.74, 0.64, and 0.74; all p < 0.05). Restricted cubic spline analysis detected no significant nonlinear relationships for either outcome. Subgroup analyses suggested potential associations within certain populations.<br><br>CONCLUSION: This cross-sectional study found an inverse association between the diet-based DI-GM score and RA, but no significant association with OA. Given the limitations of the cross-sectional design, the observed association is equally compatible with dietary changes resulting from RA diagnosis and management (reverse causality). As this study did not measure the gut microbiota, the role of the microbiome as a mediator remains speculative. Therefore, these results require confirmation in prospective studies that can account for reverse causation and directly assess the gut microbiome.}, }
@article {pmid42156216, year = {2026}, author = {Deng, X and Wang, Y and Zhu, H and Guo, Y and Wang, Q and Han, J and Yu, K and Zhou, B}, title = {Metagenomic profiling of resistome and mobilome dynamics in diverse freshwater aquaculture modes.}, journal = {Water research}, volume = {302}, number = {}, pages = {126133}, doi = {10.1016/j.watres.2026.126133}, pmid = {42156216}, issn = {1879-2448}, abstract = {The widespread presence of antibiotic resistance genes (ARGs) in aquaculture environments poses a growing threat to public health. However, comprehensive understanding of ARG distribution and transmission potential across different freshwater aquaculture modes remains limited. This study employed integrated short- and long-read metagenomic sequencing to characterize the resistome, mobilome, and associated microbial communities across three predominant freshwater aquaculture modes (grass carp, crayfish, and crab ponds), using water, sediment, and intestinal samples analyzed at both contig and metagenome-assembled genome (MAG) levels. The results revealed that aquaculture modes and environmental media jointly shaped microbial and ARG compositions. At the contig level, the crayfish system harbored the highest relative abundance of both ARGs and mobile genetic elements (MGEs), with gut samples consistently emerging as the dominant reservoir across all modes. A significant positive correlation between ARG and MGE alpha diversity indicated that the gut microbiome, particularly in crayfish, provides a selective environment that co-enriches resistance genes and their mobile carriers. High-risk core ARGs (Rank I) were at least 19 times more abundant in the crayfish gut than in any other compartment, underscoring the intestinal microbiome as a hotspot for clinically relevant resistance accumulation. At the MAG level, over half of the recovered MAGs met near-complete or high-quality thresholds, and approximately 38% of ARG-carrying MAGs were classified as multidrug-resistant (MDR). MDR MAG abundance was significantly higher in gut than in sediment and water samples, with the crayfish gut as the most enriched compartment. Critically, several crayfish-associated MDR MAGs affiliated with Klebsiella aerogenes carried virulence factor genes (VFGs) and exhibited ARG-MGE-VFG co-localization within prophage sequences, suggesting phage-mediated co-dissemination of resistance and virulence traits. These findings highlight the intestinal microbiome of aquaculture species as a critical hotspot for resistance dissemination and provide a scientific basis for evaluating freshwater aquaculture-associated ARG risks under the One Health framework.}, }
@article {pmid42156361, year = {2026}, author = {Xiang, N and Liao, T and Xie, M and Wang, Z and Mak, CH and Tang, X and McIlroy, SE and Thibodeau, B and Voolstra, CR and Luo, H}, title = {Decoding coral resistance to eutrophication through the association of hyper‑efficient denitrifiers as key microbial allies.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42156361}, issn = {2041-1723}, support = {GRF14114724//Chinese University of Hong Kong (CUHK)/ ; }, mesh = {*Anthozoa/microbiology/physiology ; Animals ; *Denitrification ; *Eutrophication/physiology ; Coral Reefs ; Nitrates/metabolism ; Hong Kong ; Symbiosis ; Climate Change ; Ecosystem ; Microbiota ; }, abstract = {Coral reefs face a perilous future due to global climate change compounded by the increasing prevalence of local stressors. Prominent among these is nutrient pollution, particularly nitrate eutrophication, which disrupts the coral-algal symbiosis and escalates reef degradation. While microbial denitrification is hypothesized to mitigate nitrate stress, the mechanisms underlying coral resilience remain unknown. Studying Hong Kong's coral "reef oases" that persist under chronic hyper-eutrophication, we discovered that resilience is not mediated by diversity or abundance shifts in denitrifier genera but by the association with specific, hyper-efficient denitrifying populations within the dominant denitrifier genus Ruegeria. By integrating population genomics, subspecies-resolution metabarcoding (resolving both the entire Ruegeria community and the denitrifying sub-community), and direct isotope-based activity assays, we identified and validated putative denitrifying "specialist" populations. These specialists were significantly enriched in corals from high-nitrate waters and exhibited 10-fold higher denitrification rates in low-oxygen incubations, converting nitrate to inert N2 with superior efficiency compared to non-specialists. Our findings reveal that critical ecosystem-scale adaptations to anthropogenic change can occur through a unique association with specialized sub-genus populations, which may be missed in conventional microbiome surveys. As such, our work sheds light into why dominant denitrifying genera are ubiquitous, yet only certain corals thrive in eutrophic conditions. It also provides a framework for future studies delineating ecologically important host-associated microbes.}, }
@article {pmid42156377, year = {2026}, author = {Hu, R and Aronson, HS and Weaver, ME and Price, MN and LaRowe, DE and Liang, Y and Deutschbauer, AM and Coates, JD and Carlson, HK}, title = {Organic carbon oxidation state shapes fermentative methanogenic microbiomes and controls greenhouse gas fluxes.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73281-z}, pmid = {42156377}, issn = {2041-1723}, abstract = {Organic compounds with a negative nominal oxidation state of carbon (NOSC) are thermodynamically recalcitrant in anaerobic ecosystems, but few studies have measured the influence of NOSC on carbon degradation rates, gaseous product yields, or microbiome composition. We amended anaerobic rice paddy sediment microcosms with water-soluble monomeric organic carbon compounds varying in NOSC. Consistent with thermodynamic and stoichiometric predictions, negative NOSC compounds are catabolized more slowly but produce more methane per mole of carbon. Negative NOSC microbiomes have higher alpha diversity, more syntrophs and methanogens, and fewer fermentative bacteria. Strikingly, fermentative bacterial taxa display genomically encoded NOSC catabolic preferences both in the lab and field. Negative NOSC-preferring fermenters have longer predicted doubling times, consistent with the thermodynamic recalcitrance of their preferred substrates. We propose that microbial NOSC catabolic preferences may reflect the thermodynamic niche of microorganisms and we anticipate that extending research on microbial catabolic preferences to a greater variety of organic carbon substrates and diverse microbiomes will improve our understanding of microbial carbon cycling and trait evolution.}, }
@article {pmid42156414, year = {2026}, author = {Maziers, N and Le Chatelier, E and Plaza Oñate, F and Fromentin, S and Thirion, F and Pons, N and Borruel, N and Casellas, F and Torrejon, A and Robles-Alonso, V and Manichanh, C and Varela, E and Derrien, M and Veiga, P and Oozeer, R and Sunagawa, S and Lombard, V and Terrapon, N and Henrissat, B and ,  and Guarner, F and Ehrlich, SD}, title = {Fecal microbiome of patients with ulcerative colitis reflects their phenotype and inflammatory level.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-44895-6}, pmid = {42156414}, issn = {2045-2322}, support = {ANR-11-DPBS-0001, MetaGenoPolis (MGP)//Agence Nationale de la Recherche/ ; FP7-HEALTH-F4-2007-201052, MetaHIT//Seventh Framework Programme/ ; }, abstract = {Inflammatory bowel diseases affect ever-increasing numbers of individuals worldwide. Alterations of the intestinal microbiome were reported for Crohn's disease and at relapse in Ulcerative Colitis (UC); they were not clearly detected in UC at remission. Here we report the characterization of the microbiome by quantitative metagenomics in a cohort of 121 individuals, composed of 65 UC adult patients in remission and 56 healthy controls. A cross-sectional comparison revealed substantial microbiome differences, patients in remission having lower microbiome richness and paucity of the Ruminococcus species driven enterotype. The observed microbiome alterations allowed robust classification of patients by intestinal species abundance, yielding an area under the curve (AUC) of 0.87 in a Receiver-Operator Characteristic (ROC) analysis. Loss of richness was linked to an aggressive UC phenotype and to the importance of past relapses; it was associated with a worse IBD quality of life score (IBDQ-36). Unexpectedly, onset of inflammatory bouts, as assessed by white blood cell count and fecal calprotectin levels, was associated with higher richness; in a longitudinal study of patients at high risk of disease flare, we observed a link between increasing gut microbiome richness over time and calprotectin level, in turn related to clinical inflammatory response and relapse.}, }
@article {pmid42156482, year = {2026}, author = {Weng, J and Hashizume, T and Ying, BW}, title = {Cleaning reshapes bacterial communities in public toilets through disturbance and random reassembly.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-52725-y}, pmid = {42156482}, issn = {2045-2322}, support = {25K02259//Japan Society for the Promotion of Science/ ; }, abstract = {Cleaning of public spaces for human activities is commonly employed and reduces the microbial load in these spaces. However, the mechanisms underlying changes in microbial community structure following cleaning remain poorly understood. As a pilot study, we investigated the bacterial community in public toilets before and after cleaning using 16S rRNA sequencing and computational simulations, as well as bacterial colony growth assays and metabolic functional prediction. The results revealed that cleaning initially imposes a strong disturbance on bacterial communities, followed by continuous stochastic loss and a concurrent influx of bacteria, resulting in changes in community structure. Culturable bacterial communities before and after cleaning showed equivalent growth properties, indicating that cleaning did not alter the original environment. Cleaning time was positively correlated with colony number but not with colony growth capacity, suggesting that bacteria surviving cleaning were fast-growing or highly abundant taxa. Metabolisms related to methane and to diverse environments showed increased contributions to survival after cleaning. Taken together, cleaning-mediated changes in bacterial community structure in public toilets were driven by a stochastic process that renewed bacterial diversity. This study provides new insights into the disturbance and recovery dynamics of the microbiome in public environments subjected to cleaning.}, }
@article {pmid42156647, year = {2026}, author = {Ravikrishnan, A}, title = {Unlocking the Metagenome: Pipeline for Microbiome Data Analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {1-23}, pmid = {42156647}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *Metagenome ; *Microbiota/genetics ; *Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; Software ; Workflow ; Sequence Analysis, DNA/methods ; Humans ; Data Analysis ; }, abstract = {Metagenomic technologies have revolutionized our understanding of microbes in different spheres of life, revealing the massive diversity and complex functionalities of microbial communities across various environments. Shotgun metagenomics, which involves sequencing the DNA of all the organisms in a sample, is emerging as a powerful tool in assessing the microbial content. Unlike the traditional culturing approach, the shotgun metagenomic technology provides a comprehensive view of the entire microbial community, including potential functions that the organisms could be performing. In this chapter, we describe a typical bioinformatics workflow to generate the taxonomic profiles from metagenomic sequencing data and demonstrate a few basic statistical analyses that can be performed from this data to generate insights. In addition, we discuss the experimental and analytical considerations that must be taken into account while generating and making inferences from metagenomic data. Lastly, we provide insights on automating the workflow for consistent and reproducible large-scale analyses.}, }
@article {pmid42156648, year = {2026}, author = {Yugandhar Reddy, BS and Sripradha, S and Kumar, A}, title = {Targeted Metagenomics Using Next-Generation Sequencing Methods.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {25-32}, pmid = {42156648}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Microbiota/genetics ; Metagenome ; Humans ; Sequence Analysis, DNA/methods ; }, abstract = {Metagenomics allows the discovery of the full diversity of all microbes present in a given niche. The technique is very powerful and has allowed very significant advances delineating the role of the microbiome in several disciplines including health, agriculture, ecology, industry, etc. Here, we describe the method required for processing of samples for metagenomic analysis using Next-Gen sequencing.}, }
@article {pmid42156649, year = {2026}, author = {Rangamaran, VR and Sushmitha, TJ and Tamilmani, KK and Murugesan, H and Gopal, D}, title = {Exploring the Ocean's Microbial World: Techniques and Protocols for Microbiome Research.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {33-46}, pmid = {42156649}, issn = {1940-6029}, mesh = {*Microbiota/genetics ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; RNA, Ribosomal, 16S/genetics ; Oceans and Seas ; *Seawater/microbiology ; Computational Biology/methods ; }, abstract = {Marine microbiomes play a crucial role in oceanic ecosystems, influencing biogeochemical cycles, climate regulation, and marine biodiversity. Accurate characterization of these microbial communities requires standardized protocols for sample collection, processing, sequencing and data analysis. This chapter provides a comprehensive guide to essential methodologies for marine microbiome research including field sampling strategies, DNA and RNA extraction techniques, high-throughput sequencing approaches (such as 16S rRNA amplicon sequencing and metagenomics) and bioinformatics pipelines for data interpretation. Additionally, we discuss quality control measures, best practices for reproducibility, and challenges associated with marine microbiome profiling. By adopting standardized methodologies, researchers can generate reliable, comparable datasets that enhance our understanding of marine microbial ecology and its broader environmental implications.}, }
@article {pmid42156651, year = {2026}, author = {Jiménez, DJ and Díaz-García, L and Aldakheel, L and Rosado, AS}, title = {Dilution-to-Stimulation: A Method for Selecting Polymer-Transforming Microbial Consortia.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {75-81}, pmid = {42156651}, issn = {1940-6029}, mesh = {*Microbial Consortia ; Soil Microbiology ; *Polymers/metabolism ; }, abstract = {The utilization of liquid enrichment cultures for selecting microbial communities has been employed to recover and increase the abundance of desired microbes capable of thriving on specific carbon sources. This strategy facilitates the development of microbial consortia designed to serve as models for studying the eco-enzymology of particular metabolic processes. In this context, we introduce a top-down method referred to as "dilution-to-stimulation" to artificially select polymer-transforming microbial consortia from soil samples.}, }
@article {pmid42156652, year = {2026}, author = {Kosmopoulos, JC and Anantharaman, K}, title = {Computational Microbial and Viral Ecology Analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {83-141}, pmid = {42156652}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *Computational Biology/methods ; Metagenome ; *Microbiota/genetics ; *Viruses/genetics/classification ; Virome ; Bacteriophages/genetics ; Bacteria/genetics ; Archaea/genetics ; }, abstract = {The explosion in known microbial diversity in the last two decades has made it abundantly clear that microbes in the environment do not exist in isolation; they are members of communities. Accordingly, omics approaches such as metagenomics have revealed that interactions between diverse groups of community members such as archaea, bacteria, and viruses (bacteriophages) are common and have significant impacts on entire microbiomes. Thus, to have a well-developed understanding of microbes as they naturally exist in the environment, biological entities of all kinds must be studied together. While numerous protocols for metagenome analysis exist, comprehensive published protocols for the simultaneous analysis of viruses and prokaryotes together are scarce. Further, as bioinformatic methods for microbiology rapidly advance, existing metagenomic tools and pipelines require frequent re-evaluation. This ensures the adherence to best practices for microbiome and metagenomic data analysis. Here, we offer an expansive approach for the joint analysis of bulk sequence data from a mixed microbial community (metagenomes) and viral-sized fraction communities (viromes). This chapter serves as a beginner's-level guide for researchers with limited bioinformatics expertise who wish to engage in multiscale metagenome and virome analyses. We cover steps from initial study design to sequence read processing, metagenome assembly, quality control, virus identification, microbial and viral genome binning, taxonomic characterization, species-level clustering, and host-virus predictions. We also provide the bioinformatic scripts used in our workflow for reuse in one's own computational methods. Lastly, we discuss additional approaches a researcher can take after processing data with this workflow.}, }
@article {pmid42156653, year = {2026}, author = {Bhusan, KK and Bose, T and Dutta, A}, title = {Identifying Differential Network Properties and Driver Microbes in Microbial Association Networks Using CompNet and NetShift.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {143-165}, pmid = {42156653}, issn = {1940-6029}, mesh = {*Microbiota ; *Software ; *Computational Biology/methods ; Microbial Interactions ; Bacteria/genetics ; Humans ; }, abstract = {This chapter describes CompNet and NetShift, two network analysis tools, which can help in comparison and analysis of microbial association networks. Biological interaction networks are basic representations of entities present in a biological system and their inter-relationships, which lies at the foundation of any modeling approaches. Inter-microbial associations define the community structure of a given microbiome and understanding these interaction networks are pivotal to modeling the microbiome. CompNet helps in the comparison of various network properties across multiple different microbial association networks that may represent communities inhabiting different/contrasting environments. NetShift helps in the identification of key microbes (driver organisms) in the network that can drive changes in community composition and interactions (network topology) characteristic of communities residing in different environments.}, }
@article {pmid42156654, year = {2026}, author = {Sambamoorthy, G and Ansari, AF and Dixit, NM}, title = {Estimating Effective Pairwise Interactions to Predict the Structures of Microbial Communities (EPICS).}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {167-174}, pmid = {42156654}, issn = {1940-6029}, mesh = {*Microbiota ; *Microbial Interactions ; Algorithms ; }, abstract = {The engineering of multispecies microbial communities is important to applications in healthcare, biotechnology, and environmental sustainability. Predicting the structures of such communities requires knowledge of the interactions between the species involved. When high-order interactions are present, bottom-up approaches, which rely on the assembly of all possible subcommunities, become prohibitive because the number of such subcommunities scales exponentially with the number of species. Here, we present an alternative, top-down approach, EPICS, which requires the assembly of subcommunities whose number scales linearly with the number of species, hugely reducing experimental effort. EPICS estimates effective pairwise interactions between species, which subsume high-order interactions, using data from monocultures and leave-one-out subcommunities and predicts community structures. The method is efficient and scalable to large communities.}, }
@article {pmid42156658, year = {2026}, author = {Roma Pi, J and Heinken, A}, title = {Personalized Constraint-Based Modeling of Microbial Communities from Metagenomic Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {233-260}, pmid = {42156658}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; Humans ; *Gastrointestinal Microbiome/genetics ; Precision Medicine/methods ; Software ; *Microbiota/genetics ; *Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; RNA, Ribosomal, 16S/genetics ; Systems Biology/methods ; }, abstract = {High-throughput metagenomic sequencing techniques such as 16S rRNA and shotgun sequencing have enabled an unprecedented understanding of the structure and function of microbiome communities such as the human gut microbiome. Tailored dietary or therapeutic interventions targeting the microbiome could advance personalized medicine; however, predicting such interventions requires predictive systems biology methods. Constraint-Based Reconstruction and Analysis (COBRA) is a mechanistic systems biology approach that relies on detailed genome-scale reconstructions of a target organism's metabolism. A resource of genome-scale reconstructions of human microbes, AGORA, and its expansion in size and scope, AGORA2, have been developed through a semi-automated refinement pipeline, DEMETER. A user-friendly analysis pipeline, mgPipe, allows building and interrogating personalized models of microbiome communities from AGORA and AGORA2. Through sample-specific simulations, mgPipe can stratify patients and controls by the distinct metabolic capabilities of their microbiomes, starting from the processed metagenomic sequencing data. Building on this functionality, the protocol provides a comprehensive workflow for the contextualization of metagenomics data through personalized, mechanistic modeling. Comprehensive tutorials for the DEMETER and mgPipe workflows are presented, which will enable both systems biologists and microbiome scientists to contextualize metagenomic data and perform mechanistic simulations of diet-microbiome-host interactions.}, }
@article {pmid42156661, year = {2026}, author = {Nawaz, A and Schaefer, JL and Centler, F}, title = {Dynamic Simulation of Growth and Cross-Feeding in Microbiomes with μbialSim.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {317-330}, pmid = {42156661}, issn = {1940-6029}, mesh = {*Microbiota ; Computer Simulation ; Software ; *Models, Biological ; Microbial Interactions ; Bioreactors/microbiology ; Computational Biology/methods ; }, abstract = {Microbial cells in natural environments are typically embedded in microbial communities consisting of few to many different species. Close proximity and high diversity of neighboring cells facilitate manifold interactions on several layers, from substrate competition, exchange of genetic material, to metabolic cross-feeding. The complexity of these ecological interaction networks makes microbiomes notoriously difficult to study. While microbiome dynamics can routinely be elucidated by meta-omics technologies, pinpointing mechanisms driving these observed dynamics remains a challenge. Mechanistic mathematical modeling with its ability to focus on individual interactions and exploring their isolated impact on overall dynamics has emerged as a suitable tool in this context. Here, we use μbialSim, an open-source simulator that extends the Flux Balance Analysis approach to microbial communities, considering substrate competition and metabolic cross-feeding but neglecting any other microbial interactions. Assuming a well-mixed bioreactor environment, simulated trajectories enable the analysis of growth behavior of individual microbiome members, dynamics of intracellular enzymatic fluxes across all species, as well as the analysis of cross-feeding behavior and how it changes over time. The MATLAB implementation of μbialSim is available from https://github.com/fcentler/microbialSim .}, }
@article {pmid42156754, year = {2026}, author = {Zhao, T and Li, B and Liu, Y and Zhang, J and Fan, X and Ao, M and Niu, Y and Li, D and He, J and Sun, D and Wu, H and Tang, T and Liu, Z and Huang, X}, title = {Enterococcus hirae QT4713-derived dopamine ameliorates intestinal inflammation and MPTP-induced Parkinson's disease in mice.}, journal = {NPJ Parkinson's disease}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41531-026-01392-x}, pmid = {42156754}, issn = {2373-8057}, support = {32200782//National Natural Science Foundation of China/ ; }, abstract = {Gut microbiota dysbiosis contributes to Parkinson's disease (PD) pathology by altering dopamine metabolism in the gut-brain axis. Although probiotics and other functional strains have been proposed as microbiome-based interventions, few naturally occurring gut microbes show therapeutic potential for PD. Here, we isolated Enterococcus hirae QT4713 (QT4713) from the hypoxic, low-pressure Qinghai-Tibet Plateau (4713 m altitude). Whole-genome sequencing revealed that QT4713 harbors a tyrosine decarboxylase gene (TyrDc), enabling conversion of L-tyrosine to dopamine in vitro. In mice, QT4713 enhanced antioxidant enzyme activity, reduced inflammatory mediators, reshaped gut microbial composition, and promoted short-chain fatty acid production. Metabolomic analyses indicated activation of L-tyrosine metabolism, with increased L-DOPA and dopamine levels in the colon and feces, accompanied by improved motor performance. In an MPTP-induced PD mouse model, QT4713 alleviated motor and gastrointestinal dysfunction, reduced oxidative and inflammatory damage, and attenuated dopaminergic neuron loss. QT4713 also increased dopamine and tyrosine levels in the striatum. Extending beyond an acute toxin model, QT4713 partially rescued PD-like phenotypes in TMEM175 knockout mice, preserving tyrosine hydroxylase-positive neurons in the substantia nigra. Together, these findings suggest that QT4713 can mitigate gastrointestinal disturbances and other PD-related deficits, consistent with combined effects on catecholamine-related metabolism and gut microbiota remodeling.}, }
@article {pmid42156769, year = {2026}, author = {Chen, R and Luo, S and Feng, Y and Maestre, FT and Sáez-Sandino, T and Gross, N and Le Bagousse-Pinguet, Y and Ochoa, V and Gozalo, B and Guirado, E and García-Gómez, M and Valencia, E and Asensio, S and Martínez-Valderrama, J and Mendoza, BJ and Abades, S and Alfaro, F and Barrett, M and Berdugo, M and Pastor, JLB and Blaum, N and Boldgiv, B and Bowker, M and Castro, H and Chu, H and Cutler, NA and Dai, Z and Deák, B and Durán, J and Espinosa, CI and Fajardo, A and Fan, K and Foronda, A and Fraser, LH and Geissler, K and Grebenc, T and Moltanvan, EG and Hart, SC and Kindermann, L and Köbel, M and Laanisto, L and le Roux, PC and Liancourt, P and Linstädter, A and Louw, MA and Macek, P and Maggs-Kölling, G and Makhalanyane, TP and Manzaneda, AJ and Marais, E and Montesinos, D and Mora, JP and Moreno, G and Munson, SM and Muñoz-Rojas, M and Nair, GR and Neuhauser, S and Nunes, A and Plaza, C and Pueyo, Y and Rey, PJ and Rey, A and Ríos, AL and Rodríguez, A and Lozano, BR and Roman, R and Ruppert, JC and Salah, A and Singh, J and Throop, HL and Travers, S and Nahberger, TU and Uuganbayar, M and Valkó, O and Wang, L and Williams, MA and Xiong, C and Xu, J and Zaady, E and Ma, B and Singh, BK and Delgado-Baquerizo, M}, title = {Functional restructuring of the global soil microbiome under multiple stressors.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73231-9}, pmid = {42156769}, issn = {2041-1723}, support = {42577352//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Microbes, as the planet's most abundant and diverse organisms, drive soil functions globally and are vulnerable to environmental stressors triggered by global change. Yet, knowledge regarding the impacts of multiple environmental stressors on their functional profiles as well as the consequences for soil functionality largely remains unknown. Here, we analyze two global-scale datasets including information on soil metagenomics and multiple environmental stressors. We find that across terrestrial ecosystems worldwide, up to 60% of all functional genes significantly shift when soil microbes experience the high-level of concurrent stressors. In this regard, the relative abundances of genes involved in microbial growth are negatively linked to the increasing number of stressors. Conversely, those genes linked to stress resistance and energy production exhibit positive responses. Taken together, our findings highlight a significant restructuring of global soil functional microbiomes in response to multiple environmental stressors. Consequently, such restructuring drives community-level shifts in matter and energy reallocations, thereby impacting the maintenance of soil functionality under the projected global change.}, }
@article {pmid42156772, year = {2026}, author = {Bamberger, T and Muller, E and Algavi, YM and Greenier, A and Adjangba, C and Slikas, E and Brassington, L and Mariner, B and McCoy, B and Harrison, BR and Partida-Aguilar, M and Marye, A and Harris, A and Rout, E and ,  and Avery, A and Promislow, DEL and Snyder-Mackler, N and Borenstein, E}, title = {Mapping the canine gut microbiome: insights from the Dog Aging Project.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73193-y}, pmid = {42156772}, issn = {2041-1723}, support = {U19AG057377//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; U19AG057377//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; U19AG057377//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; U19AG057377//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; }, abstract = {Companion dogs (Canis lupus familiaris) offer a unique model for studying the gut microbiome and its relation to aging due to their cohabitation with humans, sharing similar environments, diets, and healthcare practices. Here, we present the Dog Aging Project (DAP) Precision cohort, a large population-wide study of the canine gut microbiome. This cohort encompasses over 900 dogs of diverse breeds, environments, and demographics living across the United States. Coupling fecal shotgun metagenomic sequencing with phenotypic and environmental surveys and clinical lab tests, we explore the intricate relationships between microbiome composition, aging, and key factors such as health and living conditions. Our analyses identify multiple factors associated with microbiome composition, including dietary preferences such as commercial versus home cooked nutrition, and behaviors such as coprophagy (feces eating). In addition, we find age-associated gradual shifts in microbiome composition, supporting the development of a metagenomics-based population-level model for canine age prediction based on microbial signatures. We further examined which age-associated microbial patterns observed in humans are recapitulated in dogs by comparing our cohort with the Lifelines-DEEP cohort. Overall, these findings offer insights into the role the gut microbiome plays in our four-legged companions, with potential implications for veterinary medicine and translational aging research.}, }
@article {pmid42156980, year = {2026}, author = {Wiest, IC and Dreikhausen, L and Keller, R and Marin-Galiano, M and Albiges, L and Meran, J and Leucht, K and Rieken, S and Esteban, E and Zengerling, F and Tintelnot, J and Grimm, MO and Bozorgmehr, F and Christopoulos, P and Stein, A and Binder, M and Härtel, N and Klinghammer, K and Grünwald, V and Pogorzelski, M and Ebert, MP}, title = {Differential effects of prior versus concomitant Steroid and Antibiotic Treatment on Immunotherapy Efficacy - A Pooled Analysis of the RAMONA, INTEGA, OPTIM, ELDORANDO, FORCE, TITAN-RCC and TITAN-TCC Trials of the German AIO Study Group.}, journal = {British journal of cancer}, volume = {}, number = {}, pages = {}, pmid = {42156980}, issn = {1532-1827}, abstract = {BACKGROUND: We explored the association of immune-related adverse events (irAE), along with prior and concomitant antibiotic and steroid use, on oncological outcomes following immune checkpoint inhibitor (ICI) treatment in various solid tumours.<br><br>METHODS: Pooled data from seven trials on ICI therapy across multiple cancer types (head and neck, non-small cell lung cancer, gastroesophageal junctional adenocarcinoma, oesophageal, renal cell, and urothelial carcinoma) was analysed, focusing on overall survival (OS) and progression-free survival (PFS) and antibiotic or steroid use before and during the study.<br><br>RESULTS: Of 693 patients, 80 used steroids and 52 used antibiotics prior to the study, while 360 and 331, respectively, used them concomitantly. Lack of prior antibiotic use was associated with longer OS (No vs. Yes: HR 0.552, 95%-CI 0.370-0.822, p&#x2009;=&#x2009;0.0035) and PFS (No vs. Yes: HR 0.703, 95%-CI 0.485-1.019, p&#x2009;=&#x2009;0.0625), whereas concomitant antibiotic use had no such effect. Patients with concomitant steroid use demonstrated longer PFS (No vs. Yes: HR 1.359, 95%-CI 1.091-1.693, p&#x2009;=&#x2009;0.0061).<br><br>DISCUSSION: Our study confirmed associations between antibiotic and steroid use and ICI efficacy in cancer. Prior, but not concomitant, antibiotic use was linked to reduced OS, supporting the role of microbiome diversity in tumour response. Concomitant steroid use was associated with improved PFS, potentially reflecting its link to irAE occurrence.}, }
@article {pmid42157054, year = {2026}, author = {Cheng, S and Hao, X and Liu, S and Zhang, L and Zhang, S and Chen, Y and Wang, L and Xin, S and Li, Z and Hua, Z and Cao, H}, title = {Integrated multi-omics analysis reveals a gut microbiota-tryptophan metabolism axis contributes to sex differences in a β-aminopropionitrile-induced aortic dissection mouse model.}, journal = {Biology of sex differences}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13293-026-00925-6}, pmid = {42157054}, issn = {2042-6410}, support = {LHGJ20240212//the joint construction project of Medical Science and Technology Research Plan of Henan Province/ ; 82300717//the National Natural Science Foundation of China/ ; HNCMS202420//the Clinical Medical Scientist Training Program of Henan Province/ ; }, abstract = {BACKGROUND: Sex differences in aortic dissection (AD) have been consistently reported in epidemiological studies and experimental mouse models, with males showing markedly higher susceptibility. However, the molecular basis underlying these sex-specific differences remains insufficiently understood.<br><br>METHODS: Three-week-old male and female C57BL/6J mice were administered 0.4% &#x3b2;-aminopropionitrile (BAPN) in drinking water for 28 d to induce AD. After the induction period, fecal samples, serum, and aortic tissues were collected from all surviving animals. Integrated analyses included strand-specific transcriptomic sequencing of aortic tissues, untargeted serum metabolomics, and full-length 16&#xa0;S rRNA sequencing of fecal samples to characterize sex-related differences across transcriptomic, metabolic, and microbiome layers. Inter-omics correlations were further assessed using bioinformatic approaches. Furthermore, in vivo experiments were conducted to validate the impact of key metabolites on the progression of AD.<br><br>RESULTS: Female mice exhibited significantly lower susceptibility to BAPN-induced AD, including reduced rates of aortic rupture, lower incidence of AD or aneurysm (AAD), and attenuated aortic dilation. Transcriptomic analysis revealed that female non-dissected mice (FeNonAD) displayed diminished induction of inflammation-related genes and lower predicted immune cell infiltration. Metabolomic profiling revealed significant elevations of tryptophan-indole pathway metabolites-such as indolepyruvate, indole-3-acetic acid, and indolepropionic acid-in both FeNonAD and AAD groups. Microbiome analysis further revealed a higher relative abundance of tryptophan-metabolizing taxa, particularly key Clostridium species, in the intestinal tract of FeNonAD mice, accompanied by significant upregulation of key functional genes (tyrB and aspC) associated with indolepyruvate synthesis. Weighted gene co-expression network analysis (WGCNA)-based integration identified strong negative correlations between indolepyruvate and indole-3-acetic acid sodium salt levels and aortic gene modules linked to immune-inflammatory activation. Further in vivo experiments demonstrated that treatment with indolepyruvate delayed AD progression in male mice.<br><br>CONCLUSION: This study highlights a central "gut microbiota-tryptophan metabolism-aortic inflammation" axis that contributes to sexual dimorphism in BAPN-induced AD. These findings provide new molecular insights into sex-specific disease mechanisms and offer a conceptual basis for developing sex-tailored diagnostic and therapeutic strategies.}, }
@article {pmid42157110, year = {2026}, author = {Al Achkar, N and Privitera, GF and Arena, D and Nicotra, R and Ciccarello, L and Rizzo, GF and Pulvirenti, A and Spatafora, M and Restuccia, C and Branca, F}, title = {Exogenous microbial consortia modulate rhizosphere microbiome and yield of grafted tomato grown in the mediterranean greenhouse.}, journal = {BMC plant biology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12870-026-08962-4}, pmid = {42157110}, issn = {1471-2229}, support = {CN00000022//AGRITECH National Research Center (European Union Next-Generation EU, PIANO NAZIONALE DI RIPRESA E RESILIENZA, PNRR - MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4-D.D. 1032 17/06/2022)/ ; }, abstract = {BACKGROUND: The adoption of sustainable agricultural practices for intensive horticultural production could determine less damage to the ecosystem is a fundamental need increasing worldwide. In this trial the effect of two commercial microbial consortia, applied on two hybrid rootstocks of tomato grafted by two scions, were evaluated both on yield components and on the compositions of the rhizosphere microbiome. The rhizosphere was collected from each grafting combination, in both treated and non-treated plots. Microbiome DNA extracted was then sequenced by amplifying two specific regions ITS1-1F for fungus and 16SV34 for bacteria.<br><br>RESULTS: At the morphological level, the effect of microbial consortia application on the total production and yield showed to be highly dependent on the grafting combination, yield increased by 9.1, 10.3 and 12.6% in treated plots of Auto S2, R1/S1 and R1/S2 respectively but registered a reduction of 22.4% in NG.S2 and 9.3% in R2/S2 plots. The metagenomic sequencing revealed that fungal community composition was significantly influenced by both grafting combinations and microbial treatments (especially on the relative abundance of major phyla; Ascomycota and Basidiomycota), whereas bacterial communities exhibited stronger shifts in response to microbial consortia application than to grafting combinations. Correlation analysis between the rhizosphere microbial taxa, yield, and root weight highlighted significant associations supporting the potential of combined use of these practices. Notably, although the inoculated microorganisms were detected at low abundance or were not detectable in treated soils, pronounced shifts in the overall microbiome structure were observed, suggesting indirect yet significant ecological effects of the consortia.<br><br>CONCLUSION: This study demonstrates that microbial consortia and grafting synergistically enhance tomato productivity and modulate rhizosphere microbial communities in the monoculture degraded soil under intensive Mediterranean greenhouse conditions. These findings advance current understanding of plant genotype &#xd7; microbial consortium interactions by demonstrating that microbial inoculant relevant effects are highly modulated by plant genotype and can indirectly restructure rhizosphere microbial assemblages, contributing to the development of more sustainable and resilient horticultural systems.}, }
@article {pmid42157234, year = {2026}, author = {Shi, Y and Rao, Z and Liu, C and She, M and Yu, Y and Zhu, J}, title = {Microbial enterotype is linked to episodic and working memories via brain function in the parietal and occipital cortices.}, journal = {BMC biology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12915-026-02635-2}, pmid = {42157234}, issn = {1741-7007}, abstract = {BACKGROUND: Classification of human gut microbiome into distinct enterotypes based on gut microbial community composition has provided an attractive framework for population stratification. While empirical evidence indicates that microbial enterotype is related to brain function and memory, the neural processes underlying this interaction remain to be further characterized.<br><br>RESULTS: In 510 healthy young adults, we used 16S rDNA amplicon sequencing to perform enterotyping, acquired resting-state functional MRI data to calculate brain functional measures, and assessed both episodic and working memories. Inter-enterotype differences in brain functional measures were examined, followed by performance of correlation and mediation analyses to disentangle the potential associations between enterotype, brain function, and memory. We found significant differences in multiple brain functional measures in the parietal and occipital cortices across Bacteroides, Prevotella, and Ruminococcaceae enterotypes. Moreover, these differential brain functional measures were correlated with both episodic and working memories, and further mediated the relationship between enterotype and memory.<br><br>CONCLUSIONS: Our findings not only establish brain function as the mediating factor between enterotype and memory, but also hold translational potential for informing novel treatment for cognitive dysfunction via targeting the microbiota-gut-brain axis.}, }
@article {pmid42157265, year = {2026}, author = {Zia, B and AlKaabi, J and Agha, A and Sharma, C and Ali, BR}, title = {The diabetes exposome: interplay of environmental and genetic determinants in diabetes.}, journal = {Human genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40246-026-00987-y}, pmid = {42157265}, issn = {1479-7364}, support = {NP-25-05//College of Medicine and Health Sciences, United Arab Emirates University/ ; 12R270//United Arab Emirates University/ ; }, abstract = {Diabetes mellitus arises from complex interactions between biological susceptibility and diverse environmental influences that extend beyond traditional "genes versus lifestyle" models. The exposome is defined as the aggregate of non-genetic environmental exposures and their biological consequences across the life course. It provides a systems-level framework to evaluate this interaction, spanning chemical, physical, social, and behavioral domains while integrating them with internal molecular responses to decode how environments shape metabolic health. Emerging assessment strategies, including exposome-wide association studies (ExWAS), high-resolution mass spectrometry-based biomonitoring, geospatial and remote-sensing platforms, and wearable exposure sensors, enable characterization of multi-exposure profiles rather than single agents in isolation. Within exposome domains, air pollution, endocrine-disrupting chemicals, food-borne contaminants, exposome characteristics of the built environment, and chronic psychosocial stress have each been shown to contribute to the development and progression of both type 1 and type 2 diabetes. These diverse exposures often share common pathogenic mechanisms of chronic low-grade inflammation, oxidative and nitrosative stress, alterations in the gut microbiome, and epigenetic changes that ultimately lead to glucose dysregulation. Recent progress in metabolomics, lipidomics, and epigenomics is elucidating the "internal exposome," providing molecular fingerprints that encode prior exposure and detect early metabolic disruption. This integrated approach argues for a paradigm adjustment in diabetes prevention from behavior-centered strategies to those that also target upstream environmental determinants. Exposomic information can improve risk prediction, inform precision public health and medical practice, and inform policy regarding air pollution, chemical use, urban planning, and food systems. This review summarizes the current state of knowledge of the exposome in diabetes, describing its conceptual underpinnings, major tools of assessment, major epidemiologic findings, and biological mechanisms, and identifying the key challenges and opportunities for exposomics to inform effective approaches to diabetes prevention and planetary health.}, }
@article {pmid42157342, year = {2026}, author = {Jing, Y and Liu, S and Leng, L and He, J and Wang, T and Guan, Y and Su, Z and Zhang, W and Li, Y and Luan, P and Cheng, B and Wang, N and Li, H}, title = {Microbiota transplantation and multi-omics profiling integration unveil the mechanism of Alistipes communis-driven abdominal fat deposition in chickens.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42157342}, issn = {1674-9782}, support = {No. 2022YFF1000201//National Key Research and Development Program of China/ ; No. NK20221001//National Major Agricultural Science and Technology Project/ ; No. 32272863//National Natural Science Foundation of China/ ; No. CARS-41//The earmarked fund for CARS-41/ ; }, abstract = {BACKGROUND: Emerging evidence highlights strong correlations between the cecal microbiome and abdominal fat deposition (AFD) in chickens. However, the specific microbial species driving this process remain unclear. This study aims to identify the key microbe and elucidate its underlying mechanism in regulating chicken AFD.<br><br>RESULTS: First, cecal microbiota transplantation confirmed a causal relationship between the cecal microbiota and AFD. Subsequently, metagenomic and metatranscriptomic integrations identified Alistipes communis as a key microbe implicated in AFD. Finally, in vivo gavage integrated with multi-omics revealed that A. communis enhances AFD by disrupting host tryptophan and histidine metabolism. This was evidenced by the elevated concentrations of amino acid metabolism-related metabolites, including L-phosphoarginine and spermine in the cecum.<br><br>CONCLUSIONS: This study provides direct evidence that the cecal microbiome serves as a key driver in chicken AFD and identifies A. communis as a critical AFD regulator, offering valuable insights into the gut microbiome's role in host obesity.}, }
@article {pmid42157481, year = {2026}, author = {Garvey, K and Harris, JK and Furuta, GT and Occhipinti, KA and Wagner, BD and Fernandez, J and VeDepo, M and Fouquier, J and Hill, EB and Robertson, CE and Ackerman, S and Shandas, R}, title = {Minimally invasive capsule-string device enables spatially resolved microbiome profiling across the upper gastrointestinal tract.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2675764}, doi = {10.1080/19490976.2026.2675764}, pmid = {42157481}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Adult ; Male ; Female ; *Upper Gastrointestinal Tract/microbiology ; Middle Aged ; Young Adult ; Stomach/microbiology ; Esophagus/microbiology ; }, abstract = {Regional variation in the human gastrointestinal microbiome remains difficult to characterize because existing sampling methods either rely on invasive endoscopy or stool, which poorly reflects the upper gut. We evaluated a minimally invasive capsule-string device capable of collecting luminal and mucosal material from the esophagus, stomach, duodenum, and jejunum during natural transit. In healthy adults, compartment-level samples were anatomically localized using pH, bile staining, and string length, and microbial communities were profiled by 16S rRNA gene sequencing. The device was well tolerated and consistently recovered sufficient biomass from all upper GI regions. Distinct microbial signatures were evident across compartments, with the strongest differences observed between proximal (esophageal and gastric) and small-intestinal communities. Although the individual host exerted the dominant influence on the overall community structure, a reproducible regional signal persisted after accounting for between-person variation. These findings demonstrate that capsule-string sampling provides reliable access to spatially resolved upper GI microbiota without endoscopy. This approach enables more precise mapping of gut microbial organization in vivo and creates new opportunities for longitudinal, mechanistic, and disease-focused studies of host‒microbiome interactions in regions that have historically been inaccessible.}, }
@article {pmid42157498, year = {2026}, author = {Menadi, S and Cacan, E}, title = {Synergistic Anticancer Effects of Akkermansia muciniphila Combined With 5-Fluorouracil Through BAX/BCL2 Dependent Apoptosis in Colorectal Cancer Cells.}, journal = {Cell biochemistry and function}, volume = {44}, number = {5}, pages = {e70234}, doi = {10.1002/cbf.70234}, pmid = {42157498}, issn = {1099-0844}, support = {//Bilimsel Arastirma Projeleri/ ; }, mesh = {Humans ; *Fluorouracil/pharmacology ; *Apoptosis/drug effects ; *Colorectal Neoplasms/pathology/drug therapy/metabolism ; *bcl-2-Associated X Protein/metabolism/genetics ; *Proto-Oncogene Proteins c-bcl-2/metabolism/genetics ; *Akkermansia ; Drug Synergism ; Cell Survival/drug effects ; *Antineoplastic Agents/pharmacology ; Cell Line, Tumor ; }, abstract = {Colorectal cancer (CRC) continues to be one of the deadliest cancers worldwide, mainly due to late diagnosis, chemoresistance, and the complex interactions within the tumor microenvironment. Recent studies suggest that the gut bacterium Akkermansia muciniphila plays a key role in maintaining intestinal health and may influence the effectiveness of cancer therapies. Therefore, the main aim of this study was to explore whether a lyophilized form of A. muciniphila could support CRC treatment. First, we analyzed A. muciniphila abundance in healthy, adenoma, and CRC tissues using public datasets. Next, CRC cell lines (HT29, HCT116, and SW620) and normal stromal cells (Hs738 St/Int) were treated with increasing doses of the bacterial extract, alone and with 5-fluorouracil (5-FU). Then, cell viability measured by MTT assay, apoptosis by BAX/BCL2 expression via RT-qPCR, and physicochemical properties by zeta potential analysis. The results showed a marked reduction of A. muciniphila abundance in CRC samples, with an early decline from healthy to adenoma tissues and a slight recovery in advanced tumors. In vitro, the extract demonstrated dose-dependent cytotoxicity toward cancer cells, with HT29 showing strong sensitivity at low doses, HCT116 responding at higher concentrations, and SW620 exhibiting greater resistance. Importantly, the extract was well tolerated by normal cells, unlike 5-FU. Combining the extract with 5-FU resulted in a synergistic effect, indicating the possibility of reducing 5-FU dosage to limit its toxicity. The extract significantly upregulated BAX, downregulated BCL2, and displayed strong negative zeta potential, supporting enhanced apoptotic activation and selective interaction with cancer cell membranes. These findings suggest that A. muciniphila and its derived products may serve as promising adjuncts in personalized microbiome-based CRC therapy.}, }
@article {pmid42157503, year = {2026}, author = {Ponsero, AJ and Bahcivanci, B and Hayhoe, A and Acharjee, A and Özkurt, E}, title = {The human gut microbiome across the life course.}, journal = {FEBS letters}, volume = {}, number = {}, pages = {}, doi = {10.1002/1873-3468.70361}, pmid = {42157503}, issn = {1873-3468}, support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Across the human lifespan, the gut microbiome exhibits considerable inter-individual variation. However, individuals within the same age group often share characteristic compositional and functional patterns shaped by factors such as early microbial seeding, lifelong environmental exposures, and age-related physiological changes. Birth and early feeding establish the initial gut microbiome, with maternal transmission and milk-derived substrates typically favoring Bifidobacterium. As infants transition to solid foods and experience increasing social and environmental exposures, the microbiome undergoes substantial restructuring throughout childhood and adolescence. In adulthood, functional redundancy underpins stability despite routine perturbations; later life brings greater compositional uniqueness, with some profiles losing core taxa and accommodating opportunistic species, whereas others, particularly healthy older adults and centenarians, retain distinctive metabolic capacities that may buffer inflammaging. Efforts to build microbiome "aging clocks" highlight potential to index biological age, but progress remains constrained by technical and methodological limitations and is still maturing. This review synthesizes current evidence and identifies priorities for developing microbiome-informed, life-stage-tailored interventions.}, }
@article {pmid42157525, year = {2026}, author = {Aware, C and Woods, C and Khodakivskyi, P and Dwivedi, AK and Zuckerman, A and Govindarajan, M and Ivanich, K and Yu, W and Cui, J and Gu, Z and Goun, E and Ericsson, AC and Zafonte, R and Balchandani, P and Lin, AL}, title = {Stroke-induced gut microbiome dysbiosis accelerates Alzheimer's disease progression.}, journal = {Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism}, volume = {}, number = {}, pages = {271678X261449017}, doi = {10.1177/0271678X261449017}, pmid = {42157525}, issn = {1559-7016}, abstract = {Stroke survivors face an elevated risk of developing Alzheimer's disease (AD), yet the biological mechanisms linking these conditions remain poorly defined. Here, we show that a stroke-induced gut microbiome is a key driver of AD-related pathology. Fecal microbiota transplantation (FMT) from stroke patients into young triple-transgenic Alzheimer's disease (3xTg-AD) mice accelerated tau phosphorylation, increased neuroinflammation, and disrupted metabolic homeostasis in both the brain and gut, compared with FMT from healthy donors. Mice receiving stroke-derived microbiota exhibited persistent, donor-specific dysbiosis and broad metabolic reprogramming involving redox balance, nucleotide metabolism, and energy pathways in cecal contents and brain tissue. These metabolic disturbances were accompanied by widespread and region-specific transcriptional changes revealed by single-cell spatial transcriptomics, including glial activation, impaired neuron-glia communication, and dysregulation of mitochondrial, amyloid-processing and inflammatory pathways across cortical and hippocampal regions. Collectively, these findings identify post-stroke gut dysbiosis as a mechanistic contributor to heightened neurodegenerative vulnerability and AD risk, highlighting the gut-brain axis as a potentially modifiable target for preventing post-stroke dementia.}, }
@article {pmid42157533, year = {2026}, author = {Deriouich, M and Dompmartin, A and L'Orphelin, JM}, title = {Ultraviolet Radiations Impact on the Skin-Brain Axis: A Literature Review of our Current Knowledge.}, journal = {Photodermatology, photoimmunology &amp; photomedicine}, volume = {42}, number = {3}, pages = {e70097}, doi = {10.1111/phpp.70097}, pmid = {42157533}, issn = {1600-0781}, mesh = {Humans ; *Ultraviolet Rays/adverse effects ; *Brain/radiation effects ; *Skin/radiation effects/immunology/metabolism ; Animals ; Microbiota/radiation effects ; }, abstract = {BACKGROUND: Sunlight is essential for vitamin D synthesis and contributes to mood regulation, but it is also a major risk factor for skin aging and carcinogenesis. While the cutaneous and immune effects of ultraviolet radiation are well documented, its potential impact on brain function remains poorly understood. This review aims to synthesize current evidence on the effects of ultraviolet exposure on the central nervous system, with a particular focus on photoimmunological mechanisms and skin-derived signaling pathways.<br><br>METHODS: We conducted a narrative review of experimental and clinical studies investigating the systemic and neurological consequences of UV exposure. Findings from photodermatology, immunology, neuroscience, and microbiome research were integrated to examine potential skin-brain interactions.<br><br>RESULTS: UV exposure induces systemic inflammatory responses and immunosuppression, alters the skin microbiome, and modulates circulating neuroactive mediators. These processes are associated with changes in neurotransmitter systems, neuroplasticity, and brain structure in both animal models and human studies. Emerging evidence supports the existence of indirect pathways linking UV-induced skin and immune responses to central nervous system function, including immune and microbiota-related mechanisms.<br><br>CONCLUSION: Collectively, available data suggest that UV radiation may influence brain function indirectly through interconnected skin, immune, and microbiota pathways. As interest in balanced and "healthy" sun exposure increases, further interdisciplinary research is needed to clarify the neurological consequences of UV exposure and to assess its potential implications in photodermatology and photomedicine.}, }
@article {pmid42157753, year = {2026}, author = {Xu, H and Xu, B and Wang, H and Tao, R and Chen, R and Cheng, Y and Zheng, Z and Sun, D and Li, X}, title = {Lifestyle Modulation of Xenobiotic Stress: Aerobic Exercise Attenuates Nanoplastic-Associated Neuroendocrine Dysfunction via a Gut-Ovary-Brain Continuum.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {40}, number = {10}, pages = {e71891}, doi = {10.1096/fj.202600941R}, pmid = {42157753}, issn = {1530-6860}, support = {2025ZY01039//Central Government Funds For Guiding Local Scientific and Technological Development/ ; SHPY2025010//Scientific Research Cultivation Project of the College of Life and Environmental Sciences, Wenzhou University/ ; 2024K076//Quzhou Municipal Bureau of Science and Technology/ ; }, mesh = {Animals ; Female ; Zebrafish ; *Physical Conditioning, Animal/physiology ; *Ovary/drug effects/metabolism ; *Brain/metabolism/drug effects ; *Neurosecretory Systems/drug effects/metabolism ; Oxidative Stress/drug effects ; *Xenobiotics/toxicity ; *Nanoparticles/toxicity ; }, abstract = {Xenobiotic stress can disrupt neuroendocrine function, yet whether a modifiable lifestyle factor can alter internal burden and downstream toxicity remains unclear. Here, adult female zebrafish were exposed to polystyrene nanoplastics (NPs; 80 nm; 1.0 mg/L) for 21 days, with or without moderate aerobic exercise (AE; 12 cm/s, 20 min/day). NPs exposure alone caused significant ovarian accumulation of particle-like structures (TEM), elevated oxidative stress, increased follicular apoptosis (TUNEL), and disrupted reproductive hormones (E2, FSH, LH). It also induced anxiety- and depression-like behaviors in novel tank and shoaling tests, accompanied by elevated cortisol and altered monoamine (NE, 5-HIAA) levels. In contrast, concurrent AE markedly attenuated these effects: it reduced ovarian particle burden, improved antioxidant enzyme activities (SOD, POD), restored ovarian histoarchitecture, and normalized endocrine and neuroendocrine measures. These changes were supported by partial recovery of ovarian (ESR1, cyp19a1a, AMH) and brain (BDNF, TPH2) transcript levels. Gut microbiome profiling revealed that AE counteracted NPs-associated dysbiosis, enriching beneficial taxa, including Akkermansia and Lachnospiraceae_NK4A136_group. Predictive functional inference and correlation analyses linked these microbial shifts to enhanced fatty acid and tryptophan metabolic potential, which correlated with neuroendocrine recovery. Together, these data support a working model in which AE acts as an exposure modifier, coupling host physiology and microbiome-associated metabolic capacity to mitigate NPs-induced neuroendocrine dysfunction via a gut-ovary-brain continuum. Targeted metabolomics and causal microbiota perturbation will be needed to validate specific mediators.}, }
@article {pmid42157913, year = {2025}, author = {Nawaz, Y and Munir, S and Aslam, S and Butt, FR and Tanvir, F and Nawaz, B and Bashir, K and Tahreem, R}, title = {The Bacterial Role in the Progression of Breast Cancer through Mechanism of Gene Action: Future Prospects with Existing Studies.}, journal = {Current genomics}, volume = {26}, number = {6}, pages = {458-468}, pmid = {42157913}, issn = {1389-2029}, abstract = {BACKGROUND: Breast cancer is the main cause of death for women, even with major improvements in treatment. Through processes like DNA damage, estrogen metabolism, and immunological regulation, bacterial populations have been shown to have an impact on breast cancer development in recent studies.<br><br>OBJECTIVES: This review aimed to examine and evaluate current research on the involvement of bacteria in breast cancer progression, with an emphasis on gene action mechanisms and potential future treatments targeting the microbiome.<br><br>METHODS: A thorough literature analysis was carried out to identify pertinent research published between 1989-2024 across various databases, including PubMed, Google Scholar, Google, and Scopus.<br><br>RESULTS: Bacterial dysbiosis in the gut and breast tissue contributes to the progression of breast cancer through different pathways. Double-strand breaks in DNA are linked to various bacteria, like Escherichia coli, Staphylococcus epidermidis, Helicobacter pylori, and Fusobacterium, which contribute to genomic instability. Breast cancers are influenced by hormones that are influenced by gut microbiota, namely the estrobolome, which regulates estrogen levels. Bacteria also impact immune responses by preventing anti-tumor immunity. These results suggest that restoring microbial balance to specific bacterial taxa may open up new treatment options. Different genes may contribute to variations, including an increase in regulatory T (Treg) cells, while FOXP3+ T cells are linked to shorter relapse-free survival. Understanding the microbiota's role in DNA damage, hormone regulation, and immune modulation is important.<br><br>CONCLUSION: Bacteria contribute significantly to the development of breast cancer through gene-level processes. Probiotics, immunomodulatory techniques, and microbiome-targeted treatments are potential future developments that could improve therapy effectiveness and reduce resistance.}, }
@article {pmid42157925, year = {2026}, author = {Xiang, T and Xiao, S and Yang, C and Zhang, D and You, Y and Xie, L and Ling, Z and Wang, X and Zhang, C and Huang, G and Sun, D and Chen, Y and Luo, F}, title = {Tryptophan-Restricted Intermittent Diet Alleviates Estrogen Deficiency-Induced Osteoporosis via Regulating Coupling Effects of "Gut-Bone" Axis.}, journal = {International journal of biological sciences}, volume = {22}, number = {9}, pages = {4784-4805}, pmid = {42157925}, issn = {1449-2288}, mesh = {*Tryptophan ; Animals ; *Osteoporosis/metabolism/diet therapy/etiology ; *Gastrointestinal Microbiome/physiology ; Mice ; *Estrogens/deficiency ; Female ; Mice, Inbred C57BL ; *Bone and Bones/metabolism ; X-Ray Microtomography ; }, abstract = {Osteoporosis (OP) is a chronic and severe skeletal metabolic disorder resulting from excessive bone erosion activity and compromised bone formation. Emerging evidence highlights that the "gut-bone" axis plays a critical role in maintaining bone homeostasis via modulating gut microbiota and relevant metabolites. Individually, diet-derived tryptophan acts as one of the primary environmental factors that modulate the microbiota-bone crosstalk. Nevertheless, the promising modulatory mechanism of the "diet-microbiome-bone" axis remains unknown during OP progression. In this regard, the study focused on the dominant role of tryptophan-restricted intermittent diet during estrogen deficiency-induced OP. Upon these findings, micro-computed tomography (μCT) evaluation and histomorphometric analysis have confirmed that treatment with tryptophan-restricted intermittent diet effectively mitigated bone loss and improved bone microarchitecture. To unravel the underlying mechanism, we performed 16S rDNA gene sequencing and untargeted metabolomics to confirm the alteration of microbial community composition and metabolite profiles. Additionally, biotin was further identified as a significant microbiota-derived metabolite involved in M1 macrophage polarization and mature osteoclast apoptosis when administered with tryptophan-restricted intermittent diet. Thus, we summarized that treatment with tryptophan-restricted intermittent diet could perform a protective function during OP via modulating the coupling effects of gut microbiota and bone homeostasis, which may provide a potential therapeutic strategy for OP.}, }
@article {pmid42158361, year = {2026}, author = {Louise Jespersen, M and Kjærgaard Munk, K and Fjermedal, S and Pilgaard, B and Meyer, AS and Aarestrup, FM and Otani, S}, title = {A Hadza-enriched Prevotella/Segatella xyloglucanase shows sequence conservation and functional specialization.}, journal = {Gut microbes reports}, volume = {3}, number = {1}, pages = {2673265}, pmid = {42158361}, issn = {2993-3935}, abstract = {Bacteria can adapt to their environment through changes in their genetic material. A large proportion of gut bacteria are shaped by host-specific diet, including complex carbohydrates. The bacterial abundance, genetic content within the same bacterial species, and sequence-level variation in genes encoding similar carbohydrate-processing enzymes may therefore vary across hosts with different diets. We previously found that the abundance of diet-degrading genes varies between hominid host populations from Tanzania. We therefore hypothesized that, in addition to these abundance differences, selective pressure could act on individual gene sequences. Here, we investigated Tanzanian hominid gut microbiome differences at the taxonomic, genetic, structural, and functional levels. We analyzed 15,146 metagenome-assembled genomes (MAGs) spanning 1563 species and identified one species with striking host-associated separation. In particular, sequence variation in a xyloglucanase-encoding gene correlated strongly with the host population. This gene was highly conserved in the Hadza population, suggesting a role in the processing of diet-associated polysaccharides. Sequence differences and structural modeling revealed amino acid substitutions near the catalytic site, and biochemical assays using xyloglucan showed that representative variants differed in activity under identical assay conditions. Collectively, our findings suggest that host lifestyle and diet contribute to population-associated sequence variation in genes encoding enzymes involved in degrading polysaccharides.}, }
@article {pmid42158390, year = {2026}, author = {Zhang, J and Ren, Y and Jia, Y and Li, B and Chen, C and Hu, W and Jia, S and Li, D and Liu, Y}, title = {Effects of tangerine peel flavonoids on flavor compounds and microbial communities in cigar tobacco fermentation: insights from ion migration chromatography and microbiomics.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1793725}, pmid = {42158390}, issn = {1664-302X}, abstract = {INTRODUCTION: It is reported that addition of tangerine peel extract (flavonoids) can significantly improve the quality and flavor of tobacco leaves during fermentation. Nobiletin, tangeretin and hesperidin are the predominant flavonoids present in tangerine peel. However, their effects on the fermentation process of cigar tobacco leaves (CTL) have not yet been elucidated.<br><br>METHODS: Three major tangerine peel flavonoids, hesperidin (CPG), nobiletin (CCPS) and tangeretin (JPS), were applied during the fermentation of CTL) to evaluate their effects on fermentation outcomes. Gas chromatography-ion mobility spectrometry (GC-IMS) and microbiome analysis based on 16S rRNA and internal transcribed spacer sequencing were employed to characterize volatile flavor compounds and microbial community dynamics during the 30 days of fermentation.<br><br>RESULTS: A total of 157 volatile compounds were identified in CTL in this study. All tangerine peel flavonoid treatments improved the flavor quality of tobacco leaves by modulating the microbial community. The CPG group was enriched in esters and acids (e.g., n-amyl formate and propyl acetate), contributing to fruity aroma, with high relative abundances of Firmicutes and Staphylococcus, and a slight increase in Bacillus. The CCPS group accumulated abundant ketones (e.g., 3-methyl-2-cyclopenten-1-one, 3-pentanone, and 2-hydroxy-2-methyl-4-pentanone), providing caramel-like sweetness and enhancing the smoke body, while the enrichment of Sphingomonas, Rhizobium and other genera elevated bacterial diversity. The JPS group formed characteristic volatile compounds showed the highest fungal richness among all treatments. The mixed flavonoid (HHHT) group exhibited the highest abundance of Firmicutes and Staphylococcus, the lowest proportion of Proteobacteria, nearly undetectable harmful microorganisms, and the lowest microbial diversity. All treatment groups shared certain microbial trends, but distinct microbial profiles were observed among the CPG, CCPS, JPS, and HHHT groups, with significant correlations between key microorganisms and volatile flavor compounds.<br><br>DISCUSSION: In this study, the influence of tangerine peel flavonoids on CTL flavor quality and microbial community was systematically analyzed. These findings demonstrated that tangerine peel flavonoids enhanced flavor of CTL by modulating microbial communities during fermentation, and this provides new insights into CTL processing.}, }
@article {pmid42158396, year = {2026}, author = {McIntyre, DB and Barton, PS and Preston, S and Long, BM}, title = {Microbial succession in decomposing carrion is driven by time, modulated by insects and microbial perturbation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1773208}, pmid = {42158396}, issn = {1664-302X}, abstract = {Recent research into decomposition has shed light on the intricate interplay within multi-kingdom communities, with microbial populations emerging as key players in the breakdown process and emphasizing their interactions within the broader decomposer ecosystem. Despite this, the specific roles and regulatory mechanisms of microbial communities remain underexplored. Gaining deeper insight into these dynamics is essential for advancing ecological and forensic sciences. This study examines the role of microbes in decomposition, particularly in relation to insect activity and external microbiome alterations. We used 12 piglet (Sus scrofa) cadavers placed in a rural area in southern Australia, to investigate how experimental insect exclusion and microbial perturbation affects decomposition. Bacterial microbial composition was quantified using 16S technology and compared among treatments and time points. Results showed significant shifts in bacterial diversity and abundance across time points sampled, with early-stage decomposition characterized by a higher abundance of Firmicutes and Actinobacteria, followed by a dominance of Proteobacteria in later stages. Principal coordinate analysis confirmed these patterns, showing that while decomposition stage is the primary driver of diversity, insect access and microbial perturbation shape microbial stability and community shifts rather than overall diversity. This challenges assumptions that external factors strongly influence diversity and highlights the need to consider both time and microbial dynamics in forensic applications, particularly for post-mortem interval estimation.}, }
@article {pmid42158523, year = {2026}, author = {Muhammad, N}, title = {Nanobiotic-Enhanced Probiotics for Targeted Gut Delivery: Mechanisms, Therapeutic Applications, and Translational Challenges.}, journal = {International journal of nanomedicine}, volume = {21}, number = {}, pages = {607382}, pmid = {42158523}, issn = {1178-2013}, mesh = {*Probiotics/administration &amp; dosage/therapeutic use ; Humans ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Drug Delivery Systems/methods ; Gastrointestinal Tract/microbiology ; Gastrointestinal Diseases/therapy/microbiology ; Translational Research, Biomedical ; Nanotechnology ; Nanoparticles/chemistry ; }, abstract = {The gut microbiota plays a pivotal role in maintaining human health by influencing physiological processes such as digestion, immune regulation, and metabolism. However, disruptions in gut microbial balance, or dysbiosis, are associated with numerous disorders. Probiotics have emerged as potential therapeutic agents, but their efficacy is limited by challenges such as low survival during gastrointestinal transit, poor colonization, and lack of targeted delivery. Nanotechnology has recently provided promising solutions to these limitations by enhancing the stability, viability, and functionality of probiotics. To provide an updated perspective, this article presents a structured narrative review informed by a PRISMA-guided literature search and screening process. Relevant studies published between 2021 and 2025 were identified from PubMed, Scopus, IEEE Xplore, and Google Scholar and were narratively synthesized to examine nanoencapsulation strategies, hybrid nanobiotic systems, smart delivery platforms, therapeutic applications, and translational barriers. Nanoencapsulation techniques, hybrid nanobiotic systems, and smart delivery platforms are at the forefront of probiotic enhancement. These systems improve protection of probiotics against harsh gastric conditions and enable targeted release within specific regions of the gastrointestinal tract, thereby enhancing colonization efficiency and therapeutic potential. Moreover, nanobiotics show promise in modulating gut microbiota composition, strengthening immune responses, and opening new therapeutic avenues for the management of gastrointestinal disorders, metabolic diseases, and immune-related conditions. Despite these advances, challenges related to safety, scalability, and regulatory approval remain significant barriers to clinical translation. This review synthesizes recent progress in nanobiotic-enhanced probiotics, evaluates their therapeutic applications, and discusses key challenges and future directions for precision microbiome therapeutics.}, }
@article {pmid42158622, year = {2026}, author = {Math, RK and Javaregowda, PK and Patil, SG}, title = {Effect of Yoga and Meditation on Human Gut Microbiota: A Systematic Review.}, journal = {International journal of yoga}, volume = {19}, number = {1}, pages = {41-53}, pmid = {42158622}, issn = {0973-6131}, abstract = {The evidence from the clinical studies on the influence of yoga and meditation on gut microbiota in humans has been summarized in this systematic review. Searches were conducted until November 2023 in four electronic databases: SCOPUS, PubMed, Google Scholar, and Cochrane Controlled Registry of Trials (CENTRAL) to find relevant studies published in English. Studies on the influence of yoga and meditation on gut microbiome in human participants of any age or gender were included in the systematic review. The outcomes were modulations in the composition and function of gut microbiota and their metabolite levels. Due to the varied approaches used in the study designs and outcome measures of the included studies, a narrative synthesis was carried out. The database search resulted in 247 titles and abstracts, out of which four articles were included for qualitative synthesis. There was one nonrandomized controlled study and three observational studies. The studies were conducted on a healthy population (n = 440). The participants were followers of a vegan or vegetarian diet. The control group subjects were nonmeditators, i.e., who never received any meditation training. All the reviewed studies have shown a favorable change in the composition and function of gut microbiota and their metabolites with meditation practice when compared to controls. Yoga and meditation improved the composition and function of gut microbiota. However, all the subjects were following a vegetarian/vegan diet, so the beneficial changes demonstrated in the gut microbiota may be attributed to the combined effects of meditation and a vegetarian/vegan diet.}, }
@article {pmid42158814, year = {2026}, author = {Wu, CK and Cheng, IS and Chung, YC and Liu, MF and Lin, YK and Lin, YH and Morris, K and Chang, D and Chiang, CF and Yang, MT}, title = {The Effects of a Prebiotic Formula Promoting Akkermansia muciniphila (AKK) on Gut Health: A Single-Centre, Randomised Controlled Trial.}, journal = {International journal of medical sciences}, volume = {23}, number = {6}, pages = {1952-1965}, pmid = {42158814}, issn = {1449-1907}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Prebiotics/administration &amp; dosage ; Male ; Female ; Adult ; Middle Aged ; Verrucomicrobia ; Feces/microbiology ; Akkermansia ; }, abstract = {BACKGROUND: Gut health is closely associated with metabolic homeostasis, and alterations in gut microbiota composition have been linked to inflammation and metabolic disorders. Prebiotics targeting specific taxa, such as Akkermansia muciniphila, have attracted interest for their potential to modulate gut microbiota composition. While preclinical studies have suggested a role for A. muciniphila in gut-related metabolic pathways, clinical evidence supporting its effects on microbiome regulation and metabolic outcomes remains limited. Therefore, this study aimed to explore the effects of a prebiotic blend designed to promote A. muciniphila on gut microbiota composition and selected physiological parameters.<br><br>METHODS: Seventy participants were randomized to receive either placebo or the AKK formula for 8 weeks. Anthropometric assessments, blood tests, and stool examinations were performed at baseline and at weeks 4 and 8. The main analyses were conducted in the per-protocol population (n = 25 per group).<br><br>RESULTS: The results revealed no significant markers of liver or kidney dysfunction in either group. The AKK formula group showed an increased qPCR-derived relative abundance of A. muciniphila compared with total bacteria. Gut microbiome analysis further demonstrated selective changes in gut microbiota composition in the AKK formula group, including an increased relative abundance of Bifidobacterium and decreased relative abundances of Proteobacteria, Erysipelotrichia, and Escherichia-Shigella. A trend toward lower gastrointestinal discomfort scores was observed in the AKK formula group during the intervention period.<br><br>CONCLUSIONS: The AKK formula increased the relative abundance of A. muciniphila, was associated with selective modulation of gut microbiota composition, and showed a trend toward reduced gastrointestinal discomfort, supporting its potential relevance in future gut health research.}, }
@article {pmid42158827, year = {2026}, author = {Lin, LT and Li, CJ and Lin, PH and Cheng, SH and Raj, EN and Chen, YC and Chern, CU and Wen, ZH and Tsui, KH}, title = {Targeted Vaginal Microbiome Modulation by Postbiotic Intervention Reduces Dysbiosis-Associated Pathogens in Infertile Women: A Pilot Study.}, journal = {International journal of medical sciences}, volume = {23}, number = {6}, pages = {1921-1932}, pmid = {42158827}, issn = {1449-1907}, mesh = {Humans ; Female ; *Dysbiosis/microbiology/drug therapy/therapy ; Adult ; *Vagina/microbiology/drug effects ; Pilot Projects ; *Microbiota/drug effects/genetics ; Pregnancy ; *Infertility, Female/microbiology/therapy ; Embryo Transfer/methods ; Lactobacillus/drug effects/isolation &amp; purification/genetics ; Fertilization in Vitro/methods ; RNA, Ribosomal, 16S/genetics ; Pregnancy Rate ; *Antimicrobial Peptides/administration &amp; dosage ; }, abstract = {BACKGROUND: Vaginal dysbiosis characterized by depleted Lactobacillus populations is associated with impaired fertility outcomes in women undergoing assisted reproduction. Postbiotic interventions delivering antimicrobial peptides without live bacteria may offer targeted microecological modulation while preserving community stability. We investigated the microbial and clinical effects of an eight-week antimicrobial peptide-based postbiotic in infertile women.<br><br>METHODS: Fifteen infertile women (mean age 38.7 &#xb1; 4.1 years) with &#x2265; 2 prior in vitro fertilization failures received intravaginal postbiotic therapy (VAGINNE[&#xae;], Good-Care Biotech, Ltd.) for 8.0 &#xb1; 0.3 weeks before frozen embryo transfer (FET). Paired vaginal samples collected pre- and post-treatment underwent full-length 16S rRNA gene sequencing using PacBio Sequel platform. Microbiome composition, beta-diversity, differential abundance, and absolute bacterial load were analyzed.<br><br>RESULTS: The cohort achieved a clinical pregnancy rate of 46.7% (7/15) following postbiotic intervention and subsequent FET. Beta-diversity analysis revealed preservation of global community structure (PERMANOVA R&#xb2; = 0.05, p = 0.65), indicating ecological stability. Despite cohort-level stability, patient-specific analysis identified favorable microbiome restructuring in 73% of participants (11/15), including emergence of Lactobacillus-dominant communities in previously dysbiotic profiles. Absolute abundance quantification demonstrated selective elimination of dysbiosis-associated pathogens: Prevotella decreased from 408.47&#xb1;990.78 to 0.29&#xb1;0.83 cells/sample (p < 0.01), Pseudomonas from 419.07&#xb1;567.04 to 89.14&#xb1;114.42 (p < 0.05), and complete clearance of Howardella (3.53&#xb1;9.87 to undetectable). Conversely, Gluconacetobacter increased significantly from undetectable to 2.93&#xb1;4.18 cells/sample (p < 0.05).<br><br>CONCLUSIONS: In this pilot cohort, antimicrobial peptide-based postbiotic therapy was associated with encouraging pregnancy outcomes and targeted pathogen clearance. The intervention selectively reduced high-burden detrimental taxa while maintaining microbiome architectural integrity, supporting precision microecological modulation as a promising adjuvant strategy for reproductive health.}, }
@article {pmid42158829, year = {2026}, author = {Zhao, ZK and Ma, JL and Lu, F and Wang, SJ}, title = {Exosomes in Inflammatory Bowel Disease: Mechanisms, Diagnostic Potential, and Engineering Strategies for Precision Therapy.}, journal = {International journal of medical sciences}, volume = {23}, number = {6}, pages = {2141-2153}, pmid = {42158829}, issn = {1449-1907}, mesh = {*Exosomes/metabolism/immunology ; Humans ; *Inflammatory Bowel Diseases/diagnosis/therapy/immunology ; Biomarkers/metabolism ; *Precision Medicine/methods ; Gastrointestinal Microbiome/immunology ; Drug Delivery Systems/methods ; Animals ; }, abstract = {Inflammatory bowel disease (IBD) is a chronic gastrointestinal disorder characterized by immune dysregulation, epithelial barrier dysfunction, and microbial imbalance. Despite progress in biologic therapies, challenges such as variable efficacy, systemic side effects, and the lack of reliable biomarkers remain significant obstacles in clinical management. Exosomes, key mediators of intercellular communication, play a pivotal role in IBD's pathogenesis by transporting bioactive substances. Increasing evidence links exosomes to critical IBD processes, including Th17/Treg imbalance, inflammasome activation, and host-microbiome interactions. Exosomes also show potential as minimally invasive biomarkers for disease activity and subtype differentiation. Furthermore, advancements in exosome engineering, including surface modification and hybrid nanostructure development, enhance their potential for targeted drug delivery and immune modulation in IBD. This review summarizes the role of exosomes in IBD, their diagnostic potential, and emerging exosome-based therapeutic strategies.}, }
@article {pmid42159017, year = {2026}, author = {Baumann, PC and Pospich, R and Döhner, K and Klug, I and Guerrero, JCV and Hartmann, J and Harder, I and Lieb, W and Kind, B and Kleinheinz, A and Abraham, S and Augustin, M and Weisshaar, E and Schmitt, J and Weidinger, S and Sodeik, B and Werfel, T and Roesner, LM and Traidl, S and , }, title = {Keratinocyte Priming by Staphylococcus aureus Reduces HSV-1 Susceptibility.}, journal = {Allergy}, volume = {}, number = {}, pages = {}, doi = {10.1111/all.70392}, pmid = {42159017}, issn = {1398-9995}, abstract = {BACKGROUND: Individuals with atopic dermatitis (AD) are at increased risk for skin infections, including eczema herpeticum (EH), a severe condition caused by herpes simplex virus type 1 (HSV-1). While AD skin is often colonized by Staphylococcus aureus (S. aureus), its role in EH susceptibility remains unclear. Here we aim to investigate differences in the skin microbiome of AD patients with (ADEH[+]) and without (ADEH[-]) EH and examine the impact of S. aureus and S. epidermidis on HSV-1 infection in an in vitro keratinocyte model.<br><br>METHODS: 16S microbiome sequencing was performed on skin samples from ADEH[+], ADEH[-], and healthy controls. To investigate microbial effects on HSV-1 infection, keratinocytes were pre-incubated with heat-killed S. aureus (HKSA) or S. epidermidis (HKSE), followed by HSV-1 infection in the presence or absence of the Th2 cytokines IL-4 and IL-13, simulating the conditions of AD lesional skin. Infection rates and transcriptomic changes were analyzed.<br><br>RESULTS: ADEH[+] patients showed a reduced microbial diversity compared to ADEH[-], with increased S. aureus and S. epidermidis colonization. HKSA, but not HKSE, protected keratinocytes from HSV-1 infection and reduced the release of infectious progeny virus. Transcriptome analysis of keratinocytes revealed HKSA-induced upregulation of interferon pathways and antimicrobial peptides, and downregulation of HSV-1 entry factors.<br><br>CONCLUSION: Pre-incubation with S. aureus set basal keratinocytes into an alarmed state, restricting HSV-1 infection presumably via downregulation of receptors important for viral entry and activation of antiviral pathways.}, }
@article {pmid42159080, year = {2026}, author = {Junaid, M and Zeming, H and Zhu, Y}, title = {The Leptin Renaissance: Orchestrating the Next Endocrine Paradigm.}, journal = {Journal of cellular biochemistry}, volume = {127}, number = {5}, pages = {e70091}, doi = {10.1002/jcb.70091}, pmid = {42159080}, issn = {1097-4644}, support = {2024Z034//Major Project of 2035 Sci &amp; Tech Innovation of Ningbo/ ; 2024Z204//Major Project of 2035 Sci &amp; Tech Innovation of Ningbo/ ; //K.C. Wang Magna/Education Fund of Ningbo University/ ; }, mesh = {*Leptin/metabolism/immunology ; Humans ; Animals ; *Obesity/metabolism/immunology ; *Gastrointestinal Microbiome ; Energy Metabolism ; Endocrine System/metabolism ; Signal Transduction ; Homeostasis ; }, abstract = {Leptin, a hormone historically recognized for regulating appetite and energy homeostasis, is increasingly appreciated as a central mediator of immune function, metabolic integration, and tissue-specific signaling. Despite decades of research, leptin resistance limits the efficacy of conventional therapies, such as hormone replacement, in treating obesity and related disorders. Emerging evidence demonstrates that leptin interacts bidirectionally with the gut microbiome, influencing systemic metabolism and immune responses. Advances in multi-omics profiling, synthetic biology, and tissue-targeted therapeutics provide unprecedented opportunities to overcome these barriers. Here, we present a perspective emphasizing integrative strategies that combine precision medicine, immune modulation, engineered leptin analogs, and microbiome-targeted interventions. Leveraging these innovations could redefine leptin-based therapies, enabling system-level restoration of metabolic and immune homeostasis. Understanding leptin as a pleiotropic, multi-system hormone positions it at the forefront of the next endocrine paradigm.}, }
@article {pmid42159306, year = {2026}, author = {Sakai, M and Mori, I and Kawasaki, A and Takigawa, H and Kinoshita, K and Aosaki, T and Sakasai, M and Sugai, Y}, title = {Kytococcal and Staphylococcal strains isolated from Japanese subjects with foot malodor and their control.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxag121}, pmid = {42159306}, issn = {1365-2672}, abstract = {AIMS: Human foot malodor has been reported to be derived from volatile fatty acids, mainly isovaleric acid, generated by foot bacteria, especially staphylococcal species. However, the knowledge of foot odor is limited compared with axillary odor. Therefore, this study was conducted to identify the causative bacteria of foot malodor in Japanese individuals and to explore methods for controlling foot odor.<br><br>METHODS AND RESULTS: 16S rRNA gene-targeted microbiome analysis and qPCR analysis were performed on samples from the plantar surface and toe clefts. 16S rRNA gene sequencing was used to identify isolates. Commercially available botanical extracts were screened for their ability to inhibit microbial production of malodorous compounds, specifically the conversion of L-leucine to isovaleric acid. Microbiome analysis and qPCR indicated that Kytococcus is associated with the intensity of isovaleric acid-like odor. 16S rRNA gene analysis of isolates identified Kytococcus schroeteri and Staphylococcus hominis as isovaleric acid-producing strains. Screening of botanical extracts revealed that Sanguisorba officinalis and Eucalyptus globulus extracts effectively inhibited the generation of isovaleric acid from L-leucine.<br><br>CONCLUSIONS: Kytococcus, particularly K. schroeteri and S. hominis are implicated in isovaleric acid-mediated foot malodor in Japanese subjects. Extracts of Sanguisorba officinalis and Eucalyptus globulus show potential as control agents by inhibiting microbial production of isovaleric acid.}, }
@article {pmid42159380, year = {2026}, author = {Shao, H and Yoo, H and Cai, J-N and Jung, H-Y and Kang, C-M and Jeon, J-G and Kim, D}, title = {H2O2-producing commensal streptococci disrupt Streptococcus mutans-Candida albicans synergism.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0033326}, doi = {10.1128/aem.00333-26}, pmid = {42159380}, issn = {1098-5336}, abstract = {Microbial homeostasis is maintained by the antagonistic capacity of commensal bacteria against cariogenic pathogens. In the oral cavity, commensal Streptococcus, dominant colonizers of the tooth surface, can produce hydrogen peroxide (H2O2), modulating virulent cross-kingdom biofilm formation. To investigate their ecological role, clinical isolates from dental plaque were compared with reference strains, including Streptococcus oralis ATCC 35037 and S. oralis subsp. tigurinus J22 to determine their H2O2-producing capabilities. The antagonistic potential of S. oralis against Streptococcus mutans and Candida albicans was evaluated using microbial and biochemical assessments. In a saliva-coated hydroxyapatite disc model, S. oralis strains were co-cultured with S. mutans and C. albicans. A high H2O2-producing S. oralis J22 inhibited EPS formation in S. mutans and yeast-to-hypha transition in C. albicans, thereby reducing EPS-mediated bacterial-fungal cell colocalization. Time-lapse confocal imaging revealed that S. oralis J22 dominated the biofilm through H2O2-mediated antagonistic interactions. In contrast, the inhibitory effect of S. oralis strains lacking the spxB gene on cross-kingdom biofilms was significantly reduced. These data provide ecological insights into how physicochemical properties of early colonizing commensals shape the structure and virulence of cross-kingdom oral biofilm through antimicrobial-mediated antagonistic activity.IMPORTANCEThe co-existence of S. mutans and C. albicans accelerates the development of severe early childhood caries, particularly under frequent sucrose exposure. This study demonstrates that early colonizing and antimicrobial-producing oral commensal bacteria can disrupt these pathogenic interactions by modulating their physicochemical associations. These findings highlight the potential of enhancing commensal bacteria as part of novel caries prevention strategies. Further characterization of the functional oral microbiota, especially clinically relevant oral commensals, could advance the development of diagnostic biomarkers and microbiome-targeted therapeutics to prevent painful and costly oral diseases.}, }
@article {pmid42159387, year = {2026}, author = {Wang, X-R}, title = {mSphere of Influence: How a gut microbiota study reshaped my thinking on tick-borne pathogens.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0021326}, doi = {10.1128/msphere.00213-26}, pmid = {42159387}, issn = {2379-5042}, abstract = {Xin-Ru Wang works in tick biology and intracellular bacterial pathogenesis. In this mSphere of Influence article, she reflects on how "Gut microbiota of the tick vector Ixodes scapularis modulate colonization of the Lyme disease spirochete" by Narasimhan et al. (2014) reshaped her understanding of vector competence by placing pathogen colonization within the ecological context of the tick microbiome. Her laboratory studies Rickettsia-tick cell interactions, including autophagy, apoptosis, and innate immune signaling. Here, she examines how this ecological framework extends to the intracellular level, where pathogenic Rickettsia may encounter cellular environments already shaped by resident endosymbionts.}, }
@article {pmid42159410, year = {2026}, author = {Rodriguez, TN and Smeyne, RJ and Smeyne, M}, title = {Neurobiology of exercise in Parkinson's disease.}, journal = {Journal of Parkinson's disease}, volume = {}, number = {}, pages = {1877718X261452869}, doi = {10.1177/1877718X261452869}, pmid = {42159410}, issn = {1877-718X}, abstract = {Epidemiological, preclinical, and clinical studies increasingly support exercise as a potent neuroprotective and disease-modifying intervention in Parkinson's disease (PD). Preclinical studies, including toxin- and α-synuclein-based models, using voluntary, forced, and skilled exercise paradigms demonstrate preservation of nigrostriatal dopaminergic neurons, improved motor function, and activation of convergent pathways. Protective processes include upregulation of neurotrophic factors (BDNF, GDNF, VEGF and Irisin), enhanced mitochondrial biogenesis and oxidative resilience, reduced neuroinflammation, improved basal ganglia synaptic plasticity and increased lysosomal functions. Additional emerging mechanisms underlying exercise-induced neuroprotection involve vascular remodeling, pathways regulating cellular oxygen and hypoxia, modulation of the gut microbiome, and epigenetic reprogramming. Importantly, clinical studies mirror these preclinical findings, demonstrating improvements in motor symptoms, balance, fitness, and quality of life, along with functionally positive changes in exercise-responsive biomarkers such as BDNF, irisin, and glutathione. Collectively, these highlight exercise as a robust, multifaceted therapeutic strategy with significant implications for PD prevention and management. This review synthesizes findings from the past 5 years across preclinical models and patient studies to define how exercise reduces PD risk, slows symptom progression, and engages biological pathways relevant to neuroprotection and restoration.Lay abstractExercise, as a consistent lifestyle habit, is beneficial to overall health with cardiovascular and cognitive benefits; and also supports a better quality of life throughout aging. Exercise has been demonstrated to reduce the risk of developing Parkinsons's Disease as well as to delay the symptoms of PD. In this review we will report recent (2020-2025) preclinical and clinical studies that examine the mechanisms underlying exercise's neuroprotective benefit related to PD.}, }
@article {pmid42159601, year = {2026}, author = {Yang, Y and Lian, S and Li, X and Tang, Y and Su, Y and Zhang, Z and Li, M and Guo, Y and He, Z and Shen, Y}, title = {Unveiling metagenomic and metabolomic signatures in mild and severe pneumonia caused by Mycoplasma pneumoniae in children.}, journal = {Microbial genomics}, volume = {12}, number = {5}, pages = {}, pmid = {42159601}, issn = {2057-5858}, mesh = {Humans ; *Mycoplasma pneumoniae/genetics/pathogenicity/metabolism ; *Pneumonia, Mycoplasma/microbiology/metabolism/diagnosis ; Female ; Male ; Child, Preschool ; Child ; *Metagenomics/methods ; *Metabolomics/methods ; Prospective Studies ; Bronchoalveolar Lavage Fluid/microbiology ; Infant ; Severity of Illness Index ; Microbiota ; Machine Learning ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Background. Mycoplasma pneumoniae (MP) is a common causative pathogen of community-acquired pneumonia in children, with clinical presentations ranging in severity. Early stratification and timely intervention are essential for improving patient outcomes. However, a major clinical challenge lies in the limited ability to accurately distinguish between mild and severe cases based solely on early clinical indicators.Methods. This prospective real-world study investigated the differences in microbiome and metabolomics between mild and severe MP pneumonia (MPP) in children. Bronchoalveolar lavage fluid samples were collected from 153 children and subjected to metagenomic sequencing and non-targeted metabolomic analysis. Meanwhile, to enhance early diagnostic accuracy, this study developed a machine learning classification model and validated it using a third-party validation set.Results. The results revealed significant alterations in the abundance of specific bacterial communities in the severe group, most notably the coexistence of MP and Alphainfluenzavirus influenzae, which may contribute to disease exacerbation through synergistic pathogenic mechanisms. Furthermore, the macrolide resistant rate of MP in the severe group exceeded 80%, emphasizing the importance of appropriate antibiotic selection. Metabolomic analysis showed a significant enrichment of metabolites related to cellular energy metabolism and immune regulation in severe cases. The model demonstrated exceptional predictive performance, achieving an area under the curve ranging from 0.909 to 0.991, which significantly outperformed conventional clinical stratification methods.Conclusions. These findings elucidate the distinct pathophysiological mechanisms underlying both mild and severe MP infections and provide a promising framework for improving early diagnosis and personalized treatment strategies in paediatric MPP.}, }
@article {pmid42159807, year = {2026}, author = {Fulaneti, FS and Brasil-Neto, ES and Rumpel, VS and de Paula Ribeiro, L and Brum, LN and Cipriani, LP and Martin, TN}, title = {Microbial co-inoculation and extracellular vesicles: new frontiers for soybean productivity.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {6}, pages = {}, pmid = {42159807}, issn = {1572-9699}, mesh = {*Glycine max/microbiology/growth &amp; development ; *Extracellular Vesicles/metabolism ; Bacteria/metabolism/genetics ; Soil Microbiology ; Crops, Agricultural/growth &amp; development/microbiology ; Agriculture/methods ; *Agricultural Inoculants ; }, abstract = {Over the past decades, the intensive use of chemical fertilizers in agriculture has shown low efficiency while causing serious environmental issues and leading to soil nutrient imbalances. These challenges are compounded by climate change, increasing incidence of diseases and pests, and soil acidification, factors that jeopardize agricultural productivity and, consequently, threaten global food security. Soybean (Glycine max L.) is one of the world's most important crops, serving as a key source of protein and oil for both human consumption and animal feed. Its global relevance continues to grow with rising demand for food, biofuels, and industrial applications, with Brazil, the United States, and Argentina leading production. Beyond its economic value, soybean contributes to agricultural sustainability through symbiotic nitrogen fixation, reducing the need for synthetic fertilizers. However, maintaining high yields under changing environmental conditions requires innovative management strategies. In this context, one promising strategy to mitigate these problems is the use of plant growth-promoting bacteria (PGPB), which contribute to more sustainable crop yield. Although numerous studies are underway regarding the potential of PGPB, further research is still necessary due to the limited understanding of their mechanisms of action and the vast range of benefits they may offer. Currently, there is a wide variety of inoculants based on different bacterial species, which play a key role in stimulating plant growth and reducing reliance on agrochemicals. Among emerging technologies, noteworthy examples include molecular inoculants (still not widely adopted commercially), bacterial and fungal consortia formulated into a single product, and inoculants containing genetically edited microorganisms-all of which have shown great promise in enhancing the performance of beneficial microbial species. The selection and genetic editing of rhizosphere-associated PGPB-an essential component of the plant microbiome-are viable alternatives for promoting more sustainable agriculture. Thus, this review examines the main inoculant technologies aimed at obtaining efficient microorganisms capable of improving rhizosphere conditions and microbial community dynamics, representing a strategic opportunity for developing solutions that enhance soybean sustainability.}, }
@article {pmid42159891, year = {2026}, author = {McKay, S and Li, XM}, title = {Understanding Infantile Atopic Dermatitis: A Review of Environmental, Familial, Genetic and Microbial Influences.}, journal = {Current allergy and asthma reports}, volume = {26}, number = {1}, pages = {}, pmid = {42159891}, issn = {1534-6315}, mesh = {Humans ; *Dermatitis, Atopic/etiology/genetics/microbiology/epidemiology/prevention &amp; control ; Infant ; Female ; Pregnancy ; Microbiota ; Infant, Newborn ; *Environmental Exposure/adverse effects ; Probiotics ; Risk Factors ; Gastrointestinal Microbiome ; }, abstract = {PURPOSE OF REVIEW: This review aims to clarify the early-life risk and protective factors associated with Infantile Atopic Dermatitis (IAD)-an inflammatory skin condition that typically develops between birth and two years of age. The goal was to examine recent findings on maternal, environmental, and microbial influences on IAD.<br><br>RECENT FINDINGS: Prenatal and postpartum maternal probiotic use may reduce IAD risk, though no significant alterations in infants' gut microbiota were found. Infants with IAD exhibit higher Clostridia levels, while Verrucomicrobia are more abundant in non-IAD cases. Breastmilk from the mother of affected infants contains higher arachidonic acid and lower eicosapentaenoic acid, whereas formula-feeding may lower IAD risk. Seasonal influences such as reduced sunlight or humidity are associated with higher susceptibility. Elevated skin biomarkers, including TARC/CCL17 and IL-8, have been observed in infants who later develop IAD. Early antibiotic exposure, particularly during the first trimester, also increases risk.&#xa0; IAD is multifactorial, involving genetics, environment, and skin barrier dysfunction. Understanding the interplay between the microbiome, maternal influences, and environmental exposures may guide future preventive approaches. Further research into non-pharmacologic and microbiome-targeted interventions is warranted to delay or prevent IAD onset.}, }
@article {pmid42160091, year = {2026}, author = {Ruiz-Torres, NG and Martínez-Sánchez, S and de León-Lorenzana, A and Mercado-Juárez, RA and Salloum, PM and Poulin, R and Gaona, O and Falcón, LI and Rico-Chávez, O}, title = {Drivers of Microbiome Composition Among Helminth Parasites Sharing the Same Insectivorous Bat Host.}, journal = {Molecular ecology}, volume = {35}, number = {10}, pages = {e70389}, doi = {10.1111/mec.70389}, pmid = {42160091}, issn = {1365-294X}, support = {BV200421//PAPIIT-DGAPA, UNAM/ ; IN218020//PAPIIT-DGAPA, UNAM/ ; }, mesh = {Animals ; *Chiroptera/parasitology/microbiology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Microbiota/genetics ; *Helminths/genetics/microbiology/classification ; Trematoda/microbiology/genetics ; Host-Parasite Interactions ; }, abstract = {Parasitic metazoans are increasingly recognised to form close associations with microbial taxa. Under the holobiont concept, these associations are an eco-evolutionary unit under joint selection. However, for most parasitic helminth species and particularly those associated with wildlife, these interactions and their effect on parasite evolution remain unknown. Investigating the factors determining the composition of helminth microbiomes is the first step towards a better understanding of helminth holobionts. Using the insectivorous bat Peropteryx kappleri and its parasitic helminths as a model system, we characterised the microbiome of 41 helminth individuals of four trematode and one nematode species in various bat intestinal and biliary microhabitats, along with bat tissues and luminal fluids. Our results based on 16S rRNA metabarcoding revealed that the microbiome composition of the different helminth species is partly influenced by their microhabitat (bat tissue), but ultimately each helminth species exhibits a distinctive microbial signature. Microbiome composition among the four trematode species showed no phylogenetic signal (no correlation with genetic similarity). Compared to the bat host, each helminth species exhibited enriched microbial taxa with putative symbiotic potential, some of which are commonly found in arthropods (potential intermediate hosts of helminths) and may be conserved throughout the parasite's life cycle. We propose that helminth microbiomes are determined by ecologically relevant factors and provide a basis for future functional research with implications for parasite establishment, development, and transmission.}, }
@article {pmid42160107, year = {2026}, author = {Yan, G and Wang, S and Li, D and Liu, R and Zhang, Z and Zhang, Z and Kan, Y}, title = {Effects of dietary royal jelly supplementation on development, fecundity, and gut microbial community in Sarcophaga peregrina (Diptera: Sarcophagidae).}, journal = {Journal of economic entomology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jee/toag074}, pmid = {42160107}, issn = {1938-291X}, support = {231111111000//Key Research Project of Henan Province/ ; 251111113200//Key Research Project of Henan Province/ ; }, abstract = {Intensive laboratory rearing often reduces key phenotypic traits in farmed insects. We tested royal jelly (RJ) as a nutritional intervention in Sarcophaga peregrina (Robineau-Desvoidy) (Diptera: Sarcophagidae), assessing life-history traits and gut microbiota. Larvae were supplemented with RJ at 0%, 1%, 5%, or 10% (w/w, of the total bovine liver paste diet); a subset of emerging adults continued to receive the same RJ dose, creating "larval-only" and "larval + adult" dietary regimens. Although RJ did not alter mean larval weight at dispersal, it significantly accelerated larval growth and increased pupation rate. Adult lifespan was extended by larval supplementation and further prolonged when RJ was provided to both larvae and adults. Fecundity followed the same pattern: the "larval + adult" regimen exceeded the corresponding "larval-only" dose across concentrations. Dose-response relationships were non-linear, with modest gains at 1% and a plateau between 5% and 10%, indicating a mid-range optimum. 16S rRNA gene sequencing showed that RJ reduced gut α-diversity and shifted community composition; control-enriched taxa were suppressed under RJ. Functional predictions indicated that RJ-treated larvae harbored a gut microbiota with reduced metabolic potential, suggesting less microbial nutrient use and a lower immune challenge to the host. Together, results suggest that RJ is a promising tool to improve mass-rearing efficiency. Under our experimental conditions, a 5% RJ diet applied at both larval and adult stages appears to be an effective starting formulation, with the observed gains likely reflecting both direct nutritional benefits and microbiome restructuring.}, }
@article {pmid42160337, year = {2026}, author = {Cabirol, A and Quinn, A and Schafer, J and Neuschwander, N and Kesner, L and Liberti, J and Engel, P}, title = {A defined community of core gut microbiota members promotes cognitive performance in honey bees.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {21}, pages = {e2608600123}, doi = {10.1073/pnas.2608600123}, pmid = {42160337}, issn = {1091-6490}, support = {892574//European Commission (EC)/ ; 714804//European Commission (EC)/ ; 219829/SNSF_/Swiss National Science Foundation/Switzerland ; 180575/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {Animals ; Bees/microbiology/physiology ; *Gastrointestinal Microbiome/physiology ; *Cognition/physiology ; Memory, Short-Term/physiology ; Germ-Free Life ; Bacteria/classification ; }, abstract = {Gut microbiota across animals have been shown to influence host cognition and behavior. However, it remains unclear whether these cognitive effects are driven by specific bacterial species or arise from community-level interactions. Here, we leveraged the honey bee (Apis mellifera) as a model system, which harbors a simple and well-characterized gut microbiota that is experimentally tractable and has been previously shown to impact host cognition. We established a defined bacterial community-composed of core members of the honey bee gut microbiota. Gnotobiotic bee experiments with the full community, communities missing individual members, or individual members showed that only the full community enhanced honey bees' performances in odor discrimination learning and short-term memory compared to microbiota-deprived bees. Metabolomic analyses identified several metabolites associated with learning success that mapped to pathways modulated by microbial colonization, including tryptophan metabolism, nucleoside metabolism, and lysine degradation. However, many of these metabolites were not altered by removing individual members from the full microbial community. This suggests that microbiota-mediated improvements in cognition are emergent properties of the community as a whole, rather than the result of individual metabolites or specific bacterial taxa acting alone. Our findings support a systems-level view of the microbiome, suggesting that understanding and manipulating host development, particularly in relation to brain function, should prioritize microbial community function (e.g., metabolic pathways) over taxonomic composition alone.}, }
@article {pmid42160397, year = {2026}, author = {Liu, S and Costa, FS and Valenzano, DR}, title = {Immune surveillance and microbial escape in the aging host: Why does the microbiome lose its balance?.}, journal = {PLoS biology}, volume = {24}, number = {5}, pages = {e3003815}, doi = {10.1371/journal.pbio.3003815}, pmid = {42160397}, issn = {1545-7885}, abstract = {Host-associated microbiomes are compositionally stable across most of the life span, yet undergo consistent and marked deterioration during aging, a phenomenon linked to metabolic dysfunction and disease. What drives this late-life collapse remains poorly understood, in part because the mechanisms by which hosts actively construct and maintain the microbial niche during adulthood remain incompletely characterized. This Unsolved Mystery integrates evidence from immunology and ecosystem ecology to investigate the role of immunosenescence in age-associated dysbiosis, raising the possibility of interventions that restore immune surveillance capacity alongside ecologically informed microbiome management, rather than targeting community composition in isolation.}, }
@article {pmid42160479, year = {2026}, author = {Catley, CS and Hoedt, EC and Pockney, P and Keely, S and Hedley, KE}, title = {Unravelling Anastomotic Leak: Biological Mechanisms Underlying Intestinal Healing After Resection.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {}, number = {}, pages = {}, doi = {10.1152/ajpgi.00071.2026}, pmid = {42160479}, issn = {1522-1547}, support = {//University of Newcastle Australia (UON)/ ; //Australian Government (Federal Government)/ ; G2300020//nswgov | NSW Health (The NSW Health)/ ; }, abstract = {Understanding intestinal healing following resection and anastomosis is a challenging topic due to the complexity of underlying mechanisms. Anastomotic healing follows the fundamental phases of normal wound repair; however, the intestinal anastomosis represents a unique biological environment in which factors such as the structure of the intestines as well as the microbiome, may modify the healing process. Disruptions in any of the healing phases such as the inflammatory, proliferative and remodelling phase may result in severe complications, characterised by the intraluminal contents leaking out into the extraluminal space, termed an anastomotic leak (AL). Despite decades of surgical advancements, we are still no closer in understanding the underlying AL aetiology. It is clear that ALs are multifactorial in nature and contributed to by patient, technical and biological-related factors, however, emerging evidence suggests that biological mechanisms may play a more significant role in AL pathology than originally believed. Evidence points to an interplay between epithelial healing, tissue oxygenation and the resident microbiome in influencing mucosal healing at the anastomotic site. However, the precise contribution of these factors in failed anastomotic healing and AL aetiology remains unclear. In this review, we examine the phases of healing, discuss the existing literature on biological factors affecting anastomotic healing and the advancements made to improve AL rates by targeting the healing response.}, }
@article {pmid42161089, year = {2026}, author = {Schoenmakers, S and Nieuwenhuijse, DF and Reiss, I and van der Meeren, L and Mulders, CE and Molenkamp, R and Fraaij, PLA and van Boheemen, S}, title = {No detection of relevant virus-specific DNA or RNA sequences in the placenta.}, journal = {Placenta}, volume = {181}, number = {}, pages = {168-174}, doi = {10.1016/j.placenta.2026.05.010}, pmid = {42161089}, issn = {1532-3102}, abstract = {INTRODUCTION: The existence of a placental bacterial microbiome remains a subject of active debate, with recent studies challenging earlier claims of a resident microbial community. While the role of bacterial and viral pathogens in placental infection and adverse pregnancy outcomes is well established, the potential existence of a resident placental (non-pathogenic) virome remains largely unexplored. Given the placenta's vital role in fetal development, our study aimed to investigate whether viral genetic material is present in placental tissue, rather than to identify viral pathogens, in both uncomplicated and complicated pregnancies using viral metagenomic capture sequencing.<br><br>METHODS: Placental biopsies were obtained from three pregnancy groups: (1) delivered by elective caesarean section (n&#x202f;=&#x202f;6), (2) delivered by emergency caesarean section (n&#x202f;=&#x202f;6), and (3) complicated by preeclampsia (n&#x202f;=&#x202f;5). Samples were processed using VirCapSeq VERT, a targeted enrichment strategy for vertebrate viruses, followed by Illumina NovaSeq 6000 sequencing.<br><br>RESULTS: High quality sequencing yielded an average of 46.6 million reads per sample, with >99.6% of reads aligned to the human genome, and <0.4% of non human sequences. Across all samples, only 12 viral contigs were identified, corresponding to bacteriophages, human endogenous retroviruses, and human gammaherpesvirus 4 (not confirmed by PCR), mostly with low read counts.<br><br>CONCLUSIONS: Our study found no evidence supporting the presence of a resident placental virome. Together with existing data on the absence of a bacterial microbiome, these findings support the concept that the placenta does not harbor a detectable microbial or viral community under controlled sampling conditions.}, }
@article {pmid42161263, year = {2026}, author = {Ni, M and Junker, K and Liu, Y and Fan, Y and Li, Y and Qiao, W and Zhang, XS and Ksiezarek, M and Mead, EA and Tourancheau, A and Jiang, W and Blaser, MJ and Valdivia, RH and Davey, LE and Fang, G}, title = {Epigenetic phase variation in the gut microbiome enhances bacterial adaptation.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.04.019}, pmid = {42161263}, issn = {1934-6069}, abstract = {The human microbiome continuously adapts to variations in diet and host physiology. Epigenetic phase variation (ePV) mediated by bacterial DNA methylation can generate phenotypic heterogeneity within clonal populations. ePVs have been characterized in human pathogens, but their roles in commensals remain unclear. Here, we cataloged ePVs in infant and adult gut microbiomes, revealing genome-wide and site-specific ePV in response to antibiotics and fecal microbiota transplantation. Long-read metagenomics revealed genome-wide ePV mediated by structural variations of DNA methyltransferases. Analysis of public short-read metagenomic datasets further revealed a high prevalence of genome-wide ePVs in the human microbiome. Site-specific ePVs were identified and associated with antibiotics or probiotic engraftment. Focusing on an Akkermansia muciniphila isolate, we find a specific ePV regulating mucC, a gene of unknown function but whose heterologous expression enhances bacterial tolerance to antibiotics via a bet-hedging strategy. Thus, epigenetic modifications are used by gut bacteria to adapt to fluctuating environments.}, }
@article {pmid42161269, year = {2026}, author = {Hattori-Muroi, K and Maruta, H and Takahashi, D and Kinashi, Y and Hattori, K and Kabumoto, Y and Fujimura, Y and Tsukamoto, S and Suzuki, K and Oguchi, H and Ogihara, Y and Kodaira, Y and Hayashi, E and Takano, K and Komiyama, S and Morita, N and Naganawa-Asaoka, H and Oya, Y and Saito, Y and Ohhashi, W and Kimura, S and Shinkura, R and Matsuda, T and Hase, K}, title = {Dietary soy shapes the microbiome to induce commensal-specific T follicular helper cells and IgA production.}, journal = {Immunity}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.immuni.2026.04.013}, pmid = {42161269}, issn = {1097-4180}, abstract = {The commensal microbiota plays a crucial role in shaping mucosal immunity, particularly in the induction of T follicular helper (Tfh) cells and subsequent B cell IgA production. Here, we demonstrate that dietary soy elicits a robust Tfh cell and IgA response in Peyer's patches of weaning mice. Soy feeding promotes the expansion of two principal commensal bacterial species, Limosilactobacillus reuteri and Muribaculum intestinale. Mechanistically, L. reuteri provides cognate antigens for Tfh cell activation, while M. intestinale functions as an adjuvant by promoting IL-1β production from myeloid cells. The resulting IgA exhibits polyreactivity and enhances protection against Salmonella infection. These findings highlight the specific interplay among dietary components, intestinal microbiota, and mucosal immunity, thereby establishing a diet-microbe-immune axis that shapes host defense in early life. This axis represents a promising therapeutic target for developing future strategies to enhance resistance to enteric pathogens.}, }
@article {pmid42161933, year = {2026}, author = {Ding, X and Murayama, R and Cai, Y and Yue, Y and Yang, JJ and Hashimoto, K}, title = {Xanomeline-trospium reverses phencyclidine-induced cognitive deficits through modulation of the gut microbiota-brain axis in mice.}, journal = {Translational psychiatry}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41398-026-04097-0}, pmid = {42161933}, issn = {2158-3188}, support = {U23A20421//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82171189//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Cognitive impairment in schizophrenia remains largely unaddressed by dopamine-based antipsychotics. Xanomeline-trospium (KarXT; Cobenfy[®]), a combination of the muscarinic M1/M4 receptor agonist xanomeline and the peripherally restricted antagonist trospium, effectively reduces psychosis but is associated with gastrointestinal adverse effects. Here, we tested whether KarXT reverses phencyclidine (PCP)-induced cognitive deficits through microbiota-associated mechanisms in adult male mice. Mice received saline or PCP (10 mg/kg/day, s.c.) on days 1-5 and 8-12, followed by vehicle or KarXT [xanomeline 2 mg/kg/day + trospium 1 mg/kg/day, intragastric] on days 15-28. Recognition memory was evaluated using the novel object recognition test (NORT), and lung and intestinal microbiota (small intestine, cecum, and colon) were profiled by 16S rRNA sequencing. KarXT significantly rescued PCP-induced recognition-memory deficits without exacerbating PCP-related reductions in weight gain or fecal output. Microbiome analyses revealed region-specific dysbiosis after PCP exposure, most pronounced in the small intestine and cecum. Several taxa elevated by PCP-including Bacteroides fragilis, Veillonella ratti, Megamonas funiformis, Cupriavidus numazuensis, and Acetanaerobacterium elongatum-were normalized following KarXT treatment. Notably, restoration of multiple pulmonary, cecal, and colonic taxa correlated positively with the NORT recognition index. These findings demonstrate that KarXT reverses PCP-induced cognitive dysfunction while modulating microbial composition in a region-specific manner. Elucidating these relationships may help optimize cognitive efficacy and reduce gastrointestinal adverse effects of muscarinic therapies for schizophrenia.}, }
@article {pmid42162000, year = {2026}, author = {Zhang, Y and Schuppe-Koistinen, I and Wang, H and Tian, X and Chen, WH and Gao, G and Du, J}, title = {Vaginal microbiome and inflammation cytokines among Chinese women.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00994-w}, pmid = {42162000}, issn = {2055-5008}, support = {82161138017//NNSF-VR Sino-Swedish Joint Research Programme/ ; 2021-06112//Vetenskapsr&#xe5;det/ ; 2822//Eurostars/ ; 23 2916 Pj//Cancerfonden/ ; 251172//Radiumhemmets Forskningsfonder/ ; }, abstract = {Human papillomavirus (HPV) infection, cervical intraepithelial neoplasia (CIN), pelvic organ prolapse (POP), cervical polyps, abnormal uterine bleeding, and vaginitis are common gynecological disorders. This study characterized the vaginal microbiome and its cytokine-mediated immune interactions in Chinese women with gynecological disorders. Vaginal swabs from 310 patients diagnosed with gynecological disorders and 112 healthy controls were analyzed via 16S rRNA gene sequencing and cytometric bead array (CBA) to evaluate proinflammatory cytokines. Findings on correlation were validated through in vitro co-culture experiments. HPV infection and CIN were associated with dysbiotic microbial profiles and elevated levels of IL-1α, IL-1β, IL-6, IL-8, MCP-1, and MIG. Stratification by microbial composition demonstrated that HPV/CIN patients with non-Lactobacillus-dominant microbiomes harbored the highest IL-1α and IL-1β concentrations. Validated through computational modeling and in vitro analyses, Lactobacillus crispatus and Lactobacillus iners were identified as being strongly inversely correlated with IL-1α and IL-1β expression. Conversely, non-Lactobacillus taxa, including Bifidobacterium breve, Prevotella bivia, Gardnerella vaginalis, Sneathia amnii, Sneathia sanguinegens, Prevotella amnii, Escherichia coli, and Chlamydia trachomatis, exhibited positive correlations with proinflammatory cytokines. These findings highlight a connection between Lactobacillus species and reduced inflammation, while non-Lactobacillus dominance is linked to increased cytokine-driven responses. This study provides valuable insights into microbiome-immune crosstalk in gynecological diseases.}, }
@article {pmid42162115, year = {2026}, author = {Ranasinghe, PD and Barazanji, N and Bednarska, O and Bergman Jungeström, M and Lundberg, P and Keita, &#xc5;V and Walter, S and Simon, R}, title = {High-resolution metagenomic characterization of gut microbiota composition and functional pathways in irritable bowel syndrome.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42162115}, issn = {2045-2322}, mesh = {Humans ; *Irritable Bowel Syndrome/microbiology ; *Gastrointestinal Microbiome/genetics ; Female ; *Metagenomics/methods ; Adult ; Middle Aged ; Feces/microbiology ; *Metagenome ; Case-Control Studies ; }, abstract = {Irritable bowel syndrome (IBS) is a common functional gastrointestinal disorder characterized by abdominal pain, altered bowel habits, and frequent comorbidity with anxiety and depression. The gut microbiota has been implicated in gut-brain axis (GBA) dysfunction, but consistent microbial signatures remain unclear. We performed whole metagenome shotgun sequencing of stool samples from 63 female patients with moderate to severe IBS and 34 female healthy controls and assessed microbial composition and functional pathways. Microbial richness and diversity were slightly reduced in IBS, though with high variability and no robust separation from controls. Differential abundance analyses revealed enrichment of Streptococcus sp. and the sulfate-reducing bacterium Desulfovibrio piger in IBS, alongside reductions in Bifidobacterium and Methanobrevibacter. Functional profiling identified 39 differentially abundant pathways: amino acid biosynthesis (e.g., L-isoleucine, L-threonine) was more prominent in IBS, while carbohydrate degradation pathways (e.g., galactose, stachyose) were enriched in healthy controls. These findings indicate modest but significant IBS-associated shifts in gut microbial composition and function that may contribute to IBS symptoms. However, high intra-group variability underscores the complexity of IBS and highlights the need for larger, multi-omics studies to define robust microbial markers. These results contribute to a growing body of evidence emphasizing the complexity of gut microbiota-host interactions and the need for high-resolution, systems-level approaches in microbiome-associated disorders.}, }
@article {pmid42162530, year = {2026}, author = {Koretz, RL}, title = {JPEN Journal Club 101. Papers from Pharma.}, journal = {JPEN. Journal of parenteral and enteral nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1002/jpen.70107}, pmid = {42162530}, issn = {1941-2444}, }
@article {pmid42162563, year = {2026}, author = {Tang, YY and Zhou, YM and Lin, WK and Zhi, JR and Zou, X}, title = {The role of fungal chitinases in the tripartite interactions among insects, plants and entomopathogenic fungi.}, journal = {Pest management science}, volume = {}, number = {}, pages = {}, doi = {10.1002/ps.70955}, pmid = {42162563}, issn = {1526-4998}, support = {//the National Natural Science Foundation of China (Project No.: 32560646),/ ; //the Guizhou Provincial Basic Research Program (Natural Science) (Project number: QianKeHeJiChu-ZK[2024]YiBan002),/ ; //Natural Science Research Project of Colleges and Universities of Guizhou Provincial Department of Education (Youth Science and Technology Talent Development Project) (Project number: QianJiaoJi[2024]34),/ ; //Natural Science Project of Guizhou University (Special Post) (Project number: Gui Da Te Gang He Zi (2022) 51)/ ; //National Science Foundation of China (Project number: 31860507)./ ; }, abstract = {BACKGROUND: Chitinases are ubiquitous hydrolytic enzymes in fungi that specifically degrade chitin, a major structural component of insect exoskeletons and fungal cell walls. Increasing evidence indicates that chitinases play multifaceted roles not only in entomopathogenic fungal infection, but also in plant immune modulation and cross-kingdom interactions. However, their integrative functions within the insect-fungus-plant tripartite system remain insufficiently characterized. This review aims to systematically elucidate the molecular mechanisms and ecological functions of fungal chitinases across multitrophic interactions.<br><br>RESULTS: Accumulated studies demonstrate that: Chitinases act as critical virulence factors by facilitating fungal adhesion, cuticle degradation, and host penetration during insect infection; In plant-microbe interactions, chitinases contribute to microbial colonization while simultaneously generating chitin-derived oligomers that function as elicitors to activate plant innate immunity; Within the insect-fungus-plant tripartite system, chitinases mediate resource turnover and signal exchange, thereby shaping complex ecological networks and influencing multilevel biological interactions.<br><br>CONCLUSION: Chitinases serve as pivotal molecular hubs linking pathogenicity, symbiosis and ecological regulation across kingdoms. A comprehensive understanding of their multifunctional roles provides critical insights into cross-kingdom interaction mechanisms, and offers promising avenues for advancing biological control strategies, crop resistance improvement and microbial resource exploitation. &#xa9; 2026 Society of Chemical Industry.}, }
@article {pmid42162574, year = {2025}, author = {Panneerselvam, R and Karuppannan, M and S C, GP and Durairaj, E}, title = {Impact of Sevoflurane on the Murine Gut Microbiota: Longitudinal Characterization of Diversity Alterations and Dysbiosis Metrics Using Metagenomics.}, journal = {Asian journal of anesthesiology}, volume = {63}, number = {1}, pages = {20-29}, doi = {10.6859/aja.202503_63(1).0003}, pmid = {42162574}, issn = {2468-824X}, mesh = {Animals ; *Sevoflurane/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Male ; Mice ; Female ; *Anesthetics, Inhalation/pharmacology ; *Dysbiosis/chemically induced/microbiology ; *Metagenomics/methods ; Feces/microbiology ; Longitudinal Studies ; Sex Factors ; }, abstract = {BACKGROUND: General anesthetics can alter the gut microbiota, but the longitudinal and sex-specific effects of sevoflurane remain unclear. This study examined whether a single exposure to sevoflurane anesthesia induces significant compositional changes in the murine gut microbiome over two weeks, with a secondary focus on sex-specific patterns of alteration.<br><br>METHODS: A controlled animal exposure study was conducted at a tertiary-care academic laboratory animal facility in southern India, approved by an institutional animal ethics committee. Twenty albino mice (6-8 weeks old, ~12 g; both females and males) were randomized to sevoflurane or control groups, subdivided by sex. All animals were housed under standard conditions and completed the study protocol. Experimental animals underwent a single 4-hour exposure to sevoflurane in a controlled chamber; controls experienced identical procedures without sevoflurane. Primary endpoints were gut microbiota alpha and beta diversity (Bray-Curtis distance, Shannon, Simpson indices, richness), phylum- and genus-level differential abundance, and derived Firmicutes: Bacteroidetes and Proteobacteria metrics from serial fecal samples across five time points up to Day 14.<br><br>RESULTS: Sevoflurane exposure led to significant beta diversity separation between groups at both phylum (P = 0.004) and genus levels (P = 0.034), with additional sex effects (P = 0.035 for genus level); alpha diversity indices were significantly reduced in males (P = 0.0079), but not in females. Phylum-level differential abundance was significant in females but not in males. Group and sex effects were present throughout, and derived dysbiosis metrics varied temporally and by sex Conclusion: A single prolonged exposure to sevoflurane induces significant, durable, and sexually dimorphic shifts in the murine gut microbiome. These findings highlight the importance of considering sex as a biological variable in studies of anesthetic effects on gut health.}, }
@article {pmid42162691, year = {2026}, author = {Škutová, K and Fišar, Z and Hroudová, J}, title = {Advances in schizophrenia research and treatment: exploring neurotransmitter imbalances, genetics, and innovative therapies.}, journal = {Progress in neuro-psychopharmacology &amp; biological psychiatry}, volume = {}, number = {}, pages = {111749}, doi = {10.1016/j.pnpbp.2026.111749}, pmid = {42162691}, issn = {1878-4216}, abstract = {Schizophrenia is a severe mental disorder arising from genetic vulnerability, impaired neurodevelopment, neurobiological dysregulation, and environmental factors. Its pathophysiology involves disturbances in dopamine, glutamate, and serotonin systems, as well as neuroinflammation, oxidative stress, gut-brain axis dysfunction, and altered energy metabolism. Current dopaminergic pharmacotherapy is often complicated by insufficient efficacy, adverse effects, and patient non-compliance. This review summarizes genetic predispositions, neurotransmitter imbalances, and other contributing factors of schizophrenia, as well as therapeutic advances in novel antipsychotic therapies. Newly developed therapeutic agents preferentially target the serotonergic, muscarinic, glutamatergic, and GABAergic neurotransmitter systems. They include muscarinic agonists, glycine transporter type 1 inhibitors, trace amine-associated receptor 1 agonists, D-amino acid oxidase inhibitors, and agonists or positive allosteric modulators of metabotropic glutamate receptors, and serotonin receptor inverse agonists. Recently, the antipsychotics lumateperone and xanomeline-trospium were approved. Iclepertin, ralmitaront, roluperidone, and brilaroxazine are molecules in Phase 2 or 3 clinical trials. Novel antipsychotic drugs are being developed to effectively treat negative symptoms, cognitive deficits, and total psychopathology in patients with schizophrenia. Adjuvant treatments aimed at mitigating neuroinflammation and oxidative stress; microbiome-targeted interventions, neuroprotective and metabolic agents are being explored. Current research efforts aim to improve treatment outcomes by addressing gaps in antipsychotic therapy and mitigating its adverse effects.}, }
@article {pmid42162728, year = {2026}, author = {Suresh, G and Nath, M and Tiwari, A and Halder, N and Chawla, R and Velpandian, T}, title = {Gut Microbiome Dysbiosis in Uveitis - Mechanistic Insights and Emerging Therapeutic Strategies.}, journal = {Experimental eye research}, volume = {}, number = {}, pages = {111073}, doi = {10.1016/j.exer.2026.111073}, pmid = {42162728}, issn = {1096-0007}, abstract = {Recent studies have suggested the existence of a gut-eye axis, thus bringing the role of gut microbiota (GM) in the development of ocular inflammation in uveitis into focus. The proposed mechanisms for GM dysbiosis-induced uveitis include molecular mimicry, increased intestinal permeability by disruption of barrier integrity, immunomodulation, and alterations. Data from observational clinical studies indicate distinctive microbial signatures associated with uveal inflammation. Based on these findings, novel therapeutic modalities targeting the GM, such as antibiotics, probiotics, prebiotics, fecal microbiota transplantation, biologics, and dietary interventions have been proposed. While initial studies have shown promising results, there is limited clinical evidence supporting their therapeutic efficiency in the management of uveitis. The complexity and diversity of the GM, along with the lack of controlled clinical trials pose a significant challenge to the development of targeted therapeutics. Additionally, further studies are needed to elucidate the molecular mechanisms linking GM dysbiosis and ocular inflammation for developing specific biomarkers for diagnosis, as well as personalized GM-targeted patient interventions.}, }
@article {pmid42162795, year = {2026}, author = {Sugimoto, H and Chida, K and Toshimitsu, T and Tokunaga, S and Fujino, K and Kawakami, E}, title = {Associations Between Yogurt Consumption, Gut Microbiota Composition, and Glucose Dynamics: A Single-Arm 84-Day Intervention Study Using Continuous Glucose Monitoring.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {101572}, doi = {10.1016/j.tjnut.2026.101572}, pmid = {42162795}, issn = {1541-6100}, abstract = {BACKGROUND: Although yogurt consumption has been associated with favorable metabolic outcomes, its effect on continuous glucose dynamics and gut microbiota composition remains unclear.<br><br>OBJECTIVE: To evaluate the effects of daily yogurt intake on glucose dynamics and gut microbiota composition in healthy adults, and to examine baseline host factors associated with inter-individual variability in glycemic response.<br><br>METHODS: This single-arm, 84-day intervention study involved 303 Japanese adults without a prior diabetes diagnosis consuming 200 g of plain yogurt daily at breakfast. Continuous glucose monitoring (CGM) was used to assess mean glucose levels, standard deviation (Std), and an autocorrelation-based index (AC_Var). Fecal samples were collected at baseline and post-intervention for 16S rRNA gene sequencing. Associations between baseline clinical, microbial, and genetic characteristics and changes in the CGM-derived measures were evaluated. Differential abundance analysis was used to identify microbial taxa altered by the intervention.<br><br>RESULTS: Mean glucose levels decreased progressively, with a reduction of 4.06 mg/dL (95% CI: 2.97 to 5.14) by the final period. Significant decreases were also observed in Std (-0.86 mg/dL; 95% CI: -1.32 to -0.41) and AC_Var (-0.0059; 95% CI: -0.010 to -0.0017). Several baseline gut bacterial genera, including Gemmiger, Veillonella, Alistipes, and Butyricicoccus, were significantly associated with changes in the CGM-derived measures. Following the intervention, increases were observed in the genera Blautia, Faecalibacterium, and Coprococcus, as well as in the phylum Firmicutes, while decreases were noted in Prevotella, Oscillospira, and the phylum Bacteroidetes.<br><br>CONCLUSIONS: Daily yogurt consumption was associated with improvements in glucose dynamics and significant remodeling of the gut microbiota. Baseline microbiota profiles were linked to inter-individual differences in glycemic response. These findings suggest the potential role of the gut microbiome in modulating metabolic effects of yogurt and underscore the value of personalized dietary strategies.<br><br>UMIN000054094 (https://center6.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000061770).}, }
@article {pmid42162796, year = {2026}, author = {Xie, LX and Xu, QQ and Liu, JY and Zhang, JY and Fu, ZK and Liu, KH and Mao, CR and Deng, FX and Huang, L}, title = {Taurine in Atherosclerosis: A Multi-Target Perspective.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {101599}, doi = {10.1016/j.tjnut.2026.101599}, pmid = {42162796}, issn = {1541-6100}, abstract = {Taurine, a conditionally essential amino acid with unique sulfur-containing groups, has many fundamental physiological processes, including osmoregulation and bile acid conjugation. Atherosclerosis (AS) can lead to numerous severe vascular adverse events, such as stroke, coronary artery disease and myocardial infarction, posing a significant threat to human health. Taurine plays a role in multiple targets associated with the development of AS (Figure 1). It regulates lipid metabolism, reduces platelet activation and aggregation, and suppresses uncontrolled proliferation of vascular smooth muscle cells. Additionally, it has antioxidant effects and promotes vascular health through vasodilation and endothelial repair, making it a promising cardiovascular protective agent. Furthermore, its interactions with the gut microbiome offer new insights into its potential for managing pathological conditions that contribute to AS. Current evidence supports that taurine serves as a dietary supplement to enhance both intestinal and cardiovascular health, thereby reducing the risk of AS.}, }
@article {pmid42162932, year = {2026}, author = {Li, J and Xu, J and Wei, P and Gong, H and Tian, M and Yan, W and Ma, C and Il, D and Yang, Y}, title = {Solid-state fermentation of waste herbal medicine residues by a novel rumen-derived probiotic consortium for valorization and microbial-metabolite shifts.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134922}, doi = {10.1016/j.biortech.2026.134922}, pmid = {42162932}, issn = {1873-2976}, abstract = {Compound herbal medicine residues (CHMR) are an underutilized lignocellulosic by-product with potential for conversion into value-added feed. In this study, a rumen-derived probiotic consortium was developed for the solid-state fermentation (SSF) of CHMR, and the associated microbial and metabolic shifts were characterized. A total of 123 bacterial strains were isolated from goat rumen, of which 58 met the criteria for potential feed additives. Bacillus subtilis FB8B and Limosilactobacillus reuteri LA3 were selected as core strains based on cellulolytic activity, acidification capacity, stress tolerance, and growth performance in CHMR. The optimized consortium increased crude protein and flavonoids by 10.87% and 17.99%, respectively, while reducing NDF and ADF by 17.27% and 25.97%, respectively. Integrated 16S rRNA sequencing and untargeted metabolomics showed that inoculated fermentation restructured the bacterial community, enriched beneficial fermentative taxa, and suppressed indigenous competitors. Metabolome reprogramming was characterized by depletion of sugars and amino acids, accumulation of organic acids and phenolic derivatives, and coordinated shifts in pyruvate, amino acid, and secondary metabolite pathways. These findings demonstrate that rumen-derived probiotic fermentation is an effective strategy for CHMR valorization and provide mechanistic insight into microbiome-driven bioconversion of herbal residues into functional feed resources.}, }
@article {pmid42162964, year = {2026}, author = {Peng, C and Jiang, L and Huang, Z and Wei, X and Zhu, X and Liu, Z and Chen, Q and Shen, X and Gao, P and Jiang, C}, title = {MetaNet: a scalable and integrated tool for reproducible omics network analysis.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btag321}, pmid = {42162964}, issn = {1367-4811}, abstract = {MOTIVATION: Network analysis has become a central strategy for dissecting complex biological and environmental systems, particularly as modern omics technologies generate increasingly large and heterogeneous datasets. However, current tools often lack the scalability, flexibility, and native multi-omics support required for high-dimensional data analysis. We developed MetaNet, a high-performance R package that unifies network construction, visualization, and analysis across diverse omics layers.<br><br>RESULTS: MetaNet enables fast and scalable correlation-based network construction for datasets with more than 10,000 features, providing over 40 layout algorithms, rich annotation utilities, and visualization options compatible with both static and interactive platforms. It further offers comprehensive topological and stability metrics for in-depth network characterization. Benchmarking shows that MetaNet delivers up to a 100-fold improvement in computation time and a 50-fold reduction in memory usage compared to existing R packages. We demonstrate its utility through two representative applications: (1) longitudinal microbial co-occurrence networks revealing airborne microbiome dynamics, and (2) an integrative exposome-transcriptome network of over 40,000 features, uncovering distinct regulatory impacts of biological and chemical exposures. By offering a robust, reproducible, and biologically informed framework, MetaNet advances multi-omics network analysis across biological, ecological, and environmental domains.<br><br>AVAILABILITY: MetaNet package is freely available at https://github.com/Asa12138/MetaNet.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid42163070, year = {2026}, author = {Mohammed, H and Kohli, I and Lim, HW}, title = {From Ultraviolet to Visible Light: Emerging Concepts in Comprehensive Photoprotection.}, journal = {Photodermatology, photoimmunology &amp; photomedicine}, volume = {42}, number = {3}, pages = {e70098}, doi = {10.1111/phpp.70098}, pmid = {42163070}, issn = {1600-0781}, mesh = {Humans ; *Ultraviolet Rays/adverse effects ; *Sunscreening Agents/therapeutic use ; *Skin/radiation effects/microbiology ; *Light/adverse effects ; *Skin Aging/radiation effects/drug effects ; Erythema/prevention &amp; control/etiology ; *Skin Pigmentation/radiation effects ; }, abstract = {BACKGROUND: Photoprotection has traditionally focused on ultraviolet (UV) radiation, particularly UVB and UVA. Recent evidence highlights the significant role of long-wavelength UVA1 (LW-UVA1, 370-400 nm) and visible light (VL; 400-700 nm) in inducing pigmentation, erythema, and photoaging. This review study summarizes recent advances in LW-UVA1 and VL photoprotection and discusses emerging UV-filter formulations, non-filtering protective ingredients (PINGs), personalized photoprotection, skin microbiome, and environmental considerations.<br><br>METHODS: A literature review was conducted using PubMed and Google Scholar online databases to identify recent studies on LW-UVA1 and VL-related photoprotection. Studies were screened for direct relevance to VL and LW-UVA1 and excluded if not available in English, lacked relevance, or had insufficient methodological detail. This review represents a narrative synthesis without formal systematic quality assessment. Results are summarized.<br><br>RESULTS: LW-UVA1 and VL exert synergistic effects on the skin, resulting in erythema and sustained pigmentation. Advances include tinted mineral sunscreens with expanding shade ranges, newer UV filters with broader coverage (e.g., Mexoryl 400, TriAsorB), and oral and topical PINGs to be used as potential adjuncts. Environmental concerns for currently used UV filters persist, however. Skin microbiome has also emerged as a target and potential source for novel photoprotective agents. Personalized photoprotection recommendations now provide an individualized approach, taking skin phototype, lifestyle, and risk profile into consideration.<br><br>CONCLUSION: Photoprotection is expanding to include a broader-spectrum coverage, including LW-UVA1 and VL with new filters, formulations, and adjuncts. These innovations enhance UV protection, but environmental and long-term safety concerns highlight the need for continued research to ensure safe, effective, and inclusive photoprotection.}, }
@article {pmid42163161, year = {2026}, author = {Guan, X and Shen, XL and Hao, YN and Dong, ZQ and Chen, JM}, title = {Complex correlations between mitochondrial DNA variants and gut microbiome in major depressive disorder: a genome-wide association analysis.}, journal = {BMC psychiatry}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12888-026-08132-8}, pmid = {42163161}, issn = {1471-244X}, abstract = {BACKGROUND: Gut microbiota disturbances and impaired mitochondrial function are both linked with the development of major depressive disorder (MDD). However, little is known about how they interact in MDD.<br><br>METHODS: We used shotgun metagenomic sequencing to explore fecal microbiome based on 63 MDD patients and 30 healthy controls (HCs). Then we performed GWAS for the discriminative taxonomic features of gut microbiota to identify genetic associations between gut microbiome and mitochondrial DNA (mtDNA) in MDD.<br><br>RESULTS: Characteristic gut microbiome-based features, including significant differences in gut microbiota composition and 101 differentially enriched gut microbial species, were found in MDD group vs. HC group. 68 mitochondrial single-nucleotide polymorphisms (mtSNPs) shared between the two groups were identified through GWAS at a Bonferroni-corrected significance level of p&#x2009;<&#x2009;0.05. The genetic variants and their associated gut microbes were mapped to mitochondrial genome, most of which were located in coding regions, including MT-ND, MT-ND4L, MT-ND5, MT-ND6; MT-CO, MT-CO3; MT-RNR, MT-RNR, and MT-TE. Manhattan plots showed 9 mtSNPs in MDD group and 10 mtSNPs in HC group were associated with 20 gut microbial species at a significance of -log10(p) >20. Furthermore, Sankey diagram was used to visualize the relationships of gut microbiota and mtDNA. 36 mtSNPs (-log10(p) >5) were shown to be associated with 54 gut microbes in crosslinked patterns.<br><br>CONCLUSIONS: The current findings provide substantial evidence that complex interactions between gut microbiota and mtDNA contribute to MDD, which enables a better understanding of MDD pathogenesis and suggests new leads for future investigations.<br><br>CLINICAL TRIAL NUMBER: ChiCTR2000029703. Registration Date: Feb. 9[th], 2020. Registration Details are available at the website of Chinese Clinical Trial Registry (https://www.chictr.org.cn).}, }
@article {pmid42163413, year = {2026}, author = {Wang, M and Wang, Y and Bai, M and Peng, Q and Wu, Q and Shang, Z and Chen, G and Zhang, Z and Yang, S and Li, L and Tian, F and Jing, C}, title = {Gut microbiota-derived indole-3-propionic acid promotes lymph node metastasis in gastric cancer via the aryl-hydrocarbon receptor signaling pathway.}, journal = {Cancer &amp; metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40170-026-00438-1}, pmid = {42163413}, issn = {2049-3002}, abstract = {BACKGROUND: Gut microbiota (GM) regulates the tumor microenvironment through microbial metabolites. Indole 3-propionic acid (3-IPA) is one such metabolite that regulates gastrointestinal barrier function. In this study, we investigated the effects of 3-IPA on the progression of lymph node metastasis of gastric cancer (GC) and the molecular mechanisms that underlie them.<br><br>METHODS: The microbial metabolites were identified using a fecal metabolomic assay in GC patients. Lymphangiogenesis was evaluated using tube formation and wound healing assays in vitro. The expression of aryl hydrocarbon receptor (AHR), CYP1A1, and vascular endothelial growth factor receptor 3 (VEGFR3) were assayed using quantitative real-time PCR (qRT-PCR) and western blot (WB) analyses. Matrigel plug and popliteal lymph node metastasis model were employed to validate the influence on lymphangiogenesis and lymph node metastasis in vivo.<br><br>RESULTS: Fecal metabolomic and microbiome profiling was drastically different between GC patients with lymph node metastasis (GC-LM) and those without metastasis. The GC-LM group showed high 3-IPA expression in the feces; 3-IPA had no significant effect on GC cells; Human lymphatic endothelial cells showed greater tube formation and promoted migration after 3-IPA administration. Also, upregulation of AHR, CYP1A1, and VEGFR3 was observed. Moreover, administration of the AHR inhibitor suppressed tube formation and lymph node metastasis both in vitro and in vivo.<br><br>CONCLUSIONS: Our findings suggest that gut microbiota-derived 3-IPA functions as a lymph node metastasis promoter through the AHR/CYP1A1-VEGFR3 axis in GC. 3-IPA could serve as a prognostic biomarker and conceivably a therapeutic target for GC lymph node metastasis.}, }
@article {pmid42163541, year = {2026}, author = {Alhuwaizi, MA and Saloom, HF and Cobourne, M}, title = {Impact of clear aligners and conventional fixed orthodontic appliances on oral hygiene and periodontal health: A systematic review with GRADE assessment of the certainty of evidence.}, journal = {European journal of orthodontics}, volume = {48}, number = {3}, pages = {}, doi = {10.1093/ejo/cjaf100}, pmid = {42163541}, issn = {1460-2210}, mesh = {Humans ; *Oral Hygiene ; *Orthodontic Appliances, Fixed/adverse effects ; *Oral Health ; Randomized Controlled Trials as Topic ; Periodontal Diseases/etiology ; *Orthodontic Appliances, Removable/adverse effects ; Periodontal Index ; }, abstract = {BACKGROUND: The use of clear aligners (CA) has exponentially increased in the last decades due to their superior esthetic, ease of use and cleaning, and comfort in comparison to conventional fixed appliance (FA). However, prolonged wearing of CA could also alter oral microbiome and adversely affect oral hygiene and periodontal health.<br><br>OBJECTIVE: To assess oral hygiene level and periodontal health status in patients treated with CA versus those treated with FA using a combination of risk of bias (RoB) and Grading of Recommendations Assessment, Development and Evaluation (GRADE) tools.<br><br>SEARCH METHODS: A comprehensive electronic search was conducted in four databases, including Scopus, PubMed, Web of Science, and Google Scholar, to retrieve relevant randomized controlled trials (RCTs) in the last 10 years from 2015 to April 2025.<br><br>SELECTION CRITERIA: The study aimed to include RCTs that focused on the impact of CA and FA orthodontic treatments on oral hygiene and periodontal health.<br><br>DATA COLLECTION AND ANALYSIS: Independent eligibility assessment, data extraction, and filtering process were performed. The RoB 2 tool was used to assess the quality of the included RCTs. Data relating to oral hygiene/periodontal health assessed by different clinical periodontal indices (primary outcome) and other findings (secondary outcomes) were extracted. Certainty of evidence was determined using GRADE system.<br><br>RESULTS: Initial search process yielded 1098 records which were assessed for eligibility, screened according to titles, abstracts, and full-text reading. Six RCTs were found eligible for analysis and included for synthesis of evidence. Qualitative analyses of the included RCTs showed that periodontal parameters were significantly better in patients treated with CA than with FA. Five RCTs exhibited high RoB together with overall inconsistencies in the given oral hygiene instructions, age, follow-up, diagnosis, and measurements. Certainty of evidence ranged from very low for oral hygiene level and low for periodontal health.<br><br>CONCLUSIONS: Dual quality assessment indicated that the advantages of CA over FA in terms of oral hygiene and periodontal health are highly compliance dependent. However, due to heterogeneities, high RoB, and low to very low certainty of evidence in current RCTs, outlining a firm conclusion was impeded.<br><br>REGISTRATION: PROSPERO (CRD420251120933).}, }
@article {pmid42163554, year = {2026}, author = {Hamid, NH and Karim, MMA and Daud, HM and Hamdan, RH and Yusoff, SFM}, title = {A Stage-Aligned Disease Management Framework for Aeromonas hydrophila in Aquaculture: Implications for Antimicrobial Stewardship.}, journal = {Journal of fish diseases}, volume = {}, number = {}, pages = {e70211}, doi = {10.1111/jfd.70211}, pmid = {42163554}, issn = {1365-2761}, abstract = {Aeromonas hydrophila remains a persistent challenge in freshwater aquaculture despite extensive research and the availability of multiple disease-control strategies. Although antibiotics are widely used, alternative approaches including probiotics, immunostimulants, vaccines and bacteriophages are often evaluated in isolation. Increasing evidence indicates that disease outbreaks are not driven by pathogen presence alone, but by dynamic interactions among host condition, environmental stability and pathogen virulence. This review synthesises evidence from 45 controlled intervention studies to propose a stage-aligned framework for managing A. hydrophila, in which disease progression reflects increasing system instability. Stage I (Baseline Prevention) focuses on biosecurity, water quality management and microbiome stability. Stage II (Immune Priming) addresses early risk conditions characterised by elevated stress and immune responses alongside increasing pathogen load, where immune modulation, functional feeds and prophylactic vaccination enhance host resilience. Stage III (Containment) involves targeted interventions, including bacteriophage application, environmental correction and strengthened biosecurity to limit pathogen amplification and transmission. Stage IV (Emergency Control) represents acute outbreak conditions requiring integrated responses, including disinfectant application, emergency biosecurity measures and diagnosis-guided antibiotic use where legally permitted. Reported relative percent survival (RPS) varies substantially between laboratory and field conditions, highlighting the context-dependent performance of interventions. By prioritising intervention timing and system condition over intrinsic tool efficacy, this framework supports reduced antimicrobial reliance while maintaining production stability in intensive aquaculture systems.}, }
@article {pmid41965837, year = {2026}, author = {Munoz Briones, J and Ball, BK and Jena, S and Lescun, TB and Chan, DD and Brubaker, DK}, title = {Rumenomics: evaluation of rumen metabolites from healthy sheep identifies differentially produced metabolites across sex, age, and weight.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {41965837}, issn = {2524-4671}, support = {DGE-1842166//National Science Foundation/ ; W911NF2110372//Defense Sciences Office, DARPA/ ; }, abstract = {BACKGROUND: The rumen harbors a diverse and dynamic microbiome vital in digesting vegetation into metabolic byproducts for energy and general biological function. Although previous studies have reported connections between the rumen and the overall health of the sheep, the exact biological process by which this occurs is not well understood. Therefore, our study aimed to quantify sheep rumen metabolites to determine if enriched biological pathways are differentiable across phenotypic features of sex, age, and weight.<br><br>RESULTS: We collected and quantified metabolites of rumen samples from sixteen sheep using liquid chromatography-tandem mass spectrometry. We performed a series of univariate and multivariate statistical analyses to interpret the rumen metabolomics data. To identify metabolic pathways associated with the phenotypic features of sex, weight, and age, we used MetaboAnalyst, which identified amino acid metabolism as a distinguishing factor. Among the pathways, phenylalanine metabolism emerged as a key pathway differentiating sheep based on sex and age. Additionally, phenylalanine, tyrosine, and tryptophan biosynthesis were exclusively associated with age. In univariate linear models, we also discovered that these amino acid and protein pathways were associated with weight by age-corrected effect. Finally, we identified arginine and proline biosynthesis as a pathway linked to metabolites with weight.<br><br>CONCLUSION: Our study identified differential pathways based on the sex, age, and weight features of sheep. Metabolites produced by the rumen may act as an indicator for sheep health and other ruminants. These findings encourage further investigation of the differentially produced metabolites to assess overall sheep health.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00558-5.}, }
@article {pmid41968333, year = {2026}, author = {Chen, C and He, J and Ma, Z and Na, W and Cao, Y and Li, B and He, Z and Yuan, H and Xiao, H and Wang, S and Liu, R and Yu, S and Kang, L}, title = {Sex differences in behaviors, neuronal activation, and gut-microbiota-metabolic axis in a repeated nitroglycerin-induced chronic migraine model.}, journal = {The journal of headache and pain}, volume = {27}, number = {1}, pages = {}, pmid = {41968333}, issn = {1129-2377}, support = {82201365//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Migraine is a debilitating primary headache disorder characterized by significant sex differences in epidemiology, clinical features, comorbidities, and treatment response, yet the underlying mechanisms remain obscure. This study aims to dissect the sex difference map in chronic migraine models and explore the underlying mechanisms driving these specific phenotypes.<br><br>METHODS: A mouse model of chronic migraine was established by intraperitoneal injection of nitroglycerin (NTG, 10&#xa0;mg/kg, 5 times in 9 days). Both male and female mice were included. Mechanical withdrawal thresholds (MWTs) were measured to assess migraine-related hyperalgesia. Anxiety-like behaviors and acute malaise were evaluated using the Open Field Test (OFT), Elevated Plus Maze (EPM), and Light-Dark Box (LDB). Neuronal activation was mapped via c-Fos immunofluorescence. Medullary TNF-&#x3b1; levels were quantified by ELISA. 16S rRNA sequencing and targeted metabolomics characterized the gut microbiota composition and fecal metabolites, respectively.<br><br>RESULTS: Although male and female mice showed comparable responses in acute and chronic mechanical pain hyperalgesia, significant sex differences were observed in other migraine-like behaviors: only male mice exhibited significant acute-phase motor inhibition and anxiety-like behavior in the chronic phase. These phenotypic differences coincided with a male-restricted elevation of medullary TNF-&#x3b1; following NTG administration. In terms of regional brain activation, the AP stood out in males for its markedly elevated c-Fos cell. This sexual dimorphism extended to the gut-brain axis: while the female NTG group microbiome was enriched with g-Akkermansia, the male profile was dominated by g-Parabacteroides. Metabolomic profiling identified 29 differential metabolites (NTG vs. VEH) in males but only 3 in females. In males, these alterations were primarily enriched in the pentose and glucuronate interconversions and biosynthesis of unsaturated fatty acids pathways that are involved in neuropsychiatric disorders.<br><br>CONCLUSION: The NTG-induced chronic migraine model exhibits significant sexual dimorphism, with male mice showing greater sensitivity to acute discomfort and chronic emotional comorbidities. This exploratory study identifies the specific activation of the AP brain region, medullary neuroinflammation, and more severe disturbances in the gut microbiota-metabolic axis as potential contributors to this sex-dependent phenotype.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s10194-026-02360-9.}, }
@article {pmid42148582, year = {2026}, author = {Yu, L and Li, H and Yu, H and Zhou, Y and Wang, X and Luo, L}, title = {Inoculation of Bacillus velezensis SD24 enhancing the accumulation of tea catechin secondary metabolites.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0346925}, doi = {10.1128/spectrum.03469-25}, pmid = {42148582}, issn = {2165-0497}, abstract = {Tea (Camellia sinensis) is a globally significant economic crop, and its desirable quality and health benefits are largely credited to catechin derivatives. Plant growth-promoting rhizobacteria (PGPR), such as Bacillus velezensis, are well-known for enhancing the environmental fitness and disease resistance of plants. However, the regulation of their impact on tea catechin biosynthesis remains unclear. While previous studies have focused on PGPR-facilitated growth promotion in crops like tomatoes and rice, the physiological mechanisms by which microbes regulate secondary metabolism in tea-especially under co-inoculation conditions-remain largely underexplored. This study examined the effects of B. velezensis SD24, isolated from tea rhizosphere soil, on catechin derivative accumulation of tea leaves by altering gene expression and the rhizosphere microbiome. Strain SD24 exhibited broad-spectrum antimicrobial activity against various pathogens due to behaving antimicrobial gene clusters. Tea plants inoculated with SD24 showed significantly increased levels of catechin derivatives in their leaves. This was likely achieved by upregulation of leucoanthocyanidin reductase and anthocyanidin reductase within the phenylpropanoid pathway. Additionally, chlorophyll content was increased. Transcriptomic analysis revealed a notable enrichment in biosynthesis of secondary natural products among the tea genes activated by SD24 inoculation. Metagenomic analysis further demonstrated that SD24 inoculation led to a restructuring of the tea rhizosphere microbiome. Notably, co-inoculation with Piriformospora indica, a beneficial endophytic fungus, suppressed SD24-induced gene expression and catechin accumulation, underscoring its antagonism toward SD24. These findings suggest that B. velezensis SD24 enhances tea quality, probably by transcriptionally activating the synthesis of catechin derivatives, a process associated with the restructuring of the rhizosphere microbiome.IMPORTANCEThe mechanisms through which plant growth-promoting rhizobacteria (PGPR) influence secondary metabolism in perennial crops remain poorly understood. This study demonstrates that Bacillus velezensis SD24, a tea rhizosphere isolate, significantly enhances the accumulation of health-beneficial catechin derivatives in tea leaves. This quality improvement is associated with transcriptionally upregulating key biosynthetic genes (LAR and ANR) and concurrently restructuring the rhizosphere microbiome. Furthermore, we reveal a critical antagonistic interaction, where the beneficial fungus Piriformospora indica suppresses these SD24-induced effects. Our findings provide crucial insights into how specific PGPR strains may directly enhance tea quality by affecting host plant metabolism and the root microbiome, highlighting the complex and tailored microbial interactions that could be harnessed for sustainable agriculture.}, }
@article {pmid42148717, year = {2026}, author = {Lantz, AM and Collins, LB and Hirsch, EB and Staley, C and Nicol, MR}, title = {Prevotella bivia Influences Antiretroviral Pharmacokinetics and Viral Replication in an Ex Vivo Vaginal Tissue Model.}, journal = {Clinical and translational science}, volume = {19}, number = {6}, pages = {e70597}, pmid = {42148717}, issn = {1752-8062}, mesh = {Female ; Humans ; *Vagina/microbiology/virology/drug effects ; *Tenofovir/pharmacokinetics/pharmacology ; *Prevotella/physiology/drug effects ; *HIV Infections/virology/prevention &amp; control/drug therapy ; *Virus Replication/drug effects ; *HIV-1/drug effects/physiology ; *Anti-HIV Agents/pharmacokinetics/pharmacology ; Microbiota/drug effects ; Bacteroidaceae Infections/microbiology ; Adenosine Triphosphate/metabolism ; }, abstract = {The vaginal microbiome plays a complex role in tenofovir's mucosal pharmacology. While the relative contribution of systemic versus local concentrations to PrEP PK/PD is an ongoing debate, the development of effective HIV prevention requires an understanding of events at the site of transmission. Our objective was to further understand the relationship between tenofovir mucosal pharmacology and non-optimal vaginal microbiota using the ex vivo vaginal tissue model. Vaginal and cervical explants were produced from cadaver tissue using a biopsy punch. Explants were incubated with Prevotella bivia (10[3]-10[5] colony forming units/ml) with and without tenofovir for 24 h. TFVdp and endogenous adenosine triphosphate (dATP) were quantified using liquid chromatography tandem mass spectroscopy. Explants were then challenged with 10[6] TCID50 the viral concentration where 50% of tissue cultures are infected, of HIVJR-CSF for 3 h. Explants were cultured on gel-foam rafts for 48 h then collected for HIV RNA quantification using RT-qPCR. TFVdp formation in vaginal tissue was approximately 76% lower in anaerobic conditions (p = 0.2) compared to aerobic. While dATP concentrations did not significantly differ between any Prevotella bivia concentrations and the Prevotella-free control, TFVdp and TFVdp:dATP ratio in vaginal tissue decreased as Prevotella bivia concentrations increased, although not statistically. Unexpectedly, tenofovir efficacy increased as Prevotella bivia concentrations increased. The ex vivo tissue model was successful in demonstrating the pharmacology of TFVdp is affected by Prevotella bivia. Viral replication was also affected by Prevotella bivia; therefore, further work is needed to fully understand effects on tenofovir pharmacodynamics.}, }
@article {pmid42148776, year = {2026}, author = {Guo, J and Xiang, Z-w and Hu, F-f and Zhang, S-x and Han, W-j and Ding, X and Wang, X and Ye, M-l and Chen, J-h and Rao, T and Wu, L-l and Lian, G-h and Zhang, W and Huang, Y and Chen, Y}, title = {Turicibacter sanguinis is a candidate gut microbial pathobiont that promotes metabolic dysfunction-associated steatohepatitis.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0029226}, doi = {10.1128/msystems.00292-26}, pmid = {42148776}, issn = {2379-5077}, abstract = {UNLABELLED: Emerging evidence points to the gut microbiota's involvement in metabolic dysfunction-associated steatohepatitis (MASH), yet the specific causative microbes remain largely unidentified. This study aimed to identify and functionally characterize candidate microbial pathobionts to MASH progression. Differentially abundant microbes were identified by 16S rRNA sequencing in a choline-deficient, L-amino acid-defined, high-fat diet MASH model, validated in other animal MASH models and in public clinical metagenomic data sets, then screened for consistently altered gut taxa. A candidate underwent functional validation via directed oral administration in mice. Mechanisms were explored through bile acid profiling by UHPLC-MS/MS and FXR signaling analysis by qPCR and immunohistochemistry. Additionally, fecal samples from MASH patients before and after treatment were analyzed to correlate microbial abundance with treatment response. Turicibacter sanguinis was consistently enriched in all MASH models and public data sets, with abundance correlating positively with liver injury markers. Its increased abundance exacerbated steatosis, inflammation, and fibrosis in healthy and diseased mice. Mechanistically, Turicibacter sanguinis altered bile acid composition, thereby increasing conjugated and decreasing unconjugated species, and inhibited hepatic FXR signaling, accompanied by suppressed SHP and elevated CYP7A1 and SREBP1c expression, which is consistent with enhanced bile acid synthesis and lipid accumulation. Futhermore, after pharmacotherapy, reduced Turicibater sanguinis levels correlated positively with alanine aminotransferase (ALT) and aspartate aminotransferase (AST) improvements. In conclusion, Turicibacter sanguinis is a clinically relevant microbial pathogen that exacerbated MASH by inducing bile acid dysregulation and suppressing FXR signaling, highlighting its potential as a candidate biomarker for disease monitoring and motivating future evaluation of targeted microbiome interventions.<br><br>IMPORTANCE: Metabolic dysfunction-associated steatohepatitis (MASH) is a growing global health problem with limited treatment options. Although the gut microbiome has been implicated in MASH, the specific bacterial strains that directly drive disease progression remain largely unknown. This study identified Turicibacter sanguinis as a candidate gut microbial pathobiont that promotes MASH, demonstrating its significant enrichment in both animal models and patient samples. By disrupting hepatic metabolic signaling, this bacterium promotes bile acid synthesis and exacerbates liver fat accumulation, inflammation, and fibrosis. Following effective treatment, its abundance decreased significantly in patients. These findings indicate that Turicibacter sanguinis holds promise as a potential target for developing novel microbiome-based diagnostic and therapeutic approaches for MASH.}, }
@article {pmid42148824, year = {2026}, author = {De Biasi, J and Giménez Bastida, JA and Krupa-Kozak, U}, title = {Biotics: The Food Ingredients Supporting the Intestinal Microbiota and Immune System in Psoriasis.}, journal = {Nutrition reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/nutrit/nuaf252}, pmid = {42148824}, issn = {1753-4887}, support = {2022/45/B/NZ9/03004//National Science Centre, Poland, through project OPUS 23/ ; MICIU/AEI/10.13039/501100011033//National Science Centre, Poland, through project OPUS 23/ ; CNS2022-135253//the European Union NextGenerationEU/PRTR/ ; RyC2021-032111-I//the European Union NextGenerationEU/PRTR/ ; //MCIU/AEI/10.13039/501100011033/ ; PID2022-136915NA-I00//ERDF/EU/ ; }, abstract = {Psoriasis is a chronic immune-mediated inflammatory skin disease affecting 4 million new individuals worldwide each year. Although the etiology of psoriasis is not fully understood, genetic factors play a key role in conjunction with systemic inflammation and gut microbiota dysbiosis. Current methods of psoriasis treatment, while effective, may cause adverse reactions. Biotics (pre-, pro-, syn-, and postbiotics) are generally recognized as safe, have a good reputation, and have confirmed beneficial health effects. Considering the growing awareness of the impact of diet and lifestyle on health among individuals with psoriasis, the recognition of biotics as a potential source of health benefits with minimal constraints even during therapy has become more relevant. In this review, we highlight the therapeutic potential and beneficial effects of biotics in inflammatory skin diseases involving dysbiosis and screen the scientific data concerning recent randomized controlled trials that specifically assessed the use of biotics in psoriasis to understand the progress achieved to date. Most studies matching our screening criteria used lactic acid bacteria along with oligosaccharides as prebiotics. Probiotics have shown promising results in suppressing inflammatory pathways and alleviating the symptoms of psoriasis by modulating the gut microbiota. After several weeks of intervention, patients showed microbiome changes along with reduced levels of inflammatory biomarkers and psoriasis severity. Overall, biotics appear to be good candidates for improving the quality of life in patients with psoriasis; however, more randomized controlled trials with more rigid protocols and rigorously reported results are needed to properly assess their potential.}, }
@article {pmid42148825, year = {2026}, author = {Lim, JJX and Morgan, NR and Bhuvanendran, S and Janarthanan, P and Radhakrishnan, AK}, title = {Effects of Fat-Soluble Vitamins on Gut Microbiome Composition: A Scoping Review.}, journal = {Nutrition reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/nutrit/nuag065}, pmid = {42148825}, issn = {1753-4887}, abstract = {As the gut microbiome emerges as a key player in human health, numerous studies have reported its close association with various diseases. Consequently, increasing attention has been given to exploring whether fat-soluble vitamins can modulate gut microbiome composition as a potential strategy to maintain microbial balance. This scoping review aimed to investigate whether interventions with fat-soluble vitamins (vitamins A, D, E, and K) could alter gut microbiome composition and, in turn, improve health outcomes. A total of 17 human studies and 47 animal studies were identified across 4 databases. Most studies reported that fat-soluble vitamins effectively altered gut microbiome composition; however, evidence linking these changes to consistent improvements in health outcomes remains limited. Overall, this review maps the potential link between vitamin-driven microbiome modulation and health benefits, while highlighting current research gaps to guide future investigations.}, }
@article {pmid42148838, year = {2026}, author = {Kim, JH and Park, RY and Kim, ES and Kim, JH and Joo, BD and Yun, N and Koo, J and Kim, J and Kim, SH and Kim, J and Park, TG and Youn, SH and Kim, JH and Park, BS}, title = {Core Microbiota Drives Host-Specific Growth Enhancement: Evidence in a Harmful Algal Bloom Causing Dinoflagellate Prorocentrum lima.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c05294}, pmid = {42148838}, issn = {1520-5851}, abstract = {Bacterial microbiota influence algal growth and physiology, yet experimental validation in toxic benthic dinoflagellates remains limited. Here, we investigated the microbiota of six geographically distinct strains of the harmful benthic dinoflagellate Prorocentrum lima (P. lima) and identified core bacterial taxa shared across strains. Microbiota transplantation into an axenic P. lima strain revealed that donor consortia significantly enhanced early phase growth, increasing the specific growth rate by 61.1% compared to axenic controls. Coculture experiments with Marinobacter adhaerens (M. adhaerens), a core taxon isolated from P. lima, resulted in a significantly increased specific growth rate─up to 164.1% higher than the axenic control─while no such enhancement was observed in other tested microalgal species, indicating a host-specific interaction. Among several nutrient-limited conditions tested, this enhancement was uniquely observed under trace metal restriction. Genomic analysis and CAS assays revealed that M. adhaerens lacks canonical siderophore pathways but employs a noncanonical iron-acquisition strategy, which may contribute to enhanced iron availability under trace metal-limited conditions. These results provide experimental evidence that specific bacterial lineages closely associated with toxic dinoflagellates can promote their proliferation. Our findings highlight the ecological significance of dinoflagellate-associated core microbiota and offer new directions for microbiome-informed strategies in HAB monitoring and management.}, }
@article {pmid42149101, year = {2026}, author = {Ambi, A}, title = {The Copper-Gut-Brain Axis: A Triple Inflammatory Pathway Driving Neuroinflammation in Alzheimer's Disease.}, journal = {Aging and disease}, volume = {}, number = {}, pages = {}, doi = {10.14336/AD.2026.0375}, pmid = {42149101}, issn = {2152-5250}, abstract = {Serum copper increases progressively with normal aging, yet its downstream consequences for the gut microbiome and neuroinflammation remain unexplored. Gut microbiota dysbiosis and elevated lipopolysaccharide levels are established features of Alzheimer's disease, and growing evidence indicates that this dysbiosis drives neuroinflammatory disease progression. Yet the upstream trigger initiating this dysbiosis remains unknown. We propose that age-related copper dyshomeostasis serves as this missing trigger. The redox-active copper content of ceruloplasmin increases across the adult lifespan, and copper is selectively toxic to anaerobic bacteria, preferentially affecting butyrate-producing genera including Faecalibacterium, Roseburia, and Coprococcus while sparing copper-resistant species. This selective toxicity is supported by animal studies demonstrating copper-induced elimination of butyrate producers with reversible gut barrier damage and by Wilson's disease cohorts showing consistent depletion of butyrate-producing genera due to elevated copper levels. The resulting dysbiosis creates a triple inflammatory pathway: butyrate loss compromises gut barrier integrity and removes histone deacetylase-mediated suppression of neuroinflammation; the increase of Gram-negative bacteria elevates lipopolysaccharide translocation through the compromised barrier; and impaired blood-brain barrier integrity reduces amyloid-β clearance. These three insults trigger microglial activation through NF-κB signaling, creating a 'triple hit' on a single transcription factor that may explain the magnitude of neuroinflammatory effects observed in Alzheimer's disease. This mechanism explains the increased acetate/butyrate ratio recently identified as a biomarker distinguishing Alzheimer's-related from non-Alzheimer's cognitive impairment (AUC 0.951), since copper disrupts microbial metabolic cross-feeding networks that convert acetate to butyrate. We present specific, falsifiable predictions that can be tested in human cohorts and propose copper as a novel upstream therapeutic target for Alzheimer's disease prevention.}, }
@article {pmid42149113, year = {2026}, author = {De Allende, CC and Salter, SJ and Brigg, SE and Boardman, M and Claassen-Weitz, S and Mwaikono, KS and Workman, L and Zar, HJ and Nicol, MP and Parkhill, J and Dube, FS}, title = {Characterization of Ornithobacterium hominis colonization dynamics and interaction with the nasopharyngeal microbiome in a South African birth cohort.}, journal = {Microbial genomics}, volume = {12}, number = {5}, pages = {}, pmid = {42149113}, issn = {2057-5858}, mesh = {Humans ; *Nasopharynx/microbiology ; South Africa ; *Microbiota/genetics ; Phylogeny ; Female ; Cohort Studies ; Male ; RNA, Ribosomal, 16S/genetics ; Infant ; }, abstract = {Ornithobacterium hominis is a recently described Gram-negative bacterium that colonizes the human nasopharynx and may be associated with poor upper respiratory tract health. Here, we describe the isolation of O. hominis from samples collected from a South African birth cohort, creating the first archive of cultured strains of the species from Africa. Sequenced genomes from this archive reveal that South African O. hominis is more similar to Australian strains than those from Southeast Asia and that it may share genes with other members of the microbiome that are relevant for virulence, colonization and antibiotic resistance. Leveraging existing microbiome data from the cohort, O. hominis was found to be closely associated with bacterial co-colonizers that are rare in non-carrier individuals, including Suttonella, Rappaport, Helcococcus, Lwoffella, Moraxella and Gracilibacteria. Their collective acquisition has a significant impact on the diversity of nasopharyngeal communities that contain O. hominis. Individuals who have not yet acquired O. hominis have a higher abundance of Lwoffella lincolnii than individuals who never acquire O. hominis, suggesting that this could be a precursor state for successful colonization.}, }
@article {pmid42149451, year = {2026}, author = {Edelkamp, J and Lousada, MB}, title = {In Situ Laser-Capture Microdissection for Detection of Components of the Hair Follicle and Scalp Microbiome.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3031}, number = {}, pages = {233-242}, pmid = {42149451}, issn = {1940-6029}, mesh = {*Hair Follicle/microbiology ; *Laser Capture Microdissection/methods ; *Microbiota/genetics ; Humans ; *Scalp/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; }, abstract = {Laser-capture microdissection (LCM) enables the study of the hair follicle (HF) microbiome in relation to hair health and disease with high spatial resolution. It allows the precise excision of specific HF regions, each containing a unique and conserved microbiome, from full-length HFs encompassing all relevant HF compartments. With LCM, cross-contamination with microbiota from neighboring regions is minimized. Coupled with 16S rRNA gene or metagenomic shotgun sequencing, LCM offers great potential to assess region-specific microbiome changes, particularly in HF-associated disorders.}, }
@article {pmid42149452, year = {2026}, author = {Edelkamp, J and Lousada, MB}, title = {Viable vs. Nonviable Microbiota Evaluation of the Hair Follicle and Scalp Microbiome.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3031}, number = {}, pages = {243-259}, pmid = {42149452}, issn = {1940-6029}, mesh = {Humans ; *Hair Follicle/microbiology ; *Microbiota/genetics ; *Scalp/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; In Situ Hybridization, Fluorescence/methods ; Propidium/analogs &amp; derivatives/chemistry ; Azides/chemistry ; Microbial Viability ; Real-Time Polymerase Chain Reaction/methods ; }, abstract = {Various hair follicle (HF)-associated disorders, such as acne vulgaris, hidradenitis suppurativa, and alopecia areata, are linked to dysbiosis, an imbalance between resident and pathogenic microbes. Characterization of the HF and skin microbiome employs techniques such as 16S rRNA gene sequencing and metagenomic shotgun sequencing, with the latter providing comprehensive taxonomic and functional insights. However, relic DNA from dead microbes and free environmental DNA can persist in samples, meaning that metagenomic data does not exclusively reflect living microbiota. For functional studies on HF dysbiosis or to assess potential therapeutic interventions, we describe here how propidium monoazide (PMA) treatment can be performed before (metagenomics) sequencing to distinguish viable microbial communities. Furthermore, we exemplify qPCR and (fluorescent) in situ hybridization (ISH) of two alternative viability screening methods for the HF and scalp microbiome.}, }
@article {pmid42149786, year = {2026}, author = {Fluhr, JW and Bräutigam, MM and Proksch, E}, title = {Topical calcineurin inhibitors and the epidermal barrier in atopic dermatitis.}, journal = {Dermatology (Basel, Switzerland)}, volume = {}, number = {}, pages = {1-20}, doi = {10.1159/000552559}, pmid = {42149786}, issn = {1421-9832}, abstract = {BACKGROUND: The topical calcineurin inhibitors [TCIs] pimecrolimus and tacrolimus, offer an effective non-steroidal option for treating atopic dermatitis [AD], particularly in sensitive skin areas and for long-term use. There are several studies published on the effect of calcineurin inhibitors on the skin barrier but a comprehensive review on this topic is still missing.<br><br>SUMMARY: This review summarizes current evidence on the impact of TCIs on epidermal barrier structure and function. Clinical studies in patients with AD show that TCIs improve transepidermal water loss [TEWL], enhance stratum corneum [SC] hydration, and promote normalization of structural proteins such as filaggrin and loricrin. Unlike topical corticosteroids [TCS], TCIs do not induce skin atrophy and may even reverse steroid-induced epidermal thinning. Additionally, TCIs partially preserve antimicrobial peptide [AMP] expression in lesional AD skin, which may help reduce Staphylococcus aureus colonization and support microbial diversity. Positive effects on lipid lamellar organization and natural moisturizing factor [NMF] levels further support barrier restoration. Animal data suggesting impaired lipid synthesis under TCI treatment contrast with consistent positive findings in clinical studies. Importantly, emerging evidence indicates that TCIs may improve the skin microbiome in AD.<br><br>KEY MESSAGES: TCIs exert their beneficial effects on skin inflammation through selective T-cell modulation without disrupting keratinocyte differentiation or dermal matrix components. For this reason, the general indirect positive effects on skin barrier associated with reduction of skin inflammation is not counterbalanced by intrinsic barrier damaging mechanisms as observed with topical steroids. Further studies are needed to evaluate long-term effects on skin structure, microbiome stability, and their integration into biologic treatment algorithms.}, }
@article {pmid42149909, year = {2026}, author = {Bonacolta, AM and Kravitz, T and Mozo, R and Baker, LJ and Heuer, RM and Grosell, M and Del Campo, J}, title = {Symbiotic bacteria may support calcium carbonate precipitation in the Gulf toadfish.}, journal = {PLoS biology}, volume = {24}, number = {5}, pages = {e3003764}, doi = {10.1371/journal.pbio.3003764}, pmid = {42149909}, issn = {1545-7885}, abstract = {Marine fish play a significant yet understudied role in the oceanic carbon cycle through the production of magnesium-rich calcium carbonate (CaCO3) precipitates known as ichthyocarbonates. These deposits form in the gut of marine teleost fish in response to salinity, serving as part of their osmoregulation strategy. Through this, marine fish may contribute as much as 9.04 Pg of CaCO3 per year in global new carbonate production, being equivalent to or potentially higher than the production by coccolithophores and pelagic foraminifera. Despite their ecological relevance, the biological mechanisms driving ichthyocarbonate precipitation remain to be fully resolved. Intriguingly, bacteria are consistently found in intimate association with ichthyocarbonate precipitates. Given the widespread capacity of prokaryotes to mediate CaCO3 precipitation, this association points to a previously unexplored microbial contribution to the process. To investigate the potential role of bacteria in ichthyocarbonate production, we subjected Gulf toadfish (Opsanus beta) to salinity treatments common to their native range and known to elicit changes in CaCO3 precipitation. To assess the respective contributions of the host and its microbiota to ichthyocarbonate formation in the gut, we characterized the microbiome across the toadfish gut and performed meta-transcriptomic analysis. Across the toadfish gut, we identify a high abundance of vibrios associated with ichthyocarbonates with the metabolic potential for CaCO3 precipitation. Specifically, we observe the expression of the transcriptional activator of urease (ureR) by Photobacterium damselae subsp. damselae, which can induce the precipitation of CaCO3 via the production of bicarbonate. We demonstrate that CaCO3 precipitation in marine fish may not solely be a host-driven process, but potentially the result of a functional symbiosis with gut-associated Vibrio bacteria. We hypothesize that just as photosymbionts enable corals to build reefs, fish hosts, along with their microbial partners, may synergistically contribute to oceanic carbonate production. This discovery, if confirmed, expands the role of symbiosis in marine biomineralization and underscores its broader influence on global biogeochemical cycles.}, }
@article {pmid42150103, year = {2026}, author = {Moffatt, MF and Nishimura, T and Cox, MJ and Mcbrien, C and Burke, C and Cuthbertson, L and Lewis, K and Attanoos, R and Davies, GA and Chung, KF and Robertus, JL and Ish-Horowicz, J and O'Carroll, O and Bozeman, JM and Mcgowan, A and Hopkin, JM and Lathrop, GM and Riazalhosseini, Y and Cookson, WOC}, title = {Airway microbiome diversity, intra-mucosal bacteria, and spatial immunity in asthmatics and controls.}, journal = {American journal of respiratory and critical care medicine}, volume = {}, number = {}, pages = {}, doi = {10.1093/ajrccm/aamag232}, pmid = {42150103}, issn = {1535-4970}, abstract = {RATIONALE: Asthma is characterized by disruption of the thoracic airway mucosae and loss of microbial diversity. Spatial profiling of the mucosal transcriptome may systematically discover mechanisms for microbial influences on immunity.<br><br>OBJECTIVES: We investigated relationships between clinical measures, microbial communities, and the host mucosal transcriptome within different strata of bronchial biopsies in subjects with and without asthma.<br><br>METHODS: We bronchoscoped 65 adult asthmatics and 44 healthy controls, quantifying bacterial operational taxonomic units (OTUs) in bronchial brushings by 16S rRNA gene amplicon sequences. Biopsy histologic features were scored blind to diagnosis. Following 16S rRNA in situ hybridization of 44 biopsies, bacterial foci were scored in epithelium, basement membrane and stroma. Global human gene expression was quantified in epithelial and stromal compartments using Digital Spatial Profiling.<br><br>MEASUREMENTS AND MAIN RESULTS: Clinical asthma was independently predicted by basement membrane abnormalities (BaseMA), endobronchial bacterial diversity and circulating eosinophil counts, but not by specific OTU abundances. 16S rRNA staining revealed bacteria within epithelium and mucosa of all biopsies. Intra-mucosal bacteria (IMCBs) counts correlated negatively with spatially organized co-expression networks encoding antigen-specific immunity, neutrophil functions, and matrix activation, whereas BaseMA correlated positively with the adaptive immunity module. Eosinophil counts correlated with epithelial bacterial counts and senescence pathways. Clinical asthma was accompanied by upregulation of a Treg cell network.<br><br>CONCLUSIONS: Asthma and its related phenotypes are accompanied by complex mucosal events that extend beyond eosinophilic pathways. Components of diverse airway microbiota may modify immunity by beneficial interactions within the mucosa.}, }
@article {pmid42150350, year = {2026}, author = {Guazzini, M and Marasco, R and Radović, S and Pellegrini, E and Vuerich, M and Lodovici, A and De Wittenau, GD and Paparelli, E and Magris, G and Zanin, L and Contin, M and De Luca, E and Daffonchio, D and Di Gaspero, G and Marroni, F}, title = {Variations in the root-soil system influence the grapevine holobiont by shaping plant physiology and root microbiome.}, journal = {The Science of the total environment}, volume = {1037}, number = {}, pages = {181874}, doi = {10.1016/j.scitotenv.2026.181874}, pmid = {42150350}, issn = {1879-1026}, abstract = {Soil-dwelling bacteria and fungi play a crucial role in plant health and productivity by engaging in complex interactions that shape and are shaped by soil physico-chemical properties. In this study, we employed a multi-omics approach to investigate how variations in soil composition affect the grapevine holobiont. Grape plantlets were grown in three distinct soil types, namely sand, peat, and peat-manure. To further assess how variation in soil and root conditions affects the holobiont's response, we included treatments involving soil autoclaving and root heat treatment across all soil types. We found that soil type significantly influences leaf multielement composition and concentration, while also shaping the bacterial and fungal communities associated with the plant rhizosphere. This shift led to changes in taxa involved in nitrogen fixation, biocontrol, and pathogenicity. Autoclaving soils consistently reduced bacterial diversity across all soil types, whereas fungal communities were less affected. In contrast, thermal treatment of roots had only a minor impact on microbial community composition but did induce transcriptional changes in the root and altered leaf macronutrient concentrations. Our findings indicate that differences in soil composition reshape the entire root-soil continuum, ultimately affecting plant physiology at multiple levels-from root function to leaf nutrient status. This highlights that the soil is not a passive growth medium but a key determinant of grape holobiont structure and function. These results reinforce the view that plant health and adaptation arise from integrated, dynamic interactions among the host, its associated microbiome, and the surrounding soil matrix.}, }
@article {pmid42150447, year = {2026}, author = {Sharma, P and Iqbal, MZ and Chandra, R}, title = {The emerging insights on signaling molecule-mediated hyperaccumulation: Unlocking potential in metal-stressed plants with phytoremediation applications.}, journal = {Plant physiology and biochemistry : PPB}, volume = {235}, number = {}, pages = {111383}, doi = {10.1016/j.plaphy.2026.111383}, pmid = {42150447}, issn = {1873-2690}, abstract = {Phytoremediation, which involves plants and their associated microbiome, is a sustainable remediation strategy for removing, stabilizing, or degrading contaminants in the ecosystem. The technology revolves around hyperaccumulators that tolerate and remove contaminants through their physiological and molecular mechanisms that are facilitated by various signaling molecules [reactive oxygen species (ROS), phytohormones, calcium ions (Ca[2+]), nitric oxide (NO), and electrophysiological signals]. This review aims to define the phenomenon of phytoremediation, enumerate its types, and highlight its limitations, with an emphasis on the role of hyperaccumulator plants in environmental remediation. The major focus is on the signaling molecules-regulated molecular mechanisms of metal uptake, translocation, chelation, sequestration, and antioxidant defence. Remediation processes are optimized by regulatory networks resulting from phytohormonal cross-talk. The transgenic and CRISPR/Cas9 technologies can significantly improve the hyperaccumulator capacity through gene overexpression and gene editing of those encoding the biosynthesis of signaling molecules. The processes, phytostabilization, phytoextraction, and the microbial breakdown of organic pollutants by plants, have shown the most removal of contaminants in the in-situ experiments. The research gaps are the complexity of the pathway, the variability of the environment, and a detailed research plan, focusing on electrophysiology and the integration of Artificial intelligence/Machine learning. The concept of coupling microbial synergy, nanotechnology, and portable monitoring can accomplish the phytoremediation shift from the lab to the field. Signaling molecules can be utilized by hyperaccumulators to effectively address the global problem of contamination, thereby enabling the development of renewable and environmentally friendly solutions for the eco-restoration of contaminated sites.}, }
@article {pmid42150448, year = {2026}, author = {Wang, L and Weng, W and Zhou, Z and Liang, B and Wang, S and Hu, X and Zhu, H and Wang, H and Sui, N}, title = {A regulatory network revealing spatial distribution differences of alkaloids, flavones, and carbohydrates in Fritillaria thunbergii bulbs by multi-omics analysis.}, journal = {Plant physiology and biochemistry : PPB}, volume = {235}, number = {}, pages = {111387}, doi = {10.1016/j.plaphy.2026.111387}, pmid = {42150448}, issn = {1873-2690}, abstract = {The secondary metabolites in the bulbs of Fritillaria species display distinct spatial distribution patterns, yet the underlying mechanisms remain unclear. In this study, bulbs of Fritillaria thunbergii were divided into inside (IS) and outside (OS) layers. Integrated physiological, transcriptomic, metabolomic, and microbiomic analyses were performed to elucidate the spatial regulation of alkaloids, flavonoids, and carbohydrates. The OS was significantly enriched in secondary metabolites, with total alkaloid, peimine, and total flavonoid contents being approximately 1.18-, 1.28-, and 1.24-fold higher, respectively, than those in the IS. In contrast, carbohydrates mainly accumulated in the IS, where sucrose and starch levels were 1.37- and 2.18-fold higher than those in the OS. Transcriptomic analysis revealed that carbohydrate enrichment in the IS was associated with the upregulation of sucrose synthase (SUS) and hexokinase (HK) genes, and the downregulation of β-amylase3 (BAM3) and invertase (INV). In the OS, genes related to steroidal alkaloid biosynthesis, including 3-hydroxy-3-methylglutaryl-CoA synthase (HMGCS), 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR), and farnesyl-diphosphate farnesyltransferase 1 (FDFT1), as well as flavonoid biosynthesis genes phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), and cytochrome P450 monooxygenase CYP75B1 (CYP75B1), were upregulated. Moreover, bacterial taxa enriched in the OS, such as Actinomycetota and Ruminococcus, correlated positively with alkaloid accumulation, while the fungal genus Aspergillus was potentially associated with flavonoid regulation. Overall, the multi-omics insights provided here not only offer theoretical support for refined, region-specific processing of Zhejiang Fritillaria bulbs but also open new avenues to improve medicinal quality by manipulating host gene expression and microbial community composition.}, }
@article {pmid42150701, year = {2026}, author = {Zhu, Z and Xu, H}, title = {Distinct microbiome signatures associated with wing polyphenism in the wing-dimorphic planthopper Nilaparvata lugens.}, journal = {Journal of insect physiology}, volume = {}, number = {}, pages = {104994}, doi = {10.1016/j.jinsphys.2026.104994}, pmid = {42150701}, issn = {1879-1611}, abstract = {Wing polyphenism is crucial for the ecological adaptation of the wing-dimorphic planthopper Nilaparvata lugens, yet its underlying association with symbiotic microbiota remains poorly understood. Here, we investigated three N. lugens strains (Field, HSD, and Lab) exhibiting stable but distinct macropterous-to-brachypterous ratios. 16S rRNA amplicon sequencing revealed that the composition and structure of the microbiota differed significantly not only among the diverse strains but also between distinct wing morphs within the same genetic background and living environment. Furthermore, functional predictions demonstrated that the relative abundance of aerobic bacteria and specific metabolic pathways, notably steroid hormone biosynthesis and linoleic acid metabolism, were positively correlated with the macropterous ratio. These findings suggest that wing morph determination in N. lugens is intimately associated with distinct microbiome configurations and host-microbe metabolic interactions, providing a novel microecological perspective on insect phenotypic plasticity. However, further experimental validations are required to determine whether these microbial shifts drive wing morph development or are a consequence of divergent host physiology.}, }
@article {pmid42150752, year = {2026}, author = {Srinivasalu, VK and Subramaniam, N and Ibrahim, M and Das, M}, title = {Circulating Tumor DNA and Precision Biomarkers in Colorectal Cancer: Implications for Diagnosis, Monitoring, and Management of Advanced Disease.}, journal = {Journal of gastroenterology and hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jgh.70420}, pmid = {42150752}, issn = {1440-1746}, abstract = {Colorectal cancer (CRC) remains one of the leading causes of cancer-related mortality worldwide, with outcomes critically dependent on timely diagnosis, accurate risk stratification, and individualized treatment. Traditional markers such as CEA, KRAS/NRAS, BRAF, and MSI status, while foundational, are insufficient to address the full complexity of CRC biology. Over the past decade, a new generation of biomarkers has emerged spanning liquid biopsy, stool-based methylation, genomics, epigenomics, immune profiling, microbiome analysis, radiomics, patient-derived organoids, and multiomics integration-collectively redefining how CRC is detected, classified, and treated. This narrative review synthesizes evidence from 73 human studies published between 2010 and 2024, identified through structured searches of PubMed, Embase, Web of Science, and the Cochrane Library, and quality-assessed using QUADAS-2 and Newcastle-Ottawa tools. Circulating tumor DNA (ctDNA) emerged as the most clinically validated biomarker, demonstrating superior performance in minimal residual disease (MRD) detection, recurrence prediction, and real-time therapy monitoring. Stool DNA methylation assays showed strong sensitivity for early CRC and advanced adenoma detection. Genomic markers including BRAF V600E, POLE/POLD1, HER2, and KRAS G12C now directly inform targeted therapy selection, while immune biomarkers-MSI-H, TMB, and Immunoscore-guide immunotherapy decisions and stratify prognosis beyond TNM staging. Microbiome signatures, particularly Fusobacterium nucleatum and colibactin-producing Escherichia coli, were associated with chemo resistance and tumor progression. Radiomics and AI-driven imaging models provided noninvasive assessment of nodal involvement and neo-adjuvant therapy response. Patient-derived organoids demonstrated capacity to predict individual drug sensitivity, and multiomic integration enabled refined molecular subtyping. Despite this progress, widespread clinical adoption remains limited by assay variability, lack of prospective multicenter validation, and implementation barriers including cost and infrastructure. As these technologies mature, their integration into standardized, multidisciplinary workflows will be essential to translating biomarker innovation into improved patient outcomes across all stages of CRC care.}, }
@article {pmid42150759, year = {2026}, author = {Evans, EM and Mayday, MY and Pearce, EM and Iwanaga, K and Ly, NP and Church, GD and Reyes, G and Simon, MR and Blum, J and Kim, H and Mu, J and Baez-Maidana, J and Auletta, JJ and Shaw, PJ and Kreml, EM and Martin, PL and Duncan, CN and Rowan, CM and Godder, K and Hurley, C and Cuvelier, GDE and Qayed, M and Abdel-Azim, H and Keating, AK and Fitzgerald, JC and Hanna, R and Killinger, JS and Hume, JR and Quigg, TC and Castillo, P and Satwani, P and Moore, TB and Dvorak, CC and Zinter, MS and , }, title = {Upper and Lower Respiratory Tract Compartmentalization in Pediatric Stem Cell Transplantation.}, journal = {American journal of respiratory cell and molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/ajrcmb/aanag106}, pmid = {42150759}, issn = {1535-4989}, abstract = {RATIONALE: Lung injury after hematopoietic stem cell transplantation (HCT) occurs due to infection, chemotherapy toxicity, and alloreactive inflammation. Analyses of bronchoalveolar lavage (BAL) fluid have revealed dominant pathobiologic signatures, but minimally-invasive diagnostics are needed.<br><br>OBJECTIVES: To determine whether microbiome and gene expression perturbations are shared along the respiratory tract or isolated to the alveoli in pediatric HCT patients with lung injury.<br><br>METHODS: We performed bulk RNA sequencing on 206 paired nasal and BAL samples from 160 HCT patients and 17 healthy controls enrolled at 28 children's hospitals (2016-2025). Microbial and human transcripts were compared using multivariable models accounting for age, sex, and paired sampling.<br><br>MEASUREMENTS AND MAIN RESULTS: HCT BAL and nasal transcriptomes differed across 13,698 genes, 48 cellular components, and network interactions linking inflammation, reactive oxygen species, and immunometabolism. Minimal BAL-nasal correlation was observed in gene expression levels (median &#x3c1;&#x2009;=&#x2009;0.03, IQR -0.03 to 0.08) or fractional abundance of key cells such as neutrophils and CD8&#x2009;+&#x2009;T-cells. BAL microbiomes harbored fewer commensal bacteria and more fungi and DNA viruses. BAL bacterial RNA was associated with diminished immune signaling whereas nasal bacterial RNA aligned with inflammatory gene expression. Further, only BAL microbial RNA was linked to transcriptional shifts in epithelial injury response, keratinization, and collagen deposition. Finally, BAL commensal microbiome depletion, epithelial injury, and immune dysregulation signatures were associated with death or prolonged mechanical ventilation, whereas nasal samples provided minimal prognostic information.<br><br>CONCLUSIONS: These data support alveolar compartmentalization in pediatric HCT and emphasize the ongoing need for minimally-invasive but informative diagnostics.}, }
@article {pmid42151055, year = {2026}, author = {Dong, YH and Song, Y}, title = {[Exploring multidimensional environmental exposure and strategies for the co-prevention of multimorbidity in children and adolescents].}, journal = {Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi}, volume = {47}, number = {5}, pages = {791-798}, doi = {10.3760/cma.j.cn112338-20251118-00835}, pmid = {42151055}, issn = {0254-6450}, support = {2024YFC2707901, 2024YFC3308302//National Key Research and Development Program of China/ ; }, mesh = {Humans ; Adolescent ; Child ; *Environmental Exposure/adverse effects/prevention &amp; control ; *Multimorbidity ; Risk Factors ; Public Health ; }, abstract = {Multimorbidity in children and adolescents has become an increasingly prominent public health challenge, but the traditional single-etiology models cannot explain its complex phenotypic manifestations. This paper systematically summarizes the challenges and underlying mechanisms of the co-occurrence, multi-causal management, and co-prevention of multiple diseases associated with multidimensional environmental exposures in children and adolescents, showing that chemical (heavy metals, endocrine-disrupting chemicals, etc.), physical (PM2.5, noise, etc.), biological (microbiome, etc.), and socio-environmental factors (family stress, community resources, etc.) collectively form a mixed exposure network. These factors affect the health of multiple systems, including respiratory, metabolic, and neurodevelopmental systems, of children and adolescents through biological mechanisms such as epigenetic programming, immune-metabolic disruption, microbiome dysbiosis, and neuro-immune-endocrine network interactions, resulting in multi-disease co-occurrence. In addition, this paper introduces the co-occurrence of multiple diseases in children and adolescents in the context of "common exposure-common mechanism-common prevention" and suggests targeted intervention strategies, including risk factor identification, exposure source control and novel multidimensional environment management, to provide scientific evidence for building a co-prevention system for multiple childhood diseases and informing precision public health practices.}, }
@article {pmid42151161, year = {2026}, author = {Wang, Y and Hou, Q and Lv, X and Liu, J and Wang, H and Zhao, Y and Tong, H and Liu, Y and Du, J and Yang, X and Wu, S and He, S and Yang, X}, title = {Inorganic nitrogen metabolic reprogramming of the gut microbiome drives fecal microbiota transplantation in ulcerative colitis.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73290-y}, pmid = {42151161}, issn = {2041-1723}, support = {32172776//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Although fecal microbiota transplantation (FMT) shows promise for ulcerative colitis (UC), its clinical success appears to be contingent upon the degree of donor microbiota engraftment. Using an LD50-based ecological model, our study reveals that inorganic nitrogen utilization capacity (IN-uc) critically determines gut microbial assembly in high oxidative stress environments, which significantly influences microbial engraftment outcomes. Building on this mechanistic insight, we engineer a probiotic-metabolite consortia designed to synergistically increase IN-uc in the gut ecosystem. We find that PM-mix14 alleviates oxidative stress-mediated colonization barriers of donor microbiota by catalyzing the conversion of excess reactive nitrogen species through multi-step reactions, promotes L-glutamate biosynthesis and ATP production, thereby ensuring greater similarity in the structure and function of the recipient microbiota to those of the donor. In multiple male murine models of colitis, PM-mix14 supplementation during FMT significantly improves microbial engraftment fidelity, which is correlated with increased anti-inflammatory responses and attenuated colonic pathology. Network meta-analysis of multiple clinical datasets further substantiates the prognostic value of donor gut microbial IN-uc in UC remission. Our findings establish the gut microbial IN-uc as an ecological driver of microbiota engraftment and present a rationally designed microbial therapy that optimizes FMT efficacy through targeted metabolic reprogramming.}, }
@article {pmid42151236, year = {2026}, author = {Khalifa, AM and ElBaghdady, KZ and Hamed, MM and Mohammad, AS and Khaled, MA}, title = {Integrating spectral signatures and microbial profiling to differentiate diseased and healthy corals in the Red sea.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42151236}, issn = {2045-2322}, mesh = {Animals ; *Anthozoa/microbiology ; Indian Ocean ; Coral Reefs ; *Bacteria/classification/isolation &amp; purification ; Microbiota ; }, abstract = {Coral reef ecosystems face increasing threats from microbial diseases, especially those induced by bacterial infections. Conventional diagnostic techniques often require invasive sampling, extended processing time and are limited in their spatial applicability. Spectral reflectance analysis offers a non-invasive means for detecting subtle physiological alterations associated with coral disease; however, its application in characterizing microbiological changes remains largely unexplored. This research aimed to differentiate healthy from diseased coral colonies by analyzing the spectral fingerprints of the disease and their associated bacterial communities, using hyperspectral data, microbial profiling, and multivariate statistical analysis. The bacterial species identified in healthy coral samples included Bacillus subtilis, Cytobacillus firmus, Bacillus amyloliquefaciens, and Bacillus sporothermodurans. In contrast, the bacteria associated with diseased coral samples were Vibrio pelagius and Vibrio fortis. Healthy corals demonstrate consistently lower reflectance across all bands in comparison to diseased corals. The reflectance of diseased Favia lacuna showed a notable increase when compared to healthy specimens, especially at wavelengths of 594 nm, 649 nm, and 702 nm. In contrast, Acropora humilis exhibited heightened peaks at wavelengths of 580 nm, 693 nm, and 702 nm. The analysis of the second derivative revealed that coral colonies affected by disease exhibited distinct negative peaks at wavelengths of 450-460 nm, 580-590 nm, and 700-800 nm. The identified peaks are likely associated with tissue thinning, skeletal exposure, or microbial biofilm accumulation rather than pigment absorption, given that this region is dominated by scattering effects. In contrast, healthy colonies exhibited stable characteristics at approximately 675 nm, indicating the presence of intact symbiotic chlorophyll and preserved physiological structure. The present study demonstrates that hyperspectral reflectance profiling of bacterially infected corals shows promising potential as a non-invasive approach for differentiating healthy and diseased coral microbiomes. The integration of spectral indicators with microbial community data provides preliminary insights into coral health assessment and may contribute to the development of improved strategies for disease detection and understanding coral-microbe interactions under environmental stress.}, }
@article {pmid42151282, year = {2026}, author = {Visci, G and Notario, E and Defazio, G and Caratozzolo, MF and Cox, SN and Fosso, B and Marzano, M and Pesole, G}, title = {Benchmarking short- and long-read sequencing technologies for metagenomic profiling of microbiomes.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-49725-3}, pmid = {42151282}, issn = {2045-2322}, support = {PNC0000002 - CUP: B53C22006420001//Ministero dell'Universit&#xe0; e della Ricerca/ ; PNC-EJ-2022-23683266 PNC-HLS-DA//Ministero dell'Universit&#xe0; e della Ricerca/ ; H93C22000560003//Regione Puglia/ ; }, abstract = {Two culture-independent methods, amplicon-based sequencing and shotgun metagenomics, have significantly advanced the study of microbial communities. To date, short-read sequencing technologies have enabled high accuracy and deep coverage, while long-read sequencing approaches are increasingly being applied to improve genome assembly, despite challenges related to sequencing errors and nucleic acid input requirements. In this benchmark study, we compared the shotgun metagenomics approach across three sequencing technologies, Illumina (short reads), PacBio and Nanopore (long reads), using a 20-species commercial mock microbial community with even species representation. Specifically, we evaluated the effectiveness of the data generated by each platform in reconstructing genomes and identifying specific known taxa, as well as in understanding their functional potential, considering annotated genes, the length of predicted proteins and the number and types of inferred functions. Illumina sequencing provided high-throughput and high-quality data, but its limited read length precluded complete genome assembly. This affected the functional analysis, leading to an underestimation of coding and non-coding genes. Nanopore sequencing yielded the longest reads, resulting in more contiguous assemblies, although it was affected by higher error rates and the choice of assembly method. PacBio offered the best balance between read length and base accuracy, but with a lower number of reads. This affected genome coverage for certain taxa, influencing the quality of their assemblies, the completeness of MAGs (Metagenome Assembled Genomes), and the accuracy of functional annotation. Nevertheless, PacBio successfully retrieved MAGs for all mock community species, and the genome annotation was consistent with the reference. Evaluating the strengths and limitations of different NGS technologies and assembly strategies, this benchmark provides a practical framework for selecting the most suitable approach for optimizing data quality in microbiome genome characterization, according to study-specific goals.}, }
@article {pmid42151303, year = {2026}, author = {de Tacca, LMA and Lima, RN and de Oliveira, MA and Pascoal, PV and Bambil, D and Rosinha, GMS and Signor, D and Freire, M and Rech, E}, title = {The soil microbiome of the Caatinga drylands in Brazil.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-50433-1}, pmid = {42151303}, issn = {2045-2322}, support = {20-122//Conrad Prebys Foundation/ ; }, abstract = {Drylands cover a significant portion of the Earth's surface and play a key role in maintaining global ecological balance. The Caatinga, with its unique biodiversity adapted to the extreme conditions of this semi-arid region, offers a valuable opportunity to expand our knowledge about these ecosystems. Here, this work reveals the high microbial diversity in the soil and rhizosphere of the Caatinga, with the roots presenting more specialized communities. Bacteria such as Bacilli, Alphaproteobacteria and Firmicutes excelled in critical functions such as nutrient cycling. The Interplant differences suggested the influence of root exudates. Altogether, the metagenomic study of interactions between microorganisms in the rhizosphere of selected plants revealed microbial biodiversity and contributed to our understanding of nutrient cycling, plant growth and resistance to water stress. In addition, they demonstrate biotechnological potential to address global challenges such as desertification and food security.}, }
@article {pmid42151371, year = {2026}, author = {Monsalves-Álvarez, M and Calderón-Romero, P and Hayes-Ortiz, T and Bobadilla, S and Sánchez, F and de Tudela, CP and Utreras-Mendoza, Y and Campos, C and Reyes, &#xc1; and Gómez, J and Zara, B and Sepúlveda, C and Troncoso, R and Correa-Burrows, P and Gonzales-Billault, C and Court, FA and Flores-Opazo, M and Valladares-Ide, D}, title = {Protein yogurt and whey protein produce comparable muscle gains, but divergent microbiome shifts during strength training in older adults.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-51209-3}, pmid = {42151371}, issn = {2045-2322}, support = {FONDECYT 11230186//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; FONDECYT 1241959//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; ACT210006//Fund for Research Centers in Priority Areas/ ; 15150012//Fondo de Financiamiento de Centros de Investigaci&#xf3;n en &#xc1;reas Prioritarias/ ; FONDAP-15150012//Fondo de Financiamiento de Centros de Investigaci&#xf3;n en &#xc1;reas Prioritarias/ ; FB210008//Financiamiento Basal para Centros Cient&#xed;ficos y Tecnol&#xf3;gicos de Excelencia Centro Ciencia and Vida/ ; }, abstract = {Sarcopenia, the age-related decline in muscle mass and strength, affects the functional capacity of older adults. Strength training (ST) combined with adequate protein intake is a key element in reversing and improving functional capacity. Protein, especially Whey Protein isolates (WPI), is widely used to improve muscle mass. In contrast, high-protein products, such as protein yogurt (PY), may offer similar benefits for muscle health and drive additional effects on gut health, which is altered in older adults. For this, we aim to compare WP and PY supplementation during ST on body composition, strength, and gut microbiome in untrained older adults. Seventeen untrained adults (60-70 years) were randomized to either consume WP (25 g) or PY (24.5 g) along with an 8-week supervised ST program (3 sessions/week). Initial and final assessments included body composition (BIA), strength (10RM, isokinetic torque, handgrip), gait speed, resting metabolic rate, and gut microbiome (16 S rRNA sequencing). Data were analyzed using repeated-measures ANOVA and diversity metrics. Both groups increased skeletal muscle mass (WP: +0.47 kg; PY: +0.50 kg) and improved strength and gait speed (p < 0.01), with no between-group differences. Fat mass decreased only in WP (p = 0.02), while resting metabolic rate increased in PY (p = 0.03). Microbiome analysis revealed distinct shifts: WP increased the Firmicutes/Bacteroidota ratio and enriched Subdoligranulum, whereas PY enhanced alpha diversity and increased the abundance of Coprococcus. Functional pathway predictions indicated differential enrichment in metabolic and signaling processes. High-protein yogurt and whey protein similarly improve muscle mass, strength, and functional capacity during ST, while exerting distinct effects on gut microbiome composition. Yogurt represents a cost-effective alternative to whey protein and may confer additional gut health benefits.Trial registration: Clinicaltrials.gov identifier NCT06412302. Date of registration 06/05/2024.}, }
@article {pmid42151475, year = {2026}, author = {Kobiałka, M and Świerczewski, D and Walczak, M and Pisarek-Pacek, A and Wóycicki, RK}, title = {Complementary Microscopic and Metabarcoding Studies Allow for a Better Understanding of the Symbiotic Microbiome of Leafhopper Species Iassus lanio (Hemiptera, Cicadellidae).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02790-7}, pmid = {42151475}, issn = {1432-184X}, support = {Sonata 17, project no. 2021/43/D/NZ8/02183//National Science Centre, Poland/ ; }, abstract = {Leafhoppers' microbiome patterns were shaped by deep co-evolutionary adaptation driven by dietary specialization. Their microbiome is dominated by obligate symbionts that supplement their nutrient-poor phloem-sap diet, as well as facultative symbionts, including both bacterial and fungal microorganisms. In this study, NGS metabarcoding techniques were performed, supplemented by confocal and electron microscopy, to thoroughly investigate the symbiotic system of the Auchenorrhyncha species Iassus lanio, a representative of the poorly studied leafhopper subfamily Iassinae. The obtained results include descriptions of the composition, distribution, and ultrastructure of microorganisms, as well as the phylogeny of ancient symbionts. Two obligate symbionts were found: the ancient Auchenorrhyncha symbiont Karelsulcia bacterium and the yeast-like symbiont Ophiocordyceps. Karelsulcia bacteria occur exclusively in specialized organs called bacteriomes, while fungal microorganisms inhabit mycetocytes within the fat body. Both symbionts are transmitted transovarially from mother to offspring. The presence of Wolbachia, Sodalis and Cardinium was detected. Sodalis and Cardinium were observed in the fat body. The ultrastructure of Cardinium showed a characteristic microtubule crest inside. The obtained phylogeny of Karelsulcia bacteria indicates Iassinae affinity with the Coelidiinae and Deltocephalinae subfamily symbionts. Taxonomic profiling revealed that both sequencing methods detected the same range of bacterial taxa, while ONT exhibited improved resolution for dominant species. Differential abundance analysis emphasized platform-specific biases. These studies highlight the complementary roles of different microscopy and metabarcoding techniques, demonstrating the complexity of symbiotic systems in leafhoppers and thereby improving our understanding of the host-symbiont relationship and expanding our knowledge of the structure and localization of insect microorganisms.}, }
@article {pmid42151682, year = {2026}, author = {Blackburn, D and Rahman, B and Saroyia, AP and Parish, AJ and Driscoll, M and Szewczyk, NJ and Vanapalli, SA and Samuel, BS}, title = {Defining Microbiome Impact on Host Physiology During Spaceflight Using Caenorhabditis elegans.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3000}, number = {}, pages = {251-275}, pmid = {42151682}, issn = {1940-6029}, mesh = {Animals ; *Caenorhabditis elegans/microbiology/physiology ; *Space Flight ; *Microbiota ; Weightlessness ; *Host Microbial Interactions ; }, abstract = {Microbiome-integrated Caenorhabditis elegans cultivation methods enable investigation of host-microbiome interactions in the context of space-relevant stresses using three key innovations: introduction of live bacterial communities replacing chemically defined media, implementation of auxin-inducible degradation systems to prevent progeny production, and development of complementary hardware platforms. Polyethylene bags provide gas-permeable cultivation environments for large populations with complex microbiomes supporting downstream molecular analyses, while NemaCapsules with micropillar arrays and passive culturing chambers allow real-time phenotypic assessment through on-orbit imaging, transforming our ability to correlate molecular signatures with physiological outcomes in microgravity.}, }
@article {pmid42151788, year = {2026}, author = {Ahmed, B and Nazari, M and Elfermi, R and Kabir, AH and Hijri, M and Smith, DL}, title = {Effects of bacillin 20 on microbial community structure and cross-domain networks in the soybean root-rhizosphere interface.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05135-z}, pmid = {42151788}, issn = {1471-2180}, abstract = {BACKGROUND: Understanding how biostimulants modulate plant-associated microbiomes is critical for advancing sustainable agriculture. Here, we investigated the effects of Bacillus-derived bacillin 20 on the root and rhizosphere microbiomes of soybean (Glycine max) using amplicon-based profiling, community ecology, and network analysis.<br><br>RESULTS: Microbial community assembly was driven primarily by plant compartmentalization, with higher bacterial richness in the rhizosphere and stronger host filtering in root-associated microbiomes. PERMANOVA analysis indicated that compartment explained most of the variation in community structure, whereas bacillin 20 treatment had no statistically significant effect. Despite no meaningful shifts in alpha diversity, bacillin 20 was associated with subtle, non-significant compositional trends in specific taxa across treatments. Indicator species and core microbiome analyses revealed compartment-specific taxa with potential roles in nutrient cycling, stress tolerance, and plant growth promotion.<br><br>CONCLUSION: Bacillin 20 was associated with changes in cross-domain microbial co-occurrence patterns, including differences in network connectivity, particularly in the rhizosphere, where several fungal ASVs (e.g., ASV33, ASV5, ASV8, and ASV88) exhibited high centrality. These findings indicate that bacillin 20 is associated with changes in microbial interaction patterns while maintaining overall community diversity. Overall, treatment effects were minor relative to compartment-driven structuring of the microbiome. Together, our results suggest that microbiome-informed approaches, including the use of targeted biostimulants, may contribute to the management of plant-microbe interactions in agricultural systems. Future studies integrating multi-omics approaches will be required to elucidate the underlying mechanisms of these interactions.}, }
@article {pmid42151989, year = {2026}, author = {Deng, R and Qian, J and Liu, Y and Bu, Q and Cao, T and Gao, M and Huang, Z}, title = {The dual role of the microbiome in chronic wound management.}, journal = {Cell communication and signaling : CCS}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12964-026-02937-6}, pmid = {42151989}, issn = {1478-811X}, support = {82405398//National Science Foundation of China/ ; LKZ2024015//The key project of elderly health research in Jiangsu Province/ ; }, abstract = {Chronic wounds are characterized by delayed healing driven by persistent dysbiosis of the wound microbiome. Distinct microbial communities, often organized as biofilms, dominate different chronic wound types and impair tissue repair through metabolic disruption, immune evasion, and sustained inflammation. Emerging evidence indicates that probiotics can modulate wound-associated microbiota by suppressing pathogenic colonization, reshaping local metabolic and immune responses, and promoting a pro-regenerative microenvironment, both locally and via the gut-skin axis. Recent advances in natural product-derived biomaterials provide new opportunities to enable probiotic-based interventions through controlled delivery and protection of microbial function. This review summarizes the dual role of the microbiome in chronic wound pathology and healing, evaluates the challenges and risks of probiotic therapies, and highlights microbiome-responsive materials as translational tools. We propose that targeted microbiome interventions should evolve through a closed-loop strategy integrating microbiome profiling, strengthened product and technology development, and adaptive clinical management to achieve precision wound care.}, }
@article {pmid42152157, year = {2026}, author = {Kohl, KD and Anderson, R and Andreadis, C and Baiz, MD and Bodawatta, KH and Campos-Cerda, F and Chaves, JA and Clark, AB and Costantini, MS and Davidson, GL and Davies, CS and Dietz, MW and Florkowski, M and Hird, SM and Houtz, JL and Karasov, WH and Knutie, SA and Lim, HC and Mason, NA and Rowe, M and Rudzki, EN and San Juan, PA and Skeen, HR and Slevin, MC and Somers, S and West, AG and Worsley, SF and Videvall, E and Trevelline, BK}, title = {The elephant (bird) in the room: unknown mechanisms and unresolved impacts of low DNA yields in avian microbiome research.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {42152157}, issn = {2524-4671}, support = {2150473//Directorate for Biological Sciences/ ; }, abstract = {To holistically understand the biology of animals, we must unravel the complexities and specificities of host-microbe interactions across animal taxa. Birds represent enigmatic and scientifically compelling hosts in which to understand these interactions. Here, we present a brief summary of a series of conversations among avian microbiome researchers regarding methodological challenges facing the avian microbiome field, where most research to date has focused on bacterial communities of the gut. Collectively, we acknowledged a commonly shared but underreported issue facing the avian microbiome field: that of difficulty in obtaining high-quality and high-yield microbial DNA from avian fecal samples. We discuss some of the potential reasons underlying low DNA yields, such as inhibitory compounds and rapid DNA degradation, and provide recommendations for how researchers in the avian microbiome field might cope with these methodological challenges. Collective and dedicated efforts to address these challenges will be required for a robust understanding of host-microbe interactions in avian systems.}, }
@article {pmid42152656, year = {2026}, author = {Qiu, WJ and Chen, Y and Ye, SY and Chen, L and Zhao, CF}, title = {Critical Role of Calcitonin Gene-related Peptide (CGRP) in the Microbiome-gut-brain Axis.}, journal = {Current protein &amp; peptide science}, volume = {}, number = {}, pages = {}, doi = {10.2174/0113892037454118260504132328}, pmid = {42152656}, issn = {1875-5550}, abstract = {Calcitonin gene-related peptide (CGRP), a neuropeptide with α and β isoforms, is a pivotal regulator connecting the neural, immune, and gastrointestinal systems. This comprehensive analysis delineates the evidence-based mechanistic roles of CGRP within the microbiome-gut-brain axis, focusing on its bidirectional modulation of enteric and central nervous system pathways. Both α- and β-CGRP are widely expressed in sensory and enteric neurons, where they govern vasodilation, intestinal motility, secretion, and mucosal homeostasis. CGRP-mediated signaling integrates gut microbiota-derived cues with central neurocircuitry, influencing visceral sensitivity, immune activation, and behavioral states such as anxiety and satiety. Furthermore, CGRP interacts with major neurotransmitter systems-including serotonin (5-HT), histamine, dopamine, and glutamatethereby linking peripheral microbial activity to central pain and emotional processing. We discuss isoform-specific and receptor-level mechanisms (e.g., CLR/RAMP1) as evidence permits and highlight gaps in translating preclinical findings to human physiology. Although CGRP has significant roles in other systems, such as in metabolism and pancreatic function, these are beyond the scope of this review, which focuses specifically on the neuro-immune-gastrointestinal interface. Collectively, CGRP emerges as a critical neuroendocrine mediator in coordinating communication across the microbiota-gut-brain axis. A deeper understanding of its spatiotemporal dynamics and isoformspecific functions will be crucial for the development of targeted therapeutic strategies for CGRPrelated disorders affecting both neurological and gastrointestinal systems.}, }
@article {pmid42152808, year = {2026}, author = {Smith, RW and Jarman, EH and Francis, S and Burgess, JB and Hayashiganati, K and Sharma, A and Sanchez Rangle, U and Singh, A and Green, A and Fox, PM}, title = {Antibiotic eluting collagen-based hydrogel improves wound healing in a biofilm challenged murine stented wound model.}, journal = {Journal of applied biomaterials &amp; functional materials}, volume = {24}, number = {}, pages = {22808000261447657}, doi = {10.1177/22808000261447657}, pmid = {42152808}, issn = {2280-8000}, mesh = {Animals ; *Biofilms/drug effects ; *Wound Healing/drug effects ; Mice ; *Anti-Bacterial Agents/pharmacology/chemistry ; Pseudomonas aeruginosa/drug effects/physiology ; *Collagen/chemistry/pharmacology ; *Hydrogels/chemistry/pharmacology ; Disease Models, Animal ; Methicillin-Resistant Staphylococcus aureus/drug effects/physiology ; Male ; Gentamicins/pharmacology/chemistry ; *Pseudomonas Infections/drug therapy/pathology/microbiology ; Staphylococcal Infections/drug therapy/pathology ; }, abstract = {Biofilm-colonized chronic wounds are difficult to treat due to a constantly evolving microbiome. In this study, a cHG augmented with antibiotics was examined for the topical treatment of biofilm-challenged wounds in vivo. Two studies were performed in series using a murine stented wound model. Mice were divided into four groups: control (wound only), infection only (IO), infection + cHG (IcHG), and infection + cHG + antibiotics (IcHG + Abx). We first examined Pseudomonas aeruginosa biofilms treated with gentamicin, and then MRSA biofilms treated with clindamycin. Wound healing was assessed using photography, immunohistochemistry, and histology. Systemic symptoms were monitored with hematological laboratory tests. Pseudomonas aeruginosa infected wounds treated with cHG + Abx healed faster and were protected from bacteremia. In the MRSA infected mice, wound treatment significantly affected the outcome, explaining 5.56% of total variance (ANOVA: F(3, 366) = 17.38, p < 0.0001). Additionally, infected wounds treated with cHG + Abx demonstrated less inflammatory tissue and accelerated closure rate on day 8 (76.53% ± 7.43% vs 48.40% ± 4.95%, p < 0.0001) and day 14 (96.00% ± 3.07% vs 82.38% ± 8.24%, p = 0.003), as compared to the infection only wounds. cHG offers a biocompatible, topical option with dual functionality: antibiotic augmentation to target biofilm pathogens, and a collagen-rich dressing to accelerate wound healing.}, }
@article {pmid42152835, year = {2026}, author = {Misra, S and Motiwala, ZY and Puniyani, A and Kumar, S and Nair, D and Poddar, B and Nadeem, F and Idhrees, M}, title = {The association between gut microbiome and aortic aneurysm: a review article.}, journal = {Indian journal of thoracic and cardiovascular surgery}, volume = {42}, number = {6}, pages = {754-764}, pmid = {42152835}, issn = {0970-9134}, abstract = {Aortic aneurysm is influenced by traditional risk factors such as atherosclerosis, hypertension, and diabetes. Latest evidence states that the gut microbiome may play a crucial role in its pathogenesis. This review aims to explore the relationship between the gut microbiome and aortic aneurysm. We conducted a comprehensive literature review using PubMed, Embase, and Google Scholar to understand the association between aortic aneurysm and the gut microbiome. Relevant studies were evaluated and critically analyzed to narratively summarize existing knowledge and highlight research gaps. The analysis revealed that gut dysbiosis affects systemic inflammation and immune response. This in turn contributes to the degeneration of the vessel wall and aneurysm development. Bacterial metabolites, such as short-chain fatty acids (SCFAs), were found to influence inflammatory pathways, while microbial translocation exacerbates oxidative stress. Understanding the gut microbiome-aortic aneurysm axis can lead to the development of innovative prevention and therapeutic strategies focused on aortic aneurysm formation.}, }
@article {pmid42152993, year = {2026}, author = {Bogatyrenko, E and Dunkai, T and Kim, A}, title = {Correction: Core Bacterial Microbiome in Wild Sea Cucumbers (Apostichopus japonicus) from the Sea of Japan.}, journal = {Indian journal of microbiology}, volume = {66}, number = {2}, pages = {476}, doi = {10.1007/s12088-025-01497-6}, pmid = {42152993}, issn = {0046-8991}, abstract = {[This corrects the article DOI: 10.1007/s12088-025-01493-w.].}, }
@article {pmid42071306, year = {2026}, author = {Zhong, C and Chen, K and Lin, S and Huang, Y}, title = {Obesity-Related Cognitive Impairment: An Update Overview of Mechanisms and Treatments.}, journal = {Expert reviews in molecular medicine}, volume = {28}, number = {}, pages = {e19}, doi = {10.1017/erm.2026.10049}, pmid = {42071306}, issn = {1462-3994}, support = {NSFC 82200871//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Obesity/complications/therapy/metabolism ; *Cognitive Dysfunction/etiology/therapy/metabolism ; Animals ; Gastrointestinal Microbiome ; Brain/metabolism ; Insulin Resistance ; }, abstract = {BACKGROUND: Lifestyle changes and unhealthy eating habits have led to a sharp rise in obesity rates worldwide. Obesity is closely associated with a range of complications, including cognitive impairment and dementia. Accumulating evidence indicates that obesity negatively affects cognitive function and may increase the risk of neurodegenerative diseases. Conversely, cognitive dysfunction may further contribute to the development and progression of obesity. With growing attention in this field, obesity-related cognitive impairment has emerged as an important research focus at the intersection of metabolic and neurological disorders.<br><br>METHODS: This article reviews the potential mechanisms underlying obesity-related cognitive impairment and summarizes emerging therapeutic strategies.<br><br>RESULTS: The development and progression of obesity-related cognitive impairment involve multiple mechanisms, including insulin resistance, systemic and central inflammation, immune dysregulation, microcirculatory alterations and changes in neurotransmitters and synaptic plasticity. Recent studies have focused on the adipose tissue-brain axis and the microbiota-gut-brain axis, in particular, the targeted effects of extracellular vesicles released from adipose tissue and microbiota on the brain.<br><br>CONCLUSIONS: This article systematically reviews the mechanisms underlying obesity-related cognitive impairment and presents novel therapeutic strategies.}, }
@article {pmid42091223, year = {2026}, author = {Tagoe, J and Ojha, B and Horne, S and Prüß, B}, title = {Azospirillum brasilense and tomato exudate or cytidine increase phytopathogen resistance and modulate phyllosphere/rhizosphere.}, journal = {Canadian journal of microbiology}, volume = {72}, number = {}, pages = {1-14}, doi = {10.1139/cjm-2026-0032}, pmid = {42091223}, issn = {1480-3275}, mesh = {*Solanum lycopersicum/microbiology/chemistry/metabolism ; *Azospirillum brasilense/physiology/genetics ; *Rhizosphere ; *Plant Diseases/microbiology/prevention &amp; control ; Plant Leaves/microbiology ; Plant Roots/microbiology ; Pseudomonas syringae/pathogenicity ; *Disease Resistance ; *Plant Exudates/pharmacology ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; }, abstract = {Tomatoes are an important crop worldwide and phytopathogens can cause devastating losses. This study describes a treatment, consisting of Azospirillum brasilense Sp7 and either tomato seedling exudate or the exudate compound cytidine. The combination of A. brasilense Sp7 with cytidine showed a remarkable reduction of 83.4% in disease severity of tomatoes challenged with Pseudomonas syringae pv. tomato DC3000. Replacing cytidine with exudate was less effective at 71%, but the reduction in disease severity was still larger than by A. brasilense Sp7 alone at 55%. This reduction in disease severity was not paralleled by a decrease in P. syringae in leaf homogenates. Cytidine caused a 6.7 fold increase in A. brasilense Sp7 16S rDNA in root homogenates. In phyllosphere and rhizosphere, treatments modulated the microbial composition. In the phyllosphere, specific associations between treatment groups and bacterial orders could be computed. In the rhizosphere, principal component analysis revealed that variation along PC1 was dominated by the presence or absence of A. brasilense. Intriguingly, the inoculant caused an increase in the abundance of other Azospirillales species.}, }
@article {pmid42144148, year = {2026}, author = {Ullah, H and Huang, S and Pei, Q and Gui, P and Shi, H and Hu, X}, title = {A review on the system-level bioactivity of polysaccharides along the structure-target-microbiome axis.}, journal = {International journal of biological macromolecules}, volume = {367}, number = {}, pages = {152569}, doi = {10.1016/j.ijbiomac.2026.152569}, pmid = {42144148}, issn = {1879-0003}, abstract = {Polysaccharides are structurally diverse biological macromolecules whose functional properties extend beyond simple structure-activity relationships. This review synthesizes current literature on bioactive polysaccharides from fungal, plant, algal, marine, and microbial sources, spanning foundational studies to recent advances up to 2026, with emphasis on structural glycobiology, host-microbe interactions, and translational glycoscience. We propose the Structure-Target-Microbiome (STM) axis as a mechanistic framework in which polysaccharide bioactivity arises from the integrated interplay of molecular architecture, host receptor engagement, and microbiome-mediated biotransformation. Unlike conventional structure-activity models that correlate individual structural features with single endpoints, the STM axis integrates structural determinants (monosaccharide composition, glycosidic linkages, branching, molecular weight, and chemical modifications), microbial carbohydrate-active enzymes, metabolite production, and host physiological responses into a systems-level perspective. Accumulating evidence indicates that major polysaccharide classes, including β-glucans, pectins, hemicelluloses, arabinogalactans, sulfated marine polysaccharides, and microbial exopolysaccharides, exert biological effects through both direct host signaling and microbiota-dependent metabolic conversion. However, the literature also reveals substantial inconsistency, with many polysaccharides showing weak, absent, or context-dependent activity influenced by structural heterogeneity, purity, dosage, microbial composition, and experimental variability. Limited fermentability and inter-individual microbiome differences further contribute to divergent outcomes across experimental models. Current limitations include incomplete structural characterization, batch-to-batch variability, contamination in crude extracts, and poor reproducibility across in vitro and in vivo systems, all of which restrict translational confidence. Overall, polysaccharide bioactivity is best understood as an emergent property of structure-host-microbiome interactions rather than molecular structure alone. Future advances require standardized structural annotation, harmonized experimental protocols, microbiome-informed study design, and clinical validation to enable predictive and translational applications in functional foods and biomedicine.}, }
@article {pmid42144491, year = {2026}, author = {Voorhees, PJ and Ponek, RM and Liu, JD and Lai, SK}, title = {A Droplet Digital PCR Assay for Quantification of Bacteriophage Viral Vector Titer and Purity.}, journal = {Annals of biomedical engineering}, volume = {}, number = {}, pages = {}, pmid = {42144491}, issn = {1573-9686}, support = {2013-39274//David and Lucile Packard Foundation/ ; R21AI185808//Division of Intramural Research, National Institute of Allergy and Infectious Diseases/ ; DK007737-30/DK/NIDDK NIH HHS/United States ; }, abstract = {PURPOSE: Bacteriophage (phage)-based vectors offer considerable promise as tools for tuning the microbiome with molecular and genetic precision. However, standardized methods to rigorously characterize phage vectors remain lacking. Here, we present an optimized digital droplet PCR (ddPCR)-based assay for quantifying both the purity and potency of phage vector preparations.<br><br>METHODS: We utilized central composite design to develop a ddPCR assay capable of quantifying the number of phage vector capsids packed with the phage vector genome or packed with the transgenic DNA of interest. This assay targets 2 unique DNA barcodes, designed to be biologically inert and maximally orthogonal to existing DNA sequences.<br><br>RESULTS: Through stringent optimization, we were able to achieve assay conditions that enable a dynamic range of nearly 3 orders of magnitude and correct for systemic error in the assay. We then show that biological activity assays consistently underestimate transgene-packed vector titers, leading to overestimation of true transduction efficiency, particularly when contamination by genome-packed vectors is high. We further demonstrate how this approach facilitates optimization of vector production conditions and substantially improves the precision and reproducibility of phage vector transduction.<br><br>CONCLUSION: Compared to assays of biological activity, this optimized ddPCR assay has improved accuracy and, through design of experiments optimization, high precision (CVs&#x2009;=&#x2009;5.5&#x2009;&#xb1;&#x2009;1.3% and 4.5&#x2009;&#xb1;&#x2009;1.0% for the genome and transgene barcodes, respectively). This assay can be broadly adopted to characterize and quality control vector preparations for various applications.}, }
@article {pmid42144716, year = {2026}, author = {Shen, Y and Li, Y and Zheng, R and Xia, C and Gundel, PE and Nan, Z and Duan, T}, title = {Arbuscular Mycorrhizal Fungi Dominate Over Maternally Inherited Epichloë Endophytes in Controlling Rhizosphere Processes and Pathogen Resistance.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.70613}, pmid = {42144716}, issn = {1365-3040}, support = {32071879//National Science Foundation of China/ ; CARS-22 Green Manure//China Modern Agriculture Research System/ ; }, abstract = {Plant-microbe symbioses form a multi-layered system integrating vertically transmitted Epichloë endophytes, arbuscular mycorrhizal fungi (AMF), and the rhizosphere microbiome, with implications for nutrient acquisition and pathogen resistance. Epichloë endophytes are maternally inherited and may exert priority effects that influence subsequent associations with AMF and root microorganisms, ultimately shaping defensive pathways. Here, we manipulated symbiosis of perennial ryegrass (Lolium perenne) with Epichloë sp. LpTG-3 strain AR37 and the AM fungus Acaulospora delicata to examine exudate metabolites and the recruited rhizosphere microbiome in relation to host responses to the pathogen Bipolaris sorokiniana. Dual symbiosis with Epichloë and AMF increased host growth and pathogen resistance through enhanced nutrient uptake, elevated defensive enzyme activities in leaves and rhizosphere, and reduced malondialdehyde concentrations. It also recruited potentially beneficial microorganisms and enriched metabolites negatively associated with disease severity; notably, the metabolite Acetamide 1, which accumulated under dual symbiosis, strongly inhibited the pathogen in vitro. Significant correlations among metabolites, rhizosphere microbial communities, and rhizosphere soil properties revealed coordinated belowground responses under the synergistic regulation of AMF and Epichloë that reduced disease severity. Although both symbionts enhanced host performance, AMF played a stronger role than maternally inherited Epichloë in shaping the rhizosphere processes driving growth and pathogen resistance.}, }
@article {pmid42144903, year = {2026}, author = {de Assis, MR and Guimarães, I}, title = {Cholinergic anti-inflammatory pathway and vagus nerve stimulation in rheumatoid arthritis.}, journal = {Current opinion in rheumatology}, volume = {}, number = {}, pages = {}, doi = {10.1097/BOR.0000000000001170}, pmid = {42144903}, issn = {1531-6963}, abstract = {PURPOSE OF REVIEW: To integrate mechanistic and clinical evidence on vagal regulation of immunity via the cholinergic anti-inflammatory pathway, linking neural and inflammatory signaling in rheumatoid arthritis (RA). It highlights how reduced vagal tone contributes to disease onset and progression and frames neuromodulation as a rationale for adjunctive therapeutic strategies.<br><br>RECENT FINDINGS: Preclinical and clinical data demonstrate that vagal efferent activity modulates immune responses through noradrenergic circuits and activation of &#x3b1;7-nicotinic-acetylcholine-receptors on immune cells, inhibiting NF-&#x3ba;B nuclear translocation and reducing pro-inflammatory cytokines. This neuroimmune axis interacts with the hypothalamic-pituitary-adrenal axis and the microbiome, supporting an integrated model of inflammation. Vagus nerve stimulation (VNS) has been associated with reductions in inflammatory markers and clinically meaningful improvements in patients with RA. Implantable VNS has demonstrated efficacy and has received regulatory approval for moderate-to-severe RA refractory to disease-modifying antirheumatic drugs; however, the available evidence remains limited and requires confirmation in larger and more diverse populations. Noninvasive approaches show favorable safety profiles but heterogeneous efficacy and currently lack regulatory approval for immune-mediated diseases.<br><br>SUMMARY: VNS represents a promising adjunct to conventional immunosuppressive therapy for RA. Further well-designed trials are needed to standardize stimulation protocols, and define optimal strategies for clinical implementation.}, }
@article {pmid42144927, year = {2026}, author = {Fraser, DR and Mason, RS}, title = {Microbial biosynthesis of vitamin D2.}, journal = {The Proceedings of the Nutrition Society}, volume = {}, number = {}, pages = {1-21}, doi = {10.1017/S0029665126103073}, pmid = {42144927}, issn = {1475-2719}, abstract = {In the early history of vitamin D research most of the studies on its chemistry and function were performed with vitamin D2 which was readily obtained by UV irradiation of ergosterol from yeast. Yet, in the physiological economy of vitamin D for most vertebrates, including humans, fish and especially for birds, vitamin D3 produced in skin by solar irradiation of 7-dehydrocholesterol, is the natural form of vitamin D. Vitamin D2, as a dietary supplement, while of comparable potency to vitamin D3 in most mammals, has been found in nature only when ergosterol in fungi is inadvertently exposed to solar UV radiation. Nevertheless, some herbivorous animals, horses and elephants, seem to maintain adequate vitamin D status with vitamin D2 rather than vitamin D3. The source of that vitamin D2 has been assumed to be the traces derived from ergosterol in endophytic fungi exposed to the sun on grass being consumed. However, outdoor grazing sheep in winter maintained adequate vitamin D status with vitamin D2, yet no vitamin D2 could be detected on the grass they were consuming. Bovine rumen contents, fermenting in an artificial rumen, had an increase in vitamin D2 concentration, particularly when cellulose fibre was added as a fermentation substrate. Furthermore, mice being raised from weaning on a vitamin D-free diet had vitamin D2 in their colon contents. This review examines anaerobic microbial production of vitamin D2 in the alimentary tract, in the dark, and describes a natural function for vitamin D2 in microorganisms and potentially for gut health.}, }
@article {pmid42145141, year = {2026}, author = {Sreekumaran, S and V K, P and M N, A and Premnath, M and P S, S and P R, P and Mathew, J and E K, R}, title = {Comparative Human-Poultry Fecal Resistome Profiling from Broiler Farms Reveals Diverse Antimicrobial Resistance Genes.}, journal = {Foodborne pathogens and disease}, volume = {}, number = {}, pages = {15353141261449964}, doi = {10.1177/15353141261449964}, pmid = {42145141}, issn = {1556-7125}, abstract = {Indiscriminate use of over-the-counter antibiotics has led to the rapid emergence of resistant genes in bacteria, with the ultimate crisis to global health. One of the prominent sectors with the antimicrobial resistance (AMR) concern is the farm animals that exist in close contact with humans where the environmental conditions are favorable for the rapid dissemination of pathogenic organisms and resistance genes. Hence, to understand the threat with environmental AMR, a detailed molecular insight is very important. In this study, fecal samples from both poultry and associated humans were studied by metagenomics analysis. From the results, a primary understanding on the microbial diversity difference could be generated from the selected samples. Here, the poultry samples were identified to have more microbial diversity. At the same time, several pathogens were found to be shared commonly between the hosts. Upon detailed examination, several AMR genes were also observed to be common between the poultry and human samples. The results of the study are highly relevant in light of the "One Health" concept where an integrated approach is targeted.}, }
@article {pmid42145228, year = {2026}, author = {Lischka, J and Weghuber, D and Dinan, TG and Le Roux, CW and Schellekens, H}, title = {Optimizing Adherence and Outcomes: Potential Strategies to Enhance the Effectiveness of nutrient-stimulated hormone therapies.}, journal = {The Proceedings of the Nutrition Society}, volume = {}, number = {}, pages = {1-27}, doi = {10.1017/S0029665126103036}, pmid = {42145228}, issn = {1475-2719}, abstract = {Nutrient-stimulated hormone therapies (NuSH) therapies, a key class within obesity management medications, have reshaped obesity and type 2 diabetes care, producing substantial weight loss, improved glycaemic control, and significant cardiometabolic benefits in adults and adolescents. Yet outcomes vary widely, and NuSH therapy-induced changes in appetite, eating behaviour, and gastrointestinal function can compromise nutrient intake, lean mass preservation, and long-term adherence. This review synthesises evidence across nutrition, behavioural science, microbiota research, and metabolic-bariatric surgery (MBS) to outline supportive strategies that optimise clinical outcomes with NuSHs.Preclinical studies consistently show that NuSH therapies shift gut microbiota toward "lean-associated" profiles, while emerging human findings suggest that baseline microbial signatures may contribute to variability in response and tolerability. However, evidence in humans remains limited, heterogeneous, and underpowered. Across age groups, structured nutritional and behavioural support remains essential to ensure nutrient adequacy, manage side effects, strengthen adherence, and guide sustainable lifestyle change.Key research priorities include defining behavioural and microbial contributors of treatment response and adherence, evaluating microbiota-targeted adjuncts, and developing scalable, multidisciplinary care models for both adult and paediatric populations. NuSH therapies are powerful tools, but their long-term success depends on integrated, personalised nutrition and behavioural care, with growing opportunity for microbiome-informed approaches.}, }
@article {pmid42145481, year = {2026}, author = {Godoy-Vitorino, F and Méndez-Lázaro, P and Bolaños-Rosero, B and Baerga-Ortiz, A and Torres-Rodríguez, P and Sosa, MA and Vázquez, M and Rivera-Rivera, NL and Cardona-Cordero, N and Colón-López, V and Ortiz, AP}, title = {Environmental exposures, microbiome dynamics and chronic disease risk in climate-vulnerable regions: interdisciplinary perspectives from Puerto Rico.}, journal = {Frontiers in public health}, volume = {14}, number = {}, pages = {1807779}, pmid = {42145481}, issn = {2296-2565}, mesh = {Humans ; Puerto Rico/epidemiology ; *Microbiota ; *Environmental Exposure/adverse effects ; Chronic Disease/epidemiology ; *Air Pollution/adverse effects ; *Vulnerable Populations ; }, abstract = {Environmental factors such as air pollution, weather events, and ambient toxins are major contributors to human disease, with disproportionate impacts on vulnerable populations. In Puerto Rico, chronic exposure to air pollution and ecological disruption poses significant public health risks, particularly for cancer and other chronic conditions. These risks are unevenly distributed, disproportionately affecting children and older adults, groups central to community resilience yet highly susceptible to pollution-related health effects. This perspective review synthesizes emerging evidence linking chronic air pollution and environmental exposures to cancer, respiratory and cardiovascular disease, and microbiome alterations that may mediate long-term health trajectories. Drawing on interdisciplinary efforts from the Caribbean Cancer Research Center on Environmental and Natural Hazards, the Center for the Promotion of Cancer Health Equity, the Caribbean Collaborative Action Network, a NOAA CAP/RISA Team, and the Puerto Rico Center for Microbiome Sciences, this paper examines how environmental exposures shape health disparities. We highlight studies demonstrating that fungal spores, particulate matter, and chemical pollutants disrupt microbiome balance, immune regulation, and metabolic pathways, thereby increasing disease risk in early life and aging populations. The review also considers social determinants of health, spatial inequities, infrastructure vulnerabilities, and policy frameworks that influence exposure and resilience. By integrating environmental epidemiology, microbiome research, and public health policy, this synthesis underscores the urgency of planetary health-informed prevention, surveillance, and management strategies to mitigate pollution-related disease burdens, reduce inequities, and strengthen health in climate-sensitive regions globally.}, }
@article {pmid42145567, year = {2026}, author = {Silva, FA and da Silva, RT and Harcourt, N and Biggs, E and Magnani, M}, title = {Indigenous microbiology: Why Indigenous knowledge matters in microbial science.}, journal = {FEMS microbes}, volume = {7}, number = {}, pages = {xtag024}, pmid = {42145567}, issn = {2633-6685}, abstract = {Indigenous knowledge has long engaged with microorganisms through relationships with environment, food, and health, yet these understandings remain marginal in mainstream microbiology. In this article, we argue that Indigenous microbiology offers a broader framework for microbial science by placing microorganisms within ecological, cultural, and ecosystem-specific relationships. This perspective is relevant to current challenges in sustainable agriculture, food security, and antimicrobial resistance. Drawing on examples from environmental management, traditional fermented foods, and therapeutic practices, we show that Indigenous knowledge can deepen microbiome research and contribute to developing healthy and sustainable strategies. Indigenous microbiology should not be treated as an informal add-on to existing science, but as a valuable framework for asking better questions about microbial life and its role in human and environmental wellbeing.}, }
@article {pmid42145603, year = {2026}, author = {Waltmann, A and Puerto-Meredith, SM and Chinkhumba, J and Mzembe, E and Kayange, M and Carroll, I and Roach, J and Mathanga, DP and Gutman, JR and Juliano, JJ}, title = {Beyond malaria prevention: sulfadoxine-pyrimethamine treatment in pregnancy selectively remodels the maternal gut microbiome to increase gestational weight gain and improve birthweight.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.03.26352319}, pmid = {42145603}, abstract = {Intermittent preventive treatment in pregnancy (IPTp) with sulfadoxine-pyrimethamine (SP), an antifolate drug with antimalarial and antibiotic activity, reproducibly improves birthweight across sub-Saharan Africa and the Western Pacific. This clinical protection is independent of SP's original malaria indication: it is not diminished by widespread antimalarial resistance or reduced transmission, and SP outperforms more potent non-antibiotic antimalarials (e.g., dihydroartemisinin-piperaquine, DP) for fetal growth. The biological mechanism is unexplained. We previously showed that gestational weight gain (GWG) is a significant component of this mechanism and mediates two-thirds of SP's overall birthweight benefit (NCT03009526). In the first longitudinal characterization of antifolate antibiotic effects on the pregnant gut microbiome, we show that ∼45% of SP's GWG advantage over DP is explained by gut microbial changes consistent with its pharmacology. Microbiome-mediated GWG coincided with 126g higher birthweight in SP but not DP recipients (95%CI 22.6-229.3g; p=0.019). Relative to DP, SP suppressed gastrointestinal pathobionts and enriched anaerobic commensals with recognized roles in mucosal immunity and host metabolism, a microbiome-sparing pattern distinct from conventional antibiotic-associated dysbiosis.}, }
@article {pmid42145647, year = {2026}, author = {Xing, J and Xu, Z and Zhang, Y and Zhang, H and Zheng, L and Zhang, M and Guo, W and Liu, J and Pan, Y and Zhang, J and Jie, Z and Baele, G and Li, C and D'Souza, A and Zhao, J and Li, J and Chen, T and Wu, H}, title = {Longitudinal cross-species transmission of microbiomes and resistomes across farmers, animals and environment.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.06.26352545}, pmid = {42145647}, abstract = {Understanding the acquisition and dissemination of microbiomes and antimicrobial resistance genes (ARGs) that circulate across human-animal-environment interfaces remains a central One Health challenge, largely because of complex ecological interactions and multiple confounding factors. Although occupational exposure is known to influence the microbiomes and resistomes of farmers, how environmental compartments involve in this system is unclear. Here, we conducted a one-year longitudinal study combining strain-resolved metagenomics (500 metagenomes) with isolate-based whole-genome sequencing (28 isolates) in an ecologically managed, antibiotic-free farming ecosystem spanning animals, farmers, environmental compartments and non-exposed individuals. Assembling 6,075 species-level genomes, we show that animal-associated occupancy reshapes the microbiome and resistome of occupationally exposed farmers and their surrounding environments. Animals and their associated habitats formed the dominant interface for both strain sharing and ARG dissemination across connected ecological compartments, whereas village residents and surrounding river samples - used as ecological controls - showed limited integration into this sharing network. Tracking a frequently shared lineage further revealed within-lineage genetic turnover together with selection-consistent changes following cross-species spread, suggestive of ecological selection across hosts and habitats. Finally, we identify Klebsiella pneumoniae as the most widespread ESKAPE pathogen in this ecosystem, with repeated occurrence across animal, human and environmental compartments, consistent with a neglected but clinically critical broad profile of ecological generalist. Together, these findings identify animals as central interfaces for microbiome and resistome sharing and show how agricultural ecosystems can sustain circulation of opportunistic pathogens and resistance determinants across human-animal-environment interfaces even in the absence of routine antibiotic use.}, }
@article {pmid42145753, year = {2026}, author = {Wu, Y and Yan, H and Li, P and Liu, Y and Leng, J and Cui, Y and Lv, X and Pang, L and Zang, N}, title = {Bridging the gaps: the gut-lung axis and microbial metabolites in the pathogenesis and treatment of pulmonary fibrosis.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1817835}, pmid = {42145753}, issn = {2296-858X}, abstract = {Pulmonary fibrosis (PF) is a chronic interstitial lung disease characterized by structural damage to the lung parenchyma, excessive deposition of extracellular matrix (ECM), and irreversible decline in lung function. Current pharmacological treatments cannot effectively reverse fibrosis, highlighting an urgent need for novel therapeutic targets. Recently, the gut-lung axis and its bidirectional communication have received increasing attention for their roles in PF progression. Metabolites derived from gut microbiota, including short-chain fatty acids (SCFAs), bile acids, tryptophan metabolites, lipopolysaccharides (LPS), and trimethylamine N-oxide, regulate immune responses, modulate signaling pathways, influence epigenetic modifications, and maintain intestinal barrier integrity, thereby exerting bidirectional effects on PF. Protective metabolites primarily inhibit fibroblast activation and collagen deposition, whereas pathological metabolites promote fibrosis by inducing inflammatory responses and oxidative stress. Potential therapeutic strategies targeting the gut-lung axis include fecal microbiota transplantation (FMT), probiotic and dietary interventions, and Traditional Chinese Medicine (TCM). However, clinical applications face challenges such as donor standardization, immunological safety, and consistency of therapeutic efficacy. Critical limitations remain, including reliance on acute-injury animal models that inadequately represent the chronic, irreversible nature of human PF. Translating findings across distinct PF subtypes requires caution, as their genetic architectures, immune landscapes, and microbiome interactions may differ considerably. Additionally, the causal relationship between microbial dysbiosis and fibrosis remains unclear, and clinical translation currently lacks stratified intervention strategies based on biomarkers. Future research should prioritize large-scale longitudinal cohort studies, integrated multi-omics analyses, organoid models, and gut-lung chip platforms to identify key effector molecules and therapeutic targets, ultimately facilitating precise clinical interventions targeting the gut-lung axis.}, }
@article {pmid42145889, year = {2026}, author = {McGrath, AH and Steinberg, PD and Kjelleberg, S and Marzinelli, EM}, title = {Effects of Extreme Rainfall on a Dominant Seaweed Are Mitigated by Its Microbiota.}, journal = {Ecology and evolution}, volume = {16}, number = {}, pages = {e73644}, pmid = {42145889}, issn = {2045-7758}, abstract = {Extreme weather events are becoming more intense and frequent, driving unprecedented ecological changes globally. The effects of such extreme events can be particularly profound if they affect the performance of habitat-forming organisms (trees, corals, kelp). Further, the emergence of the "holobiont" concept in biology suggests that these impacts can occur directly on the habitat-forming "host" and/or via disruption of their associated microbiota. Following a one-in-100 year rainfall event along the coast of Sydney, Australia, we examined the effects of rainfall (in the field) and lowered salinity (in the lab) on the performance and reproductive output of a dominant, habitat-forming intertidal seaweed, Hormosira banksii. We then examined the ability of surface-associated microbes to mitigate host responses to extreme rainfall via microbial manipulations in the field. Extreme rainfall and reduced salinity (< 25 ppt) negatively affected host reproductive output. Manipulative field experiments using a combination of antimicrobial treatments applied once (pulse) or regularly (press) showed that disruption of Hormosira's microbiota after extreme rainfall affected host photosynthesis and, more importantly, inhibited the post-event recovery of host reproductive output. Press disruption of the host-microbiota prevented recovery of normal (control) levels of reproductive output and photosynthesis for over 4 months. These experiments demonstrate that host-associated microbiota can play a significant role in mediating responses of habitat-forming seaweeds to extreme weather events, with consequences for key components of fitness. Given the increased frequency of flooding and storm events experienced by many systems, the microbiome may provide a key role in influencing habitat resilience to stress.}, }
@article {pmid42145945, year = {2026}, author = {O'Sullivan, E and Solano, O and Oliveira, JS and Johnson, AJ and Dhital, S and S Pillai, PK and Dias, F and Ubbink, J and Lin, AW and Teigen, L}, title = {The food matrix as a confounder in diet‒microbiome studies: methodological challenges and research gaps.}, journal = {Gut microbes reports}, volume = {3}, number = {1}, pages = {2671724}, pmid = {42145945}, issn = {2993-3935}, abstract = {Interactions of structural and physicochemical properties of food (e.g. texture, viscosity, and solubility), known as the food matrix, are primary drivers of host digestive kinetics. While the impact of matrix-driven variability on nutrient bioaccessibility, glycemic response, and caloric absorption is well documented, these dynamics are often overlooked in diet-microbiome research. Adequately modeling the spatiotemporal availability of microbial substrate is essential to understanding how dietary patterns impact the microbiome throughout the gastrointestinal tract. This narrative review 1) synthesizes current evidence on how food processing and structure affect human digestion and absorption of macronutrients; 2) illustrates how host digestive kinetics impact forms and quantity of substrate delivered and available to the gut microbiota; and 3) identifies challenges and knowledge gaps in current diet-microbiome research regarding food structure. The challenges and knowledge gaps discussed here call for in vivo models that can better model microbial substrate availability throughout the gastrointestinal tract to improve our understanding of diet-microbiome interactions.}, }
@article {pmid42146050, year = {2026}, author = {Huang, X and Yang, X and Yu, Y and Huang, J and Tao, W and Yu, R}, title = {Bibliometric analysis of human microbiota-associated animal model (2005-2025).}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1777297}, pmid = {42146050}, issn = {1664-302X}, abstract = {BACKGROUND: The research on human microbiota-associated (HMA) animal models is an important tool for studying the human microbiome and holds great potential for elucidating disease mechanisms and microbe-based therapeutic interactions. However, a systematic bibliometric assessment of this field has been limited.<br><br>METHODS: This study employed bibliometric methods, retrieving relevant publications published between 2005 and 2025 from the Web of Science Core Collection, Scopus, and PubMed, and visualizing the data with VOSviewer and CiteSpace.<br><br>RESULTS: The analysis revealed a continuous upward trend in the number of publications on this topic. The United States and its research institutions contributed the most and maintained close collaborations with multiple countries. The majority of the articles appeared in journals such as Gut Microbes, Microbiome, and Proceedings of the National Academy of Sciences of the United States of America (PNAS). Keyword and highly-cited reference analyses focused on the application of these models in investigating disease mechanisms and therapeutic exploration, particularly for metabolic, gastrointestinal, oncological, and neurodegenerative diseases. In addition, the impact of modeling factors such as diet and host genetics on the models has also attracted attention.<br><br>CONCLUSION: HMA animal models have become a core platform linking clinical and basic microbiology research, demonstrating unique advantages in recapitulating disease-associated microbial features and phenotypes. Nevertheless, because these models are essential for testing causal links between microbiota and disease, methodological standardization and procedural refinement are needed to enhance reproducibility and clinical applicability.}, }
@article {pmid42146054, year = {2026}, author = {Li, X and Yu, X and Zhong, Y and Zhou, G and Zou, Y}, title = {Microecological modulators-new perspectives for treating sex hormone disorders.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1795152}, pmid = {42146054}, issn = {1664-302X}, abstract = {Sex hormone related disorders, characterized by complex etiology and long-term health risks, pose a significant challenge to global health. Hormone-based therapies are often accompanied by adverse effects and fail to address the underlying pathophysiological mechanisms. The "gut microbiota-sex hormone axis" maintains endocrine homeostasis through diverse pathways, including enzymatic reactions, immune modulation, metabolic regulation, and the microbiome-gut-brain axis. Dysregulation of this axis has been identified as a critical factor in the pathogenesis of sex hormone-related disorders. Probiotics have emerged as a promising adjunctive therapeutic strategy by targeting this axis. Preclinical and clinical studies have demonstrated that specific probiotic strains ameliorate hormonal imbalances, attenuate inflammation, and optimize metabolic parameters, showing positive efficacy in sex hormone-related disorders. This review systematically elaborates the regulatory mechanisms of this bidirectional axis and highlights the application of probiotics and its regulatory roles as targeted interventions in related disorders.}, }
@article {pmid42146064, year = {2026}, author = {Sin, J and Choi, D and Hwang, I and Kim, S and Bunch, H and Kim, H and Chung, DK}, title = {Culture supernatants from human-derived commensal bacteria alleviate DNCB-induced atopic dermatitis through modulation of inflammatory and barrier-associated pathways.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1813592}, pmid = {42146064}, issn = {1664-302X}, abstract = {INTRODUCTION: Atopic dermatitis (AD) is a chronic inflammatory skin disorder characterized by immune dysregulation, impaired epidermal barrier function, and recurrent episodes of itching and inflammation. Emerging evidence suggests that skin-resident microbiota influence host immune responses and may modulate AD pathogenesis. Here, we investigated the anti-inflammatory, barrier-restoring, and neuro-supportive effects of culture supernatants (CSs) derived from skin-resident bacteria.<br><br>METHODS: Human keratinocytes (HaCaT) stimulated with tumor necrosis factor-&#x3b1; (TNF-&#x3b1;) and interferon-&#x3b3; (IFN-&#x3b3;) were treated with CSs from various isolates. For in vivo evaluation, a 2,4-dinitrochlorobenzene (DNCB)-induced AD-like mouse model was utilized, receiving topical applications of the CSs. Furthermore, differentiated SH-SY5Y neuronal cells were treated with keratinocyte- or fibroblast-conditioned media, prepared after stimulation with bacterial CSs, to evaluate their neurotrophic potential.<br><br>RESULTS: CSs from Brachybacterium paraconglomeratum and Brevibacterium casei significantly suppressed interleukin-6 (IL-6) and C-C motif chemokine ligand 17 (CCL17) while restoring filaggrin expression. In keratinocytes and human dermal fibroblasts, these CSs increased brain-derived neurotrophic factor (BDNF) expression. In the DNCB-induced AD-like mouse model, topical application of B. paraconglomeratum and B. casei CSs reduced epidermal hyperplasia and immune cell infiltration, downregulated tyrosine hydroxylase (TH), and restored cutaneous BDNF, glial cell line-derived neurotrophic factor (GDNF), and filaggrin (FLG) expression. In differentiated SH-SY5Y neuronal cells, the conditioned media treatments markedly upregulated BDNF, GDNF, and nerve growth factor (NGF). Mechanistically, CS treatment inhibited p38 MAPK and JAK-STAT signaling.<br><br>DISCUSSION: Collectively, these findings demonstrate that specific skin-derived bacterial metabolites exert coordinated anti-inflammatory, barrier-reinforcing, and neurotrophic activities, thereby promoting associated changes in neurotrophic markers. Such microbial products may serve as promising biologic candidates for managing atopic dermatitis.}, }
@article {pmid42146065, year = {2026}, author = {Orwa, P and Kuhl-Nagel, T and Meinhold-Ernst, R and Jehle, JA and Mwirichia, R and Linkies, A}, title = {Linking microbiome structure to functional analysis identifies resilient Pseudarthrobacter, Pseudomonas, and Streptomyces antagonists of Phytophthora infestans in tomato.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1810932}, pmid = {42146065}, issn = {1664-302X}, abstract = {INTRODUCTION: Late blight, caused by Phytophthora infestans, remains one of the most destructive tomato diseases, driving the need for sustainable measures to reduce intensive fungicide use. Plant-associated microbial communities offer a promising but still underexplored source of biological control agents. Moreover, links between community-level microbiome patterns and functionally effective antagonists remain poorly resolved.<br><br>METHODS: In this study, we combine culture-dependent isolation, functional profiling of lytic enzymes and siderophores, with 16S rRNA Illumina-based microbiome analysis to identify ecologically relevant bacterial antagonists of P. infestans in tomato. Healthy and P. infestans-challenged tomato plants cultivated in soils from two organic tomato farms in the Rhine-Main region of Germany were analyzed.<br><br>RESULTS: Of the 594 bacterial isolates from tomato rhizosphere and phyllosphere, 84 inhibited P. infestans, and 63 of these suppressed Alternaria solani in vitro. Functional screening identified 28 isolates with broad-spectrum antagonistic potential, predominantly affiliated with the genera Pseudomonas, Bacillus, Streptomyces, Paenibacillus, and Pseudarthrobacter, characterized by broad siderophore and taxon-specific lytic enzyme activities. In planta assays identified Pseudarthrobacter sp._Pb177 as a novel and most effective antagonist of P. infestans, alongside effective Streptomyces and Pseudomonas isolates. Amplicon-based microbiome analyses of different tomato compartments under both healthy and P. infestans-challenged conditions revealed soil origin as the primary driver of bacterial community assembly, particularly in the rhizosphere and phyllosphere. Disease-associated shifts were limited to specific soil-compartment combinations (rhizosphere soil B). Key rhizosphere bacterial taxa (Acinetobacter and Chryseobacterium) remained largely stable across plant health states. Instead, disease effects are confined to shifts among rare or conditionally detected ASVs. Mapping cultured isolates to amplicon sequence variants demonstrated that most antagonists corresponded to low-abundance members of the tomato microbiome (including Bacillus, Chryseobacterium, Paenibacillus, Pseudomonas, Streptomyces, etc.), with their distribution shaped primarily by soil and plant compartment rather than disease.<br><br>DISCUSSION: These findings indicate that effective biocontrol candidates are defined less by abundance than by their resilience and function within plant-associated microbial communities. By linking microbial community profiling with functional screening and in planta assays, this study outlines a microbiome-informed approach for identifying bacterial antagonists of P. infestans and supports an ecologically grounded framework for managing tomato late blight.}, }
@article {pmid42146066, year = {2026}, author = {Matsushima, Y and Himi, E and Kitashima, M and Ogura, K and Kotani, S and Hino, A and Inoue, K and Hosoya, H}, title = {A defined synthetic algal medium enables lettuce-free culturing of unfed Paramecium bursaria while preserving host-associated microbiome composition.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1821058}, pmid = {42146066}, issn = {1664-302X}, abstract = {Paramecium bursaria is widely cultured using undefined plant-based infusions such as lettuce extract, yet the variable composition of these media remains a major obstacle to experimental reproducibility and microbiome research. Here, we tested whether a chemically defined synthetic algal medium (AF-6) can replace conventional lettuce infusion while maintaining host physiology and associated microbial communities. An unfed clonal strain of P. bursaria, established in 2023 and capable of growth without external nutrient supplementation, proliferated comparably in AF-6 and lettuce media. To confirm that these results were not specific to unfed conditions, we additionally examined a publicly maintained algae-fed strain (NIES-2891), which exhibited similar growth patterns across both media. Cell size, compression-induced extension, and symbiotic algal abundance showed no significant differences between culture conditions. rbcL metataxonomic analysis revealed that Chlorella variabilis was the sole algal endosymbiont detected in all samples. Furthermore, 16S rRNA gene sequencing demonstrated that host-associated bacterial community composition remained largely conserved after replacement of lettuce infusion with AF-6 within each strain, although clear differences were observed between strains. Together, these findings establish an "unfed strain + defined algal medium" framework as a reproducible experimental platform for investigating tripartite interactions among ciliate hosts, symbiotic algae, and associated bacteria.}, }
@article {pmid42146070, year = {2026}, author = {Chen, C and Shi, Y and Zheng, M and Han, S and Zhang, J and Sun, Z and Yue, Z}, title = {Consecutive monoculture of sweet potato reduces yield due to deteriorated soil health and disrupted nutrient cycling.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1747390}, pmid = {42146070}, issn = {1664-302X}, abstract = {Sweet potato (Ipomoea batatas L.) is a staple food with many promising health benefits. However, obstacles associated with continuous cropping are common in modern intensive sweet potato production, partially due to imbalances in the soil microbiome. This research investigates the succession of the soil microbiome and its impacts following 1, 3, and 5 years of consecutive sweet potato monoculture. The results showed significantly higher diversity and homogeneity in bacteria than in fungi. Although a large proportion of operational taxonomic units (OTUs) were shared, richness analysis indicated a significant decrease in the total number of OTUs for both bacteria and fungi, especially in the fifth year. At the phylum level, Firmicutes and Parcubacteria significantly decreased, while Cryptomycota significantly increased (p < 0.05). Further analysis of the prokaryotic community using BugBase and the Functional Annotation of Prokaryotic Taxa (FAPROTAX) database showed significant changes in many phenotypes and functions. In particular, alterations in human pathogens and Cyanobacteria, as well as differences in carbon metabolism and nitrogen conversion in soils, were revealed for the first time. It was also observed that the contents of soil organic matter (OM), total carbon (TC), and total nitrogen (TN) had a linear correlation with the abundance of Cyanobacteria. However, yield was positively correlated with soil pH but negatively correlated with disease incidence. Taken together, in addition to the distinct succession of the microbial community structure, the study indicates that consecutive monoculture of sweet potato has a significant impact on the health status of soil and nutrient cycling.}, }
@article {pmid42146094, year = {2026}, author = {Krupa-Kotara, K and León-Guereño, P and Rozmiarek, M}, title = {Editorial: Women's health in an interdisciplinary dimension - determinants of nutritional disorders: Volume II.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1844748}, doi = {10.3389/fnut.2026.1844748}, pmid = {42146094}, issn = {2296-861X}, }
@article {pmid42146321, year = {2026}, author = {Leyshon, C and Leyshon, M and Esmene, S and Leyshon, M and Clabburn, O}, title = {The Challenges Facing VCFSEs in Integrated Care Systems: A Qualitative Case Study of a Unitary Authority in England.}, journal = {International journal of integrated care}, volume = {26}, number = {2}, pages = {9}, pmid = {42146321}, issn = {1568-4156}, abstract = {INTRODUCTION: Integrated Care Systems (ICSs) in England seek ever-closer collaborative relationships between health and social care providers, local authorities, and the Voluntary, Community, Faith and Social Enterprise (VCFSE) sector to deliver public services in place. However, ICSs present significant challenges for VCFSEs.<br><br>METHODS: In-depth qualitative case study of VCFSEs in an ICS contiguous with a Unitary Authority in England.<br><br>RESULTS AND DISCUSSION: i) the role of the 'microbiome' of smallest VCFSE in the ICS is unclear; ii) current commissioning models work against the effective participation of VCFSEs in ICSs; iii) short-term and under-funded contracts threaten VCFSEs; iv) substitution and appropriation represent tangible threats to VCFSEs through increased demand and bureaucratisation; v) the degree to which ICS support a vibrant, heterogeneous, and sustainable VCFSE sector depends on 'system maturity'.<br><br>CONCLUSIONS: Integration is a process, not an event. The evolving landscape of service design presents both opportunities and challenges for VCFSEs, requiring careful management to harness strategic advantages while addressing operational risks.}, }
@article {pmid42146396, year = {2026}, author = {Mitchener, MM and Anderson, CM and Veleba, M and Teo, K and Roch, M and Chen, R and Yuan, Y and Han, I and Dziergowska, A and Pethe, K and Begley, TJ and Kline, KA and Dedon, PC}, title = {Growth-dependent tRNA Reprogramming and Codon Bias Link Translation to Metabolic State in Enterococcus faecalis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.07.723122}, pmid = {42146396}, issn = {2692-8205}, abstract = {UNLABELLED: Enterococcus faecalis is a Gram-positive commensal bacterium of the human gut microbiome and an opportunistic pathogen responsible for many hospital-acquired infections. Despite the clinical importance of E. faecalis , how gene and protein expression are coordinated with growth remains poorly defined. Here, we profiled transcript, protein, and tRNA pool dynamics across distinct phases of E. faecalis growth. Differences in protein abundance and corresponding mRNA levels suggested growth phase-dependent posttranscriptional regulation. Growth-associated genes exhibited biased synonymous codon usage, with ribosomal and glycolytic proteins enriched in low-abundance codons read by queuosine-modifiable tRNAs. Analysis of tRNA modification and tRNA isoacceptor abundance revealed growth phase-dependent changes, particularly in anticodon stem loop modifications that influence synonymous codon translation. Changes in queuosine levels preceded shifts in ribosomal proteins, suggesting a contribution to codon-biased translation. Collectively, these findings reveal growth phase-associated remodeling of the E. faecalis tRNA pool and support a model in which queuosine-dependent translational reprogramming shapes protein expression during bacterial growth.<br><br>IMPORTANCE: Enterococcus faecalis is a common cause of hospital-acquired infections. Despite its clinical importance, a comprehensive understanding of the organism's physiology and adaptation to environmental changes remains incomplete. Here, we characterized protein, transcript, and tRNA dynamics across bacterial growth phases, uncovering a role for post-transcriptional regulation marked by tRNA reprogramming and biased synonymous codon usage. These findings enhance our understanding of E. faecalis growth and support a model of translational reprogramming therein.}, }
@article {pmid42146479, year = {2026}, author = {Haran, V and Wang, J and Morimoto, M and Wong, WM and Rouyer, LSF and McDonald, JG and Meeks, JP}, title = {Bile acid chemosensation in mammals supports species and gut microbiome evaluation.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.30.721772}, pmid = {42146479}, issn = {2692-8205}, abstract = {UNLABELLED: The rodent accessory olfactory system (AOS) detects chemosignals emitted by conspecifics and other species to support beneficial behaviors. Peripheral vomeronasal sensory neurons (VSNs), the AOS' chemical sensors, detect fecal bile acids in patterns that have unknown significance to the animal. We used a combination of mass spectrometry and VSN calcium imaging to investigate the AOS' capacity to use bile acid information to discriminate between fecal samples from captive reptiles and mice with varying gut microbiome states. Mass spectrometry analysis revealed bile acid patterns that distinguished biologically relevant samples from one another, representing theoretical discrimination axes. We measured VSN response patterns to bile acid stimuli aligned with theoretical discrimination axes. We found that VSNs perform stimulus "whitening" via an inverse relationship between natural bile acid abundance and population response magnitude. VSNs showed maximum sensitivity to taurine-conjugated bile acids, which have high theoretical discriminatory value, but were found at low natural abundance levels. Individual taurine-conjugated bile acids drove threat assessment behavior when added to familiar mouse fecal extracts, suggesting high behavioral significance. Finally, we analyzed the degree to which the AOS utilizes the theoretical information about species, diet, and gut microbiome status from bile acids. We found that VSN tuning patterns align with theoretical axes for discriminating reptilian predators from vegetarians, and between mice with different gut microbiome states. VSN tuning was especially well-aligned with the information available about conspecific gut microbiome status. These results show that AOS bile acid chemosensation supports discrimination of multiple biologically relevant states.<br><br>SHORT ABSTRACT: The rodent accessory olfactory system (AOS) detects fecal bile acids via combinatorial codes with unknown biological significance. We investigated whether AOS bile acid chemosensation supports species and gut microbiome evaluation using mass spectrometry, calcium imaging in vomeronasal sensory neurons (VSNs), and analytical modeling. Bile acid excretion patterns theoretically supported discrimination of reptilian predators from vegetarians, and germ-free mice from conventionally raised counterparts. VSNs demonstrated stimulus "whitening" via an inverse relationship between natural bile acid abundance and population response magnitude. VSNs had highest sensitivity to taurine-conjugated bile acids, a novel class of chemosignals that elicited behavioral aversion. VSN tuning aligned with ideal discrimination axes, which was especially strong for gut microbiome-associated bile acid abundance patterns. These results show that AOS bile acid chemosensation supports discrimination of multiple biologically relevant states.}, }
@article {pmid42146481, year = {2026}, author = {Jensen, O and Hanson, L and Hénault, M and Haskins, BE and Trujillo, E and Brown, C and Brunetti, T and McCabe, M and Russo, BC and Heasley, L and Ost, KS}, title = {A Candida glabrata adhesin-like effector drives fitness and immunogenicity in the gut.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.04.722752}, pmid = {42146481}, issn = {2692-8205}, abstract = {Candida glabrata is a leading cause of invasive candidiasis. The gut serves as its primary reservoir, yet factors governing colonization and pathogenic potential remain poorly defined. Here, we identify immunoglobulin A (IgA) as a key regulator of C. glabrata within the intestinal microbiome. We found that C. glabrata induces an IgA response in a strain-specific manner. Comparative transcriptional and proteomic analyses of IgA-inducing and non-inducing strains identified a putative adhesin, Awp11, whose expression correlated with IgA induction. Awp11 is directly targeted by IgA and is required for inducing C. glabrata -specific IgA and Th17 responses in vivo. Functionally, Awp11 promotes colonization of a complex intestinal microbiome, and intestinal IgA limits this advantage. In most strains, AWP11 transcription is dynamic and limited by IgA in the gut. This identifies Awp11 as a key determinant of strain-dependent immunogenicity and gut colonization that C. glabrata may dynamically regulate to balance colonization and immune evasion.}, }
@article {pmid42146533, year = {2026}, author = {Steininger, HM and Iglesias-Aguirre, CE and Panzer, AR and Durack, J and McKean, M and Cabana, MD and Diamond, S and Lynch, SV}, title = {Carbohydrate Metabolism Differs in Infants by Asthma-risk Status and is Associated with the Functional Potential of Bacteroides cellulosilyticus.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.28.721144}, pmid = {42146533}, issn = {2692-8205}, abstract = {Childhood atopic disease is linked to delayed gut microbiome development and metabolic dysfunction, however microbial drivers remain unclear. To explore microbial correlates of asthma risk during a time of active gut microbiome development, we analyzed stool from 6-month-old infants at high asthma risk (HR) or healthy controls (HC), using Genome-resolved metagenomics (HR=7; HC=12) and untargeted metabolomics (HR=11; HC=15). We recovered 82 bacterial species-level metagenomic-assembled genomes (MAGs). Global Taxonomic composition did not differ by asthma risk. Anticipating that key differences might associate with specific genomes, a machine-learning approach pinpointed Bacteroides cellulosilyticus, Hungatella effluvii, and Enterocloster aldenensis as linked with asthma risk status. All three species were more abundant in HC infants and the B. cellulosilyticus genome was enriched for carbohydrate metabolism genes relative to other MAGs. Metabolomic profiling revealed variance associated with asthma risk (PERMANOVA, R2=0.069, p=0.016). HR fecal metabolomes were enriched in simple sugars, whereas HC contained more nitrogenous compounds. Integrative genome-metabolic modeling of compounds that significantly differentiate asthma-risk groups revealed risk-dependent interactions with community-encoded metabolic potential (CEP), for arabinose and agmatine, whose fecal concentrations are linked with B. cellulosilyticus and H. effluvii functional traits respectively. These findings suggest that microbial-influenced metabolic differences associate with asthma risk at 6 months, with B. cellulosilyticus and H. effluvii emerging as candidate bacteria influencing this observed metabolic remodeling.}, }
@article {pmid42146538, year = {2026}, author = {Yengo, CK and Liu, X and Langley, RJ and Avila, F and Sagar, M and Ochsenbauer, C and Bensing, BA and Hioe, CE}, title = {HIV-1 interactions with sialic acid-binding bacterial lectins promote virus infectivity in vitro and mucosal transmission in humanized mice.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.05.722898}, pmid = {42146538}, issn = {2692-8205}, abstract = {UNLABELLED: Most HIV-1 transmission occurs at mucosal surfaces, which are colonized by the host microbiota. However, interactions between HIV and bacteria or bacterial products derived from the human microbiome are poorly characterized, and their biological consequences are largely unexplored. Here, we evaluated the effects of sialic acid-binding lectins expressed by bacterial species ubiquitous in the human microbiota on HIV-1 infectivity using viruses produced in 293T cells and human primary cells. We demonstrated that these bacterial lectins enhanced HIV-1 infectivity in a sialoglycan-dependent manner. Specifically, Siglec-like binding region lectins (SLBR-N, SLBR-H, and SLBR-B) from Streptococcus gordonii and Staphylococcal superantigen-like lectins (SSL3, SSL4, and SSL11) from Staphylococcus aureus increased HIV-1 infectivity to varying extents, depending on lectin type and virus strain. Among these lectins, SLBR-N exhibited the greatest potency, corresponding with its superior ability to bind virions and promote virus-cell attachment. This enhancing activity was observed for direct infection of TZM-bl reporter cells and primary CD4+ T cells, as well as trans-infection in the presence or absence of the mannose-binding host lectin DC-SIGN. Importantly, these findings were corroborated in vivo using humanized mice, in which pre-exposure to SLBR-N promoted rectal HIV-1 transmission and increased viral burdens in plasma and splenic cells. Collectively, the data show sialoglycan-binding bacterial lectins as microbial factors that can enhance HIV-1 transmission at mucosal surfaces, highlighting a potential direct role for the microbiota in modulating HIV-1 acquisition risk.<br><br>AUTHOR SUMMARY: HIV is commonly transmitted from one person to another across mucosal surfaces, such as those lining the genital and rectal tracts, which are densely populated by bacteria that make up the human microbiota. Yet, surprisingly little is known about how these bacteria and the molecules they produce influence HIV infection. In this study, we investigated a group of bacterial proteins known as sialic acid-binding lectins that are expressed by common members of the human microbiome: Siglec-like binding region lectins from Streptococcus gordonii and superantigen-like lectins from Staphylococcus aureus . Using multiple HIV strains and several types of target cells, we demonstrate that lectin binding to HIV can increase virus attachment to target cells and thereby enhance infection, although the magnitude of this effect varies among lectins and virus strains. Lectin binding also facilitates HIV spread from cell to cell and promotes mucosal HIV infection in a humanized mouse model, resulting in a higher viral burden in the blood and tissues. These findings identify bacterial lectins as important factors that can influence HIV infection and implicate a potential role for the human microbiota in determining susceptibility to HIV infection.}, }
@article {pmid42146631, year = {2025}, author = {Madaan, T and Nieman, ML and Rakheja, T and Siddiqui, N and Gherardini, D and Sertorio, M and Kamble, NS and Thomas, SC and Hartman, A and Koch, SE and Knipper, L and Marino, VA and Sadayappan, S and Lorenz, JN and Konhilas, JP and Kotagiri, N}, title = {Modulating Cardiac-Gut Microbiome Interaction Post-Myocardial Infarction with Engineered Bacteria.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.07.10.664025}, pmid = {42146631}, issn = {2692-8205}, abstract = {The gut microbiome plays a critical role in the pathophysiology of acute myocardial infarction (MI). MI events significantly impact intestinal integrity which results in leakage of bacterial products into the systemic circulation. We demonstrate that MI not only compromises intestinal integrity, leading to systemic leakage of bacterial products like LPS, but also results in the translocation and colonization of live, intact gut bacteria in the MI heart - a novel aspect of the heart-gut axis. Our initial findings with natural murine gut microbiome were substantiated using orally administered E. coli Nissle 1917 (EcN), as a tracer bacterium. Furthermore, we engineered EcN to express the microbial anti-inflammatory molecule (MAM) derived from the probiotic Faecalibacterium prausnitzii . Treatment with this engineered strain, EcN-MAM, led to significantly improved survival and cardiac function in MI mice. This was attributed to enhanced gut barrier integrity, resulting in reduced systemic bacterial permeation and subsequent inflammation. These findings shed light on a previously unrecognized dimension of the heart-gut axis and highlight the potential of microbiome-based interventions in MI management.}, }
@article {pmid42146777, year = {2026}, author = {Mikulikova, I and Lepkova, Z and Bandouchova, H and Blahova, J and Papezikova, I and Novotna, H and Toulova, I and Kobelkova, K and Odehnalova, K and Postulkova, E and Radojicic, M and Mares, J and Mudronova, D and Palikova, M}, title = {The effect of Lactiplantibacillus plantarum probiotic supplement on rainbow trout challenged with Aeromonas salmonicida.}, journal = {Veterinarni medicina}, volume = {71}, number = {4}, pages = {156-168}, pmid = {42146777}, issn = {0375-8427}, abstract = {Two probiotic (Lactiplantibacillus plantarum) supplementation strategies (continuous and cyclic) were evaluated for their ability to enhance resistance of rainbow trout (Oncorhynchus mykiss) to Aeromonas salmonicida infection. Neither of these strategies improved post-challenge survival. Instead, cyclic administration resulted in a significantly higher mortality rate (73%) compared with continuous supplementation (52%) and the control group (46%). One week post-challenge, most haematological, plasma biochemical, and immune parameters showed no significant difference between treatments, though fish receiving cyclic supplementation did exhibit a reduced lymphocyte count. However, three weeks post-challenge, this same group showed a significant decrease in total phagocyte number and in the proportion of phagocytes within white blood cells. IgM concentrations were significantly lower in both probiotic-supplemented groups than in the control group. In the cyclic group, reductions in interleukin-10 and elevations in total protein levels were also observed. Microbiome analysis of gut content three weeks post-challenge revealed a marked decline in microbial diversity in both probiotic-treated groups. These findings indicate that, under the experimental conditions, probiotic supplementation did not provide protection against A. salmonicida infection and that cyclic administration may disrupt immune homeostasis and intestinal microbial stability, ultimately compromising host resilience.}, }
@article {pmid42146906, year = {2026}, author = {Orletskaia, VA and Olekhnovich, EI}, title = {Ecological and Functional Stratification of the Stool Microbiome Predicts Response to Immune Checkpoint Inhibitors across Cancer Types.}, journal = {Computational and structural biotechnology journal}, volume = {35}, number = {1}, pages = {0065}, pmid = {42146906}, issn = {2001-0370}, abstract = {Despite the recognized role of the gut microbiome in modulating immune checkpoint inhibitor efficacy, the ecological principles governing this relationship remain elusive. Moving beyond cataloging specific bacteria, we investigated whether general ecosystem properties determine clinical outcome. Through genome-resolved metagenomic analysis, we constructed a comprehensive catalog from 951 stool metagenomes and subsequently analyzed a curated subset of 624 samples from 11 multicancer cohorts, with melanoma (72.7%, n = 456) and other cancer types collectively accounting for 27.3% (n = 171), including gastrointestinal, non-small-cell lung, breast, ovarian, and other types. Our catalog comprises 3,816 operational genomic units and reveals the key ecological determinants of immune checkpoint inhibitor response. Clinical benefit was associated with gut ecosystems dominated by prevalent, autochthonous taxa. Indeed, the population frequency of a taxon was a positive predictor of its favorable outcome association. Functionally, responder-associated microbes were enriched in genomic capacity for complex carbohydrate metabolism, including specialized mucin degradation and amino acid biosynthesis. In contrast, nonresponse was characterized by enrichment of low-prevalence, exogenous oral and food-derived bacteria and enriched for replication-associated pathways. Our results support an ecological interpretation of the "Anna Karenina principle" in microbiomes: response is linked to a stable, functionally coherent microbial community, whereas nonresponse represents a destabilized state with high individual variability. This reframes the search for biomarkers from individual taxa to the assessment of ecosystem stability and functional coherence, providing a foundation for microbiome-targeted strategies to improve cancer immunotherapy outcomes.}, }
@article {pmid42147140, year = {2026}, author = {Vincent, SA and Devlin, PF}, title = {Fungicides disrupt total and endophytic phyllosphere bacterial communities but a salicylic acid hyperimmune mutant shows microbiome resilience.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag102}, pmid = {42147140}, issn = {2730-6151}, abstract = {Stable colonization of plants by beneficial microbes enhances disease resistance, nutrient uptake, and stress tolerance. Disruption of these communities often reduces plant fitness. The phyllosphere microbiome is especially vulnerable to agrochemicals. In this study we examined how synthetic fungicides affect the phyllosphere bacterial community of Arabidopsis thaliana. Application of several widely-used fungicides led to a pronounced decrease in bacterial diversity and depletion of beneficial taxa in both surface and internal leaf microbial communities. Moreover, these microbial responses were influenced by the host plant's genetic background. We previously showed that the phyllosphere microbiomes of plants exhibiting heightened salicylic acid-driven immune responses are enriched in xenobiotic degradation traits. We, therefore, examined whether the disrupted phyllosphere of one such line, the fhy3 far1 mutant, is buffered against fungicide-induced dysbiosis. The fhy3 far1 mutant showed reduced fungicide-induced microbiome disruption in both surface and endophytic microbiomes across both systemic and contact fungicides, supporting the hypothesis that innate plant immunity may help buffer against collateral damage from chemical treatments. Our identification of fungicide-resilient microbial taxa holds promise for the development of next-generation biostimulant products and, additionally, our findings raise the possibility that salicylic acid-mediated immunity could be strategically leveraged as a complementary tool alongside traditional fungicides.}, }
@article {pmid42147160, year = {2026}, author = {Turnbaugh, P and Zhang, S and Buttimer, C and Trepka, K and Lam, K and Hernandez, LR and Noecker, C and Soto-Perez, P and Canigiula, P and Ortega, E and Lee, J and Ramirez, L and Partipilo, G and Lawrence, H and Bottacini, F and Shkoporov, A and Draper, L and Ross, RP and Coffey, A and Hill, C}, title = {Eggerthella lenta evades bacteriophage through reversible megabase-scale inversions of capsular polysaccharide gene clusters.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-9488777/v1}, pmid = {42147160}, issn = {2693-5015}, abstract = {Bacteriophages are a promising tool for microbiome editing, yet their development has been constrained by limited insights into bacteriophage-host interactions within their shared mammalian body habitat. We isolated a lytic phage ΦKL11 that efficiently targets a disease-associated member of the human gut microbiota, Eggerthella lenta , during in vitro growth. However, ΦKL11 selects for a pre-existing and reversible bacteriophage-resistant sub-population in mice. Long-read sequencing revealed a massive genomic inversion event, representing >50% of the E. lenta genome, enriched in response to bacteriophage infection. Transcriptomics linked this inversion to the altered expression of three capsular polysaccharide synthesis (CPS) gene clusters and transmission electron microscopy confirmed differential capsule production. Finally, we show that ΦKL11 has a broad host range attributable to CPS and other strain-variable genes. These findings suggest a previously unrecognized strategy for phage evasion in the gut, involving megabase-scale genomic inversions and reversible capsule variation driving phage resistance.}, }
@article {pmid42147173, year = {2026}, author = {Ng, J and Trannguyen, J and Wilkinson, R and Conard, F and Fehrenback, S and Ebersole, B and Ghosh, D and Apewokin, S}, title = {Conditioning chemotherapy exposure is associated with epigenetic modifications in Clostridioides difficile isolates from stem cell transplant recipients.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-8865869/v1}, pmid = {42147173}, issn = {2693-5015}, abstract = {Clostridioides difficile is a highly methylated organism within the gut microbiome that is responsible for Clostridioides difficile infection (CDI), a common disease that is mediated by toxins production from the bacterium. C. difficile infection is ten times more common in chemotherapy patients than the average patient, but the reasons for this disparity are unclear. Conditioning chemotherapy (CC), an integral part of cancer treatments, has the ability to induce methylation changes in many cell types. We posit that CC induces methylation changes within C. difficile that may promote toxin production and consequently CDI. To test our hypothesis, we sought to identify the epigenetic changes, particularly methylation changes, within C. difficile isolates before and after chemotherapy and within isolates that express toxin and isolates that do not. After stool sampling, we isolated C. difficile by culture then sequenced and created a hybrid assembly of each isolate using nanopore long read sequencing and Illumina short read sequencing. Bioinformatics tools such as Dorado and Samtools were used to basecall and determine methylation states, while Unicycler was used for genome assembly. Methylartist was then used for data visualization. Genome-wide methylation profiling revealed distinct epigenetic signatures in Clostridioides difficile associated with toxin expression and chemotherapy exposure. Whole-genome 6mA analysis demonstrated significant differences between toxin-positive and toxin-negative isolates, with prominent methylation changes in tcdA and tcdE , while selected sporulation genes were unmethylated in toxin-negative strains. Chemotherapy was associated with a significant shift in global 6mA methylation patterns. Targeted 5mC analysis of the pathogenicity locus revealed reduced methylation around tcdB and across multiple toxin genes following chemotherapy, whereas sporulation genes remained unaffected. These findings suggest chemotherapy-associated epigenetic remodeling of toxin-associated loci in C. difficile .}, }
@article {pmid42147178, year = {2026}, author = {Gough, E and Basu, S and Brubaker, J and DeNeraing, B and Sack, D and Bourgeois, AL and Walker, R and Harro, CD and Chakraborty, S}, title = {Influence of Gut Microbiota on Immune Responses and Protection in Volunteers Receiving the Live Attenuated Oral ETEC Vaccine ACE257 followed by Virulent ETEC H10407 Challenge.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-9284363/v1}, pmid = {42147178}, issn = {2693-5015}, abstract = {Enterotoxigenic Escherichia coli (ETEC) remains a major cause of diarrheal morbidity with no licensed vaccines. Role of gut microbiota in vaccine immunogenicity and protection was investigated using 16S rRNA sequencing from the stool samples of 27 volunteers receiving two doses of the live attenuated oral ETEC vaccine ACE527 followed by virulent ETEC H10407 challenge. Systemic and mucosal IgG and IgA responses to heat-labile toxin-B (LTB) and colonization-factor-antigen-I (CFA/I) were quantified by ELISA in serum and antibody-in-lymphocyte-supernatant (ALS). Microbiome α-diversity, β-diversity, and taxa-immune associations were evaluated using regression models, MiRKAT, and relaxed LASSO. Vaccination increased (~ 25-30%) Eubacterium_brachy_group, Family_XIII_AD3011 and Actinomyces. Higher α-diversity (inverse-Simpson) was associated with reduced ALS anti-LTB and CFA/I IgA responses, whereas β-diversity correlated with increased serum anti-CFA/I IgA. Members of Anaerovoraceae, Peptostreptococcaceae, Oscillospiraceae, and Veillonellaceae enhanced immune responses and protection against severe diarrhea and ETEC colonization, while Ruminococcaceae, Sutterellaceae, Coriobacteria, Clostridia, and Actinobacteria showed antagonistic associations.}, }
@article {pmid42147179, year = {2026}, author = {Belger, C and Wirbel, J and Maghini, D and Carstens, N and van Coller, A and Beasley, JC and Melzheimer, J and Berkman, AY and Strauss, WM and Hetem, RS and Hazelhurst, S}, title = {The Gut Microbiome Profile of Lions in EtoshaNational Park, Namibia.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-9092464/v1}, pmid = {42147179}, issn = {2693-5015}, abstract = {Background: The gut microbiome plays a crucial role in carnivore ecology, diet, and health, yet remains poorly characterised in African lions (Panthera leo melanochaita). Previous studies of lion microbiomes have primarily focused on small numbers of captive individuals maintained on controlled diets of Asian origin, reporting Fusobacteriota and Firmicutes as dominant phyla. Some recent literature has begun to describe microbiome composition in free-living African lions; however, genome-resolved analyses and detailed functional characterisation of the wild African lion gut microbiome remain lacking. Results: We present the first comprehensive gut microbiome analysis of free-living African lions, including novel MAGs generated from examining 23 fresh faecal samples from 20 individuals in Etosha National Park, Namibia. The African lion gut was dominated by Bacteroides (22.1%) and Phocaeicola (13.3%) - two related genera - contrasting sharply with the captive lions where Fusobacterium (Bhopal, India) and Firmicutes (Rotterdam, Netherlands) predominate. This divergence likely reflects dietary differences, captivity effects and possibly allopatric separation. While recent work has begun to characterise taxonomic composition in wild African lions, our study extends these findings through the reconstruction of 318 bacterial and 102 viral metagenome-assembled genomes (MAGs) from combined short- and long-read sequencing data. Most MAGs shared <95% average nucleotide identity with existing reference genomes, indicating largely novel species. Supplementing the GTDB database with these MAGs reduced unclassified reads from 24.5% to 9.2%, demonstrating the substantial gaps in existing carnivore gut microbiome databases. Functional analysis revealed metabolic pathway enrichment, particularly for purine metabolism-critical for processing the lions' high-purine diet-with nearly complete pathways for degrading adenine and guanine to urea. Conclusions: This study provides the first in depth description of the microbial taxa in the African lion gut microbiome. Genera in the Bacteroidaceae family dominated. There are large differences with the metagenomics of the n = 3, 4 hybrid and Asiatic lions on controlled diets reported in prior studies. The discovery of over 300 novel MAGs significantly expands microbial reference databases and underscores the unique and understudied nature of apex carnivore microbiomes. These findings show critical microbial contributions to carnivore nutrition and establish a foundation for microbiome-based approaches to wildlife health monitoring and conservation management of threatened lion population.}, }
@article {pmid42147183, year = {2026}, author = {Topacio, TM and Maltz, MR and Lo, DD and Zaza, M and Porter, WC and Freund, L and Lyew, A and Cocker, D and Biddle, T and Yisrael, K and Castillo, DD and Dingilian, H and Drover, RW and Botthoff, J and Aronson, E}, title = {Chronic exposure to Salton Sea aerosols elicits pulmonary inflammation and shifts in murine lung and fecal microbiome diversity.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-9569949/v1}, pmid = {42147183}, issn = {2693-5015}, abstract = {Lung disease is rampant around the Salton Sea, California's largest inland lake and a major source of airborne particulates. To examine root causes of pulmonary disease, we investigated the exposure impacts of spatiotemporal variation in aerosols collected near the Salton Sea on lung and fecal microbiomes. We collected dust during the summer and fall at three different sites around the Salton Sea from 2020 to 2022. Dust was filtered to remove microbial cells and aerosolized for 7-day chronic murine exposures within controlled environmental chambers, after which mouse lung and fecal samples were used for 16S rRNA V3-V4 amplicon sequencing. We verified that chronic exposure to aerosols elicits neutrophilic pulmonary inflammation, particularly in mice exposed to collections from the Wister site near the Salton Sea. We found that spatiotemporal variation drove variation in lung microbiome composition in mice exposed to aerosols from 2022. The lung microbiomes of Salton Sea aerosol-exposed mice were found to increase in alpha-diversity and richness, while simultaneously decreasing in evenness. In contrast, the fecal microbiomes of aerosol-exposed mice decreased in diversity and richness. Our findings suggest that chronic exposure to aerosols from Wister, a site immediately Southeast of the Salton Sea, triggers a systemic stress response in mice characterized by high pulmonary neutrophil recruitment, increased lung microbiome diversity, and decreased fecal microbiome diversity. Back trajectory analyses for aerosol surface type frequencies revealed higher contributions from the Salton Sea in 2020 and 2022 collections from Wister. These findings suggest that chronic exposure to Salton Sea aerosols have impacts on host pulmonary and systemic health, as emphasized by significant but opposing effects on lung and fecal microbiome diversity. Furthermore, these findings demonstrate the variable capacity of environmental aerosol exposure to elicit health consequences relative to seasonal weather events.}, }
@article {pmid42147187, year = {2026}, author = {Caspi, R and Zhang, A and Horai, R and Jittayasothorn, Y and Badger, J and Wu, Z and Shi, G and Gupta, A and Arunkumar, S and Murphy, C and Nagarajan, V and McCulloch, J and Kodati, S and Sen, H and Lee, JW and Jacobs, J and Xu, X and Mattapallil, M and Peng, Z and Xu, B and Palmer, R and Majdalani, N and Honda, K and O'hUigin, C}, title = {Gut microbial interaction networks control autoimmunity to neuroretina.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-9528424/v1}, pmid = {42147187}, issn = {2693-5015}, abstract = {The gut microbiome influences the development of immune-mediated inflammatory diseases, including autoimmune uveitis, a sight-threatening ocular inflammation driven by retina-specific T cells1. Using a model of spontaneous autoimmune uveitis (sEAU) we showed that gut commensals provide immune stimuli that trigger disease2. Here we report that uveitis-promoting microbes are present in human gut flora and that colonization of germ-free (GF) mice with commensals from healthy human donors was sufficient to provoke disease. Severity of sEAU correlated with expansion of Akkermansia and contraction of short-chain fatty acid (SCFA)-producing Firmicutes, followed by decreased SCFA levels and a dominant gut Th1 effector response. Mechanistic gain-of-function experiments, enriching GF sEAU mice with Akkermansia, reproduced these microbiome, metabolite and immune phenotype shifts, and exacerbated disease, suggesting that Akkermansia promotes autoimmunity by outcompeting SCFA-producers and enhancing Th1-type responses. An inverse correlation between Akkermansia (Verrucomicrobia) and Firmicutes was also present in patients with uveitis, multiple sclerosis and Crohn's disease. These findings reveal a stereotypic gut microbial interaction network that regulates systemic immune balance, and may represent an ecologically conserved mechanism through which the gut microbiome modulates autoimmune and inflammatory diseases.}, }
@article {pmid42147198, year = {2026}, author = {Lewis, K and Patil, P and Liang, HW and Astley, E and Taher, R and Lee, MH and Norment, D and Iinishi, A and Gupta, N and Sobolevskaia, K and Chen, E and Nawab, A and Adzre, J and Moss, C and Hawkins, B and Bourgeois, J and Caimano, M and Brissette, C and Hu, L}, title = {A deformylase inhibitor expands therapeutic options for Lyme disease.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-9335039/v1}, pmid = {42147198}, issn = {2693-5015}, abstract = {Lyme disease incidence continues to rise globally. This vector-borne infection remains a major public health burden. Broad-spectrum doxycycline and ceftriaxone disrupt the gut microbiome, drive resistance in commensals, and offer suboptimal efficacy against neuroborreliosis. Here we show that forazemin, previously known as BB-83698, is an orally bioavailable peptide deformylase inhibitor with potent and selective bactericidal activity against spirochaetes, including diverse Borrelia species. Targeting the deformylation of nascent peptides, forazemin halted protein synthesis, thereby killing the spirochaetes. In murine models of Lyme borreliosis and neuroborreliosis, short oral dosing regimens cleared infection, and forazemin was more effective than doxycycline in tick-bite prophylaxis. Forazemin preserved microbiome diversity and spared beneficial gut symbionts. These findings support forazemin as a candidate for the treatment and prevention of Lyme disease.}, }
@article {pmid42147301, year = {2026}, author = {Barbosa, MC and Pellegrinetti, TA and da Cunha, ICM and da Silva, AVR and Marcandalli Boleta, EH and Losovoi, LA and Mendes, R and Tsai, SM and Mendes, LW}, title = {Genotype-dependent stability and specialization of arbuscular mycorrhizal fungal communities under drought in common bean.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1786322}, pmid = {42147301}, issn = {1664-462X}, abstract = {Arbuscular mycorrhizal fungi (AMF) represent a key biological strategy for enhancing agricultural resilience under extreme climatic events such as drought. However, how AMF interact with drought-tolerant plant genotypes to sustain performance under water limitation remains poorly understood. Here, we used high-throughput DNA sequencing to investigate AMF communities associated with drought-tolerant (BAT477 and SEA5) and drought-susceptible (IAC-Milênio and IAC-80SH) common bean genotypes, integrating taxonomic, structural, and functional perspectives under contrasting water regimes. We hypothesized that drought tolerance is not simply linked to AMF presence, but rather to the ability of host genotypes to structure and stabilize their mycorrhizal communities under stress. Our results reveal genotype-specific responses to drought, with distinct community restructuring dynamics observed across individual genotypes. Drought-tolerant genotypes maintained or increased AMF relative abundance, diversity, and functional integrity under drought, whereas susceptible genotypes displayed opposing changes in the community's structure. Although most genotypes displayed high dissimilarity in AMF community structure between control and drought conditions, tolerant genotypes reorganized their communities through increase in the relative abundance of key ASVs, whereas susceptible genotypes experienced substantial reductions in abundance, diversity, and specialist ASVs. Niche occupancy and functional guild analyses further showed that AMF communities in tolerant genotypes were dominated by specialist and symbiotrophic ASVs, whereas susceptible genotypes shifted toward rare and functionally reduced assemblages. At the plant level, AMF community stability was positively associated with root biomass and negatively associated with foliar nutrient, indicating a tight coupling between mycorrhizal community structure, host nutritional status, and growth. Collectively, our findings indicate that drought tolerance in common bean emerges, at least in part, from a cooperative host-microbiome strategy in which the host actively regulates the structure and functional stability of AMF communities under water stress. These results advance our understanding of plant-mycorrhizal interactions in drought adaptation and highlight the potential of integrating mycorrhizal functionality into plant breeding strategies aimed at developing climate-resilient crops.}, }
@article {pmid42147430, year = {2026}, author = {Liu, D and Chen, Y and Pan, J and He, Z and Zhou, Y and Dai, G and Dai, X and Lin, Z and Zhao, P and Lu, H and Zheng, M}, title = {Effect of modified Zengye decoction on age-related constipation via modulation of the host-microbial metabolic axis.}, journal = {Gastroenterology report}, volume = {14}, number = {}, pages = {goag031}, pmid = {42147430}, issn = {2052-0034}, abstract = {BACKGROUND: Constipation is a common digestive disorder in the elderly caused by weakened intestinal peristalsis and reduced mucus secretion that significantly impacts quality of life. Current treatments typically provide only temporary symptomatic relief and may lead to dependence and adverse effects.<br><br>METHODS: This study investigated the therapeutic effects of a modified traditional Chinese formula, modified Zengye decoction (MZD) on age-related constipation by modulating the gut microbiome and metabolomics. Aged constipated rats were gavage-fed with or without MZD. After detection of the indicators related to the disease, the microbial and metabolic profiles were generated for all the fecal samples by using 16S rRNA gene sequencing and [1]H nuclear magnetic resonance ([1]H NMR) spectroscopy, respectively.<br><br>RESULTS: MZD effectively alleviated constipation symptoms in aged mice by enhancing the intestinal peristalsis and antioxidant capacity. Gut microbiome analysis revealed that MZD significantly altered the abundance of Firmicutes, Bacteroidetes, and Actinobacteria. Specifically, the abundance of beneficial bacteria such as Corynebacterium, Roseburia, and Clostridium increased by 6-fold, 4-fold, and 3-fold, respectively. These changes in microbial composition enhanced the production of short-chain fatty acids (SCFAs), including acetate, propionate, and butyrate. Additionally, MZD significantly increased the expression of Mucin 2 protein and the moisture content of the small intestine, while decreasing pro-inflammatory cytokines such as tumor necrosis factor-alpha, interleukin-1 beta, and interleukin-6, and increasing anti-inflammatory interleukin-10, which may be attributed to the elevated levels of SCFAs.<br><br>CONCLUSIONS: By effectively regulating the gut microbiome and SCFA metabolism, MZD demonstrated significant anti-inflammatory and mucus-secretion-promoting effects, showing therapeutic potential for age-related constipation, enteritis, and other inflammation-related intestinal diseases.}, }
@article {pmid42147745, year = {2026}, author = {Li, W and Jiang, J and Zhou, J and Li, P and Duan, X}, title = {Gut Microbiota Metabolite, Trimethylamine N-Oxide, Aggravates Cognitive Impairment in Cerebral Ischemia-Reperfusion Injury.}, journal = {International journal of general medicine}, volume = {19}, number = {}, pages = {594053}, pmid = {42147745}, issn = {1178-7074}, abstract = {PURPOSE: Cerebral ischemia-reperfusion injury (CIRI) causes neuronal inflammation, oxidative stress, and cognitive impairment. We hypothesized that gut microbiota dysbiosis exacerbates post-ischemic cognitive deficits, with trimethylamine N-oxide (TMAO) acting as a potential mediator.<br><br>METHODS: In the primary experiment, mice received an antibiotic cocktail for 28 days to induce gut dysbiosis prior to bilateral common carotid artery occlusion (BCCAO), a model of CIRI (n = 12 per group). Gut microbial composition was analyzed using 16S rRNA sequencing, and cognitive function was assessed with the Morris water maze. Functional enrichment analyses (Kyoto Encyclopedia of Genes and Genomes and Clusters of Orthologous Groups) and microbiota-metabolite database mapping were used to identify candidate metabolites. In a separate validation cohort (n = 6 per group), TMAO (6.5 mg/day) was administered intraperitoneally for 7 days before BCCAO.<br><br>RESULTS: Antibiotic treatment markedly altered microbial diversity and composition, characterized by an expansion of Proteobacteria and a reduction in Lactobacillus. Bioinformatic analyses identified TMAO, a metabolite associated with Proteobacteria/Enterobacteria, as a potential mediator. Mice with antibiotic-induced dysbiosis subjected to CIRI exhibited impaired spatial memory, as indicated by fewer platform crossings and reduced time spent in the target quadrant. Similarly, TMAO pretreatment reproduced these cognitive deficits in BCCAO mice.<br><br>CONCLUSION: Antibiotic-induced gut dysbiosis appears to exacerbate CIRI-related cognitive impairment, at least in part through elevated TMAO levels. These findings highlight a potential microbiota-metabolite axis as a target for therapeutic intervention.}, }
@article {pmid42147973, year = {2026}, author = {Wardi, M and Amin, AB and El Belghiti, I and Lemkhente, Z and Belmouden, A}, title = {Importance of human microbiome: an update.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1787662}, pmid = {42147973}, issn = {2813-4338}, abstract = {Millions of microorganisms-including bacteria, viruses, fungi, archaea, and protists-reside on and within the human body, collectively forming the human microbiota. This complex and dynamic community plays a crucial role in modulating physiological processes, particularly the development and regulation of the immune system. Modern behaviors such as frequent washing, excessive hygiene, and widespread use of antimicrobial agents can disrupt the natural composition and functional balance of the microbiota, leading to altered immune responses and increased susceptibility to disease. In this review, we focus primarily on the bacterial component of the human microbiome. While we acknowledge the importance of viruses, fungi, archaea, and protists, these components are beyond the scope of the current review. We highlight recent advances in bacterial microbiome research that are reshaping our understanding of host-microbe interactions, immune modulation, and the health consequences of microbiota dysbiosis.}, }
@article {pmid42148043, year = {2026}, author = {Huang, CY and Nuwagira, E and Tisza, M and Kim, M and Tayebwa, M and Vieira, J and Lam, N and Wallach, E and Wiens, M and Tsai, AC and Valeri, L and Vallarino, J and Allen, JG and Lai, PS}, title = {Effect of Household Air Pollution on the Gut Microbiome and Virome of Adult Women Living in Uganda.}, journal = {Environmental health perspectives}, volume = {134}, number = {1}, pages = {75-90}, doi = {10.1021/EHP.6c00064}, pmid = {42148043}, issn = {1552-9924}, mesh = {Humans ; Uganda ; Female ; *Gastrointestinal Microbiome ; *Air Pollution, Indoor/statistics &amp; numerical data/adverse effects ; Adult ; *Virome ; Middle Aged ; }, abstract = {BACKGROUND: Emerging observational studies suggest that air pollution can influence the gut microbiome. However, this association is often highly confounded by factors, such as diet and poverty. The gut virome may influence respiratory health independent of the gut microbiome. We recently demonstrated in a randomized waitlist-controlled trial (ClinicalTrials.gov NCT03351504) that a clean lighting intervention reduced the level of personal exposure to air pollution among adult women in rural Uganda. OBJECTIVES: To determine the effect of a solar lighting intervention on changes to the gut microbiome and virome and secondarily to determine the association between these changes on lung health. METHODS: Between 2018 and 2019, we collected stool samples and assessed respiratory symptoms and spirometry from 80 adult women living in rural Uganda at baseline and 12 and 18 months postrandomization. The intervention group received a solar lighting system after randomization, while the waitlist-controlled group received one at 12 months. Deep metagenomics sequencing of stool was performed and profiled for nonviral and viral taxonomic composition. The primary analysis focused on pre- vs postintervention changes due to power considerations, adjusting for potential confounding by age, diet, antibiotic use, and season. A sensitivity analysis was conducted using intention-to-treat principles. When comparing pre- vs postintervention periods, we used sparse partial least-squares models to identify nonviral and viral signatures of reduced air pollution exposure. Mixed effects models were used to evaluate changes in health outcomes as well as associations between microbial signatures of reduced air pollution exposure and health. RESULTS: The average age was 39.2 years. The solar lighting intervention led to larger changes in viral compared to nonviral microbial community structure and differential abundance of bacteria, eukaryotes, and viruses. Provision of solar lighting systems was associated with a reduction in the presence of respiratory symptoms from 57.1% to 36.1% (p = 0.002), while there was no impact on lung function. Microbiome and virome signatures had AUCs of 0.74 and 0.76, respectively, in predicting pre- vs postintervention stool samples. Microbiome signatures were associated with a lower risk of respiratory symptoms (OR = 0.68 (0.49 - 0.94), p = 0.020). CONCLUSION: Among adult women living in rural Uganda, both nonviral and viral components of the gut microbial community changed after a clean lighting intervention. Microbiome signatures reflective of lower air pollution exposures were associated with improved respiratory symptoms. These observations suggest that air pollution may influence lung health through the gut-lung axis, warranting further exploration in future intervention studies.}, }
@article {pmid42148231, year = {2026}, author = {Niu, Y and Li, Y and Zhou, X and Kong, W and Zhou, B and Hu, X and Guo, J}, title = {Geraniol alleviates benzo[a]pyrene-induced neurotoxicity by regulating the NLRP3/Caspase-1 pathway and gut microbiome in mice.}, journal = {Food science and biotechnology}, volume = {35}, number = {7}, pages = {1905-1918}, pmid = {42148231}, issn = {2092-6456}, abstract = {Benzo[a]pyrene (BaP) exposure has been associated with an increased risk of neurotoxicity, including learning and memory impairment. As an antioxidant and a potential prebiotic, geraniol is speculated the potential preventive agent against neurotoxicity. This study aims to reveal the neuroprotection of geraniol on BaP-induced neurotoxicity. The results indicate geraniol increases immunofluorescence intensity of PSD-95, and decreases the immunofluorescence intensity of Iba-1 and GFAP, as well as the level of inflammatory cytokines, and pyroptosis biomarkers. Geraniol also up-regulates the expression of tight junction proteins markedly. In addition, lipopolysaccharide (LPS), might originate from intestinal flora and closely correlated with inflammation and pyroptosis, varies in brain and serum between each group. It is summarized that the underlying mechanism of neuroprotection effect of geraniol might be located on improving intestinal physical barrier function, decreasing LPS releasing, down-regulating pyroptosis and inflammatory response, thereby alleviating neurotoxicity induced by BaP in mice model.}, }
@article {pmid42148333, year = {2026}, author = {Szalus, K and Sakowicz-Burkiewicz, M and Pawełczyk, T and Nowicki, RJ and Trzeciak, M}, title = {The mRNA levels of COL1A1, COL2A1, COL3A1 and COL4A1 in non-lesional and lesional skin of atopic dermatitis patients.}, journal = {Postepy dermatologii i alergologii}, volume = {43}, number = {1}, pages = {94-100}, pmid = {42148333}, issn = {1642-395X}, abstract = {INTRODUCTION: Atopic dermatitis (AD) is a complex, multifactorial inflammatory disease. The multifaceted aetiology and pathophysiology consist of different elements, including genetic and immunological disorders, skin barrier defects, microbiome dysbiosis and environmental interactions. To date, little has been known about the genes involved in the relationship between extracellular matrix (ECM) expression and the pathogenesis of atopic dermatitis.<br><br>AIM: The aim of our study was to examine the mRNA transcript levels of genes encoding collagen type I, II, III and IV in the skin of atopic dermatitis patients vs. controls and to search for associations with subjective clinical symptoms and disease severity.<br><br>MATERIAL AND METHODS: A total of 18 subjects participated in the study. Nine biopsies were taken from lesions, nine from non-lesional AD skin and nine from healthy volunteers. The mRNA levels of COL1A1, COL2A1, COL3A1 and COL4A1 were determined using real-time RT-PCR. AD severity was evaluated by calculating the SCORAD score and measuring the pruritus intensity using the Visual Analogue Scale (VAS).<br><br>RESULTS: A significant increase in the mRNA levels of COL3A1 in the study group compared to the control group was associated with an increase in the intensity of clinically reported symptoms as assessed by the SCORAD and the itching scale VAS (p = 0.0293). In addition, there was a statistically significant difference in the mRNA levels of the COL3A1 gene and the mRNA levels of the COL4A1 gene between subjects in the lesional and non-lesional skin of the study group. The transcript level of mRNA COL3A1 was statistically higher in lesional skin than in non-lesional skin among subjects with AD than in healthy volunteers. Conversely, mRNA COL4A1 expression was significantly higher in non-lesional skin than in lesional skin among AD subjects; however, there was no statistical difference between AD subjects and healthy volunteers.<br><br>CONCLUSIONS: Our results suggest a role for collagen mRNA levels in AD pathogenesis. Further studies are needed to assess its role as a new potential biomarker, as a predictive element for assessing the intensity of AD or as a new target for AD therapy in the era of personalized medicine. The question to be answered is the importance of remodelling processes in AD.}, }
@article {pmid42148336, year = {2026}, author = {Kalicka, M and Biadasiewicz, M and Tekielak, A and Frątczak, A and Bergler-Czop, B}, title = {The role of the skin microbiome in modulating rosacea.}, journal = {Postepy dermatologii i alergologii}, volume = {43}, number = {1}, pages = {1-6}, pmid = {42148336}, issn = {1642-395X}, abstract = {INTRODUCTION: The skin microbiome is a contributing factor in the pathogenesis of rosacea, and disturbances in its composition may play a pivotal role in the development of the disease.<br><br>METHODS: A review of the literature in PubMed and Embase databases from inception to February 2025 to identify 13 scientific studies on the influence of the skin microbiome on the modulation of the course of rosacea.<br><br>RESULTS: Rosacea patients consistently exhibit microbial dysbiosis, which is characterized by an increased bacterial diversity, particularly involving pro-inflammatory taxa such as Staphylococcus epidermidis, Corynebacterium, and Streptococcus.<br><br>CONCLUSIONS: It seems there is growing evidence to suggest a link between the skin microbiome and the development of rosacea. This link involves changes in bacterial composition, interactions with the immune system, and the induction of inflammation. However, therapeutic implications remain largely speculative.}, }
@article {pmid42148465, year = {2026}, author = {Chang, J and Bhuvanagiri, GM and Dulkanchainun, M and Wang, C}, title = {Osteoporosis and Periodontitis: Two-Way Epidemiological and Mechanistic Evidence.}, journal = {Journal of periodontal research}, volume = {}, number = {}, pages = {}, doi = {10.1111/jre.70125}, pmid = {42148465}, issn = {1600-0765}, support = {R01 DE029200/DE/NIDCR NIH HHS/United States ; }, abstract = {Osteoporosis and periodontitis are highly prevalent, chronic inflammatory diseases that constitute a major global health burden. Strong epidemiological evidence shows an association between the two diseases, in which osteoporosis patients have an increased risk of periodontitis, specifically in postmenopausal women. Osteoporosis and periodontitis are linked by bidirectional relationships through shared inflammatory and bone-resorptive pathways. Such a connection is explained by shared osteo-immunologic pathways, particularly as highlighted by recent breakthrough findings in the field. In this review, we comprehensively examined the seven links between osteoporosis and periodontitis across microbial translocation, systemic meta-inflammation, maladaptive myelopoiesis, immune cell trafficking, masticatory dysfunction-diet interactions, underlying vulnerabilities, and functional alterations of the oral microbiome, drawing on current biological findings and clinical evidence. This bidirectional relationship underscores the importance of integrated medical and dental screening and management strategies to improve patient outcomes for both conditions.}, }
@article {pmid42148573, year = {2026}, author = {Raad, R and Mann, A and Pal, A and Parra, A and Strawn, L and Hamilton, A and Critzer, F and den Bakker, HC}, title = {Metagenomic profiling of bacterial (16S) and fungal (ITS) communities on d'Anjou pears during long-term controlled-atmosphere storage.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0411725}, doi = {10.1128/spectrum.04117-25}, pmid = {42148573}, issn = {2165-0497}, abstract = {D'Anjou pears are routinely stored for up to nine months under controlled-atmosphere (CA) conditions to meet market demands. While this practice maintains fruit quality, limited information exists on pears' natural microbiota throughout storage. The objective of this study was to describe fungal and bacterial composition on marketable and unmarketable conventional, whole, intact pears under two storage practices (bulk vs wrapped) at 3, 6, and 9 months in long-term CA cold storage. Storage practices had a significant effect on the composition and succession of both fungal and bacterial communities. No significant differences in Chao1 index were found between the bacterial and fungal communities on marketable or unmarketable pears. Trends in Chao1 indices of fungal and bacterial communities peaked at mid-storage and declined by 9 months, with wrapped pears showing parallel trends, and bulk pears exhibiting a sharper late-stage reduction. No distinct clusters could be found for 3- and 6-month fungal communities, irrespective of marketability, or whether bulk or wrapped. The principal coordinate analysis of the bacterial communities showed tight clustering by time point for the individually wrapped pears, irrespective of their marketability. Bacterial communities included genera common in food-processing and plant environments, such as Pseudomonas (19.2% relative abundance [RA]) and Acinetobacter (3.31% RA). Fungal communities shifted over time, with spoilage-associated genera like Aureobasidium (23.3% RA), Penicillium (9.28% RA), Botrytis (0.33% RA), and Mucor (0.14% RA) present at different storage stages.IMPORTANCEThis study highlights the influence of storage duration and packaging on microbial succession, establishing initial benchmarks of pear surface microbiomes. The observed lack of significant differences in microbial diversity between marketable and unmarketable pears suggests that these baseline community profiles can serve as critical reference points for identifying other influential factors. Variables such as handling practices may exert a more direct effect on microbial dynamics and, consequently, product quality. Establishing these baselines is essential because they provide a foundation for detecting deviations linked to spoilage or safety risks. Moreover, understanding these patterns can guide the development of targeted microbial control strategies in postharvest systems, enabling interventions that maintain fruit quality, reduce losses, and possibly improve food safety throughout the supply chain.}, }
@article {pmid42148579, year = {2026}, author = {Liu, M and Zhang, W and Zhang, J and Lv, N and Wu, X and Alalawy, AI and Zhao, W and Bao, H and Wu, J}, title = {Multi-site microbiomes' response to chronic obstructive pulmonary disease.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0000726}, doi = {10.1128/spectrum.00007-26}, pmid = {42148579}, issn = {2165-0497}, abstract = {This study aimed to evaluate changes in the oral, nasal, pulmonary, and gut microbiota in patients with chronic obstructive pulmonary disease (COPD) and to explore their interrelationships compared with the healthy group. This study included 33 COPD patients and 29 healthy individuals. A total of 162 oral, nasal, sputum, and fecal samples were obtained. The microbiota was determined using full-length 16S rRNA gene sequencing on the PacBio platform. Alpha diversity was significantly reduced in sputum and fecal samples of COPD patients, while oral and nasal microbiota showed no significant differences. Beta diversity revealed substantial overlap between oral and sputum microbiota in both groups, while nasal and fecal communities were clearly distinct. Linear discriminant analysis effect size analysis identified Haemophilus parahaemolyticus as a sputum biomarker. Source tracking confirmed that the majority of lung microbiota originated from the oral cavity. Interleukin-6 was inversely correlated with short-chain fatty acids (SCFAs)-producing microbiota in fecal samples, suggesting that depletion of these bacteria may contribute to systemic inflammation. Co-occurrence network analysis revealed that the sputum microbial network in COPD patients exhibited reduced robustness and lacked prominent hub nodes. Lung microbiota largely originates from the oral cavity but is changed in COPD. The lung microbiome is still more sensitive and accurate than the oral, nasal, and fecal microbiomes for COPD diagnosis. Fragmented networks in COPD indicate reduced community resilience.IMPORTANCELung and gut microbial diversity is significantly reduced in COPD patients. Oral microbiota is the primary source of lung microbes, but poorly predicts COPD status. Haemophilus parahaemolyticus was identified as a novel sputum biomarker in COPD. The bacterial network in COPD lungs is fragmented, lacking the resilience seen in healthy individuals.}, }
@article {pmid42148581, year = {2026}, author = {Wang, K and Zhang, D and Shen, K and Qiu, Y and Deng, B and Zhou, J and Qiu, S}, title = {Multi-omics characterization of new and aged Daqu reveals region-specific microbial succession and metabolic signatures in Maotai-flavor liquor fermentation.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0377525}, doi = {10.1128/spectrum.03775-25}, pmid = {42148581}, issn = {2165-0497}, abstract = {Daqu is an essential fermentation starter that drives the formation of the characteristic flavor of Maotai-flavor liquor, yet the ecological and metabolic mechanisms underlying its regional differentiation and maturation remain poorly resolved. Here, we performed genome-resolved metagenomic and untargeted metabolomic analyses on 48 new and aged Daqu samples collected from four major Maotai-flavor liquor-producing regions in Guizhou Province, China. We reconstructed 163 high-quality metagenome-assembled genomes (MAGs) spanning 16 bacterial and 3 archaeal phyla and identified 2,642 metabolites across ionization modes. Distinct regional microbial signatures were observed, with Jinsha Daqu showing the greatest genomic diversity and unique MAGs, whereas Maotai Daqu exhibited the highest community similarity with other regions. Aged Daqu significantly increased microbial richness and functional capacity, enriching thermophilic and spore-forming taxa (e.g., Bacillus, Lentibacillus, Kroppenstedtia) and enhancing carbohydrate-active enzymes (GH13, GH43, and GH3), amino acid degradation, lipid metabolism, and secondary metabolic pathways. Metabolomic profiling revealed elevated amino acid derivatives, fatty acids, esters, and phenolic compounds in aged Daqu, indicating intensified biochemical activity. Multi-omics integration linked dominant microorganisms-including Bacillus thuringiensis, Actinomycetaceae bacterium, and Methylocaldum szegediense to pyrazine biosynthesis, amino acid catabolism, and lipid oxidation, forming coordinated microbial-metabolite modules that underlie region-specific flavor precursor formation. These findings establish a mechanistic model in which microbial terroir, aging-driven succession, and metabolic specialization jointly shape the maturation and flavor potential of Maotai-flavor liquor.IMPORTANCEThis study provides the first genome-resolved, multi-omics framework for understanding how geographic origin and storage aging co-regulate the ecological assembly, functional specialization, and metabolic transformation of Maotai-flavor liquor. By linking specific MAGs, functional pathways, and key flavor precursors, our results offer mechanistic insights into microbial terroir and provide a scientific foundation for microbiome-guided optimization of Maotai-flavor liquor quality.}, }
@article {pmid42136740, year = {2026}, author = {Chen, Y and Li, J and Sun, Y and Yue, X and Tian, XH and Liu, F and Wang, DY and Shen, J}, title = {Biofilm-targeted liposomal curcumin delivery system for anti-caries therapy.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1808450}, pmid = {42136740}, issn = {2235-2988}, mesh = {*Biofilms/drug effects ; *Liposomes/chemistry ; *Dental Caries/drug therapy/microbiology ; Animals ; *Curcumin/administration &amp; dosage/pharmacology ; Streptococcus mutans/drug effects ; *Anti-Bacterial Agents/pharmacology/administration &amp; dosage ; *Drug Delivery Systems ; Rats ; Hydrogen-Ion Concentration ; Humans ; Disease Models, Animal ; }, abstract = {INTRODUCTION: Dental caries, driven by acidogenic biofilms, remains a major global health challenge. Current chemical treatments, such as chlorhexidine and fluoride, can disrupt oral microbial homeostasis and cause adverse effects, including tooth discoloration, dentin hypersensitivity, and taste disturbances. Curcumin, a natural photosensitizer, exhibits antibacterial activity and favorable biocompatibility, however, its clinical application is limited by poor stability, low aqueous solubility, and restricted biofilm penetration. There is an urgent need to develop innovative therapeutic strategies to enhance curcumin transport into acidic cariogenic biofilms.<br><br>METHODS: We developed a pH-responsive liposomal delivery system (Cur/DCPA-H2O) engineered to penetrate acidic cariogenic biofilms and enhance curcumin transport. The physicochemical characterization of Cur/DCPA-H2O was performed using a UV-1800 spectrophotometer, transmission electron microscopy (TEM), and dynamic light scattering (DLS). Biocompatibility was assessed by Cell Counting Kit-8 (CCK-8) assays, hemolysis tests, and Live/Dead cell staining. The antibacterial efficacy in vitro and ex vivo was evaluated using colony-forming unit (CFU) counting, scanning electron microscopy (SEM), confocal laser scanning microscopy (CLSM), and crystal violet (CV) staining. An in vivo caries model was established to assess the therapeutic efficacy of Cur/DCPA-H2O, using micro-computed tomography (micro-CT), Keyes' scoring, and 16S rRNA sequencing.<br><br>RESULTS: The liposomes exploit charge reversal to interact with representative caries-associated bacteria (Streptococcus mutans and the early colonizer Streptococcus sanguinis), enabling deep biofilm penetration. Upon light irradiation, Cur/DCPA-H2O was observed to generate reactive oxygen species (ROS), which may contribute to partial disruption of the biofilm matrix and reduced bacterial viability in vitro. In a rat caries model, treatment with Cur/DCPA-H2O under light irradiation reduced caries severity and decreased lesion depth by approximately 50%. It also shifted the oral microbiome composition toward a less dysbiotic profile, as confirmed by 16S rRNA sequencing.<br><br>DISCUSSION: This study demonstrates that a biofilm-targeted, pH responsive liposomal curcumin delivery system may provide a safe and effective strategy for caries prevention, highlighting the potential of natural therapeutics to modulate pathogenic biofilms with limited impact on the overall microbial community.}, }
@article {pmid42136780, year = {2026}, author = {Ahmed, SH and Islam, ZS and Zaidi, SM and Khalid, T}, title = {Surgical Solution of C-Section Associated Surgical Site Infection in LMICs: A Narrative Review.}, journal = {Pakistan journal of medical sciences}, volume = {42}, number = {411AASC}, pages = {S122-S129}, pmid = {42136780}, issn = {1682-024X}, abstract = {Cesarean section (CS) is a life-saving procedure worldwide, accompanied by a substantial burden of surgical site infections (SSIs), with the most significant impact felt in low- and middle-income countries (LMICs). This review consolidates current knowledge on the surgical management of post-cesarean infections, highlighting the vaginal microbiome as a key source of infection and the physiological immunosuppression in the postpartum period. We describe the categories of deep and organ-space SSIs that require operative management, from wound debridement to laparoscopic drainage and laparotomy. The analysis also assesses proven preventive measures, such as dual-agent antibiotic prophylaxis, advanced closure techniques, and structured care bundles. It includes a standardized, context-sensitive checklist designed for LMICs, which combines pre, intra, and postoperative measures to prevent and manage SSIs, with the aim to reduce maternal morbidity and mortality in resource-limited settings.}, }
@article {pmid42136862, year = {2026}, author = {Feng, Z and Quan, H and Li, M and He, D and Han, Y and Zou, C and Zhang, W and Chang, J and Lu, M}, title = {Distinct microbial and functional alterations across skin sites and disease severity in pediatric atopic dermatitis: a prospective study.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1805596}, pmid = {42136862}, issn = {2296-858X}, abstract = {BACKGROUND: Atopic dermatitis (AD) is a chronic inflammatory skin condition frequently associated with microbial dysbiosis.<br><br>OBJECTIVE: This study examined the diversity, composition, and functional profiles of the skin microbiome in children with varying degrees of AD in different skin regions.<br><br>METHODS: Skin samples were collected from 12&#x202f;AD patients and 12 healthy controls. Genomic DNA underwent shotgun metagenomic sequencing to analyze alpha and beta diversity, taxonomic composition, and functional profiles, including the Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), virulence factors and pathogen-host interactions (PHI).<br><br>RESULTS: Significant differences were observed in Shannon's diversity index and Chao1 diversity index between severity groups (p&#x202f;=&#x202f;0.007 and 0.004). Cluster analysis revealed partial clustering by severity, with significant differences between mild and moderate groups (p&#x202f;=&#x202f;0.042) and between moderate and severe groups (p&#x202f;=&#x202f;0.036). Staphylococcus and Streptococcus dominated the abundance profile in AD samples. Functional analysis revealed alterations in epidermal microbial activity during AD onset and across different severity levels.<br><br>CONCLUSION: Pediatric AD involves site- and severity-specific microbial shifts. This functional dysregulation and enrichment of virulence factors may push barrier dysfunction and inflammation, suggesting that the microbiome is a critical target for future therapies.}, }
@article {pmid42136892, year = {2026}, author = {Hu, CY and Pai, AH and Wang, YW and Lu, PC and Wu, HM and Huang, HY}, title = {Endobiota-Estrobolome Profiles in Reproductive-Aged Women With Ovarian Endometriosis.}, journal = {Reproductive medicine and biology}, volume = {25}, number = {1}, pages = {e70061}, pmid = {42136892}, issn = {1445-5781}, abstract = {PURPOSE: This case-control study investigated whether ovarian endometriosis is associated with altered estrogen metabolism and gut or urogenital microbiota by analyzing enzyme activity, bacterial composition, and variations of estrogen metabolites in fecal, vaginal, and urinary samples.<br><br>METHODS: Thirty-eight reproductive-aged women were enrolled, including 24 with pathologically confirmed ovarian endometriosis and 14 controls. Stool, urine, and vaginal samples were collected preoperatively. Gut &#x3b2;-glucuronidase and &#x3b2;-glucosidase activities were measured, estrogen and 14 metabolites were quantified using liquid chromatography-mass spectrometry, and gut and vaginal microbiota were analyzed by 16S rRNA gene sequencing. Microbial composition, diversity, and abundance were compared between groups.<br><br>RESULTS: Gut &#x3b2;-glucuronidase activity and overall microbial diversity were comparable between groups; however, the control group showed a higher prevalence of the genus Rothia, whereas several genera, including Megamonas and [Eubacterium] coprostanoligenes_group, were enriched in the ovarian endometriosis group. In contrast, vaginal samples from patients with ovarian endometriosis demonstrated significantly reduced bacterial abundance and diversity, accompanied by lower levels of 4-methoxyestrone, 2-methoxyestrone, and 2-hydroxyestrone-3-methyl ether.<br><br>CONCLUSIONS: Although overt dysbiosis was not observed, specific microbial shifts and altered estrogen metabolites may reflect disturbances in estrogen metabolism and urogenital-gastrointestinal microbiota in ovarian endometriosis.}, }
@article {pmid42136931, year = {2026}, author = {Mweetwa, MN and Ahsan, K and Louis-Auguste, J and Besa, E and Posma, JM and McNulty, NP and Barratt, MJ and Gordon, JI and Kelly, P}, title = {Erratum: Intestinal microbiome changes in response to amino acid and micronutrient supplementation: secondary analysis of the AMAZE trial - CORRIGENDUM.}, journal = {Gut microbiome (Cambridge, England)}, volume = {7}, number = {}, pages = {e6}, doi = {10.1017/gmb.2026.10025}, pmid = {42136931}, issn = {2632-2897}, abstract = {[This corrects the article DOI: 10.1017/gmb.2025.10011.].}, }
@article {pmid42137127, year = {2025}, author = {Ahmadi, N and Hossein Tehrani, MJ and Alamdary, A and Moukhah, R and Mardani, R and Shahali, M}, title = {Gut microbiome dysbiosis and inflammatory markers in severe COVID-19: links to atherosclerosis and potential therapeutic insights.}, journal = {Gastroenterology and hepatology from bed to bench}, volume = {18}, number = {SI}, pages = {110-120}, pmid = {42137127}, issn = {2008-2258}, abstract = {BACKGROUND: COVID-19 is implicated in the exacerbation of atherosclerosis, potentially leading to its clinical manifestations. The aim of this study was to evaluate serum biomarkers, including albumin (ALB), C-reactive protein (CRP), ferritin (FERR), CD16, CD18, NLRP3, interleukin-6 (IL-6), and tumor necrosis factor-alpha (TNF-α), in patients with COVID-19. In addition, assessment of microbiome profiles may provide insights into disease severity and gastrointestinal health.<br><br>METHOD: In this case-control study, serum samples were collected from 90 individuals: 30 patients with COVID-19 admitted to the intensive care unit, 30 hospitalized patients with COVID-19, and 30 healthy individuals. Concentrations of ALB, CRP, FERR, NLRP3, CD16, CD18, IL-6, and TNF-&#x3b1; were measured. Quantitative PCR (qPCR) was used to assess microbial diversity in stool samples.<br><br>RESULT: No significant age difference was noted between the patient (55.40 &#xb1; 10.34 years) and the control groups (58.34 &#xb1; 11.71 years). Substantial increases in CRP, CD-18, CD-16, IL-6, Alb, and TNF-&#x3b1; (P < 0.001) were observed in severe cases compared to non-severe cases. Microbiome analysis indicated a 40% decrease in Roseburia and a 35% reduction in Faecalibacterium in ICU patients.<br><br>CONCLUSION: Evaluating these biomarkers provides critical insights into atherosclerosis susceptibility in COVID-19 patients and reveals meaningful relationships among COVID-19, atherosclerosis, and gastrointestinal health.}, }
@article {pmid42137129, year = {2025}, author = {Tavanaeian, S and Feizabadi, MM and Falsafi, S and Asadzadeh Aghdaei, H}, title = {Machine learning and microbiome analysis for early detection of pancreatic cancer.}, journal = {Gastroenterology and hepatology from bed to bench}, volume = {18}, number = {SI}, pages = {76-84}, pmid = {42137129}, issn = {2008-2258}, abstract = {AIM: To develop machine learning (ML) models integrating clinical and microbial predictors for early pancreatic cancer (PC) detection.<br><br>BACKGROUND: Pancreatic cancer is a leading cause of cancer-related mortality, with a 5-year survival rate of ~12%. Limited biomarkers and non-specific risk factors hinder early diagnosis. Emerging evidence links oral and gut microbiota, such as Fusobacterium nucleatum and Roseburia species, to PC risk, offering potential for non-invasive biomarkers.<br><br>METHODS: We analyzed a retrospective cohort of 40 participants (20 PC cases, 20 controls). Clinical (e.g., age, WBC) and microbial (e.g., Fusobacterium nucleatum, Roseburia-to-Fusobacterium ratio [RI/FN]) predictors were evaluated using five ML classifiers (logistic regression, SVM, random forest, na&#xef;ve Bayes, neural network) under Leave-Group-Out Cross-Validation (LGOCV; 80/20 split, 200 repetitions). Elastic-net regularization and stability selection identified key predictors. Performance metrics included AUC, sensitivity, specificity, PPV, NPV, and accuracy. Nomograms were developed for clinical utility.<br><br>RESULTS: Age (AUC 97.4%) and microbial markers (e.g., RI/FN ratio, AUC 100%) showed excellent discrimination. Multivariable models using age and RI/FN achieved excellent performance (AUC 98-100%). Nomograms provided interpretable risk estimates.<br><br>CONCLUSIONS: Integrating clinical and microbial predictors with ML offers a promising approach for non-invasive PC detection. The RI/FN ratio and age are robust biomarkers that warrant further validation in larger cohorts. However, the small sample size limits generalizability and warrants validation in larger cohorts.}, }
@article {pmid42137133, year = {2025}, author = {Kazemifard, N and Norouzi-Beirami, MH and Baradaran Ghavami, S and Ghanbari-Maman, L and Zali, MR and Shahrokh, S and Kavousi, K}, title = {Microbiome-microRNA interactions in inflammatory bowel disease: insights from metagenomic and transcriptomic data analysis.}, journal = {Gastroenterology and hepatology from bed to bench}, volume = {18}, number = {SI}, pages = {85-96}, pmid = {42137133}, issn = {2008-2258}, abstract = {BACKGROUND: Inflammatory Bowel Disease (IBD) is a chronic inflammation of the gastrointestinal tract, the precise origins of which remain not fully elucidated. This study investigates the complex relationship between gut metagenomics and host transcriptomics in IBD patients, focusing on Ulcerative Colitis (UC) and Crohn's Disease (CD).<br><br>METHOD: One proposed theory suggests that microRNAs produced by the host may significantly influence IBD development by impacting the gut microbiota. Conversely, the gut microbiome may regulate the expression of host microRNAs, leading to dysfunction in the intestinal epithelium. An enrichment analysis was conducted to pinpoint associated pathways. To unravel this intricate interplay, the study utilized data from the IBDMDB database, selecting samples from adult individuals.<br><br>RESULT: The dataset comprised 50 paired metagenomic and host transcriptomic samples, including 8 controls, 18 UCs, and 24 CDs. Computational analyses and network constructions were applied to identify relationships between bacterial species, microRNAs, and other transcripts.<br><br>CONCLUSION: This research offers valuable insights into the dynamic relationship between the gut microbiome and human transcriptomics in IBD, providing a deeper understanding of potential disease mechanisms. Furthermore, it sheds light on the complex tripartite network connecting bacterial species, microRNAs, and transcripts, contributing to a comprehension of IBD pathogenesis and the identification of novel therapeutic targets.}, }
@article {pmid42137389, year = {2026}, author = {El Halabi, L and AlBayeh, A and Khoury, A and Katrib, M and Nasr, J and Al-Obaidi, A}, title = {Vitamins and Cancer Risk: A Comprehensive Review of Epidemiologic and Clinical Evidence.}, journal = {Kansas journal of medicine}, volume = {19}, number = {Suppl 1}, pages = {12}, doi = {10.17161/kjm.vol19.25377}, pmid = {42137389}, issn = {1948-2035}, abstract = {INTRODUCTION: Vitamin supplementation nearly is universal among patients with cancer, yet the scientific landscape is far more complex. Across decades of research, vitamins have demonstrated profound biological effects ranging from immune activation and ferroptosis modulation to paradoxical tumor promotion.<br><br>OBJECTIVE: This scoping review maps the breadth of compelling and controversial evidence surrounding vitamins A, D, E, K, C, and the B-complex in cancer prevention, treatment response, and toxicity.<br><br>METHODS: Guided by PRISMA-ScR domains, we synthesized mechanistic studies, epidemiologic cohorts, randomized trials, and therapeutic investigations addressing vitamins in the oncology context. Eligibility focused on sources examining cancer risk, progression, treatment interactions, or toxicity.<br><br>RESULTS: Several vitamins exhibit striking anticancer mechanisms: vitamin K2 triggers autophagy-driven leukemia cell death; pharmacologic vitamin C selectively kills KRAS- and BRAF-mutated colorectal cancer cells; niacin reshapes the tumor immune microenvironment; and vitamin D enhances microbiome-dependent antitumor immunity. Yet the review also identifies potential harms, including beta-carotene increasing lung cancer risk in smokers, vitamin E raising prostate cancer risk, and antioxidant supplementation potentially weakening the oxidative mechanisms essential for chemotherapy and radiotherapy efficacy. Dose-response patterns frequently are U-shaped, with both deficiency and excess linked to greater risk. High-dose intravenous vitamin C, vitamin D repletion during immunotherapy, and vitamin-targeted nanoparticles emerge as promising but unproven therapeutic strategies.<br><br>CONCLUSIONS: Across vitamins, benefits appear highly context-dependent. Routine supplementation is unsupported, while targeted correction of true deficiencies remains essential. This rapidly evolving field demands individualized decision-making and rigorously designed trials to define when vitamins act as allies, and when they become adversaries, in cancer care.}, }
@article {pmid42137425, year = {2026}, author = {Miki, T and Ito, M and Haneda, T and Okada, N and Kim, YG}, title = {Infection strategies of SalmonellaTyphimurium for gut-lumen colonization: Overcoming host defenses, exploiting host responses, and adapting to the enteric niche.}, journal = {Gut microbes reports}, volume = {3}, number = {1}, pages = {2671472}, pmid = {42137425}, issn = {2993-3935}, abstract = {Diarrheal disease is a leading cause of child morbidity and mortality globally, largely resulting from contaminated food and water and exposure to enteric pathogens. Salmonella enterica serovar Typhimurium (STm) is an enteropathogenic bacterium that infects the gastrointestinal tract using diverse strategies that are still being elucidated. Meanwhile, the gut comprises a complex ecosystem known as the microbiome, which is densely inhabited by microbial communities. The microbiome confers colonization resistance against enteropathogenic bacteria, whereas STm can overcome these defenses to establish infection. Here, we review STm infection strategies in the gut, with a particular focus on evidence from mouse models. Understanding STm virulence mechanism and adaptation strategies may inform the development of targeted interventions to prevent and treat gastrointestinal infection.}, }
@article {pmid42137495, year = {2026}, author = {Sekito, T and Hirakawa, H and Sadahira, T}, title = {Unraveling the vaginal microbiota-based etiology of recurrent cystitis: the potential role of Lactobacillus vaginal suppositories.}, journal = {Therapeutic advances in urology}, volume = {18}, number = {}, pages = {17562872261448600}, pmid = {42137495}, issn = {1756-2872}, abstract = {Recurrent cystitis is a common problem in women that substantially impairs quality of life and contributes to increasing healthcare costs. Traditionally regarded as an ascending infection originating from the gut, recurrent cystitis is now increasingly understood as a disorder rooted in vaginal dysbiosis, with the vagina acting as a key reservoir for uropathogenic Escherichia coli. Loss of a Lactobacillus-dominant vaginal microbiota and overgrowth of enteric and anaerobic bacteria are strongly associated with recurrent cystitis, particularly in postmenopausal women. Lactobacillus species promote vaginal health by producing lactic acid, maintaining a low pH, generating antimicrobial compounds, inhibiting pathogen adhesion, and modulating mucosal immune responses. At the same time, long-term antimicrobial prophylaxis, although effective in reducing recurrences, is limited by adverse effects and the promotion of antimicrobial resistance. These concerns have driven interest in strategies that restore the protective vaginal ecosystem rather than relying on repeated antimicrobial exposure. This narrative review summarizes current concepts linking vaginal dysbiosis to recurrent cystitis, highlights the protective role of Lactobacillus, and synthesizes clinical data on Lactobacillus vaginal suppositories, particularly Lactobacillus crispatus (L. crispatus)-based preparations, as a targeted, non-antimicrobial prophylactic option. Across pilot, phase II, and randomized trials, Lactobacillus vaginal therapy has demonstrated a generally favorable safety and tolerability profile, with preliminary evidence suggesting a potential to reduce recurrent cystitis episodes while restoring a Lactobacillus-dominant vaginal microbiota. However, larger, standardized studies are still needed. Collectively, these findings provide a rationale for investigating Lactobacillus vaginal suppositories as a microbiome-informed, non-antimicrobial strategy for the long-term prevention of recurrent cystitis, particularly in postmenopausal and other high-risk women, and highlight the importance of further research to define the role of vaginal microbiota-directed therapies in future recurrent cystitis management.}, }
@article {pmid42137543, year = {2026}, author = {Zhang, K and Zomer, H and Potkamp, G and Salles, JF and Tieleman, BI and Dietz, MW}, title = {Seasonal Dynamics of the Gut Microbiome in Urban Feral Pigeons Are Associated With Environmental Conditions, Not With Diet Shifts.}, journal = {Ecology and evolution}, volume = {16}, number = {}, pages = {e73682}, pmid = {42137543}, issn = {2045-7758}, abstract = {Gut microbiomes play a crucial role in host physiology and seasonal adaptation. While seasonal shifts in avian gut microbiota are often attributed to seasonal diet variation, environmental factors may be equally or more important, particularly in urban ecosystems. This study aimed to determine whether seasonal variation in the gut microbiome of free-living feral pigeons (Columba livia f. domestica) inhabiting urban environments is associated with seasonal changes in diet and environmental conditions. We captured feral pigeons at three locations in Groningen, the Netherlands, during winter (January-February 2019) and summer (July-August 2019). Cloacal swabs and fecal samples were collected to assess gut microbiota via 16S rRNA sequencing and diet via DNA metabarcoding, respectively. Microbial diversity and composition showed significant seasonal variation and location effects. At Vismarkt, one of the three urban sampling sites within the city of Groningen, Firmicutes were more abundant in summer than in winter, while Actinobacteria were more abundant in winter. Dominant genera also varied seasonally, with Lactobacillus more abundant in summer. In contrast, the diet composition was dominated by Poaceae (grasses), Fabaceae (legumes), and Asteraceae (daisies) across all seasons and locations, with no detectable differences between locations or seasons. Distance-based redundancy analysis indicated that temperature was significantly associated with microbiome composition, whereas diet as measured here showed no detectable association. This suggests that seasonal microbiome variation in urban feral pigeons may be related to seasonal environmental conditions even without detectable dietary shifts, consistent with the idea that seasonal environmental conditions can contribute to microbiome seasonality in birds.}, }
@article {pmid42137790, year = {2026}, author = {Qi, J and Zhang, K and Zhan, C and Lu, X and Chen, X and Li, X and Zhang, C and Wang, H and Tu, C and Tong, W and Dai, L and Zeng, D}, title = {Microbial and metabolic crosstalk in the rhizosphere shapes the divergent drought resilience of contrasting rice genotypes.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1788826}, pmid = {42137790}, issn = {1664-302X}, abstract = {Drought is a major constraint on rice production, yet the coordinated responses of rhizosphere microbial communities and metabolites across rice genotypes with contrasting drought tolerance remain insufficiently understood. In this study, we combined metagenomic and metabolomic analyses to investigate drought-induced changes in the rhizosphere of three rice genotypes with distinct ecological backgrounds: the drought-sensitive cultivar Bhutan, the upland rice genotype TGR78, and Oryza rufipogon K111. Field experiments were conducted under well-watered and drought conditions, and rhizosphere soil samples were collected for multi-omics profiling. Drought stress reduced plant height and panicle number in all three genotypes, but the magnitude of these effects differed among genotypes. Bhutan showed the greatest reduction in plant height (42.1%) and the largest number of differential metabolites (146), indicating a stronger drought response at both phenotypic and metabolic levels. In contrast, TGR78 and K111 displayed relatively greater phenotypic stability under drought stress. Metagenomic analysis revealed pronounced genotype-dependent shifts in rhizosphere bacterial community composition, whereas metabolomic profiling showed distinct changes in metabolite accumulation patterns among genotypes. Correlation analysis further demonstrated that drought substantially reshaped rhizosphere microbe-metabolite associations, shifting the interaction network from broadly positive and highly connected under well-watered conditions to more selective associations under drought stress. Collectively, these results indicate that rice drought adaptation is associated with genotype-dependent reorganization of the rhizosphere microbiome and metabolic profile. This study provides new insight into rhizosphere-mediated drought responses in rice and offers a basis for developing microbiome-informed strategies for drought-resilient crop improvement.}, }
@article {pmid42137793, year = {2026}, author = {Adeleke, RA and Machailoe, TME and Malemagovha, M and Olanrewaju, OS and Alayande, KA and Obi, LU and Makinde, OM}, title = {Diversity and functional potential of bacterial and fungal endophytes in traditional food wrapping leaves reveal implications for artisanal food safety and quality.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1641069}, pmid = {42137793}, issn = {1664-302X}, abstract = {Plant leaves are widely utilised globally for the packaging and serving of traditionally prepared foods. The microbial communities associated with these wrapping leaves, particularly endophytes, are recognised to potentially influence food quality, safety, and preservation. Specifically, certain endophytes can enhance sensory attributes and nutritional value through fermentative processes, while the presence of harmful microorganisms may lead to spoilage and pose a risk of foodborne illness. This study utilised 16S rRNA, ITS metabarcoding and metagenomic functional analysis (PICRUSt2) to comprehensively investigate the composition and infer the putative functional potential of putative endophytic bacterial and fungal communities present in 53 samples of four different food wrapping leaves. The leaves examined included Thaumatococcus daniellii (n = 10), Alstonia macrophylla (n = 18), Theobroma species (n = 14), and Megaphrynium macrostachyum (n = 11). Distinct microbial community profiles were observed across the different leaf types. Highest bacterial species richness and community variability were detected in A. macrophylla samples, reflected by Principal Coordinates Analysis (PCoA) values (PCoA1 = 43.97%; PCoA2 = 10.68%). Conversely, M. macrostachyum exhibited the greatest fungal species richness and variability (PCoA1 = 20.08%; PCoA2 = 8.72%). Taxonomic analysis identified Proteobacteria as the dominant bacterial phylum and Stenotrophomonas as the dominant bacterial genus. Other notable bacterial taxa included the phyla Bacteroidota and Firmicutes, and genera such as Pseudomonas, Faecalibacterium, and Bacteroides. For fungal communities, Ascomycota was the dominant phylum. Additional fungal taxa included the phylum Basidiomycota and genera Cryptococcus, Candida, and Meyerozyma. A core microbiome analysis revealed that 42 bacterial (notably Stenotrophomonas and Chryseobacterium) and 7 fungal taxa (notably Pleosporaceae and Ascomycota) were shared across all examined wrapping leaves. The identified microbial communities (e.g., Lactobacillus and Geotrichum) encompass taxa with potential beneficial roles, such as enhancing food fermentation and potentially contributing to human gut health upon consumption of the packaged food. However, the detection of potentially pathogenic and toxigenic bacterial taxa highlights a possible public health risk associated with the use of these leaves. Further investigation into the specific functionalities of these associated bacteria and fungi is essential to maximise their beneficial applications while simultaneously mitigating potential health risks posed by harmful strains.}, }
@article {pmid42137801, year = {2026}, author = {D'Amico-Willman, KM and Joglekar, P and Turner, D and Flaherty, M and Ritchie, DF and Huerta, AI}, title = {Four decades of genomic stability and adaptive divergence in Xanthomonas phages: defining Duraznoxanthovirus arenicola and its evolutionary framework.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1779411}, pmid = {42137801}, issn = {1664-302X}, abstract = {Bacteriophages (phages) are abundant and ecologically significant, yet their diversity and roles in plant-associated ecosystems remain poorly understood, limiting their application in sustainable disease management. To address this gap, we characterized 15 phages infecting Xanthomonas arboricola pv. pruni, the causal agent of bacterial spot on peach, has been isolated for over four decades from North Carolina orchards. Comparative genomic and phylogenetic analyses revealed two temporally distinct clades with >95% nucleotide identity and 63 conserved core genes, forming a new genus and species, Duraznoxanthovirus arenicola. These findings challenge assumptions of pervasive genomic mosaicism, highlighting remarkable genomic stability alongside localized variability in accessory loci. Beyond genus-level characterization, our analyses support a broader taxonomic restructuring within the family Anamaviridae, introducing a new subfamily (Terravirinae) and two new genera (Duraznoxanthovirus and Ralstopathovirus). This work provides the a family-level framework for phages exclusively infecting plant-associated bacteria, offering evolutionary insights and a foundation for ecological studies and management strategies.}, }
@article {pmid42137803, year = {2026}, author = {Liu, Y and Chen, C and Gao, J}, title = {Topological characteristics and longitudinal dynamics of co-abundance networks involving beneficial commensal bacteria in the pig gut microbiome and its association with average daily gain.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1818141}, pmid = {42137803}, issn = {1664-302X}, abstract = {Microorganisms are intricately interrelated with each other in the gut microecosystem, which influences the colonization and functional roles of probiotics. However, how these interactions dynamically change during host development and whether their topological features influence host phenotypes, such as average daily gain (ADG), remain poorly understood. In this study, we performed metagenome analysis for 2,311 fecal samples collected from a specifically designed eight genetically divergent breed intercrossed mosaic F6 and F7 population, at three developmental ages of 25 days (D25), 120 days (D120), and 240 days (D240) of each individual, covering pre-weaning to market. By constructing their microbiota co-abundance networks, we systematically characterized dynamic changes in beneficial commensal bacteria involved co-abundance networks in the pig gut microbiome across three ages. We elucidated conserved and variable co-abundance features involving these bacteria across developmental stages. We observed that the cross-age stable co-abundance correlations of beneficial commensal bacteria were maintained by a large set of weak correlations. A subset of age-shared co-abundance correlations remained variable across different ages in correlation strength and direction. Topological analysis revealed that beneficial commensal bacteria involved co-abundance networks were highly age-specific. Among the three age stages sampled in this study, the D120 stage represented a critical window for the structural and functional reorganization of gut microbiota. Using metagenomic sequencing data at the D120, we identified two guilds that were significantly associated with ADG from D120 to D240. Guild 1 included short chain fatty acid-producing taxa and was positively associated with ADG, whereas Guild 2 tended to self-utilization of energy and was negatively associated with ADG. We also inferred the ecological interaction mechanisms of ADG-associated microbial communities using genome-scale metabolic models. These findings provided a theoretical basis for stage-specific intervention in the pig gut microbiome using probiotics to improve production traits.}, }
@article {pmid42137813, year = {2026}, author = {Chiuta, NE and Pofu, KM and Mashela, PW}, title = {Short-term crop rotation interactive effects on soil microbial communities and potato yield under field conditions.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1807765}, pmid = {42137813}, issn = {1664-302X}, abstract = {INTRODUCTION: The inclusion of plant-parasitic nematode (Meloidogyne species) non-host crops in potato (Solanum tuberosum L.) -based cropping systems can sustainably manage the pest and reduce the application of greenhouse gas-emitting agro-chemicals. Nevertheless, there exists a research gap on how these cropping systems interact with soil microbiome.<br><br>METHODS: A 2-year field study was conducted at the University of Limpopo and the Agricultural Research Council to investigate the effects of potato monoculture, Cucumis africanus-potato, sorghum-potato and potato (Velum)-potato cropping sequences on soil health and tuber yield. The treatment crops, namely, sweet stem sorghum (Sorghum bicolor) cv. 'Ndendane-X1', C. africanus, potato cv. 'Mondial G3' and potato cv. 'Mondial G3'-velum (control), were assigned to 4 m[2] subplots in Sequence 1, in a randomized complete block design, with six replicates. The successor potato crop was planted in Sequence 2. Crop arrangement in Sequences 3 and 4 was as in Sequences 1 and 2, respectively. Soil organic carbon content, enzyme activity, nematode and bacterial functional diversity data were collected from Sequences 1 to 4. Final potato tuber yield was recorded in Sequence 4.<br><br>RESULTS: Based on the results, nematode indices revealed disturbed agroecosystems dominated with bacterial decomposition pathways, which is a common occurrence in intensively managed soils. High soil organic carbon content, microbial diversity and enzyme activity were observed in sorghum-potato and C. africanus-potato compared to potato monoculture (with or without velum), at both locations. In addition, sorghum-potato improved soil structure over time based on the nematode faunal results, thereby depicting its ability to promote soil health compared to other cropping systems. Tuber yield mass significantly varied (p&#x202f;&#x2264;&#x202f;0.05) among cropping sequences at both locations with potato (Velum)-potato and C. africanus-potato sequences recording higher yields than potato monoculture or sorghum-potato.<br><br>DISCUSSION: Crop diversification increased soil organic carbon content, microbial diversity and enzyme activity. Overall, sorghum-potato effectively improved soil health and soil structure over time, better than the other cropping systems.}, }
@article {pmid42137817, year = {2026}, author = {Farmakioti, I and Tegopoulos, K and Stylianopoulou, E and Siskos, N and Angelopoulou, L and Vasileiou, AR and Karagianni, E and Kandylas, D and Fragkiskatou, F and Pavlatou, C and Tsaroucha, A and Ypsilantis, P and Kourkoutas, Y and Kolovos, P and Skavdis, G and Grigoriou, ME}, title = {Genomic characterization and preclinical evaluation of the candidate probiotic strain Lactococcus cremoris FBMS_5810.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1812433}, pmid = {42137817}, issn = {1664-302X}, abstract = {This study presents a comprehensive genomic and preclinical evaluation of Lactococcus cremoris FBMS_5810, establishing its taxonomic identity, genomic uniqueness, and safety profile. Genomic analyses identified strain-specific genes linked to adhesion, colonization, and pathogen exclusion, aligning with previously observed in vitro probiotic properties. In vivo studies in healthy mice demonstrated that Lactococcus cremoris FBMS_5810 modulates gut microbiota composition. Specifically, the relative abundance of Muribaculaceae, Erysipelotrichaceae, and Streptococcaceae was significantly increased in the probiotic-treated group, whereas the relative abundance of Ruminococcaceae, Bacteroidaceae, Porphyromonadaceae, and Dehalobacteriaceae was decreased. Administration of Lactococcus cremoris FBMS_5810 was also associated with changes in intestinal gene expression: in the ileum, Tnf and Il1b expression increased, while in the cecum, Zo1 expression was elevated. These findings may indicate a role in supporting intestinal homeostasis and could be linked to reduced susceptibility to diet- and inflammation-related disorders. Overall, these results suggest that Lactococcus cremoris FBMS_5810 may be a useful candidate for further investigation in the development of health-oriented microbial products. By integrating genomic characterization with preclinical evaluation, this study not only highlights Lactococcus cremoris FBMS_5810 as a promising candidate but also provides a systematic approach for the identification and validation of probiotics, advancing both fundamental understanding and translational applications in molecular microbiology.}, }
@article {pmid42137872, year = {2026}, author = {Parrino, J and Sunshine, J and Tripp, K and Shaffer, M and Sughra, U and Procházková, N and Jara, M and Moll, JM and Noble, R and Muir, L and McIntyre, E and Guduk, E and Zachariah, D and Vernochet, C and Frahm, N and Schmidt, AC}, title = {Impact of Bifidobacterium infantis supplementation on growth, health outcomes, and gut microbiome features in underweight infants from Pakistan.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1783141}, pmid = {42137872}, issn = {2296-861X}, abstract = {BACKGROUND: Alterations in the gut microbiome are implicated in infant malnutrition. Bifidobacterium longum subspecies infantis (B. infantis), a commensal common in breastfed infants, has been shown to have reduced abundance in malnourished infants. This trial (NCT05952076) evaluated if B. infantis strain Bi-26 supplementation could improve growth and health outcomes in underweight infants in Pakistan.<br><br>METHODS: In this double-blind, randomized, placebo-controlled trial, 40 infants aged 30-120&#x202f;days (d) with a weight-for-age Z score (WAZ) below -2 received daily oral Bi-26 or placebo for 28d, with follow-up to d90 for safety. The primary endpoint was change in WAZ from baseline to d56. The intended sample size was 396 infants but study was terminated early due to operational delays. Total B. infantis levels microbiome, metabolome, and cytokine profiles were assessed.<br><br>RESULTS: Bi-26 supplementation increased fecal B. infantis levels at d28 (p&#x202f;=&#x202f;0.001) and d56 (p&#x202f;=&#x202f;0.03) but did not result in significant change in WAZ (p&#x202f;=&#x202f;0.69) or weight gain (p&#x202f;=&#x202f;0.56) compared to placebo. Fewer adverse events (AEs) occurred in the Bi-26 group compared to placebo (40% vs. 80% of infants; 17 vs. 49 events). Probiotic engraftment was impacted by presence of baseline endogenous B. infantis, suggesting that Bi-26 complemented rather than outcompeted endogenous strains. Bi-26 altered microbiome composition with transient alterations in function and metabolite abundance that reverted to baseline by d56, without cytokine differences between groups. B. infantis levels and Bifidobacterium-community types were associated with fewer AEs but not changes in WAZ or weight.<br><br>DISCUSSION: Bi-26 supplementation had an acceptable safety profile but did not improve growth. The findings of this trial support further evaluation of B. infantis strains in larger studies of underweight infants across diverse LMIC settings. Future trials should determine whether sustained metabolic and functional remodeling can translate into measurable improvements in growth and health outcomes.<br><br>CLINICAL TRIAL REGISTRATION: https://www.clinicaltrials.gov/study/NCT05952076, NCT05952076.}, }
@article {pmid42138066, year = {2026}, author = {Allwang, M and Wipplinger, M and Akbarimoghaddam, P and Alonso-Roman, R and Cseresnyes, Z and Dietschmann, A and Wegner, V and Feile, A and Bachelot, Y and Warschinke, M and Hassan, MIA and Mittag, S and Huber, O and Hube, B and Gresnigt, MS and Figge, MT and Mosig, AS}, title = {Human Colitis-on-Chip Model Reveals Dual Roles of Butyrate in Epithelial and Macrophage Defense Against Candida albicans Tissue Invasion.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {}, number = {}, pages = {e00074}, doi = {10.1002/smll.202600074}, pmid = {42138066}, issn = {1613-6829}, support = {434385622/GR 5617/1-1//German Research Foundation/ ; //Exploration Grant of the Boehringer Ingelheim Foundation (BIS)/ ; //Free State of Thuringia and co-funded by the European Union/ ; 390713860//DFG Cluster of Excellence "Balance of the Microverse"/ ; FKZ: 13N15713 13N15716//DFG Cluster of Excellence "Balance of the Microverse"/ ; //Collaborative Research Center "PolyTarget"/ ; //Scholarship from the Interdisciplinary Center of Clinical Research of the Jena University Hospital/ ; }, abstract = {Microbial dysbiosis in inflammatory bowel disease (IBD) reduces intestinal butyrate levels, compromising epithelial barrier integrity and enabling overgrowth of opportunistic pathogens such as Candida albicans. Here, we present a human immunocompetent colitis-on-chip model (CooC) that mimics key features of inflamed gut mucosa, including DSS-induced epithelial damage and C. albicans tissue invasion. Using this model, we uncover dual protective roles of microbiota-derived butyrate: (i) stabilization of epithelial adherens junctions and promotion of epithelial renewal, thereby restricting fungal invasion; and (ii) modulation of macrophage function to enhance antifungal activity while attenuating inflammasome-mediated inflammation. Butyrate pretreatment preserves barrier function, limits fungal translocation, and promotes macrophage viability through the inhibition of histone deacetylase (HDAC) and the suppression of NLRP3 inflammasome activation. These findings position butyrate as a key metabolite in orchestrating epithelial-immune defense against fungal exacerbation in colitis, supporting its therapeutic and preventive potential in restoring mucosal resilience in IBD.}, }
@article {pmid42138097, year = {2026}, author = {Kozajda, A and Miśkiewicz, E and Gawor, J and Gromadka, R}, title = {Bacteria and associated antibiotic resistance in air filter-derived biological material from utility vehicles at mechanical-biological treatment plants.}, journal = {International journal of occupational medicine and environmental health}, volume = {}, number = {}, pages = {}, doi = {10.13075/ijomeh.1896.02785}, pmid = {42138097}, issn = {1896-494X}, abstract = {OBJECTIVES: The study objective was to assess occupational exposure to bacteria and antimicrobial resistance genes (ARGs) present on air filters of utility vehicles used in the working environment of mechanical-biological treatment (MBT) facilities, in the context of workers health risks.<br><br>MATERIAL AND METHODS: The study was conducted in summer 2024 in 9 air filters from utility vehicles used in MBT plants in Poland. External filters were removed from the vehicle's ventilation system, packed and shipped according to instructions. From the duplicate filters samples DNA was isolated and high-throughput next-generation sequencing (NGS) was carried out. Bioinformatic data analysis was conducted to detect bacteria and ARGs in air filters' surfaces.<br><br>RESULTS: Totally, 34 bacterial taxa were detected in relative abundance &#x2265;0.5%. The genera most frequently present at the highest relative abundances: Saccharomonospora, Thermobifida, Nocardiopsis, Pectobacterium, Aerococcus, Thermoactinomyces, Novibacillus and Streptomyces. Across all bacteria isolated from the analyzed filters, regardless of their relative abundance, a total of 91 taxa were classified into risk groups 2 or 3 (86 and 5 taxa, respectively). The most frequently detected ARGs were those encoding resistance to a single class of antibiotics (AAC(3)-VIIa, aadA2, ANT(6)-Ia, APH(3'')-Ia, APH(3'')-Ib, APH(6)-Id, cml, cmx, lnuA, lnuD, novA, parY, sul2, vanHF, vanJ, vanRA, vanRI, vanRO - each at least on 4 air filters). Antimicrobial resistance genes encoding multi antibiotic resistance were also detected: CRP, emtA, erm(34), erm(36), ermA, ermC, ermF, ermG, ermT, ermX, ernB, H-NS, mel, msrA, msrE, mtrA, optrA, ramA, ykkD - each at least on 1 air filter.<br><br>CONCLUSIONS: Despite the limited number of analyzed filters, the study demonstrated a high bacterial species diversity in the MBT plant environment. The MBT workers are exposed to bacteria with high pathogenic potential and to ARGs encoding resistance to antibiotics used exclusively in human medicine, used in human and veterinary medicine, and not intended for human use. Int J Occup Med Environ Health. 2026;39(2).}, }
@article {pmid42138193, year = {2026}, author = {Ma, X and Zhao, Y}, title = {Gut‑brain axis in anesthesia and critical illness: Molecular crosstalk and its impact on delirium and outcome (Review).}, journal = {International journal of molecular medicine}, volume = {58}, number = {1}, pages = {}, doi = {10.3892/ijmm.2026.5859}, pmid = {42138193}, issn = {1791-244X}, mesh = {Humans ; Critical Illness ; *Delirium/etiology/metabolism ; *Gastrointestinal Microbiome ; *Brain/metabolism ; *Anesthesia/adverse effects ; Animals ; }, abstract = {The gut‑brain axis (GBA) has emerged as a critical mediator of acute brain dysfunction, particularly postoperative delirium and sepsis‑associated encephalopathy, in surgical and critically ill patients. Anesthesia, surgical stress, and critical illness collectively disrupt gut microbiota composition and intestinal barrier integrity, leading to increased systemic translocation of microbial products. This process triggers neuroinflammation and compromises blood‑brain barrier function through defined molecular pathways, including alterations in microbe‑derived short‑chain fatty acids, tryptophan metabolites, and potent neuroimmune signaling via the LPS‑TLR4‑NF‑κB axis. The present review synthesizes current evidence on the molecular crosstalk within the GBA, highlighting how perioperative and intensive care interventions drive dysbiosis and subsequent neurological sequelae. Furthermore, it evaluates promising GBA‑targeted therapeutic strategies, including dietary modulation, biotherapeutics and pharmacological interventions, are evaluated for their potential to mitigate delirium and improve long‑term cognitive outcomes. A deeper understanding of these mechanisms is essential for developing novel preventive and therapeutic approaches in vulnerable patient populations.}, }
@article {pmid42138225, year = {2026}, author = {Jamieson, PE and Gu, I and Reichart, NJ and Maier, CS and Ho, E and Sharpton, TJ and Metz, TO and Bradley, R and Stevens, JF}, title = {Modulation of Microbiota-Derived Bile Acids Linked to Symptom Amelioration in Crohn's Disease: Insights From a Randomized Clinical Trial With Xanthohumol Supplementation.}, journal = {Molecular nutrition &amp; food research}, volume = {70}, number = {10}, pages = {e70501}, doi = {10.1002/mnfr.70501}, pmid = {42138225}, issn = {1613-4133}, support = {R01 AT010271/NH/NIH HHS/United States ; R01 AT010271-02S1/NH/NIH HHS/United States ; S10OD026922/NH/NIH HHS/United States ; }, mesh = {Humans ; *Flavonoids/pharmacology/therapeutic use ; *Crohn Disease/drug therapy/microbiology ; *Bile Acids and Salts/metabolism ; *Propiophenones/pharmacology/therapeutic use ; Male ; Female ; *Gastrointestinal Microbiome/drug effects ; Adult ; Dietary Supplements ; Middle Aged ; Feces/microbiology/chemistry ; Interleukin-10/blood ; Young Adult ; Humulus/chemistry ; }, abstract = {Xanthohumol (XN), a dietary flavonoid from hops (Humulus lupulus), possesses anti-inflammatory and microbiome-modulatory properties with potential therapeutic benefits for Crohn's disease (CD). To investigate the effects of XN on the gut environment in CD, we conducted a randomized, placebo-controlled clinical trial-the XN Microbiome and Signature (XMaS) trial (NCT4590508). 19 participants with clinically active CD completed the study. They were randomized to receive 24 mg/day of XN or placebo for 8 weeks, with clinical assessments at baseline and every 2 weeks. We assessed changes to Crohn's disease activity index (CDAI) scores, systemic inflammation, gut barrier function, profiling of microbial metabolism of XN, and gut microbiota composition and metabolism. Integration analysis of gut microbiota abundance, fecal metabolites, and inflammatory markers with CDAI scores revealed a pattern in which reductions in secondary bile acids and increases in IL-10 were associated with improved CDAI score in XN-treated individuals. These findings suggest that XN beneficially modulates the gut environment in CD by influencing microbial bile acid metabolism and host inflammatory response, thereby improving symptoms in individuals with severe innate immune activation.}, }
@article {pmid42138268, year = {2026}, author = {Camps-Massa, P and Pérez-Mormeneu, J and Guevara-Nuñez, D and Saiz-Escobedo, L and Calatayud, L and González-Díaz, A and Sanllorente, A and Vicens-Zygmunt, V and Santos, S and Morros, R and Salvador-González, B and Domínguez, M&#xc1; and Martí, S and , }, title = {Gut microbiome shift in long COVID: impact of disease and montelukast treatment.}, journal = {Journal of global health}, volume = {16}, number = {}, pages = {04164}, pmid = {42138268}, issn = {2047-2986}, mesh = {Humans ; *Cyclopropanes/therapeutic use ; *Sulfides/therapeutic use ; *Quinolines/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; *Acetates/therapeutic use ; *COVID-19/microbiology/complications ; Male ; Female ; Cross-Sectional Studies ; Middle Aged ; SARS-CoV-2 ; Feces/microbiology ; Adult ; Aged ; Longitudinal Studies ; *COVID-19 Drug Treatment ; }, abstract = {BACKGROUND: Long COVID-19 is a post-infectious syndrome with persistent symptoms that can involve multiple organ systems. Evidence suggests that SARS-CoV-2 infection may disrupt gut microbiome composition, potentially contributing to long-term effects. As treatment remains symptom-based, interest has grown in repurposing drugs like montelukast. However, non-antibiotic medications may also alter gut microbial communities, raising questions about their impact. Here, we compare gut microbiota between long COVID patients and healthy controls and examine how montelukast treatment affects microbial composition.<br><br>METHODS: We analysed stool samples from long COVID patients and healthy controls using 16S rRNA gene sequencing (Illumina MiSeq). We evaluate alpha (Shannon) and beta (Bray-Curtis) diversity, followed by relative abundance and linear discriminant effect size analysis, to identify differentially abundant taxa. This proof-of-concept study included a cross-sectional comparison and a longitudinal analysis of montelukast-treated patients vs. placebo.<br><br>RESULTS: Cross-sectional analysis revealed a significant structural reorganisation of the gut microbial community in long COVID patients, although overall species richness was largely maintained. Linear discriminant effect size analysis revealed that this architectural shift was driven by an enrichment of Firmicutes (Agathobacter and Faecalibacterium genera) in the long COVID group, while healthy controls were characterised by higher abundances of the phyla Verrucomicrobiota and Actinobacteriota, as well as genera Alistipes and Akkermansia. Longitudinal analysis demonstrated that the broader community structure remained stable in both groups; however, montelukast treatment led to a specific enrichment of the genus Dialister, suggesting targeted and potentially transient effects without disrupting the overall microbial landscape.<br><br>CONCLUSIONS: Long COVID is characterised by a significant restructure of the gut ecosystem. This qualitative dysbiosis reflects a shift in homeostatic balance, where the core microbial community remains present, but its proportions are altered. Short-term montelukast treatment shows a minimal impact on the microbial landscape, suggesting treatment does not further destabilise the gut environment. These findings highlight the specific and targeted nature of gastrointestinal involvement in long COVID.}, }
@article {pmid42138670, year = {2026}, author = {Khanna, S and Allegretti, JR and Hashash, JG and Feuerstadt, P}, title = {AGA Clinical Practice Update on Management of Clostridioides difficile Infection in Inflammatory Bowel Disease: Expert Review.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2026.03.008}, pmid = {42138670}, issn = {1528-0012}, abstract = {DESCRIPTION: Clostridioides difficile infection (CDI) remains a significant driver of disease flares and poor outcomes in patients with inflammatory bowel disease (IBD), leading to increased hospitalization, intensified or failed therapy, and higher surgical rates. Compared with the non-IBD population, patients with IBD face greater CDI risk and severity and higher recurrence risk, creating clinical dilemmas when considering antibiotic selection and the timing or necessity of IBD-related therapy adjustments. Emerging evidence highlights microbiota-based therapies such as unapproved fecal microbiota transplantation or US Food and Drug Administration-approved donor-derived therapies as a promising therapeutic avenue for recurrent CDI in patients with IBD, reflecting a growing emphasis on microbiome-directed interventions. This review examines the evolving literature, considering the diagnosis and management strategies and offering pragmatic guidance to optimize outcomes for patients with IBD challenged by concomitant CDI and recurrent CDI.<br><br>METHODS: This Expert Review was commissioned and approved by the American Gastroenterological Association (AGA) Institute Clinical Practice Updates Committee and the AGA Governing Board to provide timely guidance on a topic of high clinical importance to the AGA membership and underwent internal peer review by the Clinical Practice Updates Committee and external peer review through standard procedures of Gastroenterology. These practical Best Practice Advice statements were drawn from a review of the best available published evidence, including existing clinical studies, systematic reviews and practice guidelines, and expert opinion. Because a formal systematic review was not performed, these Best Practice Advice statements do not carry formal ratings of the quality of evidence or strength of the presented considerations. The focus is on the management of both CDI and IBD in patients with underlying IBD who develop CDI. Best Practice Advice Statements BEST PRACTICE ADVICE 1: In patients with IBD who have new or worsening diarrhea, CDI should be excluded, especially among those with colonic involvement, as they are at increased risk of CDI. Clinicians should consider and treat CDI in patients with end ileostomy or ileo-anal pouch anastomosis with worsening diarrhea. BEST PRACTICE ADVICE 2: In patients with IBD and suspected CDI, a multistep toxin-based assay should be used for diagnostic evaluation. BEST PRACTICE ADVICE 3: In patients with IBD and recent CDI who have been treated successfully with antibiotics, recurrent diarrhea should prompt retesting for CDI. BEST PRACTICE ADVICE 4: In patients with IBD who develop an initial episode of CDI, clinicians should preferentially use fidaxomicin or use vancomycin if fidaxomicin is unavailable or cost-prohibitive. Metronidazole should not be used. BEST PRACTICE ADVICE 5: Clinicians should strongly consider hospitalization for patients with IBD and CDI who demonstrate features of severe colitis or systemic toxicity (eg, more than 6 bowel movements per day, severe abdominal pain, marked leukocytosis, hemodynamic instability, or other evidence of sepsis). BEST PRACTICE ADVICE 6: When selecting an immunosuppressive therapy to treat IBD, no class or mechanism of action has a differential risk of CDI and, therefore, clinicians should choose the therapy that is best to treat the IBD. BEST PRACTICE ADVICE 7: In patients with IBD and acute CDI, concurrent treatment of IBD is critical and clinicians should continue therapy with the required immunosuppressive therapies (ie, immunomodulators, biologics, or small molecules). Steroids can also be used if deemed necessary while CDI is treated with antibiotics. BEST PRACTICE ADVICE 8: Clinicians should consider endoscopic evaluation for IBD activity and exclusion of concomitant cytomegalovirus infection if symptoms persist 48-72 hours after initiation of treatment for CDI. BEST PRACTICE ADVICE 9: Clinicians may consider loperamide in patients with improving inflammation and infection but ongoing diarrhea. BEST PRACTICE ADVICE 10: Clinicians should offer microbiome-based therapies (eg, fecal microbiota, live-jslm, fecal microbiota spores, live-brpk, or unapproved fecal microbiota transplantation) to patients with IBD with at least 1 recurrence of CDI to prevent future infection. BEST PRACTICE ADVICE 11: In patients with IBD, clinicians should not advise probiotics for primary or secondary prevention of CDI. BEST PRACTICE ADVICE 12: In patients with IBD and a history of CDI who are receiving systemic antibiotics, clinicians may consider oral vancomycin prophylaxis as secondary prevention.}, }
@article {pmid42138705, year = {2026}, author = {Zhu, L and Wang, M and Zhang, X and Dou, T and Hua, H and Tang, X and Niu, X and Kou, Q and Chen, Y and Pan, M and Ma, B}, title = {Early supplemental feeding improves post-weaning growth restriction in lambs via the gastrointestinal-metabolic axis.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0242125}, doi = {10.1128/aem.02421-25}, pmid = {42138705}, issn = {1098-5336}, abstract = {The weaning period often induces growth restriction in lambs due to gastrointestinal immaturity and dietary transition. Although early supplemental feeding (ESF) shows promise, its systemic mechanisms via the rumen microbiota-gut-metabolism axis remain incompletely understood. Sixty Tan lambs were assigned to a control group (suckling only), Trial Group I (free-access ESF from 10 days), and Trial Group II (free-access + forced isolation from 15 days). Growth performance, rumen fermentation, intestinal morphology, serum metabolites, and rumen microbiota were comprehensively analyzed. The supplemental feeding regimen in Trial Group I significantly improved body weight, average daily gain, and body size before and after weaning. Rumen butyrate and acetate concentrations increased markedly, with enrichment of beneficial microbiota (Bifidobacteriaceae and Sharpea). Intestinal villus height and villus-to-crypt ratio were enhanced in the jejunum and ileum. Regarding serum metabolism, lambs in both supplemental feeding groups showed significantly increased levels of albumin and urea and decreased total cholesterol. The activities of antioxidant enzymes (catalase, superoxide dismutase, and glutathione peroxidase) and the levels of oxidative products (malondialdehyde and hydrogen peroxide) in the serum of lambs from both supplemental feeding groups were significantly higher than those in the control group. Correlation analysis revealed positive associations between beneficial microbiota, fermentation parameters, intestinal development, and growth performance. ESF alleviates post-weaning growth restriction by remodeling the rumen microbiota, enhancing volatile fatty acid production, improving intestinal development, and optimizing host nutrient utilization. The free-access ESF regimen is recommended for efficient lamb production.IMPORTANCEThis study reveals that different regimens of early supplemental feeding differentially alleviate post-weaning growth restriction in lambs by distinctly remodeling the host's "rumen microbiota-gut-metabolism axis." The optimized regimen enriches beneficial rumen microbiota (e.g., Bifidobacteriaceae and Sharpea), increases key metabolite production (e.g., butyrate), and synergistically improves intestinal development and host protein/lipid metabolism, thereby elucidating the mechanism of growth promotion via microbe-host interactions. These findings advance the understanding of "nutrition-microbe-host" crosstalk in young ruminants and provide a theoretical framework for precision nutrition through microbiome modulation. The identified key microbes and metabolic functions offer potential targets for developing eco-friendly feed additives, aiding in reducing antibiotic reliance and promoting sustainable lamb production.}, }
@article {pmid42138826, year = {2026}, author = {Chen, X and Shen, M and Zhang, R and Huang, Z and Niu, H and Yu, Q and Chen, Y and Pan, X and Rong, L and Wen, H and Yang, J and Xie, J}, title = {Sulfated Cyclocarya Paliurus Polysaccharide Sorchestrates the Gut Microbiome to Mobilize a Host-Derived 12-HEPE Against Ulcerative Colitis.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e75681}, doi = {10.1002/advs.75681}, pmid = {42138826}, issn = {2198-3844}, support = {2023YFF1104001//National Key Research and Development Program of China/ ; 82460642//National Natural Science Foundation of China/ ; }, abstract = {Despite extensive evidence supporting the therapeutic potential of natural product-derived compounds in Ulcerative colitis (UC), their precise mechanisms have yet to be fully elucidated. In this study, structurally modified Cyclocarya paliurus polysaccharide (CP) derivatives were evaluated in a dextran sulfate sodium (DSS)-induced UC mouse model. Among the variants tested, sulfated Cyclocarya paliurus polysaccharide (SCP) emerged as the most therapeutically potent. SCP administration markedly attenuated colitis severity, as evidenced by relieved disease symptoms and reinforced intestinal barrier function. Mechanistically, SCP restored gut microbial homeostasis by enriching beneficial Bacteroidetes and enhancing short-chain fatty acids (SCFAs) production. This remodeled microbial ecosystem orchestrates the upregulation of host-derived 12-hydroxyeicosapentaenoic acid (12-HEPE), which exerts anti-inflammatory effects via direct inhibition of Toll-like receptor 4 (TLR4) signaling. The gut microbiota's functional relevance was substantiated by fecal microbiota transplantation and antibiotic-mediated exhaustion studies. Notably, the therapeutic benefits of 12-HEPE were abrogated upon co-administration of a TLR4 agonist, confirming its target specificity. Elevated serum 12-HEPE levels were observed in a human UC cohort, implying a potential compensatory immunoregulatory response. Our findings elucidate a novel microbiota-host interaction axis wherein SCP alleviates UC by modulating the gut microbiota to enhance endogenous 12-HEPE production, thereby suppressing TLR4-mediated inflammation.}, }
@article {pmid42138982, year = {2026}, author = {Pereira, VH and Cassiano, GH and Ferreira, PHN and Abreu, LGF and Sousa, JES and Carazzolle, MF and Pereira, GAG and Silva, NV}, title = {An integrated microbiological analysis of the soil and rhizosphere of Agave spp. under minimum technological input farming systems.}, journal = {Microbiology (Reading, England)}, volume = {172}, number = {5}, pages = {}, pmid = {42138982}, issn = {1465-2080}, mesh = {*Agave/microbiology/growth &amp; development ; *Rhizosphere ; *Soil Microbiology ; *Soil/chemistry ; Microbiota ; Agriculture/methods ; Bacteria/classification/isolation &amp; purification/genetics ; Crops, Agricultural/microbiology ; }, abstract = {The expansion of arid and semi-arid regions, consequent to the intensification of desertification processes attributable to global warming, exerts a deleterious effect on the agricultural production of energy crops, with current estimates indicating that a further 23% of global agricultural areas will suffer from desertification by 2100, precipitating crises in these sectors. Agave species have the capacity to thrive in these marginal environments characterized by aridity and elevated temperatures. These plants can serve as a source of biomass for the production of biofuels, a process that mitigates the environmental impacts of the transport sector while promoting the utilization of drylands, thereby eliminating competition with food crops. Given the paucity of knowledge regarding the soil microbiota and rhizosphere in minimal technological input Agave plantations, the objective of this study was to evaluate the microbiological and chemical soil properties of Agave sisalana and Agave hybrids (H11648 and H400f) farming systems. The analyses, which were carried out using microbial quantification, enzyme stoichiometry and enzymatic vector calculations, demonstrated that the microbiome of these plants is active and well-structured in terms of nutritional acquisition. It was observed that the Agave fields' microbiome is very similar to that of the native vegetation. This finding suggests that the soil and rhizosphere microbiota are healthy and stable in the Agave fields evaluated, even with the implementation of agronomic exploitation models, as the chemical analysis of the soil reveals that all measured parameters are consistent with those of soils suitable for crop production. These observations persist even in long-established Agave plantations of varying ages that have never received any type of implement or soil correction. Thus, the integration of the chemical and biological data through principal component analysis, redundancy analysis and Permutational Multivariate Analysis of Variance (PERMANOVA) enabled the differentiation of the soil among the three Agave species, which shows the influence of the plant genotype on its microbiota.}, }
@article {pmid42139081, year = {2026}, author = {Shen, H and Song, J and Li, J and Hu, Y and Peng, N and Zhao, S}, title = {Dietary Niches Drive Microbial Community Assembly, Network Reorganization, and Symbiont Evolution in Freshwater Fish Gut Microbiomes.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag125}, pmid = {42139081}, issn = {1751-7370}, abstract = {Host diet is a fundamental ecological factor shaping the assembly and evolution of host-associated microbiomes, yet how dietary niches influence the structure of microbial associations and functional adaptation in freshwater fish remains poorly understood. This study selected five dominant farmed freshwater fish species in China with distinct feeding habits (herbivory, omnivory, filter-feeding, and carnivory) and systematically investigated the adaptive mechanisms of their gut microbiomes by integrating metagenomics, targeted cultivation, comparative genomics, and in vitro assays. We show that dietary niches exert a strong deterministic effect on microbial community assembly, leading to pronounced differences in ecological network topology, including connectivity, modularity, and keystone taxa. Cetobacterium was detected in all five fish species but exhibited a higher relative abundance in omnivorous (16.0%) compared to carnivorous fish (5.4%), suggesting that it may be a core genus within the gut microbiota of freshwater fish. Comparative genomics further revealed that Cetobacterium symbionts exhibit streamlined genome architectures and conserved core metabolic functions, indicative of adaptive evolution toward stable host-associated lifestyles. Guided by metagenomic insights, we isolated multiple Cetobacterium strains displaying host-adapted functional traits, linking community-level ecological patterns to cultivable symbiont resources. In summary, our findings demonstrate that freshwater fish guts function as ecological niches that deterministically structure microbial community assembly and drive symbiont evolution, providing a conceptual framework for understanding host-microbiome co-adaptation in aquatic ecosystems.}, }
@article {pmid42139085, year = {2026}, author = {Sidhom, J and Balla, SB and Tadakamadla, SK and Tadakamadla, J}, title = {The Association Between Self-Reported Nicotine Vaping and the Human Oral Microbiome: A Systematic Review.}, journal = {Nicotine &amp; tobacco research : official journal of the Society for Research on Nicotine and Tobacco}, volume = {}, number = {}, pages = {}, doi = {10.1093/ntr/ntag103}, pmid = {42139085}, issn = {1469-994X}, abstract = {INTRODUCTION: Nicotine Vapes have experienced a rise in their popularity, and our understanding of how vapes affect our oral microbiome remains to be reviewed. This systematic review explores whether the use of vapes is associated with measurable alterations in the diversity and taxonomic composition of the oral microbiome compared to non-vapers or conventional cigarette smokers.<br><br>METHODS: A comprehensive and systematic search of 6 databases was meticulously conducted, covering published literature up to the end of August 2024. The data was then extracted and underwent a qualitative analysis. Studies' risk of bias was assess using Newcastle Ottawa Scale Eligible studies needed to have a comparison group of either non-smokers or tobacco users or both and a group of sole e-cigarette users.<br><br>RESULTS: The search yielded 18 articles, with sixteen being cross-sectional and the remaining two were cohort studies. There were 1418 participants across the studies, ranging from 30-125 participants in each study. Majority of the included literature indicated e-cigarettes can alter the taxonomic composition and diversity of their user's oral microbiome.<br><br>CONCLUSIONS: Vaping was found to be associated with changes in oral microbiome. Since, the majority of the existing literature relied on self-reporting to see if participants were sole vapers, and mainly focused on bacterial genera, the exact impact of these changes are difficult to ascertain. However, the existing literature demonstrates a relationship in a few bacterial genera associated with periodontal disease among e-cigarette users, highlighting the need for further comprehensive studies with sound methodological approach to recruit sole e-cigarette users.<br><br>IMPLICATIONS: This study concludes that nicotine vapes do have a demonstratable impact on the oral microbiome that is unique to vapes. E-cigarette use may be associated with an increase periodontal pathogens which may predispose e-cigarette users to worse periodontal disease, however, further research is required.}, }
@article {pmid42139269, year = {2026}, author = {Wein, H and Iglesias-Moreno, P and Apostolov, A and Salumets, A and Muzzio, DO and Sola-Leyva, A}, title = {Bacterial Extracellular Vesicles: New Hype or Hope to Explain Reproductive Host-Microbiota Interactions.}, journal = {Journal of extracellular vesicles}, volume = {15}, number = {5}, pages = {e70296}, pmid = {42139269}, issn = {2001-3078}, support = {PSG1082//Estonian Research Council/ ; PRG1076//Estonian Research Council/ ; 2024-02530//Vetenskapsr&#xe5;det/ ; 101236395//Horizon Europe / Marie Sk&#x142;odowska-Curie Staff Exchange/ ; TK214//Estonian Ministry of Education and Research/ ; 101120075//HORIZON EUROPE Health/ ; NNF24OC0092384//Novo Nordisk Fonden/ ; MU 4404/3-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Humans ; *Extracellular Vesicles/metabolism ; Female ; Pregnancy ; *Microbiota ; *Host Microbial Interactions ; Animals ; *Reproduction ; *Bacteria/metabolism ; }, abstract = {Rapid advances in microbiome research are transforming our understanding of human health and disease, with growing focus on the female reproductive tract as a critical but understudied niche. Evidence for a local microbiome largely derives from bacterial nucleic acid detection; however, the biological relevance of these signals remains debated, with whether they reflect viable microbial communities, transient colonisation, or mere microbial remnants with immunomodulatory effects. Bacterial extracellular vesicles (BEVs) have emerged as pivotal mediators of host-microbiota crosstalk. Their small size enables them to traverse tissue barriers, enter systemic circulation and access barrier-protected anatomical sites like the placenta, thereby extending their biological reach beyond the site of origin. Although BEVs have been extensively characterised in the context of gastrointestinal, respiratory and systemic diseases, their relevance within the reproductive tract remains insufficiently defined. Understanding whether BEVs contribute to processes such as endometrial receptivity, gamete interaction, embryo implantation and immune tolerance in early pregnancy may reveal novel mechanisms of reproductive physiology and pathology. Furthermore, unravelling the role of BEVs could help resolve the ongoing debate regarding the existence of a functional upper reproductive tract (URT) microbiota, reframing it in terms of microbial activity rather than microbial presence alone. This review synthesises the limited but growing body of evidence on BEVs in the reproductive tract, with a particular emphasis on their potential influence on female fertility and early pregnancy outcomes. We also outline the major methodological challenges, including the discrimination of BEVs from host-derived extracellular vesicles (EVs), the technical limitations of current detection approaches and the risk of contamination in low-biomass environments that complicate research in this field. Finally, we highlight conceptual frameworks and future research directions needed to establish BEVs as important players in reproductive biology and to harness their diagnostic and therapeutic potential in reproductive medicine.}, }
@article {pmid42139619, year = {2026}, author = {Dorohavtseva, HA and Dorofieiev, AE and Myroshnychenko, MS}, title = {Clinical, endoscopic, morphological and microbiological characteristics of diverticular disease in patients with metabolic disorders.}, journal = {Wiadomosci lekarskie (Warsaw, Poland : 1960)}, volume = {79}, number = {4}, pages = {803-810}, doi = {10.36740/WLek/220666}, pmid = {42139619}, issn = {0043-5147}, mesh = {Humans ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; Colonoscopy ; Aged ; *Diverticular Diseases/microbiology/pathology/complications ; *Obesity/complications ; Adult ; Intestinal Mucosa/pathology/microbiology ; *Metabolic Diseases/complications ; Overweight/complications ; }, abstract = {OBJECTIVE: Aim: The aim of the study was to identify the clinical course and endoscopic activity features in patients with uncomplicated diverticular disease (UDD) associated with diabetes mellitus (DM), overweight, and obesity and perform an analysis of the gut microbiome and morphological characteristics of the colonic mucosa in such patients.<br><br>PATIENTS AND METHODS: Materials and Methods: 259 patients with UDD, hospitalized in the Department of Gastroenterology of Feofaniya Clinical Hospital of the State Administration of Affairs during the period of 2020-2024, were included in the study. Among all patients with DD included in the study, 43 had no metabolic disorders (MD) (DM, overweight, obesity), while 216 presented with varying degrees of MD. All patients underwent total colonoscopy with assessment of endoscopic activity of diverticular inflammation using the Diverticular Inflammation and Complication Assessment (DICA) score. The clinical course of DD was evaluated according to the classification proposed by the German Society of Gastroenterology, Digestive and Metabolic Diseases and the German Society of General and Visceral Surgery in 2021. The microbiome analysis was conducted only in 172 patients who had the financial means to undergo this test. During endoscopic examination of the colon in all patients, mucosal biopsies were obtained from the diverticular orifice. Histological, histochemical, and immunohistochemical methods were used. The obtained digital indicators in the groups were analyzed using statistical methods.<br><br>RESULTS: Results: This study evaluated clinical, endoscopic, morphological, and microbiological characteristics of DD in patients with metabolic disorders. A recurrent course of diverticular inflammation was observed more frequently in patients with metabolic dysfunctions. Endoscopic assessment of inflammatory activity correlated with histological changes of colon mucosa and alterations in mucin expression (MUC2 and MUC4). Microbiological analysis revealed a reduction in butyrate-producing flora (Akkermansia muciniphila, Faecalibacterium prausnitzii) with predominance of Bacteroidetes in metabolic disorder patients.<br><br>CONCLUSION: Conclusions: The clinical, morphological, microbiological and endoscopic features of DD identified by the authors highlight pathophysiological links between metabolic dysfunction (DM, overweight, obesity) and DD progression.}, }
@article {pmid42139623, year = {2026}, author = {Khudhair, HM and Alhamdani, ASH and Al Tameemi, AMH}, title = {Microbiology of dental decay and periodontal disease: A review.}, journal = {Wiadomosci lekarskie (Warsaw, Poland : 1960)}, volume = {79}, number = {4}, pages = {829-846}, doi = {10.36740/WLek/216932}, pmid = {42139623}, issn = {0043-5147}, mesh = {Humans ; *Periodontal Diseases/microbiology/therapy ; *Dental Caries/microbiology/therapy ; Biofilms ; Porphyromonas gingivalis/pathogenicity ; Mouth/microbiology ; }, abstract = {OBJECTIVE: Aim: This review attempts to examine the microbiology, pathogenesis and current therapeutic approaches of dental caries and periodontal diseases with a special focus on the role of polymicrobial biofilms, the host-microbe interaction and the major pathogenic species involved in disease progression.<br><br>PATIENTS AND METHODS: Materials and Methods: A thorough literature review was performed using major scientific databases such as PubMed, Scopus, Web of Science and Google Scholar. Studies that were published between 2000 and 2025 were included. Relevant experimental, clinical and review articles that focused on the etiology, microbial composition, virulence mechanisms, host immune responses and therapeutic approaches of dental caries and periodontal disease were analyzed.<br><br>CONCLUSION: Conclusions: The oral cavity harbors over 700-800 bacterial species, of which the primary cariogenic pathogen is Streptococcus mutans and Porphyromonas gingivalis has been implicated as a major cause of periodontal disease. Dental caries progression is mostly attributed to acid production and demineralization of enamel, whereas periodontal disease is a result of dysbiotic shift in the subgingival microbiome with destructive host inflammatory responses. The "red complex" (P. gingivalis, Treponema denticola and Tannerella forsythia) has a high degree of synergistic virulence in advanced periodontitis. Biofilm formation, production of extracellular polysaccharide (EPS) matrix, quorum sensing and immune components (neutrophils, macrophages and matrix metalloproteinases or MMPs) are all factors that contribute to disease formation. Prevention strategies include oral hygiene measures, fluoride exposure, dietary modification, and antimicrobial agents, whereas treatment measures include mechanical debridement, systemic antibiotics, antimicrobial peptides, probiotics, and photodynamic therapy. Dental caries and periodontal diseases are the result of complex interactions between polymicrobial biofilms and immune responses by the host. A better understanding of the microbial ecology, virulence pathways and host-pathogen interactions is crucial in the process of improving prevention and treatment. Advances in targeted antimicrobial therapies and innovative therapeutic approaches hold promise for enhancing global oral health outcomes.}, }
@article {pmid42139793, year = {2026}, author = {Jibril, AH and Alencar, ALF and Olsen, JE and Hounmanou, YMG}, title = {Effect of age, severity of diarrhoea, number of pathogens present and blooming of E. coli on metagenomic characteristics of stools from Danish dairy calves with diarrhoea.}, journal = {Veterinary microbiology}, volume = {319}, number = {}, pages = {111070}, doi = {10.1016/j.vetmic.2026.111070}, pmid = {42139793}, issn = {1873-2542}, abstract = {BACKGROUND: Calf diarrhoea causes substantial welfare and economic losses, and it is one of the major drivers of antimicrobial use. This study aimed to characterize the faecal microbiome of diarrhoeic calves, with a specific focus on Escherichia coli, and to assess whether microbial profiles vary with age, diarrhoea severity, and high E. coli abundance in the absence of other detectable enteric pathogens.<br><br>METHODS: Stool samples from Danish diary calves (n&#x202f;=&#x202f;32) below 4 weeks of age were collected from 11 herds and were analysed using direct long-read sequencing (mgt) as well as analyses of a subset of samples by swiping microbiota from faecal samples grown on McConkey agar plates (plate-swipe). Metagenomes were analysed to characterise community structure (Shannon &#x3b1;-diversity; Bray-Curtis PCoA with PERMANOVA) and to assess differential abundance at the species level while adjusting for sample type (mgt/plate swipe), herd, age, number of other pathogens detected by qPCR (rotavirus, coronavirus, Cryptosporidium parvum, Salmonella Dublin, Clostridium perfringens A, B, C, Eimeria and Escherichia coli F5) and recorded as presence/absence and summarised into infection classes (None/Mono/Co-2/Co-3&#x202f;+). Binning was performed to build metagenome assembled genomes (MAGs) of E. coli.<br><br>RESULTS: Microbiome structure was dominated by methodological and contextual factors: sample type (direct metagenomic vs plate swipe) and herd explained far more variation than clinical severity and age. Metagenomic species profiles from plate swabs were comparatively homogeneous and E. coli-rich, whereas direct metagenomes captured higher diversity. Differential abundance identified species enriched with increasing diarrhoea severity and with infection classes, while pathogen-specific contrasts (e.g., C. perfringens A-positive vs negative) revealed discrete sets of bacterial co-occurrences. Classical pathotype markers (virulence-genes) were uncommon among E. coli MAGs.<br><br>CONCLUSIONS: Long-read metagenomics revealed insignificant influence of severity of diarrhoea, age below 4 weeks and number of pathogens detected in stool samples on diversity and microbial communities in diarrheic dairy calves. In contrast, large variation was observed between herds. On average, E. coli constituted about half of the microbiota. MAGs generated by binning indicated non-specific blooming of strains without particular virulence genes.}, }
@article {pmid42140024, year = {2026}, author = {Mu, Y and Zhang, H and Pan, Y and Tian, Z and Huang, Y and Yang, L and Zhang, C and Zhao, C and Li, D and Liu, X and Jiang, L}, title = {Deciphering the mechanisms underlying regional heterogeneity of high-temperature Daqu through integrated electronic sensory, volatilome, and microbiome analysis.}, journal = {International journal of food microbiology}, volume = {457}, number = {}, pages = {111847}, doi = {10.1016/j.ijfoodmicro.2026.111847}, pmid = {42140024}, issn = {1879-3460}, abstract = {High-temperature Daqu (HTD) is crucial for shaping the style of Moutai-flavor Baijiu, but its quality characteristics exhibit geographical and spatial heterogeneity, resulting in diminished typicity of products from non-core production regions. Therefore, this study employed multiphase detection techniques to analyze HTD samples from the typical region (Guizhou) and emerging region (Shandong), along with their surface and inner layers. Guizhou HTD possessed superior biochemical activity (especially on the surface) and higher response values for W1W, W2W, umami, and salty sensors. It also showed higher concentrations of key flavor compounds, such as pyrazines, acids, and alcohols. Targeted amplicon sequencing showed Kroppenstedtia, Thermoascus, and Thermomyces dominated all samples, but Guizhou HTD had greater microbial diversity and richness. Metagenomics indicated a higher proportion of bacteria in Guizhou HTD, represented by Kroppenstedtia eburnea and Oceanobacillus indicireducens, whereas fungi were more prevalent in Shandong HTD, with Paecilomyces varioti, Aspergillus chevalieri, and Rasamsonia emersonii as the dominant species. Functional annotation demonstrated that carbohydrate metabolism and amino acid metabolism were core biological functions of HTD, with gene abundances showing Guizhou > Shandong and inner > surface. Furthermore, species-enzyme contribution and metagenome-assembled genomes analyses confirmed that HTD exhibited functional redundancy at the ecological scale, yet the species responsible for these functions displayed regional specificity, explaining the phenotypic heterogeneity between Guizhou HTD and Shandong HTD. These findings highlight the pivotal role of the production region in HTD quality and offer insights for improving Moutai-flavor Baijiu flavor in non-core regions.}, }
@article {pmid42140124, year = {2026}, author = {Lu, Y and Wu, Y and Zhang, H and Gao, D and Xie, H and Fu, S and Wang, H and Li, X}, title = {Multi-omics and in silico assessment of ecological risks posed by agrochemical coatings: Disruption of rhizosphere stress signaling and induction of bulb rot in Fritillaria cirrhosa.}, journal = {Ecotoxicology and environmental safety}, volume = {318}, number = {}, pages = {120276}, doi = {10.1016/j.ecoenv.2026.120276}, pmid = {42140124}, issn = {1090-2414}, abstract = {Agrochemical seed coatings are widely used to control soil-borne pathogens. However, their unintended ecological effects on rhizosphere interactions and plant health remain unclear. Here, we combined a field transplantation trial, multi-omics analyses, and molecular docking to investigate the effects of fungicide-based seed coatings on the rhizosphere microecology of Fritillaria cirrhosa.The field trial showed that coating treatment unexpectedly increased bulb rot incidence by 2.8-fold compared with untreated controls (P < 0.001). Multi-omics analyses further indicated that coating application disrupted rhizosphere microecology, as evidenced by a 25.1% decline in bacterial diversity, reduced network complexity, and enrichment of pathogenic Fusarium species. Metabolomic analysis revealed the accumulation of exogenous xenobiotics along with downregulation of pyrimidine metabolism pathway, suggesting altered plant-microbe chemical communication. Stress-related metabolites, including salicylic acid (SA), L-carnitine, and ethylmalonate, accumulated, whereas key signaling molecules, such as adenosine, monoacylglycerol (18:3), Lysophosphatidylethanolamine 15:1 were depleted (0.03-fold) in the treatment group. Moreover, the decrease in jasmonic acid coupled with an increase in SA suggests immune hijacking associated with necrotrophic pathogens such as Fusarium, a pathological cascade further supported by the accumulation of mycotoxins such as T-2 triol. Cross-domain network and molecular docking analyses further clarified interactions between hub metabolites and the microbial community. Notably, adenosine exhibited strong binding affinities (< -6.0 kcal/mol) to both plant defense-related proteins (JOX2 and CotA laccase) and fungal pathogenicity targets, indicating a key role for endogenous plant defense signals in maintaining rhizosphere ecological balance. Collectively, these findings provide robust correlative evidence linking agrochemical seed coatings to rhizosphere microecological dysbiosis, characterized by reduced metabolite-mediated recruitment of beneficial microbiota and disrupted interkingdom signaling. This pathogen-favoring environment highlights the often-overlooked ecological impacts of seed coatings and underscores the urgent need for microbiome-compatible disease management strategies in perennial bulbous crop production.}, }
@article {pmid42140291, year = {2026}, author = {Ojeda-Martinez, D and Boter, M and Ortego, F and Santamaria, ME}, title = {Unveiling CAZyme modularity patterns: Comparative genomics links domain architecture to arthropod diets and life histories.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {152547}, doi = {10.1016/j.ijbiomac.2026.152547}, pmid = {42140291}, issn = {1879-0003}, abstract = {Carbohydrate-active enzymes (CAZymes) are proteins that assemble, remodel, and depolymerize complex carbohydrates. They are ubiquitous across the tree of life, underpinning energy capture, cell-wall architecture, microbiome interactions, and host-pathogen dynamics. CAZymes are modular in structure and function, being tightly related to the overall enzyme architecture. Domain architecture constrains folding, substrate range, and integration into metabolic pathways. Arthropods, the most species-rich animal phylum, offer a powerful system to study enzymatic modularity because their enzymatic machineries must function in extremely diverse ranges of diet, niche, and abiotic conditions. Here we built a genome-scale framework to characterize CAZyme modular organization across Arthropoda and to test how domain architecture is influenced by diets, life histories and clades while revealing emergent functional relationships. We find that unimodular architectures dominate CAZyme repertoires, while multimodular and class-exclusive arrangements remain rare but highly variable. We identify herbivory as responsible for the discrimination on three CAZyme structural strategies (saprophagous, leaf-stem-root, and pollen-nectar feeders) differing in class composition, modular complexity, and catalytic emphasis. Correlation and co-occurrence analyses at genomic and protein levels show that expansions of glycosyltransferases, glycoside hydrolases, carbohydrate-binding modules, and auxiliary activities are tightly coupled, especially in myriapods and crustaceans, and that intra-protein networks of CAZyme families are denser in hexapods, holometabolans, and herbivores. Within these networks, GT2 and hydrolytic domains occupy central positions in co-occurrence clusters. Together, our findings indicate that arthropod CAZymes evolve as integrated macromolecular systems whose modularity and class balance track ecological demands, providing a scalable framework for engineering CAZyme networks for biotechnological and pest-management applications.}, }
@article {pmid42140378, year = {2026}, author = {Tan, MW and Clister, D and Chandra, QM and Wangsa, CE and Simone, CN and Umaya, C and Choi, J and Park, S and Rani, A and Akter, S and Kim, B and Kim, SH and de Azambuja Ribeiro, RIM and Syahputra, RA}, title = {Circulating microbial metabolites and the gut-prostate axis in prostate cancer: Implications for laboratory biomarkers and therapeutic response.}, journal = {Clinica chimica acta; international journal of clinical chemistry}, volume = {590}, number = {}, pages = {121086}, doi = {10.1016/j.cca.2026.121086}, pmid = {42140378}, issn = {1873-3492}, abstract = {Prostate cancer progression and treatment response are influenced not only by tumor genomics and androgen receptor signaling but also by systemic host-microbiome interactions along the gut-prostate axis. Increasing evidence indicates that gut microbial metabolism produces bioactive compounds that circulate in human body fluids and can influence immune regulation, hormone metabolism, and therapeutic outcomes. This review synthesizes current evidence on microbiome-derived metabolites that may serve as measurable biomarkers relevant to prostate cancer biology and clinical laboratory diagnostics. Microbial metabolism of dietary substrates generates circulating molecules-including short-chain fatty acids, secondary bile acids, indole derivatives, polyamines, and endotoxin-associated signals-that can modulate inflammation, epithelial barrier integrity, and systemic immune responses involved in tumor progression. In addition, intestinal microbes participate in steroid transformation and enterohepatic cycling of hormones, potentially influencing circulating androgen and estrogen levels that contribute to androgen-driven prostate cancer development and adaptation under androgen deprivation therapy. Importantly, many of these microbial metabolites are detectable in serum or plasma using validated analytical platforms such as liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry, supporting their potential integration into laboratory biomarker panels. Emerging multi-omics approaches combining metagenomics, metabolomics, host transcriptomics, and immune profiling are beginning to clarify mechanistic links between microbial activity and therapy response, including variability in outcomes with androgen-targeted agents, chemotherapy, radiotherapy, and immune checkpoint inhibitors. From a clinical chemistry perspective, characterization of circulating microbiome-derived metabolites may enhance the diagnostic and prognostic performance of established biomarkers such as prostate-specific antigen while providing new opportunities for non-invasive monitoring of disease progression and treatment response. Establishing reproducible microbial metabolic signatures across diverse patient populations will be essential to translate microbiome-informed biomarkers into next-generation diagnostic and prognostic tools in prostate cancer management.}, }
@article {pmid42140385, year = {2026}, author = {Li, Y and Zhang, J and Liu, H and Noman, M and Rizwan, MA and Isiaka, ID and Chen, H and Li, W and Zhao, N and Li, Y and Sun, Y and Lu, X and Liu, D and Yan, Y}, title = {Age-related pharyngeal microbiome and host transcriptomic signatures underlying fever responses in RSV bronchiolitis.}, journal = {Virologica Sinica}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.virs.2026.05.002}, pmid = {42140385}, issn = {1995-820X}, abstract = {Respiratory syncytial virus (RSV) bronchiolitis is the leading cause of hospitalization in infancy and exhibits pronounced age-dependent clinical heterogeneity. Fever becomes increasingly prevalent with age, yet whether febrile representation reflects a uniform inflammatory and immune phenotype across infancy remains unclear. In this prospective cohort of infants hospitalized with RSV bronchiolitis, we performed an integrated analysis of clinical features, pharyngeal microbiome composition, host transcriptomic profiles, and host-microbe interaction networks, with particular attention to age-related variation in fever-associated patterns. Clinically, fever prevalence exhibited a strong age-dependent increase across infancy. Correspondingly, canonical correspondence analysis identified age and fever as dominant gradients related to variation in both pharyngeal microbiome composition and host gene expression. Although no significant age-dependent correlations were observed at the global microbial and host transcriptomic levels in the fever-age interaction model, distinct patterns of microbial and host responses related to fever were observed across different age groups. Specifically, ranked gene set enrichment analysis indicated that febrile infants in early infancy showed relative attenuation of host defense-related programs, whereas older infants showed stronger enrichment of antiviral and inflammatory effector pathways, with more selective regulatory and signaling-associated patterns in late infancy. Integrated host-microbe network analysis further delineated a coherent developmental trajectory of fever-associated interaction architectures, evolving from densely interconnected regulatory networks in early infancy to modular, selectively coupled, host-centered configurations with advancing age. Together, febrile responses in RSV bronchiolitis should not be interpreted as a uniform biological phenotype across infancy and support age-aware interpretation of fever in pediatric RSV infection.}, }
@article {pmid42140394, year = {2026}, author = {Linton, S and Sjaarda, C and Hossenbaccus, L and Davis, A and Greenlaw, J and Douchant, K and Thiele, J and Garvey, S and Botting, H and Steacy, LM and Sheth, PM and Ellis, AK}, title = {Characterizing the Nasal Microbiome Using a Nasal Allergen Challenge Model.}, journal = {The Journal of allergy and clinical immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jaci.2026.05.003}, pmid = {42140394}, issn = {1097-6825}, abstract = {BACKGROUND: The role of the nasal microbiome in allergic rhinitis (AR), particularly following direct allergen exposure using a controlled model, remains incompletely understood. Understanding microbiome dynamics after allergen challenge could provide insights into AR pathophysiology.<br><br>OBJECTIVE: To evaluate nasal microbiome changes following a nasal allergen challenge (NAC) with ragweed pollen extract in individuals with ragweed-induced AR compared to non-allergic controls.<br><br>METHODS: Nineteen ragweed-allergic and twelve non-allergic participants completed an out-of-season NAC. Middle meatus and the adjacent nasal cavity secretions were collected at baseline and 6, 24, and 48 hours post-challenge. Microbial composition was characterized using 16S rRNA sequencing. Alpha diversity was assessed using Shannon and Chao1 indices, and beta diversity using Bray-Curtis dissimilarity with principal coordinate analysis. Ragweed-specific IgE (sIgE), total IgE (tIgE), and Staphylococcus aureus nasal carriage were also evaluated.<br><br>RESULTS: Nasal microbial community composition differed according to biological sex (beta diversity P = 0.001) and S. aureus carriage (P = 0.015). However, allergic status and NAC exposure had no significant effect on alpha or beta diversity over time. Genus-level differences between allergic and non-allergic participants emerged at 24 and 48 hours post-challenge (P = 0.028 and P = 0.0062), with greater relative abundance of Streptococcus and Veillonella observed in non-allergic individuals. Stratification by sIgE demonstrated significant differences in microbial community structure (P = 0.001), with higher sIgE levels associated with increased relative abundance of Streptococcus, Rothia, and Neisseria. Higher tIgE levels were also associated with distinct microbial community profiles and reduced Shannon diversity.<br><br>CONCLUSION: The nasal microbiome remained stable following acute allergen exposure despite clinical responses, while host factors including IgE levels, sex, and S. aureus carriage were associated with differences in microbial community composition.}, }
@article {pmid42140492, year = {2026}, author = {Corcione, S and Benech, N and Kuijper, E and , }, title = {Microbiome science at a turning point: from descriptive ecology to clinical decision-making in infectious diseases.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmi.2026.05.017}, pmid = {42140492}, issn = {1469-0691}, }
@article {pmid42140743, year = {2026}, author = {Lee, JB and Baek, S and Kim, DK and Kwon, BE and Ahn, JS and Nagasaka, M and Davar, D and Park, H and Kim, H and Im, J and Yang, J and Yang, E and Shin, GH and Choi, S and Kwon, JE and Kim, JM and Kang, SY and Kim, Y and Park, SY and Kim, JH and Oh, HS and Chalita, M and Min, A and Cho, BC}, title = {Phase I trial of CJRB-101 plus pembrolizumab in patients with metastatic non-small cell lung cancer, head and neck squamous cell carcinoma and melanoma.}, journal = {Journal for immunotherapy of cancer}, volume = {14}, number = {5}, pages = {}, doi = {10.1136/jitc-2025-014702}, pmid = {42140743}, issn = {2051-1426}, mesh = {Humans ; *Antibodies, Monoclonal, Humanized/pharmacology/therapeutic use ; Female ; Male ; Middle Aged ; *Carcinoma, Non-Small-Cell Lung/drug therapy/pathology ; Aged ; *Squamous Cell Carcinoma of Head and Neck/drug therapy/pathology ; *Melanoma/drug therapy/pathology ; *Lung Neoplasms/drug therapy/pathology ; Mice ; *Head and Neck Neoplasms/drug therapy/pathology ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use/pharmacology ; Animals ; Adult ; }, abstract = {BACKGROUND: Dysbiosis of gut microbiome leads to resistance to immunotherapy in various advanced solid tumors. CJRB-101 is a live biotherapeutic product consisting of a novel strain belonging to the species Leuconostoc mesenteroides. To modulate the tumor microenvironment, CJRB-101 was combined with pembrolizumab.<br><br>METHODS: Preclinical efficacy and mechanistic studies were performed using humanized non-small cell lung cancer (NSCLC) patient-derived xenograft (PDX) models. This is a multicenter, first-in-human, two-part, phase I, open-label study of CJRB-101 (1&#xd7;10[11]&#x2009;or 4&#xd7;10[11]&#x2009;colony forming unit (CFU)/day) plus pembrolizumab (200&#x2009;mg every three weeks (Q3W)) in advanced NSCLC, melanoma, and head and neck squamous cell carcinoma in both immune checkpoint inhibitor (ICI)-naive and ICI-refractory settings. The primary endpoint was to assess the dose-limiting toxicities (DLTs), adverse events, and preliminary activity of the combination treatment. Exploratory endpoints included stool metagenomics analysis and pharmacodynamics parameters.<br><br>RESULTS: In four PDX models, CJRB-101 with pembrolizumab demonstrated enhanced antitumor efficacy, showing a tumor growth inhibition (TGI) of 77.3% in the CJRB-101 monotherapy group and 61.9% in the combination group, which was significantly improved compared with pembrolizumab alone. A distinct M2-to-M1 repolarization was observed and validated in vitro. Notably, increased activation of cytotoxic T cells was observed, suggesting an immune-mediated antitumor mechanism of CJRB-101. A total of 42 patients were enrolled in the low-dose cohort (one capsule once a day; n=6) and high-dose cohort (two capsules two times a day, n=36). Metastatic NSCLC accounted for 86% (n=36) and 67% (n=28) of the patients were refractory to ICIs. None of the patients experienced DLT. In ICI-na&#xef;ve NSCLC (n=12) with programmed death-ligand 1 (PD-L1) >50%, the overall response rate (ORR) and disease control rate (DCR) were 58% and 75%, respectively. The ORR was 5% and DCR was 41% in the ICI-refractory NSCLC (n=22) with an ORR of 5% and DCR of 41%. After a median follow-up of 15.6 months and 8.9 months for ICI-na&#xef;ve and ICI-refractory NSCLC, the median progression-free survival was 9 months (95%&#x2009;CI 5.6 to not reached) and 1.8 months (95%&#x2009;CI 1.6 to 4.3), respectively. CJRB-101 plus pembrolizumab was well-tolerated, and none of the patients experienced grade >3 treatment-related adverse events.<br><br>CONCLUSIONS: Early clinical data show encouraging antitumor response of CJRB-101 plus pembrolizumab in ICI-na&#xef;ve metastatic NSCLC with PD-L1 >50%.<br><br>TRIAL REGISTRATION NUMBER: NCT05877430.}, }
@article {pmid42140787, year = {2026}, author = {Singh, N and Srivastav, M}, title = {Comment on "Distinct gut microbiota signatures and predicted lipid metabolism pathways in Taiwanese patients with acute versus chronic coronary syndromes".}, journal = {Journal of the Formosan Medical Association = Taiwan yi zhi}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jfma.2026.05.046}, pmid = {42140787}, issn = {0929-6646}, }
@article {pmid42140850, year = {2026}, author = {Fagundes, D and Costa, LMS and Cagliari, A and de Vargas, DP and Rieger, A}, title = {Microbial Community Shifts and Plant Performance Improvements Driven by Bacillus firmus in Pampa Agroecosystems.}, journal = {Environmental microbiology reports}, volume = {18}, number = {3}, pages = {e70315}, pmid = {42140850}, issn = {1758-2229}, mesh = {*Bacillus/physiology ; *Soil Microbiology ; *Microbiota ; Rhizosphere ; *Glycine max/growth &amp; development/microbiology/parasitology ; Plant Roots/growth &amp; development/microbiology ; Animals ; Fungi/classification/genetics/isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; Nematoda ; Ecosystem ; Soil ; }, abstract = {The impact of Bacillus firmus-based bionematicides on rhizosphere microbiota and plant performance remains poorly understood in complex agroecosystems. This study evaluated the effects of B. firmus application on soil microbial communities, nematode dynamics, and soybean productivity in the Pampa biome. Our results demonstrate that B. firmus significantly modulates the composition and diversity of soil microbiota, with effects varying across locations and over time. Treated areas exhibited shifts in bacterial communities, including increased abundance of beneficial taxa, while fungal diversity tended to decrease, likely due to the combined effect of the fungicide used in seed treatment. Despite persistent populations of target nematodes such as Pratylenchus brachyurus and Heterodera glycines, treated areas showed reduced root infestation in specific stages and locations. Importantly, the application of B. firmus consistently enhanced soybean shoot and root growth, resulting in productivity gains of 6%-7% across all sites. These findings reveal that B. firmus not only contributes to plant growth promotion but also induces significant, yet context-dependent, shifts in rhizosphere microbial communities. The study highlights the ecological complexity of microbial responses to biocontrol agents and underscores the importance of integrating microbiome dynamics into sustainable nematode management strategies in agroecosystems.}, }
@article {pmid42140946, year = {2026}, author = {Zheng, R and Li, Y and Shang, P and Shen, Y and Nan, Z and Duan, T}, title = {Anthracnose drives assembly of phyllosphere epiphytic bacterial communities to increase disease resistance.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00991-z}, pmid = {42140946}, issn = {2055-5008}, support = {grant no. 2023-NK-147//the Fundamental Research Funds for the Leading Scientist Project of Qinghai Province/ ; }, abstract = {The phyllosphere microbiome plays crucial roles in plant health, but evidence of 'cry for help' strategy in the face of pathogen attack in the phyllosphere remains limited, particularly for the microbiomes of distinct leaf ecological niches. We investigated whether foliar pathogen anthracnose (Colletotrichum lentis) influenced the assembly and functions of microbiomes in epiphytic and endophytic niches of the phyllosphere of common vetch (Vicia sativa) leaves. We also evaluated synthetic microbial communities (SynComs), including representatives of disease-associated strains, for pathogen protection. Anthracnose mediated the deterministic assembly process of epiphytic bacterial and endophytic fungal communities, and increased the complexity of bacterial co-occurrence networks. Iron competition and antifungal genes were also enriched in the epiphytic bacteria, which produce siderophores and degrade fungal cell walls to counteract pathogens. SynComs of beneficial epiphytic bacteria partially protect hosts by regulating bacterial interactions and inducing host immune responses. These findings suggest that disease drives the deterministic assembly of distinct phyllosphere microbiomes, their diversity and their function. Moreover, SynComs from the epiphytic niche can confer host plant disease resistance.}, }
@article {pmid42140950, year = {2026}, author = {Garrido-Castro, AC and Graham, N and Li, KX and Bi, L and Crowdis, J and Bi, K and Park, J and Pastorello, R and Li, Y and Gupta, H and Kuntz, T and Petry, R and Pasquina, LW and Patel, A and Lange, P and DiLullo, M and Attaya, V and Frey, AM and Childress, MA and Wesolowski, R and Sinclair, N and Sinclair, S and Lo, S and Tung, N and Faggen, M and Kaufman, PA and Block, CC and Walsh, J and Toke, M and Chen, W and Wucherpfennig, KW and Tian, Y and Williams, AJ and Mukhopadhyay, S and Dasgupta, T and Schnitt, S and Cherniack, AD and Barroso, R and Ligibel, J and Lin, NU and Mittendorf, EA and Tayob, N and Van Allen, E and Tolaney, SM}, title = {Carboplatin with or without nivolumab in metastatic triple-negative breast cancer: a randomized phase II trial.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73085-1}, pmid = {42140950}, issn = {2041-1723}, abstract = {This multi-institutional randomized phase II clinical trial (NCT03414684) investigated the efficacy and safety of carboplatin plus nivolumab compared to carboplatin in metastatic triple-negative breast cancer (mTNBC). The primary endpoint was progression-free survival (PFS) in a modified intention-to-treat (mITT) population of patients with chemotherapy-naïve (i.e., first-line) mTNBC. Secondary endpoints included overall survival (OS), confirmed objective response rate, confirmed clinical benefit rate, time to and duration of confirmed objective response, safety, and tolerability. Clinical outcomes were evaluated in the PD-L1-positive subgroup (≥ 1% immune cells; SP142 clone) per central review. Biospecimens were collected for correlative analyses. 75 patients were enrolled and treated between 2/2018-9/2020. Among the mITT population (n = 62), median PFS was 4.2 months with carboplatin plus nivolumab vs 5.5 months with carboplatin. Median OS did not significantly differ between arms (16.8 vs 11.1 months, respectively). In PD-L1-positive mTNBC patients (n = 24), median PFS was 8.3 vs 4.7 months; median OS was 17.6 vs 10.7 months. Grade ≥3 adverse events occurred in 56.8% of patients in the combination arm and 65.8% in the carboplatin arm. Carboplatin plus nivolumab did not significantly improve PFS compared to carboplatin in patients overall; however, a trend toward improved outcomes was observed in PD-L1-positive mTNBC patients. High mutational burden, interferon-gamma signaling, early circulating tumor DNA reduction, low baseline serum thymidine kinase activity, and urea cycle dysregulation in the microbiome emerged as potential predictors of response to immune checkpoint inhibitors with platinum.}, }
@article {pmid42141277, year = {2026}, author = {Jiao, S and Pan, H and García-Palacios, P and Tu, H and Zhang, Y and Liu, Y and Gao, H and Chen, B and Peng, Z and Chen, S and Qi, J and Liang, C and Li, X and Wang, Y and Jin, C and Gao, M and Liu, J and Wang, Y and Zhao, J and Jiang, L and Romero, F and Banerjee, S and Yang, Y and Lu, Y and Delgado-Baquerizo, M and van der Heijden, MGA and Wei, G}, title = {Agricultural soil microbiomes are structurally and functionally more resistant to warming than adjacent natural ecosystems.}, journal = {Nature food}, volume = {}, number = {}, pages = {}, pmid = {42141277}, issn = {2662-1355}, abstract = {Agricultural soil microbiomes experience frequent disturbance from intensive management and may therefore be better equipped to withstand climate warming than microbiomes in undisturbed natural soils. Here we test this by combining a continental-scale warming microcosm experiment across 100 paired agricultural-natural sites with a global meta-analysis and three microbiome manipulation experiments (microbial suspensions, cross-inoculation and synthetic communities). Agricultural soils showed a higher resistance of soil multifunctionality to warming than natural soils, consistent across the meta-analysis. Resistance of microbial community composition was the strongest predictor of functional resistance and was confirmed in artificial soils inoculated with agricultural versus natural microbial suspensions. Introducing soil microbiomes from agricultural ecosystems into previously undisturbed natural soils enhanced functional resistance to warming. Metagenomic analysis revealed that microbial life-history strategies play a crucial role in regulating the resistance of soil microbial community to warming, with communities dominated by stress-tolerant strategies conferring significantly stronger resistance. Our work highlights the potential of microbiome engineering to strengthen ecosystem functioning under climate change.}, }
@article {pmid42141284, year = {2026}, author = {}, title = {Even mild blows to the head disrupt the microbiome.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {42141284}, issn = {1476-4687}, }
@article {pmid42141351, year = {2026}, author = {Sarkar, S and Roy, S and Choudhury, L}, title = {Importance of the inflammasome in gut-brain axis: from pathological driver to therapeutic target.}, journal = {Inflammopharmacology}, volume = {}, number = {}, pages = {}, pmid = {42141351}, issn = {1568-5608}, abstract = {The inflammasome, a supramolecular complex, plays important role in the gut-brain axis (GBA), acting as a sensor of cellular stress and danger signals. It activates inflammatory responses, and its dysregulation has been implicated in neurological diseases. Various inflammasomes, such as NLRP3, NLRC4, and AIM2, contribute to disease progression by promoting inflammation, tissue damage, and oxidative stress. These inflammasomes recognize and get activated by different stimuli, such as ATP, fluctuations in ion fluxes, nucleic acids, and molecular signatures associated with pathogens, eventually releasing inflammatory cytokines, and triggering inflammatory responses. Although the inflammatory response is orchestrated, sometimes it might happen that its dysregulation causes excessive and sustained inflammation leading to cellular damage and tissue injuries. Inhibiting or modulating these inflammasomes can therefore, provide therapeutic benefits. Targeting NLRP3, like MCC950, has shown promise in reducing inflammation. Some natural compounds have also been found to inhibit NLRP3 and other inflammasomes. Interestingly, regulating the gut microbiome can impact inflammasome activation, and reduce unsolicited inflammation. This review explores the bidirectional communication network between the gut and brain, and emphasizes the importance of understanding the role of inflammasomes in the GBA which can lead to novel therapeutic strategies for neurological diseases like Multiple Sclerosis, Parkinson's, and Alzheimer's.}, }
@article {pmid42141362, year = {2026}, author = {Baeuerle, E and Semwal, MK and Nie, J and Zhang, N and Liang, H and Ganapathy, V and Sathavarodom, N and Fernandez, R and Wang, CP and Espinoza, S and Dong, Q and Gao, X and Yang, Z and Kostic, A and Musi, N}, title = {Effect of Sevelamer and B. longum on Insulin Sensitivity in Participants With Obesity: A Randomized Clinical Trial.}, journal = {Obesity (Silver Spring, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1002/oby.70224}, pmid = {42141362}, issn = {1930-739X}, support = {7-13-GSK-01//American Diabetes Association/ ; R01DK080157//Foundation for the National Institutes of Health/ ; P30AG044271//Foundation for the National Institutes of Health/ ; P30AG094848//Foundation for the National Institutes of Health/ ; U01AR071130//Foundation for the National Institutes of Health/ ; R01AG075684//Foundation for the National Institutes of Health/ ; U54AG075941//Foundation for the National Institutes of Health/ ; T32GM113896//Foundation for the National Institutes of Health/ ; //South Texas MSTP/ ; }, abstract = {OBJECTIVE: This study evaluated whether two interventions with putative lipopolysaccharide (LPS)-lowering properties, the phosphate binder sevelamer or a synbiotic, improve insulin sensitivity in humans.<br><br>METHODS: We conducted a randomized, double-blind, placebo-controlled, three-arm parallel-group trial. Twenty-two&#xa0;lean and twenty-eight&#xa0;participants with obesity completed the trial. Participants were randomized to: (1) sevelamer; (2) synbiotic (oligofructose plus Bifidobacterium longum Rosell-175); or (3) placebo, three times a day for 4&#x2009;weeks. The primary outcome was change in peripheral insulin sensitivity (M) assessed by hyperinsulinemic (60&#x2009;mU/m[2]&#x2009;min) euglycemic clamp versus placebo.<br><br>RESULTS: In participants with obesity, sevelamer improved the M (+2.176 [0.314, 4.038] mg/kg&#x2009;min vs. placebo; p&#x2009;=&#x2009;0.022) and lowered LDL-C (-29.675 [-53.794, -5.556] mg/dL vs. placebo; p&#x2009;=&#x2009;0.016). Synbiotic had no effect on insulin sensitivity or lipids in either group. No changes in markers of endotoxemia were observed with any intervention. Sevelamer increased plasma levels of metabolites linked to improved glucose and lipid metabolism, such as bile acids, amino acids (citrulline, betaine), NAD+ precursors (trigonelline), and xenobiotics (genistein, umbelliferone).<br><br>CONCLUSIONS: Sevelamer improves insulin sensitivity and LDL-C in participants with obesity. Further investigation is warranted to elucidate sevelamer's metabolic mechanisms, potentially involving the mediation of bile acids and other host-microbiome-derived metabolites.<br><br>TRIAL REGISTRATION: ClinicialTrials.gov NCT02127125.}, }
@article {pmid42141481, year = {2026}, author = {Roslund, MI and Uimonen, L and Kummola, L and Cerrone, D and Ojala, A and Luukkonen, A and Holopainen, E and Korhonen, A and Penttilä, R and Saarenpää, M and Venäläinen, M and Haveri, H and Rajaniemi, J and Laitinen, OH and Sinkkonen, A and Group, TBR}, title = {Neighborhood deadwood and yard rewilding modulate commensal microbiomes and inflammatory signals among urbanites.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02413-w}, pmid = {42141481}, issn = {2049-2618}, support = {346136//Strategic Research Council/ ; 346137//Strategic Research Council/ ; 346138//Strategic Research Council/ ; }, abstract = {BACKGROUND: Urbanization and biodiversity loss reduce human exposure to diverse microbiomes. Current evidence suggests that the vanishing microbiomes in industrialized populations are a central factor in the rising prevalence of non-communicable immune-mediated diseases. Rewilding has been proposed as an approach to diversify urban microbial communities and promote immunological resilience.<br><br>RESULTS: We rewilded 21 urban private yards with deadwood, vegetation, and microbially rich soil. Control yards (15) were analyzed for comparison. We analyzed skin bacteria and oral microbiomes and used vegetation and deadwood inventories, satellite data, and questionnaires to determine the effects of rewilding, living environment, and lifestyle factors on skin and oral microbiota, functional gene pathways, and cytokine levels (IL-6, IL-10). Neighborhood deadwood within 200-m radii around home yards was used as an indicator of environmental biodiversity. Samples were collected before the rewilding in summer and three months later in autumn. Skin microbial diversity stayed constant and was associated with plant richness in the rewilding group, despite the normal seasonal decline and reduced outdoor time in autumn. Rewilding was associated with a decrease in tetrahydrofolate biosynthesis and salvage, and L-histidine degradation&#xa0;gene pathways and other&#xa0;changes in oral microbiota.&#xa0;In the rewilding group&#xa0;in autumn, picking of berries and fruits&#xa0;was&#xa0;directly associated with immunoregulatory IL-10 and pleiotropic IL-6 in saliva,&#xa0;and neighborhood deadwood abundance with the fatty acid biosynthesis superpathway in oral microbiomes.&#xa0;When groups were analyzed jointly,&#xa0;the diversity of oral microbial functional gene pathways was negatively correlated with IL-6 levels,&#xa0;and neighborhood deadwood&#xa0;abundance&#xa0;was directly linked to&#xa0;skin&#xa0;Gammaproteobacterial&#xa0;taxa,&#xa0;and&#xa0;typically soil-derived&#xa0;Cytobacillus&#xa0;sp. CY-G&#xa0;and&#xa0;Streptomyces&#xa0;sp. HSG2 in&#xa0;saliva.<br><br>CONCLUSIONS: Our findings are consistent with the biodiversity hypothesis, suggesting that biodiversity exposure may influence commensal microbiomes and biological pathways involved in host-microbe interactions. Our results suggest that the amount of decaying deadwood in the neighborhood, in addition to conventional measures of greenness and vegetation diversity, may provide advantageous information in studies examining human-environment microbiome interactions. This may inform biodiversity-related ecosystem services related to impacts on human health. Our findings provide an incentive for future studies and strategic investments for rewilding urban microbiomes to support planetary health. Video Abstract.}, }
@article {pmid42141512, year = {2026}, author = {Li, Y and Sun, J and Dai, Z and Jin, LN and Chen, Z and Lin, D and Zhu, L}, title = {Antibiotic Metabolites Are an Overlooked Driver of Resistance Dissemination in Plant Systems.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c04146}, pmid = {42141512}, issn = {1520-5851}, abstract = {Antibiotic pollution in agroecosystems is widely recognized, yet the risks posed by their metabolites remain insufficiently addressed. Using lettuce as a model, we investigated how tetracycline (TC) and its metabolites, anhydrotetracycline (ATC) and epitetracycline (ETC), contribute to the dissemination of antibiotic resistance genes (ARGs). TC primarily accumulated in roots and declined during translocation, whereas ATC exhibited greater persistence and became the predominant residue through in planta transformation. At environmentally relevant concentrations (≤0.1 mg·L[-1]), ATC more effectively expanded the mobilizable resistome than the parent compound by inducing reactive oxygen species, activating the SOS response, increasing membrane permeability, and promoting RP4 plasmid conjugative transfer. These processes facilitated the acquisition of multidrug resistance and the colonization of plant tissues by human pathogens, including Stenotrophomonas maltophilia and Pseudomonas aeruginosa, thereby increasing ARG burdens in both rhizosphere and phyllosphere compartments. Metagenomic analysis further confirmed the coselection of nontetracycline ARGs, such as aph3'-I and catB, and the enrichment of efflux systems (acr/emr) in pathogenic bacteria. Our findings challenge the parent-compound-centered paradigm of antibiotic risk assessment by identifying ATC as a key high-risk driver of ARG dissemination in food plants and highlighting the need to incorporate transformation products into future management strategies.}, }
@article {pmid42141788, year = {2026}, author = {Garcia-Godos, C and Jauhal, MK and Khan, MA and Mendoza-Cozatl, DG}, title = {Plant-microbiome interactions provide novel insights into the regulation of iron-sulfur metabolism in plants.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/erag224}, pmid = {42141788}, issn = {1460-2431}, abstract = {Iron-sulfur (Fe-S) clusters are at the core of photosynthesis, respiration, and redox homeostasis, yet their biogenesis and stability are highly sensitive to fluctuations in iron (Fe) and sulfur (S) availability. Although the molecular players of Fe and S assimilation pathways are well characterized, the mechanisms mediating the crosstalk between these nutrient networks remain largely unknown, particularly within the context of plant-microbiome interactions. Recent work has revealed that plant-associated microbial communities play active roles in shaping Fe-S metabolism through metabolite exchange, hormonal modulation, and redox signaling. Here we discuss recent research demonstrating how root-associated microbes and synthetic microbial communities (SynComs) can influence Fe and S homeostasis, including the reprograming of plant transcriptional and metabolic networks to preserve photosynthesis under nutrient limitation. We also highlight key microbial strategies, including siderophore-mediated Fe mobilization, S-containing metabolites release, and microbial modulation of hormonal pathways that collectively enhance Fe and S use efficiency. Finally, we discuss future directions for AI-driven trait-based design of SynComs, multi-omics integration, and field-level validation to translate these novel insights into agricultural solutions. Harnessing the power of plant-microbe interactions to improve Fe-S metabolism offers a promising path toward sustainable agriculture and crop productivity under stress and challenging environments.}, }
@article {pmid42141942, year = {2026}, author = {Ebersole, JL and Gonzalez, OA}, title = {Characteristics of the Health-Associated Oral Microbiome in Young Nonhuman Primates.}, journal = {Molecular oral microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/omi.70033}, pmid = {42141942}, issn = {2041-1014}, support = {R56DE029954//The National Institutes of Health/ ; P40RR03640//Caribbean Primate Research Center/ ; //Microarray Core of the University of Kentucky/ ; }, abstract = {Nonhuman primates have been shown to develop periodontitis with clinical and demographic features similar to humans. This preclinical disease model is well-positioned to advance the elucidation of novel biologic-based preventive and therapeutic approaches to controlling periodontitis, a chronic infection and immunoinflammatory disease. In this analysis, the oral microbiomes of younger (10-19 human years; n = 30) nonhuman primates are compared for matriline (an indicator of heritability), sex, and age variations. A holistic assessment of the microbiome similarities/differences suggested two primary conclusions in this younger group of orally healthy nonhuman primates. First, at the microbiome level of phyla, orders, and families, the ecology was relatively similar across sexes, matrilines, and age groups. However, at the genus level, matriline, sex, or age differences were observed. Of interest was that the principal differential genus proportions with matriline and age were similar, but somewhat unique with the sex comparison. These genus differences encompassed microorganisms generally considered as human commensals, albeit Fusobacterium, Tannerella, and Treponema genera did show some variation. The second, broader observation was the rather extensive species variation across these nonhuman primates. Nevertheless, the data could define a "core microbial species" pattern that included species across the Actinobiota, Bacteroidota, Desulfobacterota, Firmicutes/Bacillota, Fusobacteriota, Proteobacteriota, and Spirochaetota phyla. The results provide seminal details of the oral microbiome in this disease model and underpin the ability to elucidate specific microbial changes that can occur related to early-life oral environmental stimuli that may presage a greater risk for periodontitis in adulthood.}, }
@article {pmid42142239, year = {2026}, author = {Khattab, R}, title = {Artificial Sweeteners and Gut Microbiota: Mechanistic Insights and Implications for Metabolic Health.}, journal = {Current nutrition reports}, volume = {15}, number = {1}, pages = {}, pmid = {42142239}, issn = {2161-3311}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Sweetening Agents/pharmacology/adverse effects ; Energy Metabolism/drug effects ; Animals ; Insulin Resistance ; Fatty Acids, Volatile/metabolism ; Signal Transduction/drug effects ; Aspartame/pharmacology ; }, abstract = {PURPOSE OF REVIEW: Artificial sweeteners (ASs) are widely used as sugar substitutes to reduce caloric intake. Emerging evidence indicates that these compounds are not metabolically inert and can alter gut microbiota composition and downstream metabolic regulation. This review synthesizes recent mechanistic and clinical evidence on how commonly used ASs-particularly sucralose, saccharin, acesulfame-K, aspartame, and steviol glycosides-modulate intestinal microbiota.<br><br>RECENT FINDINGS: Experimental and human studies show that AS exposure is associated with alterations in microbial diversity, short-chain fatty acid (SCFA) production, and gut barrier integrity. These alterations are linked to changes in glucose homeostasis, insulin sensitivity, and energy metabolism. Proposed mechanisms include modulation of nutrient-sensing G-protein-coupled receptors, interference with bile acid metabolism, and receptor-independent activation of intracellular signaling pathways such as PI3K/Akt and mTORC1. Notably, responses in human studies appear highly individualized and dose-dependent, highlighting substantial interindividual variability. This review integrates microbiome, metabolic, and mechanistic perspectives to identify areas of emerging consensus, conflicting results, and critical research gaps in AS-microbiota-metabolism interactions. Current evidence suggests that ASs can modulate host metabolism through both microbiota-dependent and independent mechanisms. These findings have direct implications for clinical dietary guidance and risk stratification, particularly among individuals with obesity, insulin resistance, or other metabolic disorders.}, }
@article {pmid42142240, year = {2026}, author = {Xiang, W and Yang, Q and Ji, J and Qiao, H and Khan, A and Salama, ES and Mao, C and Wu, Y and Li, X}, title = {Food-Derived Limosilactobacillus fermentum GR-3 Enhances Anti-PD-1 Immunotherapy Efficacy.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {42142240}, issn = {1867-1314}, support = {GZC20251840//The Postdoctoral Fellowship Program of CPSF/ ; 32370110//National Natural Science Foundation of China/ ; 24ZDWA005//Gansu Province Science and Technology Major Project/ ; }, abstract = {Immune checkpoint blockade (ICB) has improved the cancer treatment, its application remains constrained by heterogeneous response rates and immune-related adverse events. While gut microbiome modulation represents a promising avenue to optimize ICB, rationally selected probiotics with defined mechanistic actions are critically lacking. Here, we selected Lactobacillus fermentum GR-3 (L. fermentum GR-3), a food-derived strain pre-screened for exceptional gastrointestinal resilience (maintaining > 10[7] CFU/mL), antioxidant activity (87.4% DPPH-Scavenging efficiency), and immunomodulatory potential, as an oral combination strategy to enhance anti-PD-1 therapy. In the MC38 murine colorectal cancer model, oral L. fermentum GR-3 synergistically enhanced ICB efficacy, yielding significantly greater tumor suppression than anti-PD-1 monotherapy (51.7% volume reduction vs. untreated controls), while attenuating therapy-associated weight loss. Locally within the tumor microenvironment (TME), the combination therapy promoted dendritic cell maturation (MHC-II[+] DCs reaching 56.0%), favored pro-inflammatory macrophage polarization (M1 increased to 20.8%, while M2 reduced to 2.57%), and suppressed regulatory T cell infiltration (Tregs decreased to 2.32%). These shifts strongly correlated with enhanced cytotoxic responses, with Granzyme B[+] CD8[+] T cells reaching 40.4% (doubling the effect of PD-1 monotherapy). Mechanistically, L. fermentum GR-3 colonization partially reversed tumor-associated gut dysbiosis, enriching short-chain fatty acid (SCFA)-producing consortia (e.g., Lachnospiraceae and Bacteroides) and increasing intestinal SCFA concentrations (e.g., propionic and butyric acids recovering to 70.13 and 26.07 μM/g, respectively)). This microbial-metabolic shift was accompanied by upregulated expression of mucosal tight junction genes (ZO-1, Occludin). Furthermore, L. fermentum GR-3 facilitated a balanced immune response. Systemically, it alleviated oxidative stress and buffered peripheral inflammatory signals, contributing to immune homeostasis in non-tumor tissues (spleen and colon). Collectively, these findings position L. fermentum GR-3 as a grounded, translatable strategy to simultaneously enhance ICB efficacy and improve therapeutic tolerability.}, }
@article {pmid42142274, year = {2026}, author = {Mari, PV and Carriera, L and Saviano, A and Ricci, A and Coppola, A and Ielo, S and Lipsi, R and Dodaj, M and Gennari, F and Gullà, M and Stivalini, D and Pellegrino, MG and Migneco, A and De Corso, E and Ojetti, V}, title = {Impact of IL-4/IL-13 Blockade with Dupilumab on the Microbiome in Type 2 Inflammatory Diseases: A Systematic Review.}, journal = {Current allergy and asthma reports}, volume = {26}, number = {1}, pages = {}, pmid = {42142274}, issn = {1534-6315}, mesh = {Humans ; *Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology ; *Microbiota/drug effects ; *Interleukin-13/antagonists &amp; inhibitors ; *Interleukin-4/antagonists &amp; inhibitors ; Skin/microbiology ; *Inflammation/drug therapy ; *Dermatitis, Atopic/drug therapy/microbiology ; Gastrointestinal Microbiome/drug effects ; Sinusitis/drug therapy/microbiology ; }, abstract = {PURPOSE OF REVIEW: To systematically review current evidence on microbiota changes associated with dupilumab treatment across different anatomical sites in type 2 inflammatory diseases.<br><br>RECENT FINDINGS: Fifteen studies were included, comprising two randomized trials and thirteen observational studies, mostly in atopic dermatitis, with fewer data in chronic rhinosinusitis with nasal polyps and NSAID-exacerbated respiratory disease. The skin was the most frequently investigated site, followed by the sinonasal tract and gut. Across skin studies, dupilumab was consistently associated with reduced Staphylococcus aureus, increased microbial diversity, and enrichment of commensal taxa. Sinonasal studies suggested shifts toward more eubiotic microbial communities. Gut evidence was limited, although one study suggested modulation of tryptophan metabolism-related pathways.&#xa0; Dupilumab appears to exert compartment-specific and disease-dependent effects on the microbiome. The strongest evidence concerns the skin and sinonasal compartments, whereas gut microbiota changes remain poorly defined. Further prospective studies are needed to assess microbiota signatures as potential biomarkers of response.}, }
@article {pmid42142639, year = {2026}, author = {Afresham, S and Khan, MK and Mughal, MAS and Bashir, M and Mehmood, MS and Ali, S and Abbas, Z and Azeem, A and Latif, M}, title = {Ecological and Biomedical Functions of Parasitofauna: Mechanistic and Evolutionary Perspectives.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {108561}, doi = {10.1016/j.micpath.2026.108561}, pmid = {42142639}, issn = {1096-1208}, abstract = {Parasites have traditionally been viewed primarily as pathogenic organisms associated with disease and economic burden. However, growing evidence indicates that parasitofauna-the diverse assemblage of parasitic organisms across ecosystems-plays fundamental roles in ecological regulation, host evolution, and biomedical innovation. Despite increasing recognition of these functions, existing literature largely treats ecological, immunological, and translational aspects of parasitism in isolation, lacking an integrated mechanistic framework that links these domains across biological scales. This review synthesizes current knowledge to provide a cross-disciplinary perspective on the ecological and biomedical functions of parasitofauna. Ecologically, parasites act as regulators of host population dynamics, modulators of biodiversity, and contributors to nutrient cycling and ecosystem stability. Evolutionarily, they impose strong selective pressures that shape host genetic diversity, immune system architecture, and behavioral adaptations through mechanisms such as allele frequency shifts and fitness trade-offs. From a biomedical standpoint, parasite-derived molecules demonstrate promising immunomodulatory, anti-inflammatory, and anticancer properties, with evidence derived primarily from in vitro studies and preclinical animal models, and limited support from early-phase clinical trials. In addition, interactions between parasites and the gut microbiome highlight their role in immune regulation and potential implications for inflammatory and metabolic disorders. By integrating ecological theory, evolutionary biology, and translational research, this review proposes a unified conceptual model of parasitofauna as multi-level regulators rather than solely pathogenic agents. This perspective supports a shift toward evidence-based parasite management strategies that balance disease control with ecological and therapeutic considerations. The synthesis also identifies key knowledge gaps and emphasizes the need for mechanistic, multi-system studies to better understand context-dependent outcomes of host-parasite interactions.}, }
@article {pmid42142662, year = {2026}, author = {Montenegro, J and Oliveira, CLP and Nguyen, NK and Armet, AM and Berg, A and Sharma, AM and Mereu, L and Cominetti, C and Ghosh, S and Cani, PD and Richard, C and Walter, J and Prado, CM}, title = {The effects of a powdered meal replacement intake on inflammation, gut microbiota, and metabolism compared to habitual diet in people with excess body weight - results from a randomized controlled trial.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {101595}, doi = {10.1016/j.tjnut.2026.101595}, pmid = {42142662}, issn = {1541-6100}, abstract = {BACKGROUND: Excess body weight is associated with chronic low-grade inflammation and metabolic abnormalities, such as insulin resistance, and dyslipidemia.<br><br>OBJECTIVE: This study aimed to assess the impact of a soy protein-yogurt-honey powdered meal replacement (PMR) on inflammation, gut microbiota, and metabolism in individuals with excess body weight and in weight-stable conditions.<br><br>METHODS: The Premium Study was a 12-week, parallel-arm, randomized controlled trial. Participants (body mass index 25-37 kg/m[2]) were randomized into either control (CON; usual diet, n=34) or PMR (two daily doses added to usual diet, n=29) groups, maintaining a stable body weight. Assessments occurred at baseline, week 6, and week 12, and included inflammation markers (primary outcome: interleukin-6 [IL-6]), gut microbiota diversity and composition (secondary outcome), metabolic blood markers (glucose and lipid profile), body composition (via dual-energy X-ray absorptiometry), and dietary intake. Data of completers was analyzed by two-way repeated measures analysis of variance or generalized estimating equations with Bonferroni-corrected post-hoc tests. Between-group differences in changes over time are expressed as mean and 95% confidence intervals.<br><br>RESULTS: Adherence to PMR was 98% of total doses, which increased protein intake (6.53 [5.04, 8.02]%, p<0.001) and decreased fat intake (-5.23 [-7.10, -3.35]%, p<0.001) compared to CON. By design, body weight remained stable. There were no changes in IL-6 (0.01 [-0.47, 0.45] pg/mL, p=0.412, with a low statistical power of 13.7%). Minor changes in gut microbiota composition included an increase in relative abundance of Subdoligranulum (0.72 Log2 fold-change, q=0.002). In exploratory outcomes, PMR increased lean soft tissue (LST; 0.57 [0.12, 1.02] kg, p=0.014) and reduced total cholesterol (-0.33 [-0.58, -0.08] mmol/L, p=0.01) and low-density lipoprotein cholesterol (-0.28 [-0.46, -0.10] mmol/L, p=0.003).<br><br>CONCLUSIONS: In this population, PMR intake did not improve chronic low-grade inflammation and had limited effects on gut microbiota. Improvements in LST and lipid profile warrant further exploration.<br><br>CLINICAL TRIAL REGISTRY: Number NCT03235804 registered on August 1[st], 2017: https://clinicaltrials.gov/study/NCT03235804.}, }
@article {pmid42142668, year = {2026}, author = {Keber, C and Schmitt, M and Visekruna, A and Brichkina, A and von Strandmann, EP and Bartsch, JW and Huber, M and Bauer, UM and Gress, TM and Lauth, M}, title = {Emerging concepts, hot topics, and open questions in today's pancreatic cancer research.}, journal = {Biochimica et biophysica acta. Reviews on cancer}, volume = {}, number = {}, pages = {189614}, doi = {10.1016/j.bbcan.2026.189614}, pmid = {42142668}, issn = {1879-2561}, abstract = {Despite intense research, pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal malignancies to date. The low 5-year survival rate of currently 8-10% has only marginally improved over the last years, necessitating novel approaches and a thinking "outside the box". We as translational basic and medical scientists working in a clinical research unit on tumor-stroma interactions in PDAC (the DFG-funded CRU325) have sought to identify emerging concepts in current pancreatic cancer research. We have addressed recent developments and open questions, covering a wide spectrum of topics, including clinical treatment, lifestyle, the tumor microenvironment, drug targeting, vaccination, and the microbiome. This selection of topics is highly personal and does not claim to be complete, yet it represents those areas that we believe may contribute to relevant developments in the near future. In our review, we not only briefly describe the state of the art but also pinpoint the potential of recent advances, while not ignoring current contradictions or uncertainties. Taken together, we provide our subjective view on upcoming topics in today's PDAC research landscape.}, }
@article {pmid42142727, year = {2026}, author = {Li, M and Liu, T and Yue, Y and Bae, S}, title = {Gut Microbiome and Metabolic Responses of Adult Zebrafish (Danio rerio) to the Co-exposure of Polyethylene Microplastics and Levofloxacin.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128358}, doi = {10.1016/j.envpol.2026.128358}, pmid = {42142727}, issn = {1873-6424}, abstract = {The co-occurrence of microplastics (MPs) and antibiotics in aquatic environments poses complex ecological risks. This study investigated the combined toxicity of polyethylene microplastics (PE MPs) and levofloxacin (LEV) in zebrafish using integrated untargeted metabolomics and gut microbiome profiling. Zebrafish were exposed to environmentally relevant concentrations of LEV (0.1 μg/L, 1 μg/L, 100 μg/L), PE (1 mg/L), and their combinations for 96 hours. LEV exposure produced concentration-dependent metabolic toxicity, progressing from energy conservation at 0.1 μg/L to inflammatory activation at 1 μg/L, and ultimately to system-wide metabolic perturbation at 100 μg/L. PE independently disrupted oxidative stress and membrane integrity pathways. Co-exposure generated emergent interactive effects exceeding additive predictions, with PE+LEV 0.1 μg/L affecting 387 metabolites versus 245 for LEV alone. Crucially, co-exposure elicited synergistic toxicity with unique metabolic fingerprints-including neuroendocrine activation (dynorphin B) and mTOR signaling modulation-that were absent in individual treatments. Conversely, microbiome analysis revealed an antagonistic interaction; while LEV alone caused significant dysbiosis and enrichment of resistant taxa, co-exposure stabilized microbial diversity and composition, likely due to LEV adsorption onto PE particles reducing luminal bioavailability. These findings highlight a "microbiome-host interaction paradox": PE mitigates antibiotic-induced gut dysbiosis yet exacerbates host systemic toxicity through mechanisms of epithelial barrier disruption and pharmacokinetic modulation. This study demonstrates that microbiome stability does not reliably predict host physiological health under multi-stressor conditions, underscores the importance of integrative, multi-omics approaches to assess the emergent risks of complex environmental mixtures.}, }
@article {pmid42142802, year = {2026}, author = {Stalder, M and Raurich, S and Finzel, A and Schlifke, A and Ghanbari, M and Campiche, R and Pagac, MP}, title = {3-Dimensional Facial Skin Microbiome Mapping: An Integrated Technology for Continuous Visualization of Absolute Microbial Densities.}, journal = {The Journal of investigative dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jid.2026.04.037}, pmid = {42142802}, issn = {1523-1747}, }
@article {pmid42142804, year = {2026}, author = {Zheng, F and Gao, J and Han, X and Kang, S and Zhou, T and Zhu, D and Neilson, R and Zhang, Z and Chen, B}, title = {Nematode gut microbiota confers cadmium tolerance through microbial-dependent activation of detoxification and innate immune pathways.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2026.05.035}, pmid = {42142804}, issn = {2090-1224}, abstract = {INTRODUCTION: Soil heavy metal pollution, especially cadmium (Cd) contamination, represents a serious threat to ecosystem health and agricultural sustainability. Understanding how soil organisms and their associated microbiota respond to such stress is crucial for developing bioremediation strategies.<br><br>OBJECTIVES: This study aimed to investigate the response of the gut microbiota in the model soil nematodeCaenorhabditis elegansunder Cd(II) stress, identify key bacterial taxa involved in metal detoxification, and elucidate the underlying mechanisms of microbe-mediated host resistance.<br><br>METHODS: We employed an integrated multi-omics approach, combining 16S rRNA gene sequencing, metatranscriptomics, and culturomics. The structural and functional differences between the nematode gut microbiome and the soil microbial community were compared. A core Cd(II)-tolerant gut bacterium was isolated and used for colonization experiments inC. elegansunder Cd(II) exposure. Host responses were assessed via transcriptomic analysis, antioxidant enzyme activity assays, and physiological fitness measurements.<br><br>RESULTS: Nematode gut microbiota exhibited lower diversity but higher compositional stability compared to soil communities, with deterministic host selection (R[2]&#x202f;=&#x202f;0.480) overriding stochastic assembly. The gut community was dominated by Proteobacteria, particularly Pseudomonadaceae and Sphingomonadaceae, which maintained conserved abundances across cadmium gradients. Phenotype prediction and functional analysis revealed enhanced stress tolerance and enrichment of glutathione S-transferase (GST) in the gut microbiota. From 100 isolated colonies, we identified Brucella pseudogrignonensis (formerly Ochrobactrum) as a core gut symbiont with high Cd(II) tolerance. B. pseudogrignonensis successfully colonized the C. elegans gut, significantly improving host survival, reproduction, and growth under Cd(II) exposure. Transcriptomic analysis identified 1929 bacteria-Cd(II) interaction genes, with significant enrichment in glutathione metabolism, cytochrome P450 pathways, and lysosome function. Mechanistically, live bacteria primed host immunity (e.g., clec-67, lys-2) and activated a two-phase defense program: Phase I involved lysosome pathway activation and basal immune priming; Phase II featured GST-mediated detoxification (gst-4, gst-5, and gst-6) coordinated by transcription factors DAF-16 and SKN-1, with GSH-Px activity increasing 213% under Cd(II) stress while maintaining stable ROS levels.<br><br>CONCLUSION: Using C. elegans as a model system, we demonstrate that the gut bacterium B. pseudogrignonensis enhances host Cd(II) resistance through synergistic activation of detoxification and immune pathways. These findings provide mechanistic insights into microbe-mediated heavy metal tolerance in soil fauna and identify B. pseudogrignonensis as a promising microbial candidate for developing bioremediation strategies for cadmium contaminated soils.}, }
@article {pmid42143007, year = {2026}, author = {Zhang, XD and Shen, XN and Liu, CX and Liu, ZH and Ao, X and Che, TY and Ran, TJ and Li, HL and Zhang, Y and Zhou, CH and Zou, DW}, title = {Analysis of gut microbiome dynamics in patients with type 1 autoimmune pancreatitis before and after glucocorticoid treatment.}, journal = {Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.]}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pan.2026.05.002}, pmid = {42143007}, issn = {1424-3911}, abstract = {BACKGROUND: Type 1 autoimmune pancreatitis (AIP) is a rare inflammatory pancreatic disease. Emerging evidence suggests that gut microbiota dysbiosis may contribute to the pathogenesis of type 1 AIP. However, no study has systematically characterized gut microbiota alterations before and after glucocorticoid treatment in patients with type 1 AIP.<br><br>METHODS: Fecal samples were collected from 45 healthy controls (HC), 61 patients with type 1 AIP before glucocorticoid treatment, and 27 patients after glucocorticoid treatment for metagenomic sequencing. To investigate the potential role of Streptococcus anginosus in the development of type 1 AIP, heat-killed Streptococcus anginosus was administered by oral gavage in an AIP mouse model.<br><br>RESULTS: Significant differences in both &#x3b1;-diversity and &#x3b2;-diversity were observed among HC and the pre- and post-treatment groups. Compared with the HC group, the pre-treatment group showed increased abundances of Streptococcus, Streptococcus anginosus, and Streptococcus salivarius, along with decreased abundances of Blautia and Dorea formicigenerans. Moreover, the abundances of Streptococcus and Streptococcus anginosus were reduced in the post-treatment group. In the AIP mouse model, oral gavage with heat-killed Streptococcus anginosus significantly increased the pancreatic pathological injury score.<br><br>CONCLUSIONS: Compared with the HC group, the pre-treatment group showed increased abundances of Streptococcus and Streptococcus anginosus, which were reduced in the post-treatment group. In addition, heat-killed Streptococcus anginosus exacerbated pancreatic injury in the AIP mouse model.}, }
@article {pmid42143054, year = {2026}, author = {Eom, JA and Park, IG and Hyun, JY and Lee, NY and Kwon, GH and Yoon, SJ and Won, SM and Ham, YL and Lee, KJ and Han, SH and Yang, DH and Kim, DJ and Suk, KT}, title = {Pharmabiotics, Phocaeicola dorei, ameliorates cholestatic liver fibrosis by alleviating macrophage efferocytosis of neutrophils.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73166-1}, pmid = {42143054}, issn = {2041-1723}, support = {NRF-2020R1I1A3073530 and NRF-2020R1A6A1A03043026//National Research Foundation of Korea (NRF)/ ; }, abstract = {Phocaeicola dorei has been reported to ameliorate metabolic diseases. Its role in liver fibrosis remains unclear. We evaluated the hepatoprotective effect of P. dorei in liver fibrosis. Fecal samples were collected from healthy controls and patients (n = 285) to assess the clinical relevance of P. dorei. In male mice models (3,5-diethoxycarbonyl-1.4-dihydrocollidine [DDC] diet), P. dorei (10[9] CFU/g twice/week) was orally administered. Primary HSCs, LX-2, THP-1, and HL-60 cell lines were used for mechanical validation. The relative abundance of P. dorei increased with worsing liver disease in human. P. dorei administration significantly reduced neutrophil degranulation and efferocytosis pathways (Ly6g and F4/80). The dysregulated expression of neutrophil-associated chemokines (Cx3cl1 and Cx3cr1) was restored by P. dorei. P. dorei culture supernatant inhibited macrophage-mediated efferocytosis. P. dorei attenuates liver fibrosis by suppressing neutrophil and macrophage infiltration and disrupting efferocytosis. Our results identify P. dorei as a potential microbiome-based therapeutic candidate for cholestatic liver fibrosis.}, }
@article {pmid42143215, year = {2026}, author = {Martínez, S and Cerdeiras, MP and Douterelo, I and Ijaz, UZ}, title = {Biofilm and sediment phases as key components of microbial community dynamics within secondary drinking water distribution systems.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05149-7}, pmid = {42143215}, issn = {1471-2180}, support = {EP/V030515/1//Engineering and Physical Sciences Research Council/ ; }, abstract = {BACKGROUND: Secondary drinking water distribution systems (SDWDS), particularly rooftop storage tanks, are critical components of water supply infrastructure in many regions, yet the ecological processes governing microbial community development within these systems remain poorly characterized. Here we present a year-long, phase-resolved metagenomic study of an operational full-scale SDWDS in Uruguay to assess how environmental conditions and surface materials are associated with microbiome dynamics across bulk water, biofilm and sediment phases. We integrated amplicon sequencing, whole-genome sequencing (WGS) metagenomics, culture-based microbiology and physicochemical analyses over a one-year period.<br><br>RESULTS: Microbial communities associated with biofilm and sediment phases consistently exhibited higher richness and diversity than bulk water, with marked seasonal variation. Biofilms formed on concrete and polyethylene surfaces followed distinct successional trajectories, indicating material-associated patterns in community development. Seasonal increases in temperature were associated with greater similarity in community composition across phases, while functional richness remained comparatively stable over time. Functional pathways related to energy production, stress response, and antibiotic resistance showed phase- and time-dependent enrichment, particularly in mature biofilms. Across the system, Proteobacteria, Actinobacteriota, and Bacteroidota were persistent taxa. Temperature and pH were the primary variables associated with temporal shifts in water-phase microbial communities, with chlorine residuals contributing to additional variation.<br><br>CONCLUSIONS: Together, these findings provide in situ ecological insight into microbial succession and phase-specific community dynamics in drinking water storage systems, highlighting the importance of long-term observations in real-world engineered environments.}, }
@article {pmid42143340, year = {2026}, author = {Yu, C and Lin, Y and Cui, X and Huang, X and Zhang, Y and Kang, M and Lu, J}, title = {Characteristics of gut microbiota changes in patients with nasopharyngeal carcinoma during radiotherapy.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-08265-0}, pmid = {42143340}, issn = {1479-5876}, support = {GXHL202305//the Scientifc research project of Guangxi Nursing Society/ ; Excellent nursing talent 202202//"Nursing Talents" Research and Innovation Ability Training Program of the First Affiliated Hospital of Guangxi Medical University/ ; No. 2021KY0126//Adolph C. and Mary Sprague Miller Institute for Basic Research in Science, University of California Berkeley/ ; Key No: S2023075//Health Promotion Administration, Ministry of Health and Welfare/ ; }, abstract = {BACKGROUND: This study aimed to characterize the longitudinal and dynamic changes of gut microbiota in patients with nasopharyngeal carcinoma (NPC) during radiotherapy, to inform the development of strategies for maintaining gut microbiota homeostasis.<br><br>METHODS: Thirty-one newly diagnosed NPC patients were recruited from the Department of Radiotherapy, First Affiliated Hospital of Guangxi Medical University, and 31 age-matched healthy controls from the same Hospital Physical Examination Center between August and December 2023. Fecal samples were collected from NPC patients at three key time points, including days 1-3 pre-radiotherapy (T0), days 14-18 of mid-radiotherapy (T1), and days 28-32 at end of radiotherapy (T2). Meanwhile, fecal samples from healthy controls were collected on the morning of their physical examination. 16S rDNA sequencing, combined with bioinformatics and statistical analyses, was used to compare the structural characteristics and dynamic changes of gut microbiota in NPC patients during radiotherapy.<br><br>RESULTS: Alpha diversity analysis showed significantly lower Shannon and Chao1 indices in NPC patients compared with healthy controls. Beta diversity analysis based on the Bray-Curtis distance revealed distinct gut microbial community structures between NPC patients and healthy controls. In this intergroup comparison, a total of 16 core differentially abundant taxa were consistently identified by two complementary analytical methods (LEfSe and ALDEx2). Linear mixed-effects models demonstrated that the Chao1 index at T0 was significantly lower than at T1 and T2 in NPC patients. Following adjustment for multiple confounding variables, mucositis grade was the only factor significantly associated with gut microbiota alpha diversity during radiotherapy. Radiotherapy time points, treatment regimen, and most clinical and demographic variables showed no such association. Beta diversity analyses based on the Bray-Curtis and unweighted Unifrac distances revealed significant compositional and structural differences linked to radiotherapy time points (T0/T1/T2) in the gut microbiota of NPC patients. This temporal variation was abrogated by stratification according to chemotherapy regimen. Beta diversity based on Bray-Curtis distance showed no significant differentiation across time points in either the concurrent chemotherapy (CCRT) alone cohort or the induction chemotherapy plus CCRT cohort. LEfSe and ALDEx2 concordantly identified seven core differentially abundant taxa across all NPC patients in the longitudinal T0 vs. T1 vs. T2 analysis. Stratification by chemotherapy regimen revealed such core taxa in the CCRT alone cohort, whereas no core differentially abundant taxa were detected by either method in the induction chemotherapy plus CCRT cohort.<br><br>CONCLUSION: Our findings demonstrate that NPC patients exhibit significant gut microbial dysbiosis compared with healthy controls, characterized by reduced alpha diversity and altered genus-level composition. Longitudinal analyses further revealed that radiotherapy is associated with dynamic alterations in gut microbial diversity, composition, and structure in NPC patients. Notably, these temporal shifts in the gut microbiota are strongly stratified by chemotherapy regimen, with pronounced changes observed in patients receiving CCRT alone but a stable microbial profile in those receiving induction chemotherapy followed by CCRT. Collectively, these results highlight the profound impact of oncological treatment on the gut microbiome in NPC patients and identify treatment regimen as a critical modifier of microbial dynamics during radiotherapy.}, }
@article {pmid42143365, year = {2026}, author = {ChenLiu, Z and Tang, D}, title = {Neuron-tumor interplay in colorectal cancer: from mechanisms of onset and progression to targeted therapies.}, journal = {Cell communication and signaling : CCS}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12964-026-02938-5}, pmid = {42143365}, issn = {1478-811X}, support = {SJCX22_1816//the Graduate Research- Innovation Project in Jiangsu province/ ; }, abstract = {Colorectal cancer (CRC) is a major cause of cancer-related mortality worldwide, traditionally attributed to genetic mutations and epigenetic alterations. However, with the emergence of cancer neuroscience, a paradigm shift has occurred, revealing the central role of the nervous system in the initiation, progression, and metastasis of CRC. The gastrointestinal tract, being the only organ in the body with an independent peripheral nervous system - the enteric nervous system (ENS) - provides a unique anatomical and functional basis for neuro-tumor interactions. This review systematically explores the mechanisms by which the nervous system regulates CRC cell proliferation, invasion, and immune microenvironment remodeling through neurotransmitters (such as norepinephrine and acetylcholine) and neurotrophic factors (including NGF and BDNF). We also delve into the role of the brain-gut-microbiome axis, particularly its influence on tumor progression through metabolic reprogramming and neuroimmune crosstalk. Finally, we discuss novel therapeutic strategies based on the bidirectional communication between the nervous system and CRC, offering new perspectives for precise interventions in CRC.}, }
@article {pmid42143575, year = {2026}, author = {Zhang, P and Zhao, M and Cheng, Z and Ding, Y and Xia, S and Guo, J}, title = {Bile acid metabolism dysregulation following Helicobacter pylori eradication promotes plasmid-mediated antimicrobial resistance in the gut microbiome.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag126}, pmid = {42143575}, issn = {1751-7370}, abstract = {Antimicrobial resistance (AMR) transmission within the gut microbiome poses a major health risk during antibiotic exposure, primarily via horizontal gene transfer (HGT). However, how antibiotic-induced metabolic remodeling of the intestinal environment modulates plasmid-mediated AMR dissemination remains unclear. Herein, integrating metagenomics, metabolomics, in vitro conjugation assays, and in vivo mouse models, we show that Helicobacter pylori eradication therapy reshapes gut metabolism in ways that enhance transfer of antibiotic resistance genes (ARGs). Metagenomic analysis revealed the expansion of Escherichia populations and the enrichment of plasmid-borne ARGs after H. pylori eradication. Fecal filtrates from treated individuals significantly increased conjugation frequencies of the broad-host-range plasmid RP4 in E. coli. Metabolomic profiling identified a pronounced accumulation of primary bile acids, including glycocholic acid, taurocholic acid, glycochenodeoxycholic acid, and taurochenodeoxycholic acids, which could increase bacterial membrane permeability, induce the SOS response, and upregulate conjugation and pilus assembly genes, thereby accelerating ARG transfer. Molecular docking further suggested these bile acids may likely participates in interacting with global plasmid repressors KorA/KorB, derepressing conjugation operons. In mice, H. pylori eradication therapy elevated fecal primary bile acid levels and significantly promoted in vivo plasmid transfer, with the critical role of bile acids further confirmed through interventions using the bile acid sequestrant cholestyramine or glycocholic acid. Together, these findings demonstrate that dysregulation of bile acid metabolism due to H. pylori eradication creates a permissive gut niche for plasmid-mediated ARG dissemination, providing mechanistic insight into how clinical antibiotic regimens can unintentionally promote microbiome-associated AMR risk.}, }
@article {pmid42143576, year = {2026}, author = {Xu, X and Tan, Y and Xiecun, S and Wang, J and Zhao, W and Wang, L and Dai, R and Tang, L and Li, X and Jin, D and Fan, Y}, title = {Galactosaminogalactan orchestrates Verticillium dahliae virulence and rhizosphere microbial ecology through multi-partite interactions.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag123}, pmid = {42143576}, issn = {1751-7370}, abstract = {The infection of plants by soil-borne fungal pathogens is a complex process and depends on their adhere ability to host surfaces and interactions with the rhizosphere bacteria. In this study, we identify galactosaminogalactan (GAG) as a pivotal virulence determinant in the pathogenesis of Verticillium dahliae. By characterizing the VdGAG biosynthetic gene cluster, we show that the glycosyltransferase VdGtb is essential for GAG synthesis. The knockout of GAG increased fungal sensitivity to the cell wall-perturbing agent calcofluor white (CFW) and reduced mycelial ball formation in liquid culture. The absence of GAG polysaccharides reduced root-binding capacity by 50% and increased cotton immune responses 1 day post fungal infection. The ΔVdGtb mutant exhibited a significant 30.5% decrease in the pathogenicity toward cotton seedlings compared with the wild type V991. Microbiome and bacterial enrichment analysis indicate that the GAG polysaccharides promote the enrichment of soil bacteria and alter the bacterial community structure in the plant rhizosphere. Several bacteria enriched by GAG-contained fungal cells, including Achromobacter animicus, Pseudomonas aeruginosa, and Acinetobacter pittii exhibited strong growth-inhibitory effects against V. dahliae and showed distinct effects on fungal virulence in a GAG-dependent manner. Together, these results reveal that GAG is not merely a cell wall component but a multi-functional molecule that orchestrates fungal protection, host infection, and inter-kingdom microbial communication.}, }
@article {pmid42143583, year = {2026}, author = {Kim, J and Kim, WI and Lee, K and Kim, N and Hwang, AY and Suh, DH and Cho, D and Ji, Y and Kang, H and Jung, ES}, title = {Systems-level restoration of vaginal and gut microbiota by lactobacillus helveticus 20 838 alleviates Gardnerella vaginalis-induced dysbiosis.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag118}, pmid = {42143583}, issn = {1751-7370}, abstract = {Bacterial vaginosis (BV), often driven by Gardnerella vaginalis overgrowth, is characterized by epithelial disruption, inflammation, and microbiome dysbiosis across the vaginal and gut ecosystems. Affecting a majority of women during their reproductive years, BV increases the risk of infection and reproductive complications. Here, we identify a novel probiotic strain, Lactobacillus helveticus 20 838, exhibiting potent antagonistic activity against G. vaginalis and evaluate its ecological and immunological effects in a murine model of vaginitis. Comparative genomics revealed distinct adaptive and antimicrobial traits of L. helveticus 20 838 relatives to the reference strain DPC4571. Both oral and intravaginal administration reduced G. vaginalis colonization, suppressed Tnf-α and Il-1β expression in vaginal tissue, and prevented pathological epithelial thickening. Multi-omics profiling of fecal and vaginal samples demonstrated restoration of microbial alpha and beta diversity disrupted by infection. The L. helveticus 20 838 reduced dysbiosis-associated taxa such as Staphylococcaceae whereas enriching protective Lactobacillus species, with intravaginal delivery achieving superior local recolonization of Lactobacillaceae. Collectively, these findings identify L. helveticus 20 838 as a next-generation probiotic that alleviates G. vaginalis-induced dysbiosis by restoring microbial and immune homeostasis across interconnected mucosal niches, providing a systems-level framework for microbiota-targeted therapy in women's health.}, }
@article {pmid42143599, year = {2026}, author = {Dong, A and Paju, S and Leskelä, J and Manzoor, M and Putaala, J and Ylikotila, P and Könönen, E and Pussinen, P and Zaric, S}, title = {Microbial burden of periodontal diseases and its clinical application: The stage, grade, and furcation matter.}, journal = {Journal of periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1002/jper.70140}, pmid = {42143599}, issn = {1943-3670}, support = {SGL023/1035/AMS_/Academy of Medical Sciences/United Kingdom ; //Medical Research Council Impact Acceleration Account/ ; 202108410182//Engineering and Physical Sciences Research Council/ ; //Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral &amp; Craniofacial Sciences/ ; //Revealing the Etiology/ ; //Sigrid Jus&#xe9;lius Foundation/ ; TYH2014407//Helsinki and Uusimaa Hospital District/ ; TYH2018318//Helsinki and Uusimaa Hospital District/ ; //Finnish Medical Foundation/ ; //Finnish Dental Society Apollonia/ ; //King's-China Scholarship Council/ ; }, abstract = {BACKGROUND: Periodontal diseases are associated with dysbiotic oral microbial communities, but clinically applicable measures that reflect microbial burden across disease severity and progression remain limited. This study aimed to assess the oral microbial burden of periodontal diseases by evaluating salivary and subgingival lipopolysaccharide (LPS) activity and lipoteichoic acid (LTA) levels, to explore their relationships with microbial dysbiosis and clinical periodontal parameters in individuals with periodontal health (n = 52), gingivitis (n = 194), and periodontitis of varying stages, grades, and furcation involvement (n = 78), and to assess their diagnostic potential.<br><br>METHODS: Saliva and subgingival plaque samples from 324 SECRETO cohort participants were analyzed for microbial virulence factors using a recombinant Factor C assay for LPS and enzyme-linked immunosorbent assay (ELISA) for LTA. Microbial dysbiosis was assessed using a sequencing-derived, simplified dysbiosis index, calculated from subgingival 16S rRNA gene sequencing and salivary shotgun metagenomic profiles, based on the relative abundances of health-associated and periodontitis-associated taxa.<br><br>RESULTS: Subgingival LPS activity was significantly higher in periodontitis patients compared to healthy individuals and increased progressively across disease stages and grades. Salivary LPS activity differed only by periodontal diagnosis and correlated with full-mouth bleeding score (FMBS). LTA levels showed no statistical variations across periodontal conditions. Subgingival LPS activity and LPS/LTA ratio were strongly associated with simplified dysbiosis index. Salivary dysbiosis index was significantly higher in patients with furcation involvement. Receiver operating characteristic (ROC) analyses identified subgingival LPS, salivary LPS, and simplified dysbiosis index as diagnostic biomarkers with good clinical utility (area under the curve [AUC] 0.59-0.87).<br><br>CONCLUSIONS: This study highlights the importance of periodontitis diagnoses, stages and grades of periodontitis and furcation involvement as determining factors for increased salivary and subgingival bioburden. In addition, LPS activity could be used as a reliable periodontal biomarker, while the LPS/LTA ratio is an indirect indicator of microbial dysbiosis.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT01934725.<br><br>PLAIN LANGUAGE SUMMARY: Periodontitis is a common inflammatory disease that affects the tissues supporting the teeth and can lead to tooth loss and broader health consequences if not properly managed. This study explored whether measures of oral microbial burden, particularly bacterial components such as lipopolysaccharide (LPS) and lipoteichoic acid (LTA), could help explain differences in periodontal disease severity and progression. Saliva and subgingival plaque samples were analyzed from individuals with periodontal health, gingivitis, and different stages and grades of periodontitis. We found that microbial burden, especially subgingival LPS activity, increased consistently with more severe and rapidly progressing forms of periodontitis and was closely associated with clinical signs of inflammation. In contrast, LTA levels showed limited variation across disease categories. Importantly, LPS-related measures demonstrated good ability to distinguish periodontal health from disease. These findings suggest that assessing microbial burden, particularly LPS activity, may provide clinically useful information beyond traditional periodontal assessments and could support improved disease classification, risk assessment, and the development of more personalized periodontal care strategies.}, }
@article {pmid42143685, year = {2026}, author = {T, K and T, B and M S, K and T, S}, title = {Simulating the impacts of ocean deoxygenation on coral reef resilience using adaptive ecosystem modeling.}, journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances &amp; environmental engineering}, volume = {}, number = {}, pages = {1-15}, doi = {10.1080/10934529.2026.2664333}, pmid = {42143685}, issn = {1532-4117}, abstract = {Adaptive ecosystem modeling provides a proactive approach to mitigating ocean deoxygenation and enhancing coral reef resilience. This study proposes an integrative framework that combines machine-learned dissolved oxygen (DO) reconstructions with a multispecies reef ecosystem model, augmented by Bayesian uncertainty quantification to identify intervention strategies that maximize ecological recovery. By explicitly linking oxygen dynamics with biological feedbacks and management actions, the framework addresses critical gaps in current hypoxia mitigation research. The approach is applied to the central Great Barrier Reef using long-term in situ measurements and satellite observations for model calibration. Simulation results indicate that targeted aeration, watershed nutrient reduction, and microbiome manipulation can reduce cumulative hypoxic stress by up to 43% over two decades, while increasing live coral cover by 28% relative to baseline projections. Sensitivity analyses reveal that model outcomes are particularly influenced by microbial acclimation rates and seasonal DO minima, highlighting the importance of fine-scale biogeochemical monitoring. Overall, the findings demonstrate the value of an adaptive, data-driven decision-support framework that integrates ecological processes, high-resolution environmental data, and management interventions, offering scalable guidance for hypoxia resilience planning in threatened coral reef systems.}, }
@article {pmid42143767, year = {2026}, author = {Zhang, Y and Zhang, X and Wang, S and Xu, Z and Wei, Q and Hua, S}, title = {Intestinal Alkaline Phosphatase Alleviates Ruminal Acidosis in Dairy Cows Fed High-Concentrate Diets Improves Their Overall Health.}, journal = {Journal of animal physiology and animal nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1111/jpn.70073}, pmid = {42143767}, issn = {1439-0396}, abstract = {The pursuit of high milk yields via high-concentrate diets risks ruminal acidosis and microbial dysbiosis, triggering lipopolysaccharide (LPS) release, subacute ruminal acidosis (SARA) incidence, and substantial economic losses. This study evaluated the efficacy of the dietary intestinal alkaline phosphatase (IAP) against high-concentrate feeding effects, hypothesizing it prevents SARA by degrading LPS, modulating microbiota, stabilizing ruminal pH, and improving gut health. Thirty-six lactating cows were stratified into three groups (n = 12): a high-concentrate diet group (HC, 5:5 concentrate:forage), an HC group supplemented with IAP (HC + IAP), and a low-concentrate control group (LC, 3:7). Key biomarkers such as ruminal pH, ruminal and fecal LPS, inflammatory cytokines (IL-6, IL-1β), and acute-phase proteins (SAA, LBP)--were monitored at 30-day intervals from calving through lactation. SARA status was defined by ruminal pH: < 5.6 (SARA), 5.6-5.8 (at-risk), and ≥ 5.8 (healthy). Fecal microbiome analysis was conducted on HC and HC + IAP cows at 90 days in milk (DIM). The HC group exhibited a high incidence of SARA, peaking between 90 and 120 DIM. In stark contrast, dietary supplementation with IAP (0.5 kg per 1000 kg of concentrate feed) effectively stabilized ruminal fluid pH, thereby completely preventing the incidence of SARA throughout the entire lactation period. This prophylactic effect was associated with significantly reduced systemic concentrations of SAA, LBP, IL-6, and IL-1β. Moreover, IAP treatment markedly enhanced gut microbial diversity and the relative abundance of beneficial bacteria. Therefore, IAP acted primarily in the rumen to detoxify LPS, thereby stabilizing pH and preventing the occurrence of SARA, while also entering the intestine to regulate the structure of gut microbiota, thereby maintaining the health of dairy cows under high-concentrate feeding conditions.}, }
@article {pmid42135082, year = {2026}, author = {Saranya, RG and Ramesh Babu, K and Viswanathan, P}, title = {Corrigendum to "Investigating gut microbiome dysbiosis in adults with chronic kidney disease: Diabetes-induced alterations via metagenomics and qPCR" [Life Sci. 393 (2026) 124336].}, journal = {Life sciences}, volume = {}, number = {}, pages = {124457}, doi = {10.1016/j.lfs.2026.124457}, pmid = {42135082}, issn = {1879-0631}, }
@article {pmid42135208, year = {2026}, author = {He, F and Lin, Q and Tan, Y and Yan, Z and He, H and Lin, L}, title = {Drug-Induced Alterations of Mouse Aorta Lipidome and Their Potential Correlations with the Gut Ecosystem.}, journal = {Journal of proteome research}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jproteome.6c00103}, pmid = {42135208}, issn = {1535-3907}, abstract = {Drug-induced cardiovascular risk is one of the primary concerns in drug development and clinical practice. Meanwhile, drugs can also alter the gut microbiome, the disturbance of which is correlated with cardiovascular diseases. However, the detailed molecular information underlying these associations is still unclear. Here, we comprehensively investigated the impact of 33 commonly used drugs on the mouse aorta lipidome and gut metaproteome, revealing that 6 out of 8 (75.0%) anticancer drugs and 2 out of 16 (12.5%) cardiovascular drugs significantly altered the aorta lipids, with the majority being downregulated. Drugs triggered a greater increase in phosphatidylethanolamine (PE) with longer fatty acyl chains and higher degrees of unsaturation rather than hydrophobicity. Drugs also tend to suppress gut microbial producers of short-chain fatty acids. Antibiotic pretreatment and conventional mouse models revealed potential drug-host-microbe interactions on the gut-vascular axis. This study provides a deeper insight into the pharmacological actions of the studied drugs with a molecular basis for the management of cancer treatment-related cardiovascular diseases.}, }
@article {pmid42135319, year = {2026}, author = {Chuanjian, L and Hao, Z and Xinyang, L and Wenjin, G and Yang, Z and Qianyu, W and Hongmingxiu, F and Zhihui, L}, title = {Naringin alleviates periodontitis via direct AMPK/Nrf2 activation and NLRP3 inhibition, amplified by gut microbiota/Arg-Gln modulation.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01007-6}, pmid = {42135319}, issn = {2055-5008}, support = {82370934//National Natural Science Foundation of China/ ; YDZJ202401160ZYTS//Jilin Provincial Natural Science Foundation/ ; }, abstract = {Periodontitis, driven by oral-gut microbiota dysbiosis and NLRP3 inflammasome activation, lacks effective natural therapeutic strategies. This study investigated naringin (Nar), a grapefruit peel flavonoid, using ligature-induced periodontitis in rats and LPS-stimulated RAW264.7 cells. Nar treatment significantly reduced alveolar bone loss, inhibited NLRP3 inflammasome activation (NLRP3, IL-1β), and suppressed inflammatory mediators (COX2, iNOS, IL-6, TNF-α) while improving collagen organisation. Microbiome analysis revealed that Nar suppressed pathogenic bacteria (Veillonella orally, Escherichia-Shigella in the gut) and enriched beneficial Lactobacillus. Metabolomics analysis revealed a significant decrease in the abundance of arginyl-glutamine (arg-gln) in the intestines of rats with periodontitis. Both Nar and arg-gln activated the AMPK/Nrf2 pathway, suppressing NLRP3 activation. FMT from Nar-treated donors had similar anti-inflammatory effects. In conclusion, Nar alleviates periodontitis primarily by directly activating the AMPK/Nrf2 pathway and inhibiting NLRP3 inflammasome activation in periodontal tissues. Additionally, Nar reshapes the gut microbiota to elevate arg-gln levels, which further amplifies AMPK activation and contributes to inflammation control, but is not sufficient alone to drive structural repair. These findings provide a novel theoretical basis for natural compound-mediated microbiota and inflammatory regulation in periodontitis treatment.}, }
@article {pmid42135323, year = {2026}, author = {Park, JH and Kim, SY and Lim, HS and Kim, HJ and Lee, JY and Chung, J and Na, HS}, title = {A cross-sectional study of supragingival microbiome depending on age in Korean population.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-47336-6}, pmid = {42135323}, issn = {2045-2322}, support = {NRF-RS-2024-00349457//National Research Foundation of Korea/ ; NRF-RS-2024-00349457//National Research Foundation of Korea/ ; NRF-RS-2024-00349457//National Research Foundation of Korea/ ; }, abstract = {Age is a key factor influencing the composition of the oral microbiome, but its age-related dynamics remain unclear as most studies focus on specific age groups or disease-related changes. The objective of this study was to characterize age-related differences in the supragingival microbiome. Supragingival plaque samples were collected from 533 participants across four age groups including Child (3 ~ 5 year), Young adult (18 ~ 34 year), Mid-age (35 ~ 65 year) and Elder (over 65 year) groups. Microbial DNA was extracted and analyzed using 16S rRNA gene sequencing. Alpha and beta diversity were assessed. Taxonomic classification was performed using a Naïve Bayes classifier trained on the eHOMD database. Differential abundance analysis was conducted using LEfSe, and microbial network interactions were examined using SparCC. Alpha diversity differed among age groups, and beta diversity also showed significant differences among groups, except between the Mid-age and Elder groups. The relative abundance of Firmicutes and Proteobacteria was lower in the Mid-age and Elder groups, whereas Bacteroidetes and Fusobacteria were more abundant. Early colonizers such as Streptococcus, Veillonella, and Haemophilus were less abundant in these groups, while periodontopathogens including Porphyromonas, Fusobacterium, and Treponema were more abundant. Core microbiome analysis revealed Streptococcus dominance in the Child group, the presence of Rothia and Actinomyces in the Young adult group, and more pathogen-enriched microbiome in the Mid-age and Elder groups. Microbial network complexity also differed across age groups, with denser and more pathogen-centered networks observed in the older groups. Distinct age-related differences in the oral microbiome were observed in this cross-sectional study, with microbial diversity, taxonomic composition, and microbial interaction patterns. These findings suggest that understanding age-related microbial variation may be important for long-term oral health.}, }
@article {pmid42135341, year = {2026}, author = {Huang, Y and Hong, L and Li, S and Zhang, L and Guo, X and Han, J and Yu, W and Chen, H and Luo, N and Chen, J and Peng, W and Zhou, Y and Hong, S and Yan, W and Jiang, S and Cao, Y}, title = {Neonatal intensive care unit exposures reprogram microbiome-metabolome trajectories and modulate host calprotectin in preterm infants: a longitudinal multi-omics study.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01008-5}, pmid = {42135341}, issn = {2055-5008}, support = {82402017//National Key Research and Development Program of China/ ; 82402017//National Key Research and Development Program of China/ ; }, abstract = {Early-life gut microbiota development is critical for orchestrating mucosal barrier function and immune priming, as disruptions in this process can increase susceptibility to life-threatening diseases such as necrotizing enterocolitis (NEC) and sepsis. This longitudinal multi-omics study of 186 preterm infants (<32 weeks of gestation or <1500 g birth weight) explores the impact of early-life exposures in the neonatal intensive care units (NICUs) on gut microbiota, metabolism, and immune responses. We analyzed 1153 stool samples using quantitative microbial profiling, untargeted metabolomics, and fecal S100A8/A9 (calprotectin) levels. Antibiotic exposure suppressed anaerobic colonization and microbial diversity in a cumulative exposure-dependent manner, with breastmilk feeding partially mitigating these effects. The stool metabolome correlated with microbial colonization, showing antibiotic-driven disruptions in polyamine metabolism linked to anaerobe abundance. Host calprotectin levels followed a biphasic pattern, correlating with microbial diversity and polyamine metabolites. Mediation analysis identified anaerobe suppression and polyamine depletion as key drivers of antibiotic-associated reductions in calprotectin. This study reveals that NICU interventions, particularly antibiotics, reprogram the preterm gut ecosystem and immune response, with anaerobes and polyamines being key mediators linking microbial ecology to immune maturation during early life.}, }
@article {pmid42135536, year = {2026}, author = {Adedire, DE and Onilude, AA and Odeniyi, OA and Nash, O and Semenya, K and Unuofin, JO}, title = {Snapshot reflection of the seasonal resilience and diversity of fungal phylotypes in the tropical Ikogosi spring.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {42135536}, issn = {1614-7499}, abstract = {Freshwater ecosystems like rivers, streams, and springs harbour diverse microbial communities, including fungal and bacterial phylotypes. These communities are an important part of the aquatic ecosystem, playing key roles in biogeochemical cycles. However, research on the seasonal differences concerning the fungal diversity of Ikogosi Warm Spring's sediments and water has been lacking. In this pilot study, we aimed to bridge this gap by employing high-throughput DNA sequencing to examine the fungal microbiome of this spring during the wet and dry seasons. Metagenomic DNA was extracted from water and sediment samples from different locations of the spring, and the fungal ITS1 region was sequenced using Illumina HiSeq technology. Sequences were processed with the DADA2 pipeline in R, enabling comprehensive taxonomic and diversity analyses. In addition, the spring's sediment and water physicochemical characteristics were assessed, and the impact of environmental variables on fungal communities was examined using redundancy analysis. Taxonomic analysis revealed that the spring was dominated by Ascomycota and Basidiomycota, irrespective of seasonal differences. In water samples, Ascomycota represented 62.0% (wet season) and 89.0% (dry season), while Basidiomycota accounted for 37.7% and 10.7%, respectively. Sediments exhibited a similar dominance, with Ascomycota comprising 65.1% in both seasons and Basidiomycota contributing 34.8% (wet season) and 33.5% (dry season). Alpha diversity indices indicated that fungal diversity was higher during the dry season than in the wet season, with no significant difference at p < 0.05. Redundancy analysis showed that some physicochemical factors, such as potassium and sulphate ions in water samples, were associated with seasonal patterns. These factors also influenced fungal communities in the spring, such as Cladosporium, Trichosporon, and Meyerozyma.}, }
@article {pmid42135574, year = {2026}, author = {Yang, Y and Vega, A and Holck, J and Planas, A and Biarnés, X and Zeuner, B}, title = {Computationally guided enzyme engineering for regioselective synthesis of fucosylated human milk oligosaccharides.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-026-13860-8}, pmid = {42135574}, issn = {1432-0614}, abstract = {Human milk oligosaccharides (HMOs) are key bioactive components of human milk that support infant health and microbiome development. Prevalent HMOs include the internally fucosylated pentasaccharides lacto-N-fucopentaose II (LNFP II) and lacto-N-fucopentaose III (LNFP III), which are absent from infant formula. Their enzymatic synthesis from simpler HMOs such as 3-fucosyllactose (3FL), lacto-N-tetraose (LNT) and lacto-N-neotetraose (LNnT) represents an important step towards bridging this gap, especially now that these simpler HMOs are available on an industrial scale. We evaluated the use of the GH29B α-1,3/4-L-fucosidase SpGH29[C] from Streptococcus pneumoniae for transfucosylation at equimolar donor-to-acceptor ratio and applied the computational pipeline BindScan to design variants with reduced hydrolytic activity to avoid undesirable product hydrolysis. Guided by these predictions, we generated and tested 21 variants of SpGH29[C], achieving significantly reduced hydrolysis and enhanced transglycosylation yields. Variants W264F and D257N reached LNFP II yields of up to 73% and 68%, respectively, while A173H improved LNFP III formation to 53%. Importantly, the product levels remained stable over 24 h as the variants displayed significantly decreased product hydrolysis as intended. Further binding analyses with BindScan enabled rational targeting of regioselectivity, identifying W211 as a key position influencing branched vs. linear product formation for LNFP II synthesis, while F202 and D257 variants improved regioselectivity in LNFP III synthesis. This study demonstrates that computationally guided protein engineering can optimize glycosidase-catalyzed transglycosylation and provides a framework for designing regioselective biocatalysts for complex oligosaccharides synthesis. KEY POINTS: • BindScan designs fucosidase variants with improved transglycosylation performance • SpGH29[C] variants efficiently synthesize LNFP II and LNFP III with low hydrolysis • SpGH29[C] positions W211, F202 and D257 influence regioselectivity.}, }
@article {pmid42135633, year = {2026}, author = {Basu, U and Ahanger, SA and Song, T and Gai, X and Hu, X}, title = {Ecological and genomic dynamics of the soil microbiome under sustained pressure from Phytophthora nicotianae, the causal agent of tobacco black shank disease.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05137-x}, pmid = {42135633}, issn = {1471-2180}, support = {202405AD350100, 2023530000241003/YNDG202302XJ02//Yunnan Applied Fundamental Research Projects and the Yunnan Provincial Tobacco Monopoly Bureau/ ; }, abstract = {BACKGROUND: Soil-borne pathogens threaten global agriculture, yet soil microbiome adaptation to persistent pathogen pressure is poorly understood. This study characterized the ecological and genomic long-term shifts in a tobacco field soil microbiome under sustained Phytophthora nicotianae pressure. We conducted a six-year longitudinal metagenomic study in a field with a documented history of tobacco black shank disease. Comparative analysis of the rhizosphere microbiome from Year_1 and Year_6 was performed using shotgun sequencing, non-redundant gene catalog construction, and functional annotation against specialized databases.<br><br>RESULTS: Our analysis revealed a profound genetic remodelling, with 45.6% (116,529) of 255,258 genes showing significant differences in abundance (p&#x2009;<&#x2009;0.05, |log2FC| &#x2265; 1). This restructuring was systematic, characterized by significant enrichment of the soil antibiotic resistome, where 45.88% of antibiotic resistance genes were differentially abundant and showed a distinct trend toward increased abundance. The functional potential for carbohydrate metabolism was reorganized, with 53.2% of CAZymes (Carbohydrate-Active enZYmes) genes showing differential abundance and a predominant depletion. Analysis of COG (Clusters of Orthologous Groups) revealed a strategic functional trade-off, with significant enrichment of defense-related categories like secondary metabolite biosynthesis (+&#x2009;52.9%) alongside a reduction in growth-related processes. Such functional changes were ultimately driven by an taxonomically homogenized community, as indicated by a major reduction in species level alpha diversity (Shannon index: 5.52 to 5.31) that coexisted with a 14.8% significant increase in species level abundance, which showed a selective enrichment of a subset of dominant taxa.<br><br>CONCLUSION: Sustained pathogen pressure triggers a coordinated, multi-level adaptive succession, reshaping the genetic, functional, and taxonomic structure of the soil microbiome into a more defended and specialized state.}, }
@article {pmid42135724, year = {2026}, author = {Jiang, S and Shang, G and Ning, W and Liu, D and Huang, J and Lan, X and Bai, Y and Hao, Y and Wang, H and Zhang, H}, title = {Lactobacillus-derived indole-3-lactic acid suppresses meningioma malignant phenotypes by direct anti-proliferative effects and macrophage reprogramming.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-08222-x}, pmid = {42135724}, issn = {1479-5876}, abstract = {BACKGROUND: The intratumoral microbiome influences cancer progression, but its role in meningiomas is unknown. We characterized the meningioma intratumoral microbiome and investigated its functional significance.<br><br>METHODS: 16&#xa0;S rRNA sequencing was performed on 80 meningioma specimens (44 benign, 36 non-benign). Microbial findings were validated via fluorescence in situ hybridization (FISH) and transmission electron microscopy. Among differentially abundant genera, Lactobacillus was identified as the core genus due to its 100% detection rate and significant enrichment in benign tumors, and was thus selected for functional interrogation. We employed in vitro assays (proliferation, migration), non-targeted metabolomics, RNA sequencing, and co-culture systems with primary human macrophages derived from peripheral blood mononuclear cells (PBMCs) and THP-1 cells to dissect microbial-metabolite-immune interactions.<br><br>RESULTS: Meningiomas harbor a distinct intratumoral microbiome dominated by Firmicutes and Bacteroidota, with beta diversity revealing significant compositional differences between benign and non-benign tumors. The Lactobacillus genus was identified as a core genus enriched in benign tumors, and its abundance negatively correlated with the Ki-67 proliferation index. Logistic regression analysis further indicated an association between Lactobacillus abundance and low-aggressiveness tumor phenotypes (benign histology and low Ki-67 index); however, this association was not independent after adjusting for key clinical confounders. Functionally, the supernatant from cultured Lactobacillus intestinalis (putative L. intestinalis, a species belonging to the Lactobacillus genus that showed a differential abundance pattern between benign and non-benign meningiomas) suppressed IOMM-Lee cell proliferation and migration. Non-targeted metabolomics identified indole-3-lactic acid (ILA) and niacin as the predominant metabolites in the bacterial supernatant. ILA was established as the primary effector, recapitulating the direct antitumor effects and skewing human macrophages towards an M1-polarized phenotype with enhanced secretion of IL-12 and IL-6. While niacin also promoted M1 cytokine secretion, it lacked direct antiproliferative activity. Transcriptomic profiling of ILA-treated tumor cells confirmed the suppression of multiple oncogenic pathways.<br><br>CONCLUSION: This study characterizes the intratumoral microbiome of meningiomas and reveals that the Lactobacillus genus may serve as a potential microbial marker for a low-proliferation, low-necrosis tumor microenvironment. Furthermore, we uncover a tumor-suppressive mechanism mediated by Lactobacillus, identifying its metabolite, indole-3-lactic acid (ILA), as a key effector. As an exogenous compound, ILA exerts dual anti-tumor activity through direct anti-proliferative effects and immunomodulation in vitro experiments. While these findings are preliminary and require further validation in vivo, they suggest ILA as a potential preclinical candidate for informing future therapeutic strategies.}, }
@article {pmid42135886, year = {2026}, author = {Wang, X and Song, F and Zhang, L and Jiang, L and Li, D and Huang, Z}, title = {Advances in Protein-Based Delivery Systems: From Structural Design to Smart Responses and Intestinal Microbiome Modulation.}, journal = {Comprehensive reviews in food science and food safety}, volume = {25}, number = {3}, pages = {e70504}, doi = {10.1111/1541-4337.70504}, pmid = {42135886}, issn = {1541-4337}, support = {ZDYF2025XDNY084//Hainan Province Science and Technology/ ; ZDYF2025XDNY065//Hainan Province Science and Technology/ ; GHYF2025001//International&#xa0;Science &amp; Technology Cooperation Program of Hainan Province/ ; }, mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Drug Delivery Systems ; *Proteins/chemistry/administration &amp; dosage ; }, abstract = {While bioactive compounds hold significant potential for health promotion, their application is severely constrained by issues such as poor stability, low oral bioavailability, and susceptibility to degradation in the gastrointestinal environment. Protein-based delivery systems (PBDS), as novel carriers, demonstrate the potential to overcome these challenges through encapsulation and targeted release technologies. This paper provides a systematic review of the latest research advances in various PBDS systems, including Pickering emulsions, protein-small molecule complexes, protein-polysaccharide complexes, nanogels, nanoparticles, core-shell microcapsules, self-assembled nanotubes, and nanofibers, along with their performance and characteristics in encapsulation, protection, and controlled release. PBDS enables smart stimulus-responsive release through pH, temperature, enzymatic reactions, redox reactions, and receptor recognition, thereby enhancing targeted delivery and controlled release efficiency. Furthermore, PBDS interacts with the gut microbiota to modulate microbial composition and strengthen intestinal barrier function, positively impacting systemic metabolic health. In summary, PBDS offers a solution for developing next-generation functional foods with improved nutritional properties, sensory qualities, and storage performance. Future research should focus on novel protein sources, multi-stimulus response design, scalable preparation processes, and in-depth exploration of PBDS-microbiome interaction mechanisms to advance personalized nutrition and smart food applications.}, }
@article {pmid42136241, year = {2026}, author = {Singh, R and Monika,  and Mazumder, R and Mazumder, A and Singh, M and Majee, C and Padhi, S and Das, S}, title = {Chronic Inflammation (A Silent Killer) - Molecular Mechanisms and Emerging Therapeutic Approaches.}, journal = {Current drug targets}, volume = {}, number = {}, pages = {}, doi = {10.2174/0113894501450885260409050432}, pmid = {42136241}, issn = {1873-5592}, abstract = {Chronic inflammation is a dysregulated and persistent immune response that underlies numerous serious health conditions, like heart problems, diabetes, nerve damage, cancer, or conditions where the body attacks itself. Recently, scientists have gained a better understanding of how molecules such as cytokines and chemokines, along with dysregulated immune cells, contribute to excessive oxidative stress and impaired healing processes. New tools now help identify this condition as early as possible through biomarkers, advanced laboratory techniques, integrated data approaches, and smart sensors that track biological changes in real time. However, despite this knowledge, effective strategies for early prevention and long-term treatment remain limited. Daily habits, particularly anti-inflammatory dietary patterns, regular physical activity, and stress management, play a critical role in reducing the risk of disease. Emerging therapies, including inflammasome inhibitors, cytokine-targeted biologics, immunometabolic modulators, and specialized pro-resolving mediators, may restore immune homeostasis rather than merely suppressing symptoms. Additionally, microbiome-targeted interventions-such as probiotics, prebiotics, bacteriophage therapy, and fecal microbiota transplantation-are increasingly being recognized as potential strategies to modulate systemic inflammation. Daily habits, especially eating patterns that fight inflammation, walking regularly, or handling stress, are critically important for lowering the chances of illness. Chronic inflammation is a complex, multifactorial process; therefore, its effective management requires integrated efforts in basic research, therapeutic innovation, and population- level healthcare strategies. Innovations in personalized medicine, AI-based analytics, digital health technologies, and microbiome science are poised to significantly enhance diagnostic and therapeutic approaches. Sustained cross-disciplinary collaboration will be critical in mitigating the worldwide impact of chronic inflammatory disorders and improving long-term health outcomes.}, }
@article {pmid42136267, year = {2026}, author = {Saraswati, BD and Wicaksono, AW and Valles, SL and Poeggeler, B and Singh, SK}, title = {Exploring the Gut Microbiome as a Promising Frontier in Alzheimer's Disease Therapy.}, journal = {Current neuropharmacology}, volume = {}, number = {}, pages = {}, doi = {10.2174/011570159X444975260408044214}, pmid = {42136267}, issn = {1875-6190}, abstract = {Alzheimer's Disease (AD) is a major global health challenge, particularly in ageing populations, and current therapies offer limited modification of disease progression. Emerging evidence indicates that the gut microbiome contributes to AD pathogenesis through metabolic, immune, and neuroendocrine mechanisms. Microbial metabolites, including Short-Chain Fatty Acids (SCFAs), bile acids, and trimethylamine-N-oxide (TMAO), regulate neuronal signalling and blood-brain barrier integrity, and dysbiosis has been linked to amyloid-β (Aβ) accumulation, tau hyperphosphorylation, chronic neuroinflammation, oxidative stress, and synaptic dysfunction. Host genetic factors, particularly APOE ε4 and immune-regulatory variants such as TREM2 and CD33, further influence microbial composition and susceptibility to metabolite-driven pathology. This review provides a deeper synthesis of current evidence by integrating findings across multi-omics studies and identifying key unresolved issues in the microbiome-AD field. The discussion evaluates whether microbiome alterations act as early initiators or downstream consequences of neurodegeneration, examines sources of heterogeneity in microbiome-targeted interventions, and considers how inter-individual variability in host genetics and microbial ecology may inform precision therapeutics. Conceptual frameworks presented here, including a two-phase dysbiosis trajectory and a metabolite "tipping-point" network, aim to reconcile conflicting results and support the development of testable mechanistic hypotheses. Microbiome-directed strategies, such as probiotics, prebiotics, dietary modulation, faecal microbiota transplantation, and antiviral therapies, demonstrate promise but require rigorous mechanistic validation and methodological standardisation. Continued advancement in longitudinal, genotype-stratified, and multi-omics research will be essential for translating microbiome science into clinically actionable approaches. Overall, current evidence positions the gut microbiome as a compelling frontier for the development of personalised, diseasemodifying strategies in AD.}, }
@article {pmid42136277, year = {2026}, author = {Saxena, V and Singh, V and Sanskriti, }, title = {Translational Perspectives on Anti-Inflammatory Interventions for Neurodegenerative Disorders: Evidence from Gut-Brain Axis.}, journal = {Central nervous system agents in medicinal chemistry}, volume = {}, number = {}, pages = {}, doi = {10.2174/0118715249430752260407050033}, pmid = {42136277}, issn = {1875-6166}, abstract = {The Gut-Brain Axis (GBA) has a complex role in chronic neuroinflammation, which is increasingly connected to neurodegenerative diseases (NDDs) such as Multiple Sclerosis (MS), Parkinson's Disease (PD), and Alzheimer's Disease (AD). Through neuronal, endocrine, and immunological pathways, the GBA enables twoway communication between the gastrointestinal tract and the central nervous system. According to recent research, the pathophysiology of neuroinflammatory responses in NDDs may be significantly influenced by gut dysbiosis, increased intestinal permeability, and modified microbial metabolites, such as Short-Chain Fatty Acids (SCFAs) and polyphenols. This study summarizes preclinical and clinical data supporting several anti- inflammatory approaches targeting GBA. Probiotics and fecal microbiota transplantation are two examples of microbiota-based treatments that have demonstrated promise in reducing neuroinflammatory responses and enhancing cognitive performance. Mediterranean and polyphenol-rich diets are among the dietary therapies that show promise in modifying the composition of microorganisms, lowering pro-inflammatory signaling, and enhancing neuroprotection. Through microbiota regulation, pharmacological substances such as curcumin, resveratrol, and SCFA mimetics also have anti-neuroinflammatory benefits. However, a number of translational challenges still exist, including limitations in animal models, a lack of standardized therapies, and inter-individual microbiome heterogeneity. In order to provide precise, GBA-targeted therapies, future views place a strong emphasis on integrating multi-omics, artificial intelligence, and personalized medicine. This study highlights a new therapeutic approach to treating neurodegeneration by examining the translational potential of anti- inflammatory therapies targeting GBA. It also emphasizes the necessity of strong clinical studies to confirm these findings.}, }
@article {pmid42136303, year = {2026}, author = {Rahimkhani, M and Hosseini, M}, title = {From Microbes to Minds: The Impact of Gut Bacteria on Infant Cognitive Growth.}, journal = {CNS &amp; neurological disorders drug targets}, volume = {}, number = {}, pages = {}, doi = {10.2174/0118715273391751251125075624}, pmid = {42136303}, issn = {1996-3181}, abstract = {Recent advances underscore the pivotal role of the gut microbiota in shaping infant brain development, emphasizing how the diversity and function of microbial communities regulate neurodevelopmental processes. This review synthesizes current literature on how maternal and early-life microbial exposures influence the infant gut ecosystem, producing cascading effects on cognitive and behavioral outcomes. Perturbations in gut microbial composition during sensitive developmental windows may increase the risk of conditions such as autism spectrum disorder (ASD) and attention- deficit/hyperactivity disorder (ADHD). Furthermore, research highlights the significance of the gut-brain axis, particularly the impact of nutrition and environmental factors on both microbiome composition and neurodevelopment. This review aims to provide an integrated overview of current evidence and to outline future directions for microbiota-targeted interventions that may enhance cognitive and neurological outcomes in children.}, }
@article {pmid42136370, year = {2026}, author = {Wu, C and Liu, H and Carvalhais, LC and Guo, J and Cai, P and Zhong, J and Zhang, H and Jin, B and Li, G and Yang, J and Chen, J and Ge, T}, title = {Root exudate-associated microbiome assembly contributes to viral disease resistance in wheat.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71254}, pmid = {42136370}, issn = {1469-8137}, support = {CARS-08-G09//China Agriculture Research System from the Ministry of Agriculture of P.R. China/ ; U24A20404//National Science Foundation of China/ ; 42477341//National Science Foundation of China/ ; 2022YFD1400700//National Key Research and Development Program of China/ ; 2022YFA1304401//National Key Research and Development Program of China/ ; 2024YFC3406003//National Key Research and Development Program of China/ ; //K.C. Wong Magna Fund of Ningbo University/ ; YLS-2025-ZY01012//Yuelushan Laboratory Breeding Program/ ; }, abstract = {Early mutualistic interactions between host plants and their rhizosphere microbes have the potential to provide soil-borne disease resistance. However, it remains unclear how the early rhizosphere microbiome protects against viral diseases such as wheat yellow mosaic virus, which is a major threat to global wheat production. We combined field trials with microbiome transplantation experiments to investigate the role of early rhizosphere microbiomes in suppressing wheat yellow mosaic disease. To uncover the underlying mechanisms, we further performed integrated multi-omics analyses of microbial communities, functional genes, and metabolic profiles. Disease-resistant wheat cultivars were consistently associated with distinct seedling rhizosphere microbiome assembly, including a lower Polymyxa graminis abundance, lower community compositional variation, and enrichment of beneficial taxa such as Bacillus, Pseudomonas, and Trichoderma. Resistant cultivars also exhibited distinct rhizosphere metabolite profiles, including higher levels of glyceraldehyde and N-acetyltryptophan, which were positively associated with keystone microbial taxa and stimulated representative isolates in vitro. Isolate-based and synthetic community validation further supported the functional relevance of these taxa, while microbial inoculation was associated with reduced vector abundance, lower virus accumulation, and activation of host defense-related pathways. Our findings showed that early cultivar-dependent rhizosphere microbiome assembly was closely linked to resistance against soil-borne viral disease in wheat.}, }
@article {pmid42136372, year = {2026}, author = {Mawer, CMA and Stanel, SC and Ward, EM and Smith, DJF and Hull, RC and Mehta, P}, title = {A framework for translational research in interstitial lung disease (ILD) using bronchoalveolar lavage (bal).}, journal = {Expert review of clinical immunology}, volume = {}, number = {}, pages = {}, doi = {10.1080/1744666X.2026.2675640}, pmid = {42136372}, issn = {1744-8409}, abstract = {INTRODUCTION: Bronchoalveolar lavage (BAL) offers a minimally invasive window into the distal airspaces and is an important tool in the study of interstitial lung disease (ILD). As chest imaging has obviated the need for diagnostic surgical biopsies, research tissue is increasingly limited, strengthening the rationale for BAL. By sampling the epithelial lining fluid, BAL captures cellular and acellular host- and microbe-derived signals relevant to inflammation and fibrogenesis, enabling multi-omic mechanistic and biomarker studies. However, variation in technique, dilution, and pre-analytical handling limits reproducibility and cross-center comparability.<br><br>AREAS COVERED: Here, we summarize key biological insights gained from BAL fluid-based studies, divided into cellular, acellular and microbiome compartments. We highlight current guidance, methodological challenges, and outline standardized frameworks to maximize translational scientific yield and multi-center validation.<br><br>EXPERT OPINION: Standardized protocols will maximize the value of BAL samples. Paired multi-compartment analysis can expand actionable readouts: multimodal cellular pipelines combining single-cell RNA and protein profiling, aligned with clinical annotation, may define ILD endotypes and prognostic/predictive biomarkers. Acellular BALF bioassays coupled to transcriptional and proteomic signatures can support mechanistic validation and pharmacological targeting, while microbiome profiling integrated with host multi-omics may improve risk stratification. Ultimately, these data could inform clinical decision-making and regulatory endpoints.}, }
@article {pmid42136474, year = {2026}, author = {Javadi, B}, title = {The Modulating Effects of Alkaloids on Gut Microbiota: Insights and Implications for Parkinson's Disease Management.}, journal = {Mini reviews in medicinal chemistry}, volume = {}, number = {}, pages = {}, doi = {10.2174/0113895575413113251031045342}, pmid = {42136474}, issn = {1875-5607}, abstract = {Parkinson's Disease (PD) is a neurodegenerative disorder characterized by the selective degeneration of dopaminergic neurons in the substantia nigra, leading to motor and non-motor symptoms. Recent research highlights the importance of the microbiome-Gut-Brain Axis (GBA) in PD pathogenesis, particularly the role of gut microbiota dysbiosis and inflammation. This review aims to explore the potential of alkaloids, a diverse group of naturally occurring compounds, in modulating gut microbiota and their implications for PD management. We evaluated studies that investigated the effects of various alkaloids on gut microbial composition, neuroinflammation, and dopaminergic neuron health using PubMed, Scopus, Web of Science, and Google Scholar databases. The search strategy combined Medical Subject Headings (MeSH) and free-text keywords. The primary search terms included: "Parkinson's disease" OR "PD", "gut-brain axis" OR "gut microbiota" OR "intestinal dysbiosis", "alkaloids" OR specific compound names (e.g., "berberine," "harmine," "galantamine," "nicotine," etc.). Evidence suggests that alkaloids such as berberine, protopine, and palmatine, matrin, etc., can restore microbial balance, reduce inflammation, and enhance neuroprotective effects, potentially mitigating both gastrointestinal and neurological symptoms associated with PD. This review underscores the need for further research, particularly human clinical trials, to validate the therapeutic efficacy and safety of alkaloids in the context of PD. By elucidating the mechanisms through which alkaloids influence the GBA, we can pave the way for innovative treatment strategies that enhance the quality of life for PD patients.}, }
@article {pmid42136577, year = {2026}, author = {Serdo, DF and Németh, Z}, title = {The Integrative Imperatives of Locust Phase Polyphenism Research: A Bibliometric Analysis.}, journal = {Integrative organismal biology (Oxford, England)}, volume = {8}, number = {1}, pages = {obag018}, pmid = {42136577}, issn = {2517-4843}, abstract = {Locust phase polyphenism, a classic example of phenotypic plasticity, has been studied for over a century, generating an extensive body of literature. However, a quantitative synthesis of the field's structure, evolution, and disparities has been lacking. Here, we present the first comprehensive bibliometric analysis of locust phase polyphenism research, quantitatively mapping its intellectual structure, collaborative networks, and thematic evolution. Analyzing 400 peer-reviewed primary studies published from 1921 through February 2025, we reveal a field at a critical inflection point. Publication trends demonstrate robust growth since the 1990s, reflecting the refinement of classical methods and the emergence of molecular and neurobiological approaches. However, this expansion rests upon a narrow foundation: research concentrates almost exclusively on two model species-Schistocerca gregaria and Locusta migratoria-while ecologically important non-model taxa remain critically understudied. Co-authorship network analysis exposes significant geographical disparities: research leadership concentrates in a small number of countries (UK, China, Japan, Belgium, Israel, Kenya, Germany, and USA), while most other locust-affected regions across the Sahel, the Horn of Africa, and the Middle East remain peripherally integrated. Keyword co-occurrence mapping identifies critical thematic blind spots within the phase polyphenism literature, including a complete absence of explicit climate change framing and limited representation of socioeconomic dimensions and non-model species. The field thus exhibits a notable disconnect: deep mechanistic knowledge of how phase change occurs exists alongside limited understanding of when and why outbreaks occur under changing environmental conditions. Transformative advances require strategic reorientation: from model-organism focus to comparative ecology, from episodic collaboration to equitable partnership with range-state scientists, from descriptive mechanism to functional validation, and from neglected frontiers (microbiome, epigenetics, and climate) to systematic investigation. This bibliometric mapping provides an evidence-based framework to guide future research toward greater impact on global food security.}, }
@article {pmid42136643, year = {2026}, author = {Wan, Y and Zheng, M and Fu, W and Zhu, H and Li, Y and Lin, H and Chen, J and Li, J and Mo, Q and Tai, W and Yang, J}, title = {Research trends on autoimmune liver diseases and gut microbiota (1989-2025): a bibliometric and visualization analysis based on the web of science core collection database.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1785064}, pmid = {42136643}, issn = {1664-3224}, mesh = {*Gastrointestinal Microbiome/immunology ; Humans ; Bibliometrics ; *Hepatitis, Autoimmune/microbiology/immunology/epidemiology ; Cholangitis, Sclerosing/microbiology/immunology ; *Autoimmune Diseases/microbiology ; *Biomedical Research/trends ; *Liver Diseases/immunology/microbiology ; Databases, Factual ; }, abstract = {Autoimmune liver diseases (AILD) encompass autoimmune hepatitis (AIH), primary biliary cholangitis (PBC), primary sclerosing cholangitis (PSC), and IgG4-related sclerosing cholangitis (IgG4-SC), with both incidence and prevalence showing an upward trend in recent years. Increasing evidence indicates that the onset and progression of AILD are inextricably linked to the gut microbiota. So far, no comprehensive and objective bibliometric study on AILD and gut microbiota has been conducted. This study retrieved literature from the Web of Science Core Collection (WoSCC) and Scopus database up to October 13, 2025, for analysis and validation respectively. VOSviewer, CiteSpace, R, Bibliometrix, SciExplorer, and WPS Office analysis tools were employed to systematically evaluate research trends, hot topics, and knowledge structures in the field. Our analysis indicates a growing research trend in AILD-gut microbiota interactions, involving 58 countries, 981 institutions, and 3,528 authors. Influential journals in this field include Frontiers in Immunology, GUT, and World Journal of Gastroenterology. Gershwin M. Eric stands as an authoritative author in this domain. Hot topics include "Mendelian randomization","primary sclerosing cholangitis", "primary biliary cholangitis", "bile acids", and the "gut-liver axis". Exploring therapeutic targets in AILD patients through the gut microbiome and its metabolites may emerge as a key future research direction. In summary, this study employed bibliometric methods to evaluate the application and development of gut microbiota in the field of AILD. Research in this area has experienced rapid growth in recent years, progressively focusing on the mechanisms of the gut-liver axis and genetics. Future efforts should further explore the potential of gut microbiota modulation in AILD treatment.}, }
@article {pmid42136650, year = {2026}, author = {Shao, M and Zhang, Y and Tang, H and Zhou, Z and Zhai, M and Zhou, X and Bi, X and Liao, J and Zhang, C and Jiang, L}, title = {Multi-omics insights into immune tolerance at the maternal-fetal interface in recurrent pregnancy loss: mechanisms, integration challenges, and translational perspectives.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1811970}, pmid = {42136650}, issn = {1664-3224}, mesh = {Humans ; Female ; Pregnancy ; *Abortion, Habitual/immunology/metabolism/genetics/etiology ; *Immune Tolerance ; Translational Research, Biomedical ; Animals ; Metabolomics ; Proteomics ; Genomics/methods ; *Maternal-Fetal Exchange/immunology ; Multiomics ; }, abstract = {Recurrent pregnancy loss (RPL) is a heterogeneous reproductive disorder in which dysregulation of maternal-fetal immune tolerance, aberrant decidual immune remodeling, and altered inflammasome signaling have been implicated within a complex multi-omics landscape. Multi-omics profiling (genomics, epigenomics, single-cell/spatial transcriptomics, proteomics, metabolomics, microbiome analyses, and immunomics) is increasingly being used to characterize mechanistic heterogeneity in RPL and to support biomarker discovery and immune-informed stratification. Genomic studies have associated chromosomal abnormalities and pathogenic variants with early embryonic developmental failure, while epigenomic profiling has highlighted aberrant methylation patterns and imprinting disturbances. Single-cell and spatial transcriptomics have revealed altered cellular composition and disrupted communication among decidual stromal cells, uterine natural killer (uNK) cells, macrophages, regulatory T cells (Treg), T helper 17 (Th17) cells, and trophoblast lineages. Proteomic and metabolomic studies have further identified immune-metabolic signatures associated with impaired trophoblast function and vascular remodeling, while emerging microbiome studies suggest a gut-reproductive axis that may modulate systemic immune homeostasis. Integration of multi-omics datasets with computational frameworks (e.g., weighted gene co-expression network analysis (WGCNA), multi-omics factor analysis (MOFA), and deep-learning models may improve RPL subtype classification, risk prediction, and the identification of potentially actionable pathways. However, current studies remain limited by small cohort sizes, especially in single-cell datasets, cross-platform heterogeneity, insufficient longitudinal validation, and a lack of multicenter reproducibility. Future work should prioritize standardized multi-omics pipelines, clearer evidence stratification, and immune-centric analytical frameworks to improve the robustness and translational relevance of RPL research. These advances may ultimately support immune-informed risk assessment and contribute to the gradual development of more individualized management strategies for RPL.}, }
@article {pmid42136651, year = {2026}, author = {Jin, W and Tang, L and Yang, J and Hu, X and Guo, W and Ai, H and Zuo, Y and Jin, Z}, title = {The oral - X axis: from periodontal dysbiosis to systemic disease.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1806445}, pmid = {42136651}, issn = {1664-3224}, mesh = {Humans ; *Dysbiosis/immunology/microbiology ; *Mouth/microbiology/immunology ; *Periodontitis/microbiology/immunology ; Animals ; Microbiota ; }, abstract = {Chronic oral inflammatory diseases, particularly periodontitis, are increasingly recognized as important contributors to the onset and progression of systemic disorders. Accumulating epidemiological, clinical, and mechanistic evidence indicates that the oral cavity is not an isolated organ, but rather a critical hub and early window for systemic disease development. Through microbial translocation, chronic low-grade inflammation, immune dysregulation, oxidative stress, and epigenetic reprogramming, oral diseases engage in bidirectional communication with distant organs.We conceptualize this integrated network as the "oral-X axis, " encompassing the oral-cardiovascular, oral-metabolic, oral-respiratory, oral-gastrointestinal, oral-oncologic, oral-immune, oral-brain, and other systemic axes. At the core of these interactions lies periodontitis-associated microbial dysbiosis dominated by key pathogens such as Porphyromonas gingivalis, Fusobacterium nucleatum, and Aggregatibacter actinomycetemcomitans. The ensuing inflammatory response compromises periodontal barrier integrity, facilitating the dissemination of bacteria, virulence factors, and inflammatory mediators into the systemic circulation. These processes promote endothelial dysfunction, insulin resistance, breakdown of immune tolerance, neuroinflammation, and the formation of pro-tumorigenic microenvironments, thereby mechanistically linking oral inflammation to a broad spectrum of systemic diseases. This review systematically summarizes the current evidence supporting the oral-X axis, with a particular focus on epidemiological associations and underlying molecular and cellular mechanisms. In addition, we discuss periodontal interventions and oral microbiome modulation as potential strategies for the prevention and treatment of systemic diseases. A deeper understanding of the oral-X axis may provide novel insights into integrated oral-systemic healthcare and precision medicine.}, }
@article {pmid42136652, year = {2026}, author = {Hou, Y and Chen, C and Chen, X}, title = {Advancing precision immuno-oncology in melanoma: the synergistic convergence of personalized neoantigen vaccines and multi-omics biomarker profiling.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1831047}, pmid = {42136652}, issn = {1664-3224}, mesh = {Humans ; *Melanoma/immunology/therapy/genetics ; *Cancer Vaccines/immunology/therapeutic use ; *Precision Medicine/methods ; *Antigens, Neoplasm/immunology ; *Biomarkers, Tumor/genetics/immunology ; Tumor Microenvironment/immunology ; *Immunotherapy/methods ; Genomics/methods ; *Skin Neoplasms/therapy/immunology/genetics ; Proteomics ; Multiomics ; }, abstract = {Cutaneous melanoma represents a paradigm of immunological complexity, where multifactorial primary and acquired resistance often undermine the clinical efficacy of conventional immune checkpoint blockades and targeted therapies. This review provides a comprehensive analysis of the strategic shift toward precision immuno-oncology, focusing on the mechanistic synergy between personalized neoantigen-directed vaccines and integrated multi-omics profiling. Rather than viewing these as independent pillars, we propose an integrated framework where multi-omics data functions as the indispensable 'operating system' that drives the entire lifecycle of neoantigen vaccines. By targeting patient-specific somatic mutations, bespoke vaccines are capable of orchestrating de novo, high-avidity T-cell responses with superior specificity and minimal off-target toxicity. We evaluate the clinical evolution and immunological foundations of advanced vaccine platforms-including mRNA, synthetic long peptides (SLPs), and engineered exosome-based systems-highlighting their transformative potential in the neoadjuvant and adjuvant settings. Central to this paradigm is the deployment of a robust multi-omics ecosystem (encompassing genomics, transcriptomics, epigenomics, proteomics, and the host microbiome) to decipher the dynamic landscape of the melanoma tumor microenvironment (TME). Facilitated by artificial intelligence (AI) and real-time liquid biopsy monitoring, this framework enables an iterative, biologically informed feedback loop for adaptive clinical management. We emphasize that the integration of personalized vaccines with immune checkpoint inhibitors (ICIs) and MAPK pathway inhibitors is essential to dismantle resistance barriers, providing a definitive roadmap for achieving durable clinical remission and curative outcomes in the era of personalized oncology.}, }
@article {pmid42136670, year = {2026}, author = {Gidaro, A and Guarino, MD and Arcoleo, F and Bignardi, D and D'Antonio, C and Brussino, L and Accardo, P and Nicola, S and Pucci, S and Cognigni, M and Popescu Janu, V and Cogliati, C and Bizzi, E and Cancian, M}, title = {Probiotic supplementation to mitigate berotralstat gastrointestinal side effects: a multicenter case series from the ITACA network.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1790199}, pmid = {42136670}, issn = {1664-3224}, mesh = {Humans ; *Probiotics/therapeutic use/administration &amp; dosage ; Female ; Male ; Middle Aged ; Adolescent ; Adult ; Aged ; Child ; Young Adult ; Aged, 80 and over ; *Gastrointestinal Diseases/chemically induced/prevention &amp; control ; *Angioedemas, Hereditary/drug therapy ; Pilot Projects ; }, abstract = {INTRODUCTION: Berotralstat, the first oral plasma kallikrein inhibitor approved for hereditary angioedema (HAE) prophylaxis, may be associated with gastrointestinal (GI) side effects, particularly during the first three months of therapy. Probiotics have been shown to reduce GI disturbances in several conditions. This pilot study described GI tolerability in patients receiving initiation-phase probiotic co-administration alongside berotralstat and explored whether this supportive strategy merits further controlled evaluation.<br><br>MATERIALS AND METHODS: We analyzed 25 adolescents and adults with HAE treated with berotralstat across six Italian centers (December 2023-November 2025). All patients received probiotics during the early treatment phase. Demographic and clinical data, side effects, and monthly HAE attack rates were collected. Severity of complaints was graded using the Common Terminology Criteria for Adverse Events (CTCAE).<br><br>RESULTS: Participants were 60% females, and the mean age for the cohort was 45 years (range 12-82). The most common probiotics were Lacteol[&#xae;] , Codex[&#xae;] , and Lactoflorene Plus[&#xae;] . GI complaints occurred in 5/25 patients (20%); only 3/25 (12%) experienced GI side effects while receiving probiotics. 2/25 GI complaints occurred after probiotic discontinuation. No serious side effects were reported. Mean monthly attack rate decreased from 2.6 to 0.8 attacks per month, ~3.3-fold reduction from baseline.<br><br>CONCLUSION: Probiotic co-administration during early berotralstat therapy was accompanied by a low incidence of GI side effects, while clinical effectiveness was maintained. These preliminary findings support further controlled studies to validate probiotics as a supportive strategy for improving the tolerability of berotralstat.}, }
@article {pmid42134890, year = {2026}, author = {Mohan, S and Selvam, PK and Vasudevan, K}, title = {Advances in immunomodulation: From dietary influence to computational precision.}, journal = {Advances in protein chemistry and structural biology}, volume = {151}, number = {}, pages = {29-44}, doi = {10.1016/bs.apcsb.2025.10.004}, pmid = {42134890}, issn = {1876-1631}, mesh = {Humans ; *Diet ; *Immunomodulation/drug effects ; Machine Learning ; Gastrointestinal Microbiome/immunology ; Animals ; *Immunologic Factors/therapeutic use/pharmacology ; }, abstract = {Immunomodulators are bioactive agents that play a crucial role in modulating immune responses, making them essential for managing autoimmune disorders, infections, and cancers. This chapter provides a thorough examination of immunomodulators, highlighting their clinical importance and therapeutic potential. It begins with an overview of immunomodulators and their applications, followed by a detailed classification into two primary categories: immunosuppressants and immunostimulants. Additionally, the chapter explores the influence of dietary and lifestyle factors on immunomodulation, emphasizing how specific nutritional components can enhance or suppress immune function, ultimately affecting health outcomes. The integration of computational approaches in immunomodulation is discussed, particularly focusing on the interactions between immunomodulators and the gut microbiome. This section underscores the significance of computational modeling and data analytics, including Artificial Intelligence (AI) and Machine Learning (ML), for predicting therapeutic efficacy and optimizing treatment strategies. Challenges and limitations are critically assessed, addressing the complexities of immune system interactions and the variability in individual responses to immunomodulatory therapies. The chapter concludes with future directions in the field, advocating for continued research to fully unlock the potential of immunotherapeutic interventions. This comprehensive review aims to clarify the interplay between dietary factors, computational advancements, and immunological strategies, ultimately contributing to the development of more effective and personalized therapeutic approaches in immunomodulation.}, }
@article {pmid42134973, year = {2026}, author = {Nagamine, T}, title = {The Gut-Muscle Axis in Sarcopenia: From Parallel Aging to a Self-Perpetuating Vicious Cycle.}, journal = {Geriatrics &amp; gerontology international}, volume = {26}, number = {5}, pages = {e70538}, doi = {10.1111/ggi.70538}, pmid = {42134973}, issn = {1447-0594}, mesh = {*Sarcopenia/physiopathology/microbiology/metabolism ; Humans ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/complications ; *Muscle, Skeletal/metabolism ; *Aging/physiology ; Aged ; }, abstract = {Sarcopenia and gut dysbiosis form a bidirectional vicious cycle where microbial changes drive systemic inflammation and muscle loss. Conversely, declining muscle metabolism further disrupts the microbiome. While "bottom-up" microbial interventions show promise in restoring muscle integrity, more research is needed on "top-down" muscle rejuvenation to fully confirm this interaction.}, }
@article {pmid42127905, year = {2026}, author = {Shen, J and Sun, Z and Song, H and Pu, Y and Wang, P and Hailili, G and Huang, Y and Mei, Z and Chen, H and Huang, L and Yuan, C and Wang, X and Zheng, Y}, title = {Healthful plant-based diet, gut enterotype, and cognition in a rural Chinese elderly cohort: A longitudinal multi-omics study.}, journal = {Cell reports. Medicine}, volume = {}, number = {}, pages = {102797}, doi = {10.1016/j.xcrm.2026.102797}, pmid = {42127905}, issn = {2666-3791}, abstract = {The gut microbiome may shape how diet influences cognitive aging, but population-based evidence remains limited. In 784 older adults living in rural China (70-98 years old) with fecal metagenomics and structured dietary assessment, a modified healthful plant-based diet index (mHPDI) is associated with distinct gut microbial structure and taxonomic shifts (15 species, 17 genera). Among participants with repeated cognitive measurements, higher mHPDI is associated with better global cognition, with stronger benefits in participants with non-Prevotella-dominant enterotypes (highest versus lowest tertile β = 0.34, 95% confidence interval [CI], 0.16 to 0.52) than in those with a Prevotella-dominant enterotype (0.04, -0.22 to 0.29; p interaction = 0.04). Enterotype-associated differences in microbial metabolic pathways, including preQ0 and L-isoleucine biosynthesis, parallel this heterogeneity. Moreover, 12 circulating microbiota-related metabolites (primarily amino acids and short-chain fatty acids) are linked to mHPDI. A composite score comprising these metabolites mediates 11.0% of the mHPDI-cognition association (p mediation = 0.02), with branched-chain amino acids as major contributors. These findings suggest that gut microbial context may shape diet-cognition associations.}, }
@article {pmid42128003, year = {2026}, author = {Gutsfeld, S and Wray, C and Schweiger, N and Röhrig, A and Paschke, H and Fu, Q and Kasmanas, JC and Abdulkadir, N and Kader, S and Rocha, U and Ebert, A and Tal, T}, title = {N-Ethyl Perfluorooctane Sulfonamide (N-EtFOSA) Exposure Alters Microbiome Composition and Causes Microbiome-Dependent Behavior Effects in Larval Zebrafish.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c16330}, pmid = {42128003}, issn = {1520-5851}, abstract = {We hypothesized that host-associated microorganisms can alter host behavior by modifying perfluorooctane sulfonamides to produce perfluorooctanesulfonic acid (PFOS) or other potentially neuroactive metabolites. Zebrafish larvae (Danio rerio) were exposed to PFOS (0.28-5 μM), N-ethyl perfluorooctane sulfonamide (N-EtFOSA, 0.07-1.25 μM), or perfluorooctane sulfonamido ammonium iodide (PFOSAmS, 0.83-15 μM) from 5 to 6 days post fertilization (dpf). This resulted in altered dark-phase swimming behavior at 8 dpf. Exposure to PFOS, or N-EtFOSA, but not PFOSAmS caused a similar shift in community structure. We exposed microbiome-depleted (axenic, AX), conventionally colonized (CC), or axenic conventionalized on day 1 (AC1) zebrafish larvae to N-EtFOSA (0.22-0.7 μM) from 5 to 6 dpf. In comparison to CC and AC1 larvae, AX-larvae did not exhibit concentration-dependent hypoactivity at 8 dpf. Chemical analysis at 7 dpf revealed a significant increase in N-EtFOSA levels in AX-larvae and AX-water samples, relative to colonized cohorts. The main metabolite detected was perfluorooctane sulfonamide (FOSA), which was not microbiome-dependent. Perfluorooctane sulfonamidoacetic acid (FOSAA) was detected at lower levels in AX-larvae, relative to colonized groups. This study revealed that the presence of the microbiome enhanced N-EtFOSA-dependent behavior effects at the level of the host. This supports the concept that chemical-microbiome interactions can influence host phenotypic outcomes.}, }
@article {pmid42128073, year = {2026}, author = {Wang, X and Xi, J and Gong, H and Yin, Y and Jin, C and Zhao, Y and Wang, S and Zhao, D and Liu, S and Wang, W and Liu, M}, title = {Intestinal CncC gene activation mediates the sleep-protective effects of Ziziphus jujuba alcohol extract via the gut-brain axis in Drosophila.}, journal = {Journal of ethnopharmacology}, volume = {368}, number = {}, pages = {121859}, doi = {10.1016/j.jep.2026.121859}, pmid = {42128073}, issn = {1872-7573}, abstract = {Ziziphus jujuba var. spinosa (Bunge) Hu ex H.F.Chow (Ziziphus jujuba) has been used in Chinese folk medicine for over 2000 years, with the Shennong Bencao Jing noting that the "main worry is not sleeping." More than 100 health foods and Chinese patent medicines, feature Ziziphus jujuba as the core ingredient, embodying the traditional concept of "nourishing heart and tranquilizing mind."<br><br>OBJECTIVE: This study investigated microbiome-targeted phytotherapeutic strategies for sleep disorders, which are often linked to gut dysbiosis and systemic oxidative stress.<br><br>MATERIALS AND METHODS: Chronic sleep-deprived Drosophila were orally treated with a Ziziphus jujuba alcohol extract (ZJAE). Sleep architecture was recorded using a Drosophila activity monitor. Intestinal microbiota shifts were assessed by gnotobiotic colonization and 16S rRNA sequencing. Quantitative PCR, western blotting, and reactive oxygen species (ROS) imaging assessed intestinal signaling of the Nrf2 homolog cap 'n' collar C (CncC) gene, antioxidant gene expression, gut barrier integrity, and systemic ROS. Gut-specific RNA interference was used to targeted the CncC gene.<br><br>RESULTS: ZJAE restored total sleep time and reduced motor hyperactivity, consistent with reduced systemic ROS and restoration of intestinal barrier function. Acetobacter was enriched. Antibiotic-treated flies colonized with acetic acid bacteria and treated with ZJAE showed the highest CncC gene expression. Knockdown of the CncC gene knockdown in intestinal epithelial cells abolished improvements in both sleep parameters and redox status.<br><br>CONCLUSION: ZJAE recruits commensal Acetobacter to activate an intestinal Nrf2-dependent redox axis, normalizing oxidative stress-linked sleep deficits. These findings provide the first preclinical evidence of a microbiota-dependent mechanism, supporting a rationale for the development of jujube-based functional foods targeting oxidative sleep disorders.}, }
@article {pmid42128097, year = {2026}, author = {Wang, R and Liang, C and Li, Y and Zhu, L}, title = {Insights into Lower Reproductive Tract Aging: Mechanisms and Perspectives.}, journal = {Mechanisms of ageing and development}, volume = {}, number = {}, pages = {112192}, doi = {10.1016/j.mad.2026.112192}, pmid = {42128097}, issn = {1872-6216}, abstract = {Rising global life expectancy intensifies the health impact of female lower reproductive tract aging, particularly affecting the uterus, cervix, and vagina. This process is primarily driven by estrogen depletion triggering hormonal imbalance, chronic inflammation, cellular senescence through senescence-associated secretory phenotype mediators, and systemic oxidative stress. These interconnected mechanisms accelerate structural degeneration leading to uterine fibrosis with endometrial atrophy, pelvic organ prolapse, cervical susceptibility to persistent HPV infections and subsequent malignancy development, vaginal microbiome disruption, and genitourinary syndrome of menopause. Future advances will require addressing the pronounced research imbalance across anatomical sites, resolving the causal links between immune aging and tissue-specific pathologies, and integrating multi-omics and organoid technologies to enable personalized, site-specific interventions.}, }
@article {pmid42128146, year = {2026}, author = {Su, YJ and Kuo, BY and Lin, LY and Lin, YH and Chen, CC and Sheu, JJ}, title = {High fat diet-induced diversity reduction in gut microbiota facilitates the development of systemic lupus erythematosus.}, journal = {The Journal of nutritional biochemistry}, volume = {}, number = {}, pages = {110398}, doi = {10.1016/j.jnutbio.2026.110398}, pmid = {42128146}, issn = {1873-4847}, abstract = {Systemic lupus erythematosus (SLE) is influenced by environmental, genetic, and dietary factors. The impact of a high-fat diet (HFD) on SLE pathogenesis remains unclear. To investigate this, we utilized an imiquimod (IMQ)-induced SLE mouse model under HFD and normal diet conditions. Mice receiving both HFD and IMQ exhibited aggravated inflammation, tissue damage, and enhanced B-cell infiltration in the colon, alongside significant reductions in gut microbial diversity. Notably, HFD alone induced similar microbiome and immune alterations, suggesting a pro-SLE intestinal microenvironment. Microbiome analysis identified specific species shifts, including Parabacteroides goldsteinii and Bacteroides caccae, associated with disease progression. Metabolomic profiling revealed dysregulation of several pathways, including amoebiasis, with marked reduction of dl-o-phosphoserine. These findings suggest that HFD-induced microbial and metabolic changes may exacerbate SLE development. Our study highlights the interplay between diet, gut microbiota, and immune regulation in SLE, providing potential targets for microbiome- or diet-based interventions.}, }
@article {pmid42128216, year = {2026}, author = {Ackermann, RE and Brayton, KA and Oosthuizen, MC and Matthee, CA and Makgabo, SM and Ngoveni, H and Fagir, DM and van Wyk, I and Quan, V and Rossouw, J and Weyer, J and Blumberg, LH and Frean, J and Collins, NE}, title = {Microbial networks and pathogen detection: Insights from ticks and patients with acute febrile illness.}, journal = {Acta tropica}, volume = {}, number = {}, pages = {108138}, doi = {10.1016/j.actatropica.2026.108138}, pmid = {42128216}, issn = {1873-6254}, abstract = {Ticks are vectors of diverse pathogens, with transmission risk elevated in regions of close human-livestock-wildlife contact. In rural South Africa, non-malarial acute febrile illness (AFI) is common, yet the microbial diversity of ticks and human patients remains underexplored. We applied microbiome sequencing (16S rDNA for bacteria; 18S rDNA for eukaryotes) to four sample groups from Bushbuckridge, Mpumalanga, South Africa: Rhipicephalus sanguineus s.l. (n16S = 175, n18S = 30), Amblyomma hebraeum (n16S = 74, n18S = 21), human AFI patients (n16S = 168, n18S = 14), and apparently healthy humans (n16S = 67, n18S = 3). Bacterial alpha diversity did not differ significantly between groups (Shannon p = 0.81, Inverse-Simpson p = 0.36), whereas eukaryotic diversity was lower in human patients (Shannon p = 0.00026, Inverse-Simpson p = 0.00415). Beta diversity exhibited clear differences between groups, with ticks showing greater variability (bacteria p = 0.001; eukaryotes p = 0.001). Co-occurrence networks revealed structured clusters reflecting organised community interactions. Pathogen DNA detected included Plasmodium falciparum in an AFI patient, and sequences similar to several spotted fever group Rickettsia species, including the first report of Rickettsia barbariae in ticks from South Africa. This result requires confirmation by multi-gene sequence analysis. Novel Rickettsiales with uncertain pathogenicity were detected across sample groups. Opportunistic pathogens were detected including Acanthamoeba, Aspergillus and Malassezia. These findings provide baseline evidence on microbial diversity in a rural community in South Africa, underscoring the need for integrated surveillance to address AFI burden within a One Health framework.}, }
@article {pmid42128223, year = {2026}, author = {Li, J and Jong, MC and Li, P and Yu, K and Bao, Y and Song, Z and Shen, Y and Yew-Hoong Gin, K and He, Y}, title = {Size-Dependent Toxicity Cascades of Microplastics in Perna viridis: Mechanistic Insights into Membrane Damage, Microbial Dysbiosis, and Persistent Genotoxicity.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128330}, doi = {10.1016/j.envpol.2026.128330}, pmid = {42128223}, issn = {1873-6424}, abstract = {Microplastics are pervasive contaminants in coastal ecosystems, but their size-dependent toxicity cascades across multiple biological levels remain poorly resolved. This study integratively assesses the 0.5-, 5-, and 50-μm microplastics toxicity in Perna viridis through multi-endpoints (cellular membrane stability, microbial homeostasis, haemolymph DNA integrity) across exposure (14-day) and depuration (7-day), revealing a size-dependent cascade. Exposure to 0.5-μm MPs triggered intracellular organelle stress, leading to oxidative stress responses marked by elevated ROS and MDA along with progressive ATP depletion. This was accompanied by downregulation of cytoskeletal genes (Actin and Tubb4b) and upregulation of the membrane repair gene preCOL-p. Concurrently, 0.5-μm MPs triggered severe intestinal dysbiosis reflected in reduced Shannon and Chao indices, enrichment of virulence genes and significant haemolymph DNA damage as measured by the Genetic Damage Index. Although membrane biomarkers recovered after depuration, irreversible DNA damage persisted exclusively in the 0.5-μm groups. GO enrichment analysis showed consistent top functions across MPs sizes but divergence in lower-ranked terms, while KEGG analysis revealed distinct size-dependent upregulation of metabolic pathways in exposed microbial communities. We propose a size-dependent cascading toxicity framework in which internalized small MPs first perturb cell membranes, then drive microbiome dysbiosis and microbiome-derived inflammatory signals, ultimately leading to sustained DNA damage.}, }
@article {pmid42128400, year = {2026}, author = {Han, E and Nam, JH and Lee, I and Ku, CR and Lee, YH}, title = {Metformin beyond Glycemic Control: New Mechanistic Insights and Expanding Therapeutic Horizons.}, journal = {Diabetes &amp; metabolism journal}, volume = {50}, number = {3}, pages = {435-449}, pmid = {42128400}, issn = {2233-6087}, support = {2021F-4//Korean Diabetes Association/ ; RS-2024-00352467//National Research Foundation of Korea/ ; RS-2025-02214844//National Research Foundation of Korea/ ; //Ministry of Science and ICT/ ; }, mesh = {Humans ; *Metformin/therapeutic use/pharmacology ; *Hypoglycemic Agents/therapeutic use/pharmacology ; Gastrointestinal Microbiome/drug effects ; *Glycemic Control ; Aging/drug effects ; Animals ; Neoplasms/drug therapy ; }, abstract = {Metformin, while central to diabetes management, functions as a highly pleiotropic agent with mechanisms that extend far beyond simple glycemic control. In age-related degenerative diseases, including neurodegenerative disorders, it may modulate mitochondrial function, reduce oxidative stress, and influence longevity-related pathways, suggesting possible anti-aging effects. Emerging evidence also points to anticancer activity, with studies reporting reduced incidence and improved outcomes across several malignancies, potentially through mammalian target of rapamycin (mTOR) inhibition, metabolic reprogramming, and suppression of inflammatory signaling. Furthermore, the 'intestinal glucotonic effect' has been proposed to involve glucose excretion from the circulation into the gut lumen through reactive oxygen species-dependent upregulation and membrane localization of glucose transporter type 1 (GLUT1), an adenosine monophosphate-activated protein kinase (AMPK)-independent process that may contribute to the reprogramming of systemic glucose flux and provides metabolic substrates for the microbiota. Metformin also alters the gut microbiome by increasing the abundance of multiple short-chain fatty acid-producing bacteria and enhancing intestinal barrier function, which may contribute to systemic metabolic and immunologic benefits. Collectively, metformin is a pleiotropic agent with broad effects on aging biology, cancer pathophysiology, host-microbiome interactions, and immunometabolic regulation. Despite decades of clinical use, important gaps remain in understanding how these mechanisms converge to influence outcomes in individuals with diabetes and beyond.}, }
@article {pmid42128407, year = {2026}, author = {Pati, NB and Chung, BK and Holm, K and Sætre, F and Reims, HM and Aasebo, AT and Gedde-Dahl, T and Sreelakshmi, KV and Domanska, D and Hov, JR and Bækkevold, ES and Jahnsen, FL}, title = {Ultra long-lived plasma cells in the human small intestine produce microbiota-reactive IgA antibodies.}, journal = {Beneficial microbes}, volume = {}, number = {}, pages = {1-13}, doi = {10.1163/18762891-bja00120}, pmid = {42128407}, issn = {1876-2891}, abstract = {A large fraction of the intestinal microbiota is highly coated with secretory IgA, and bacteria-specific IgA is believed to shape the composition of the microbiota. A hallmark of the adaptive immune system is immunological memory to specific antigens. However, whether there is strong and persistent memory of secretory antibodies to bacterial antigens has not been determined. Here we show that ultra long-lived CD19-CD45- (age > 20 years) plasma cells (PCs) residing in the human small intestine produce IgA that binds to most taxa of a diverse anaerobic microbiota culture. Long-lived CD19-CD45+ (age > 10 years) and short-lived CD19+CD45+ (age < 2 years) PCs also produced IgA with broad bacterial reactivity. A clear correlation between high-binding and low-binding taxa was observed across the PC subsets. We also found that host PCs were depleted in acute intestinal graft versus host disease, a condition strongly associated with loss of microbiota diversity. Together, we show that bacterial antigens in the intestine induce an extremely stable, long-lasting humoral immune memory that may be important for the long-term stability and resilience of the intestinal microbiome.}, }
@article {pmid42128724, year = {2026}, author = {Alam, A and Mayengbam, SS and Senchanthisai, S and Bektas, EI and Dey, P}, title = {Microbiome: a driver of pancreatic inflammation and tumorigenesis.}, journal = {Trends in cancer}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.trecan.2026.04.006}, pmid = {42128724}, issn = {2405-8025}, abstract = {The human microbiome plays a crucial role in regulating various physiological processes, including immune responses, inflammation, gut permeability, and overall homeostasis. Recent studies have identified bacterial and fungal components in the tumor microenvironment of multiple malignancies, including pancreatic ductal adenocarcinoma (PDAC). These intratumoral microbiomes drive tumorigenesis by activating oncogenic signaling cascades and reprogramming both innate and adaptive immune responses, ultimately establishing a protumorigenic niche. In this review, we highlight the advances, limitations, and challenges of studying the intratumoral microbiome and its cellular products in PDAC tumorigenesis, with a specific focus on their modulation of the immune axis. Finally, we evaluate existing and emerging therapeutic strategies, including microbiome-targeted drugs, antibiotics, probiotics, and engineered microbes, to disrupt protumorigenic microbial influences and improve clinical outcomes.}, }
@article {pmid42128741, year = {2026}, author = {Lefranc, M and Ramel, E and Marsh, R and Tricker, JM and van der Gast, C and Bomberger, JM and Delhaes, L}, title = {Towards a gut-lung axis role in pwCF on CFTR modulators: rationale, clinical evidence and perspectives.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jcf.2026.04.011}, pmid = {42128741}, issn = {1873-5010}, abstract = {Recent data support the existence of a "gut-lung axis" (GLA), yet it's role in chronic respiratory diseases, like cystic fibrosis (CF), is under investigation. In this review we explore the potential linkages and underlying mechanisms for gut-lung interaction axis, in terms of rationale (same embryonic and anatomical origins), microbial and immune interactions, and recent advances on GLA role in chronic lung diseases, with a focus on GLA research relevant to CF. The introduction of CFTR modulators has revolutionized CF management, dramatically reshaping the disease's clinical course by improving ion transport, mucosal hydration and mucociliary clearance. CFTR modulators are known to improve anion channel function, which has resulted in physiological and microbiological changes to the respiratory tract and gastrointestinal tract, which are likely to impact the GLA and are explored in this review. While there is a growing literature for the role of the GLA in regulating lung physiology in health and disease, additional work is warranted to elucidate molecular mechanisms by which the GLA mediates pathogenesis of disease. The ultimate goal would be to apply mechanistic understanding from the bench to the bedside to enable more personalized treatment strategies that both guide and improve lung disease management, especially in the CF field.}, }
@article {pmid42129074, year = {2026}, author = {Veenstra, TD}, title = {The Pathology of Viral Infections.}, journal = {Advances in experimental medicine and biology}, volume = {1511}, number = {}, pages = {127-158}, pmid = {42129074}, issn = {0065-2598}, mesh = {Humans ; *Virus Diseases/pathology/virology ; Viruses/pathogenicity ; Microbiota ; Animals ; Host-Pathogen Interactions/physiology ; }, abstract = {If you were to ask, "Biologically speaking, what are humans made of?", almost everyone would reply "Human cells and molecules, of course." This seemingly logical answer, however, does not truly capture the diversity of the human organism. Over the past couple of decades scientists have discovered that humans are a collective of cohabitating human, bacteria, and fungi cells along with countless numbers of viruses. Collectively, these microorganisms are referred to as the microbiome (Lederberg and McCray, The Scientist 15:8, 2001). The most recent estimates suggest the biological material from these microorganisms makes up as much as half of every human. Considering the size of the microbiome, it is not surprising that humans share an intimate relationship with viruses since they will be found wherever life exists.}, }
@article {pmid42129076, year = {2026}, author = {Veenstra, TD}, title = {Proteomic Characterization of HIV Infection.}, journal = {Advances in experimental medicine and biology}, volume = {1511}, number = {}, pages = {189-222}, pmid = {42129076}, issn = {0065-2598}, mesh = {Humans ; *HIV Infections/metabolism/virology ; Male ; *Proteomics/methods ; Homosexuality, Male ; *HIV-1/metabolism ; }, abstract = {In the summer of 1981, young gay men began falling ill and dying of opportunistic infections. The strange thing was that these infections should have been easily rebuffed by their immune systems (Greene WC, Eur J Immunol 37(Suppl 1):S94-S102, 2007). These men become emaciated and developed dark purple lesions primarily on their arms and faces. These lesions were due to Kaposi's sarcoma, a relatively rare and aggressive form of cancer (Antman K and Chang Y, N Engl J Med 342:1027-1038, 2000). Physicians in cities such as New York, Los Angeles, and San Francisco were dumbfounded by the presence of young men who appeared elderly (Greene WC, Eur J Immunol 37(Suppl 1):S94-S102, 2007; Premeaux TA and Ndhlovu LC, Curr Opin HIV AIDS 18:237-245, 2023). Fear initially spread throughout the gay male community as this group was disproportionately impacted. As their health rapidly deteriorated, doctors were unable to prevent patients from dying from opportunistic infections and malignancies. The condition was recognized in 1981 as acquired immune deficiency syndrome (AIDS) (CDC, MMWR Morb Mortal Wkly Rep 30:305-308, 1981). As it became more publicized, the shock and stigma surrounding individuals who died from AIDS grew. The first major figure to reveal their AIDS diagnosis was Rock Hudson. This revelation was followed by other well-known individuals including Robert Reed (i.e., the father on the Brady Bunch), Arthur Ashe, and Freddie Mercury (webmd.com/hiv-aids/ss/slideshow-celebrities-hiv-aids).}, }
@article {pmid42129181, year = {2026}, author = {Dobranowski, P and Duan, H and Butcher, J and Mayne, J and Figeys, D and Mack, DR and Stintzi, A}, title = {Individual variability shapes ex vivo responses to resistant starch in inflammatory bowel disease derived microbiomes.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01003-w}, pmid = {42129181}, issn = {2055-5008}, support = {OGI-149//Government of Canada through Genome Canada and the Ontario Genomics Institute/ ; project number 13440//Ontario Ministry of Economic Development and Innovation/ ; }, abstract = {Fiber-based therapies focus on butyrate production, a process often dysregulated in inflammatory bowel disease (IBD), but seldomly examine other metabolites or functional pathways. Here, we systematically profiled ex vivo responses of 66 pediatric IBD microbiomes to nine resistant starches (RS), with extensive multi-omic characterization in a subset. Our study demonstrates that inter-individual variability dominates over RS-specific effects, yielding consistent yet highly personalized fermentation phenotypes, microbial compositional shifts, and metabolite outputs. Beyond butyrate, we identify previously unreported RS fermentation metabolites, revealing hidden functional pathways and cross-feeding interactions not captured by conventional short chain fatty acid-focused analyses. Metaproteomic profiling further revealed a coordinated shift from host mucin-degrading activity toward RS utilization. Together, these findings show that RS fermentation is shaped by both RS type and participant microbiome composition, and establish the RapidAIM ex vivo platform as a fiber personalization pipeline fit for interventions aimed at restoring microbial functions disrupted in human diseases.}, }
@article {pmid42129189, year = {2026}, author = {Lacruz-Pleguezuelos, B and Pérez-Cuervo, A and Coleto-Checa, D and Bazán, GX and Romero-Tapiador, S and Freixer, G and Fernández-Cabezas, J and Aguilar-Aguilar, E and Martín-Segura, A and Cárdenas-Roig, N and Carrasco-Guijarro, L and Fernández, LP and Espinosa-Salinas, I and Ramírez de Molina, A and Morales, A and Tolosana, R and Ortega-Garcia, J and Pancaldi, V and Marcos-Zambrano, LJ and Carrillo de Santa Pau, E}, title = {Network topology of the gut microbiome associates with metabolic health in obesity.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42129189}, issn = {2041-1723}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; Male ; Female ; *Obesity/microbiology/metabolism ; Middle Aged ; Cross-Sectional Studies ; Adult ; Feces/microbiology ; Metagenomics ; *Obesity, Metabolically Benign/microbiology/metabolism ; Dysbiosis/microbiology ; Phenotype ; }, abstract = {Obesity is a heterogeneous condition comprising a continuum of phenotypes with various metabolic and inflammatory profiles. Metabolically healthy obesity (MHO) identifies individuals with obesity but a relatively preserved metabolic state, although little is known about the gut microbiome features underlying this phenotype. Here, we analyzed gut microbial network structures of 931 individuals living with metabolically healthy non-obesity (MHNO), MHO, metabolically unhealthy non-obesity (MUNO), and metabolically unhealthy obesity (MUO), performing cross-sectional analyses on feces shotgun metagenomics data. Individuals with MHNO and MHO harbor more robust and functionally cohesive microbial networks, while communities from MUO and MUNO phenotypes exhibit a potentially dysbiotic state with reduced connectivity. A nutritional intervention cohort showed an improvement in network connectivity in parallel with metabolic improvements. Our findings show differences in microbial connectivity and association patterns across metabolic and obesity phenotypes, shedding light on how distinct microbial network structures may associate with host metabolic health and disease.}, }
@article {pmid42129350, year = {2026}, author = {Parkin, K and Christophersen, CT and Verhasselt, V and Palmer, DJ and Cooper, MN and Prescott, SL and Silva, D and Martino, D}, title = {Chlorinated drinking water exposure enriches antimicrobial resistance pathways in the infant gut microbiome: a randomized trial.}, journal = {Communications medicine}, volume = {}, number = {}, pages = {}, doi = {10.1038/s43856-026-01626-2}, pmid = {42129350}, issn = {2730-664X}, abstract = {BACKGROUND: Water chlorination is essential for controlling harmful microbes in drinking water; however, the antimicrobial effects of chlorine-based disinfectants present in tap water may influence early-life gut microbial ecology.<br><br>OBJECTIVE: To investigate the functional and compositional impact of chlorinated drinking water on the gut microbiome of infants.<br><br>DESIGN: The waTer qUality and Microbiome Study (TUMS) was an Australian-based double-blinded, randomised controlled trial. Six-month-old infants (n&#x2009;=&#x2009;197) received either de-chlorinated drinking water via benchtop filtration (treatment, n&#x2009;=&#x2009;99), or regular chlorinated water (control, n&#x2009;=&#x2009;98) for twelve months. Tap water and stool samples were collected at baseline and at end of intervention. Metagenomic sequencing was used for faecal microbiome analysis. Primary outcomes were differences in gut microbiota between groups, secondary outcomes included incidence of allergic sensitization and respiratory conditions.<br><br>RESULTS: At baseline, 170 stool samples (83 control, 87 intervention) were collected, with 130 samples obtained at the end of the intervention (65 control, 65 intervention). Overall community structure was similar between groups after the intervention, including beta diversity (0.56% variance explained; p&#x2009;=&#x2009;0.84), richness (-4.25, 95% CI; -14.85 to 6.35, p&#x2009;=&#x2009;0.43) or Shannon Index (-0.14, 95% CI; -0.32 to 0.04, p&#x2009;=&#x2009;0.12). The chlorinated water group showed enrichment of antibiotic resistance MetaCyc groups and pathways (adjusted p&#x2009;<&#x2009;0.05). Stratified analysis suggested this effect was potentiated by clinical antibiotic use.<br><br>CONCLUSION: Chlorinated drinking water may enhance resistance functions in the infant gut microbiome. While remaining vital for public health, future studies should explore whether adjusting the timing or method of drinking water disinfectants into the infant diet can reduce selective pressures.<br><br>TRIAL REGISTRATION: ACTRN12619000458134; https://www.anzctr.org.au.}, }
@article {pmid42129442, year = {2026}, author = {Shinde, RM and Kotasthane, AS and Agrawal, T}, title = {Bio decomposition of paddy straw waste using laccase producing novel soil bacterial isolates: An eco-friendly and sustainable approach.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-50628-6}, pmid = {42129442}, issn = {2045-2322}, abstract = {The soil microbiome plays a pivotal role in carbon sequestration, particularly through the degradation of lignocellulosic biomass such as paddy straw, which is often disposed of through environmentally harmful practices like open-field burning. This study investigates the isolation and characterization of novel lignocellulolytic bacterial strains capable of efficiently degrading paddy straw, thereby contributing to sustainable carbon management. A diverse collection of 27 bacterial isolates was obtained from soil samples, demonstrating significant cellulase, laccase, and lignin-degrading activities. Detailed biochemical and phenotypic analyses revealed distinct metabolic profiles and carbon source utilization patterns among the isolates. Notably, strains SH2A, AK17, AK15, U6, and SH2 achieved up to 94% degradation of paddy straw within 25 days, with isolate GS5A exhibiting an 18% reduction in recalcitrant lignin content in paddy straw within just 10 days leading to enhanced bioavailability of structural polysaccharides, and accelerating microbial-mediated degradation processes. Enzyme kinetic studies indicated optimal laccase activity at temperatures of 45-55 °C and pH levels of 4-7, with isolates TR32, SH2A, and AK17 producing laccase activities exceeding 90 U/L. Molecular characterization via 16 S rRNA sequencing identified these isolates as belonging to genera such as Pseudomonas, Enterobacter, Acinetobacter, and Klebsiella, known for their lignocellulolytic enzyme production. The findings underscore the potential of these bacterial strains exhibiting rapid lignin degradation enabling faster and more effective paddy straw decomposition compared to previously reported strains. Thereby leading faster carbon sequestration through effective biomass management, contributing to the development of a circular bio-economy and sustainable agricultural practices.}, }
@article {pmid42129646, year = {2026}, author = {Mannan, SJ and Roqunuzzaman, M and Mannan, ABA and Begum, K and Yasmin, M and Yihune, E and Al-Mutairi, AA and Zaki, MEA and Ahsan, CR}, title = {Exploring genetic variations and plasmid diversity in Escherichia coli strains isolated from Hospital Wastewater.}, journal = {BMC genomics}, volume = {27}, number = {1}, pages = {}, pmid = {42129646}, issn = {1471-2164}, mesh = {*Wastewater/microbiology ; *Escherichia coli/genetics/isolation &amp; purification/pathogenicity/classification ; *Plasmids/genetics ; *Genetic Variation ; Hospitals ; Polymorphism, Single Nucleotide ; Phylogeny ; Drug Resistance, Multiple, Bacterial/genetics ; beta-Lactamases/genetics ; Whole Genome Sequencing ; }, abstract = {The multidrug-resistant (MDR) Escherichia coli, particularly β-lactamase producing strains, has become a global health challenge, where wastewater systems, specially from hospitals, serve as critical reservoirs for the dissemination of resistance genes. The objectives of the study were to investigate the whole genome sequence diversity and genetic variations focusing on their evolutionary relationships, genetic similarity, and single nucleotide polymorphisms (SNPs) of pathogenic β-lactamase producing E. coli strains. A total of four β-lactamase producing E. coli strains, from differently located tertiary care hospitals, were included in this study. A heatmap of genetic similarity revealed near-identical genetic makeup among the strains. A number of genes including AcrAB-TolC, β-lactamases, and resistance determinants such as glpT, gyrA, msbA, and tet(M) were identified in these strains. However, the presence of virulence genes of the aerobactin synthesis gene (iucA, iutA) and type III secretion systems (espX1, espX4, espX5) in the strain has the potential for pathogenicity. These resistance genes were identified at the genomic level; however, their transcriptional expression was not evaluated and the detection of virulence-associated genes suggests that the isolates have the potential to cause disease and pathogenicity. These findings provide insights into the whole genome sequence diversity of E. coli in urban based tertiary care hospital wastewater, emphasizing the genetic variation and plasmid diversity in these E. coli strains, which may have implications in public health and microbial ecology of the environment.}, }
@article {pmid42129938, year = {2026}, author = {Zhao, L and Wu, L and Yin, S and Gao, W and Xiang, X and Xie, Y and Guo, Y and Wang, Z}, title = {Multi-omics reveals effects of several rumen bacteria on reproductive performance of sheep.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02426-5}, pmid = {42129938}, issn = {2049-2618}, support = {2025SNJF019//Three Agriculture Nine Party Science and Technology Cooperation Project/ ; 32573211//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Mounting evidence indicates that the rumen microbiota plays a crucial role in the reproductive health of sheep. However, the potential beneficial effects of rumen microbiota on lambing performance in sheep across different stages of the reproductive cycle and the precise mechanisms underlying these effects remain unclear. We aimed to elucidate the rumen microbial regulatory network underlying differences in reproductive performance in sheep by integrating multi-stage metagenomics and metabolomics.<br><br>RESULTS: No significant difference was observed in the ruminal microbial &#x3b1;-diversity between sheep with high and low litter size. However, significant stage-specific segregation was observed in their community structures. We identified a cohort of key species strongly associated with litter size. These included Asaia bogorensis, Methanolobus zinderi, Erwinia gerundensis, Marinobacter sp. BSs20148, and Lactobacillus amylolyticus enriched during pregnancy; Rhizobium gallicum, Aeromonas caviae, Pseudolysobacter antarcticus, Mucilaginibacter rubeus, Thermococcus paralvinellae, and Janthinobacterium svalbardensis enriched during lactation; Pseudomonas mandelii, Gordonia sp. HY186, Arachidicoccus sp. BS20, Mesotoga prima, Acidovorax ebreus, Donacia cinerea, and Salmonella enterica enriched during estrus. Host plasma metabolomics analysis further revealed an enrichment of a set of core metabolites in the blood of high-fertility sheep, including Inositol, 2-Linoleoylglycerol, lysophosphatidylcholines and neuromodulatory substances such as tyramine and sphingosine-1-phosphate. We constructed stage-specific "rumen microbe-rumen metabolite-plasma metabolite" regulatory axes. These results suggest the influence of the rumen microbiome on plasma metabolic profiles and subsequent fertility outcomes in sheep.<br><br>CONCLUSION: We elucidate the dynamic mechanism by which the rumen microbiota in high-fertility sheep is associated with superior reproductive performance through stage-adaptive community succession and functional remodeling, which in turn may modulate the host's neuroendocrine and lipid metabolic profiles. These findings provide a new perspective for understanding the regulation of fertility in ruminants and lay a theoretical foundation for improving reproductive efficiency through nutritional strategies targeting the rumen microbiota. Video Abstract.}, }
@article {pmid42129966, year = {2026}, author = {LaRochelle, L and Morningstar, JL and Hoch, C and Rodriguez Materon, S and Hashioka, H and Scott, DJ and Gross, CE}, title = {Does Implanted Ankle Hardware Harbor Bacteria? Identification of the Microbial Profile Using Next-Generation DNA Sequencing? A Short Report.}, journal = {Foot &amp; ankle international}, volume = {}, number = {}, pages = {10711007261438460}, doi = {10.1177/10711007261438460}, pmid = {42129966}, issn = {1944-7876}, abstract = {BackgroundNext-generation DNA sequencing (NGS) has improved detection of bacterial species and expanded understanding of the microbiome's influence on postoperative outcomes in orthopaedic patients. Although NGS has identified organisms linked to reoperations in shoulder surgery, its application in the foot and ankle remains unexplored. This study uses NGS to determine whether patients undergoing hardware removal exhibit a unique microbiome profile.Methods:A prospective study recruited 34 patients undergoing hardware removal surgery from the foot or ankle during 2020-2023. Patients were excluded based on any concern for infection prior to surgery. During the operation, the surgeon collected the removed hardware for analysis at a CLIA (Clinical Laboratory Improvement Amendments of 1988)-licensed molecular diagnostic laboratory. Majority of patients underwent surgery for painful orthopaedic hardware (70.6%). The cohort was predominantly female (62.2%) and mean age was 53.3 years (range 17-78). The mean time from primary implantation to hardware removal was 40.1 months (range 2.8-276.6 months).ResultsNGS identified bacterial DNA in 5 cases (14.7%), detecting 9 total organisms. Staphylococcus species were most common (44.4%), followed by Corynebacterium (22.2%). No significant associations were found between bacterial detection and patient demographics or with hardware removal performed for painful implants.Conclusion:This study found no consistent microbiome among patients undergoing hardware removal surgery, with Staphylococcus species being the most frequently detected organisms. These preliminary findings suggest that foot and ankle hardware does not consistently harbor bacteria detectable by NGS, although the small sample size limits generalizability and further investigation is warranted.}, }
@article {pmid42130174, year = {2026}, author = {Pesenti, L and Lengrand, S and Kahn, A and Michot, L and Marchandise, F and Focant, C and Richet, S and Debode, F and Bragard, C}, title = {Xylem endophytes of Salicaceae: potential role in mitigating disease symptoms from Xylella fastidiosa or Brenneria salicis.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71230}, pmid = {42130174}, issn = {1469-8137}, support = {40006265//FRIA-FNRS/ ; }, abstract = {Increasing pressure from xylem-limited pathogens has driven the search for beneficial xylem-inhabiting endophytes that can enhance growth, stress tolerance, and disease resistance in woody plants. This study characterized the culturable xylem microbiota of Salicaceae species (willow and poplar) and evaluated their potential as biological control agents against vascular pathogens. A combination of microbial isolation, metabarcoding, and whole-genome sequencing was used to characterize xylem-associated bacteria. Functional traits were assessed through in vitro assays, while genome mining identified genes linked to plant-beneficial activities. Interactions between endophytes and pathogens were tested using fluorescently labeled strains in tobacco (Nicotiana tabacum) and in vitro-grown willow (Salix caprea). Bacterial genera (Bacillus, Pseudomonas, Erwinia) exhibited plant growth-promoting traits and strong antagonism against bacterial and fungal vascular pathogens, including Xylella fastidiosa, Brenneria salicis, Fusarium spp., and Verticillium dahliae. Genome analyses revealed functions related to nutrient acquisition, biofilm formation, and antimicrobial production. Co-inoculation assays significantly reduced pathogen load and disease symptoms in tobacco and mitigated symptoms in willow. Xylem endophytes act as context-dependent allies in woody plant defence. This study provides a functional and genomic framework supporting microbiome-based strategies to enhance resistance against vascular pathogens in long-lived woody hosts.}, }
@article {pmid42130196, year = {2026}, author = {Cheng, X and Lei, Y and Zhang, S and Chen, L and Wang, Y}, title = {Butyrate Alleviates Hyperuricemia by Selectively Targeting the Metronidazole/Neomycin-Sensitive Bacterium Dubosiella newyorkensis.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c13934}, pmid = {42130196}, issn = {1520-5118}, abstract = {Hyperuricemia (HUA), a metabolic disorder resulting from disrupted uric acid (UA) homeostasis, is the principal etiological factor for gout. This study investigated the therapeutic potential of gut microbiota modulation in HUA using antibiotic-treated mouse models with butyrate intervention. Selective antibiotic screening identified the Dubosiella-type strain Dubosiella newyorkensis (Dn) as an effective intervention for HUA. Dn treatment significantly reduced UA production, improved renal function markers, and decreased oxidative stress. Dn enriches Bacteroides and Romboutsia while suppressing the pathobiont Thomasclavelia, thereby enhancing the production of acetate, propionate, and butyrate. Molecular analyses demonstrated that Dn downregulated the expression of URAT1 while upregulating ABCG2, thereby promoting UA excretion. Histopathological evaluation confirmed that Dn restored the glomerular atrophy, tubular dilation, and collagen deposition induced by HUA. These findings suggest that Dn is a promising multitarget therapeutic agent for HUA and provides a scientific foundation for the development of novel microbiome-based strategies against HUA.}, }
@article {pmid42130486, year = {2026}, author = {Dichter, J}, title = {Fermented Dairy Products as Modulators of the Gut Microbiome: Greek Yogurt as a Model System.}, journal = {Food science &amp; nutrition}, volume = {14}, number = {}, pages = {e71872}, pmid = {42130486}, issn = {2048-7177}, abstract = {Greek yogurt, characterized by its thick texture and higher protein content, contains reduced lactose levels while still preserving large colonies of active bacteria when compared to conventional (or "traditional") yogurt. The starter cultures listed on its label do more than just ferment milk; they actively reshape the gut microbiome and adjust host physiology. This review examines currently available observations about distinct bacterial types within this product, especially regarding its effects on intestinal balance. The ability to produce short-chain fatty acids is a property linked to these strains, along with the potential to stabilize gut lining function, adjust immunity patterns, aid blood sugar regulation, and even offer possible cardiovascular benefits. Greek yogurt's properties and potential differ from other fermented food items. Findings from experimental and clinical research suggest the lactic acid and Bifidobacterium species found in Greek yogurt contribute to increased microbiota variety, encourage growth of butyrate-producing bacteria, and strengthen the intestinal lining. Inflammation levels are reduced by these microbes, leading to greater lactose tolerance, smoother digestion, and balanced metabolic activity. Still, much of the available data is limited because most studies do not distinguish Greek yogurt from conventional yogurt in their analyses, even though differences exist in live cultures, survival through digestion, and manufacturing. Fermented vegetables may offer wider microbe variety; however, consistency in bacterial strains and stronger clinical evidence gives Greek yogurt significance in nutritional and microbiome research. Future investigations should focus on Greek yogurt and prioritize direct comparisons to other fermented foods. To credibly refine dietary recommendations, improved microbial methodologies and expanded trials among diverse populations are warranted.}, }
@article {pmid42130645, year = {2026}, author = {Ali, N}, title = {Vitamin D Roles Across Developmental Stages in Pediatric Pneumonia: Linking Genetics, Microbiome, Maternal Status and Immunity.}, journal = {Health science reports}, volume = {9}, number = {}, pages = {e72520}, pmid = {42130645}, issn = {2398-8835}, abstract = {BACKGROUND: Pneumonia remains a leading cause of morbidity and mortality among children globally, especially in low- and middle-income countries, where poor nutrition and limited access to healthcare increase vulnerability. Vitamin D deficiency is common among children and has emerged as a significant risk factor associated with respiratory infections. This review aims to synthesize current evidence on the role of vitamin D across developmental stages in pediatric pneumonia.<br><br>METHODS: A comprehensive literature search was conducted in PubMed, Scopus, Web of Science, and Google Scholar to identify relevant studies on vitamin D and pediatric pneumonia. Peer-reviewed articles, including observational studies, randomized controlled trials, and reviews, were screened. Evidence was synthesized from immunology, genetics, maternal health, and microbiome research to provide an integrated perspective on vitamin D-mediated immune responses and clinical outcomes.<br><br>RESULTS: Mechanistically, vitamin D enhances host defense by inducing antimicrobial peptides such as cathelicidin and &#x3b2;-defensins. It improves macrophage phagocytic function, modulates Toll-like receptor signaling, and preserves airway epithelial barrier integrity. Vitamin D also modulates adaptive immunity by suppressing pro-inflammatory Th1 and Th17 responses while promoting regulatory T-cell activity and anti-inflammatory cytokine production. Epidemiological studies consistently show an association between low serum 25-hydroxyvitamin D levels and increased risk and severity of pneumonia, although results from supplementation trials remain heterogeneous. Recent evidence highlights additional modifiers of vitamin D-mediated immunity, including maternal vitamin D status, vitamin D receptor (VDR) genetic polymorphisms, early-life immune programming, and respiratory microbiome interactions, which may explain variability in clinical outcomes across populations and developmental stages.<br><br>CONCLUSION: Overall, this review provides a comprehensive framework linking vitamin D biology with immune system development in children and their risk of pneumonia. It emphasizes the importance of age-specific supplementation strategies and well-designed mechanistic and clinical studies to improve prevention and management.}, }
@article {pmid42130741, year = {2026}, author = {Long, J and Zhao, J and Gu, X and Huang, C}, title = {Post-transplant diabetes mellitus after kidney transplantation: pathogenesis, risk factors, and management strategies.}, journal = {Frontiers in endocrinology}, volume = {17}, number = {}, pages = {1829579}, pmid = {42130741}, issn = {1664-2392}, mesh = {Humans ; *Kidney Transplantation/adverse effects ; Risk Factors ; *Postoperative Complications/etiology/therapy ; *Diabetes Mellitus/etiology/therapy ; Gastrointestinal Microbiome ; Immunosuppressive Agents/adverse effects ; }, abstract = {Post-transplant diabetes mellitus (PTDM) affects 7-39% of kidney transplant recipients and substantially worsens cardiovascular, infectious, and allograft outcomes. Although PTDM shares core pathophysiological features with type 2 diabetes-peripheral insulin resistance and impaired β-cell secretion-its etiology is fundamentally shaped by immunosuppressive therapy. Calcineurin inhibitors suppress insulin gene transcription via NFAT inhibition and exacerbate lipotoxicity; corticosteroids drive hepatic gluconeogenesis and impair GLUT4-mediated glucose uptake; and mTOR inhibitors reduce β-cell mass through mTORC1-dependent mechanisms. Chronic NF-κB/JNK-driven inflammation further amplifies insulin resistance and promotes β-cell apoptosis. Beyond these established mechanisms, we propose a unifying "gut-immune-metabolic axis" in which immunosuppression-induced gut microbiota dysbiosis-characterized by depletion of short-chain fatty acid-producing taxa (Roseburia, Faecalibacterium prausnitzii) and Akkermansia muciniphila-drives intestinal barrier dysfunction, endotoxemia, impaired FXR/TGR5-mediated GLP-1 secretion, and TMAO-associated metabolic inflammation, collectively perpetuating glucose dysregulation. Risk stratification integrates non-modifiable factors (advanced age, African American/Hispanic/South Asian ethnicity, TCF7L2 polymorphisms, autosomal dominant polycystic kidney disease) with modifiable determinants (pre-transplant dysglycemia, obesity, hypomagnesemia, hepatitis C and cytomegalovirus infections, acute rejection, and diuretic use). Diagnosis requires OGTT-centered assessment per the 2024 International Consensus guidelines, with cautious interpretation of HbA1c during the early post-transplant period. Management encompasses personalized immunosuppression (corticosteroid minimization, tacrolimus trough levels <10 ng/mL, and belatacept-based regimens in high-risk patients), structured lifestyle interventions, and emerging pharmacotherapies-particularly SGLT2 inhibitors and GLP-1 receptor agonists-which offer cardiometabolic benefits beyond glycemic control. Microbiome-targeted strategies, including prebiotics, probiotics, and fecal microbiota transplantation, represent a conceptually compelling frontier warranting prospective investigation. This framework reframes PTDM as a multi-hit, immunometabolic syndrome and provides a translational roadmap toward precision prevention and improved long-term transplant outcomes.}, }
@article {pmid42130766, year = {2026}, author = {Li, Y and Sun, Y and Shi, L and Wang, A and Gao, X and Leng, H}, title = {The nasal-oral microbiome axis in allergic rhinitis: environmental triggers, microbial dysbiosis, and immune dysregulation.}, journal = {Frontiers in allergy}, volume = {7}, number = {}, pages = {1799085}, pmid = {42130766}, issn = {2673-6101}, abstract = {Allergic rhinitis (AR) is a common chronic inflammatory disease, which affects about 400 million people around the world. The role of the upper airway microbiota in the development of AR has recently emerged and seems to be an important player in its pathology, but there are still no detailed mechanistic models that incorporate exposure to the environment, dysbiosis of microbes or dysregulated immunity as a whole. In this review we summarize the state of the art about the microbiome nose-mouth connection in AR to understand how environmental stimuli change the microbiota composition as well as how an imbalance can induce allergy-related inflammation. This review follows a narrative approach. Literature was identified through systematic searches of PubMed, Web of Science, and Scopus databases (up to March 2025) using the following key terms and their combinations: "allergic rhinitis', "nasal microbiome", "oral microbiome", "dysbiosis", "epithelial barrier", 'short-chain fatty acids', "Th2 inflammation", and "probiotics". Inclusion criteria encompassed original research articles, systematic reviews, and meta-analyses published in English; conference abstracts, case reports, and purely non-human studies were excluded unless they provided mechanistic insights not available from human data. Environmental exposures substantially alter upper airway microbial communities. Air pollutants such as PM2.5 and diesel exhaust particles (DEP) damage epithelial tight junction proteins via reactive oxygen species (ROS), increasing nasal permeability. DEP additionally functions as an immune adjuvant by promoting pro-Th2 immune polarization. Antibiotic treatment during early childhood may affect GI tract development by altering resident bacterial populations, being considered as a strong risk factor for developing AR. On the other hand, farm exposure and microbial diversity provide protection by enhancing regulatory T cell induction. AR patients exhibit characteristic nasal dysbiosis, including overgrowth of Staphylococcus aureus and Moraxella catarrhalis alongside depletion of protective commensals such as Dolosigranulum pigrum and Corynebacterium spp. This dysbiosis disrupts the epithelial barrier, triggering alarmin release (TSLP, IL-25, IL-33) and amplifying type 2 inflammation. The oral microbiota also contributes via the oral-nasal-pulmonary axis whereby periodontal pathogens are pro-inflammatory while commensals have immunomodulatory roles. Mechanistically, microbiome-derived metabolites-especially short chain fatty acids and tryptophan derivatives-regulate the immune system via G protein-coupled receptors, histone deacetylase inhibition, and aryl hydrocarbon receptor activation. Dysbiosis promotes Th2 polarization, Treg/Th17 imbalance, and the activation of ILC2s, whereas neuro-immune interactions via TRPV1/TRPA1 enhance neurogenic inflammation. Translation to clinical opportunity: Microbiome based diagnostic biomarker; Probiotic (nasal/oral); Prebiotics; postbiotics, and engineered bacteria. Multi-omics based precision medicine using ML to stratify patient and tailor intervention. In summary, this review offers an insight into the theory of the microbiome-immunology interplay in AR as well as new avenues to consider regarding treatment of this condition through the nasal-oral microbiota axis.}, }
@article {pmid42130962, year = {2026}, author = {Tomar, SS and Khairnar, K}, title = {Disruption in the Host-Phage Dynamics and Altered Microbial Diversity in the Upper Respiratory Tract of SARS-CoV-2-Infected Individuals.}, journal = {PHAGE (New Rochelle, N.Y.)}, volume = {7}, number = {1}, pages = {9-20}, pmid = {42130962}, issn = {2641-6549}, abstract = {BACKGROUND: The upper respiratory tract (URT) is an important site for the predisposition and multiplication of the SARS-CoV-2 virus. Therefore, URT is a critical site for investigating the changes in the microbiome caused by the SARS-CoV-2 infection. This study aims to compare phageome diversity and investigate the correlation of the phageome profiles with the sample type (SARS-CoV-2 or control) to determine the nature of phage-host interactions in the human URT microbiome and to assess the effect of SARS-CoV-2 viral load on host and phage abundance.<br><br>MATERIALS AND METHODS: In this study, we have used the whole-genome shotgun metagenomic approach to investigate URT swab samples (n = 96) collected from SARS-CoV-2-positive individuals (n = 48) (nonhospitalized but symptomatic) and healthy controls (n = 48) belonging to five districts of central India.<br><br>RESULTS: The results revealed distinct phageome profiles among the groups; Detrevirus dominated the composition in the control samples, while Maxrubnervirus was dominant in SARS-CoV-2 samples. Microbial diversity analysis showed significantly higher richness in the SARS-CoV-2 group compared to controls for both bacteria (Chao1: 886.00 vs. 351.00, p < 0.0001) and phages (Chao1: 39.00 vs. 16.00, p = 0.0002). Bacterial diversity (Simpson index) was lower in the SARS-CoV-2 group (0.88 vs. 0.93, p = 0.0024), whereas phage diversity was higher in the SARS-CoV-2 group (0.86 vs. 0.79, p = 0.0384). Viral load, as reflected by cycle threshold (Ct) values, significantly influenced both bacteria (H = 6.69, p = 0.035) and phage (H = 8.97, p = 0.011) abundances. Host-phage interaction networks appeared disrupted in SARS-CoV-2 samples, with a weaker logistic model fit (R [2] = 0.7425) than controls (R [2] = 0.9265).<br><br>CONCLUSION: SARS-CoV-2 infection alters URT microbiome composition, increasing microbial diversity but disrupting host-phage dynamics. SARS-CoV-2 Viral load correlates with the shifts in microbial abundance, indicating infection-driven shifts in microbiome stability compared to healthy controls.}, }
@article {pmid42131067, year = {2026}, author = {Glynn, TR and Broedlow, CA and Rodriguez, V and Nogueira, NF and Londono, V and Brophy, T and Pallikkuth, S and Roach, M and Pahwa, S and Fein, LA and Hurwitz, BE and Jones, D and Alcaide, ML and Klatt, N and Martinez, C}, title = {Microbiota, Gender-Affirming Hormone Therapy, and Inflammatory Biomarkers in Transgender Women with HIV: Potential Implications for Cardiovascular Disease.}, journal = {Transgender health}, volume = {11}, number = {2}, pages = {114-125}, pmid = {42131067}, issn = {2688-4887}, support = {T32 AI007433/AI/NIAID NIH HHS/United States ; }, abstract = {PURPOSE: The intersecting disparities of human immunodeficiency virus (HIV) and cardiovascular disease (CVD) among transgender women have raised questions about the role of the gut microbiota and gender-affirming hormone therapy (GAHT) in the pathogenesis of CVD in the context of HIV. The purpose of this study was to provide an early exploration of the associations between these possible mechanisms driving inflammatory CVD risk markers among transgender women with HIV.<br><br>METHODS: We conducted a preliminary study with 21 transgender women with HIV exploring the relationship between GAHT use (self-report), gut/rectal microbiota composition (rectal swabs), and inflammatory markers linked to CVD (plasma). Microbiota measures included alpha (richness, evenness, and Shannon diversity) and beta (Bray-Curtis, un/weighted UniFrac) diversity metrics. Inflammatory biomarkers included intestinal fatty-acid binding protein, monocyte chemoattractant protein-1, soluble CD163, intercellular adhesion molecule 1, tumor necrosis factor alpha (TNFa), soluble TNF receptor I (sTNF-I), sTNF-II, interleukin (IL)-6, IL-8, IL-1b, IL-1a, soluble CD14, d-dimer (domain dimer), vascular cell adhesion molecule 1, and high-sensitivity C-reactive protein. Wilcoxon rank sum test, log-level regression, Spearman's rho, permutational multivariate analysis of variance, and differential abundance testing assessed relationships between constructs.<br><br>RESULTS: Key inflammatory markers linked to CVD were associated with GAHT use-an increased sTNF-I and sTNF-II levels and decreased IL-1a levels. Microbiota composition was not related to GAHT use but was variably associated with inflammatory biomarkers related to CVD risk.<br><br>CONCLUSIONS: Although preliminary, these findings suggest a potential association between inflammation linked to CVD risk and microbiota composition and GAHT. The results contribute to the characterization of interconnecting factors that may inform understanding and interventions to enhance overall health and well-being in transgender women with HIV. Further research is essential to elucidate the mechanisms underlying these associations, ultimately striving for health equity.}, }
@article {pmid42131202, year = {2026}, author = {Sivamaruthi, BS and Kesika, P and Chaiyasut, C and Ragu Varman, D}, title = {Microbiome driven modulation of neurotransmitters: implications for neurotransmission and mood disorders.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1750377}, pmid = {42131202}, issn = {1664-302X}, abstract = {The human gut microbiome has emerged as a crucial regulator of neurophysiological processes by engaging with the central nervous system (CNS) via the microbiota-gut-brain (MGB) axis. One of the most significant ways gut microorganisms influence brain functions is by altering the levels of neurotransmitters. A significant relationship exists between microbial activity and mood, behavior, and cognition. Gut microorganisms can make or break down bioactive substances like serotonin, dopamine, γ-aminobutyric acid (GABA), glutamate, acetylcholine, and histamine. These microbial modulations influence precursor availability, receptor sensitivity, synaptic signaling dynamics, and neuroimmune modulation, thereby indirectly shaping neurotransmission within central circuits. These neurochemical effects, particularly involving serotonergic, dopaminergic, GABAergic, and glutamatergic pathways, are mediated through microbial metabolites such as short-chain fatty acids (SCFAs), alterations in tryptophan metabolism, immune system activation, vagal nerve transmission, and the control of the hypothalamic-pituitary-adrenal (HPA) axis. Changes in the composition of the microbiome have been frequently linked to mood disorders, such as depression, anxiety, bipolar disorder, and schizophrenia. The current review integrates findings from preclinical and clinical studies on microbiome-related neurotransmitter modulation, emphasizing novel therapeutics such as probiotics, prebiotics, fecal microbiota transplantation, and dietary alterations. Unlike previous reviews that primarily focus on microbiome composition or therapeutic interventions such as probiotics and fecal microbiota transplantation, this review adopts a neurotransmitter-centered framework, integrating microbial regulation of serotonergic, dopaminergic, GABAergic, glutamatergic, cholinergic, and histaminergic systems with the pathophysiology of mood disorders. Connecting microbiota-driven modulation of neurochemistry to mental outcomes offers a promising adjunctive avenue for mood disorder management, pending rigorous mechanistic and clinical validation.}, }
@article {pmid42131203, year = {2026}, author = {Zahra, M and Ouf, A and Azzazy, HME and Moustafa, A}, title = {Metagenomic profiling of gut microbiome signatures across liver disease stages and HCV-related hepatocellular carcinoma in Egyptian patients.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1758563}, pmid = {42131203}, issn = {1664-302X}, abstract = {INTRODUCTION: Dysbiosis in the gut microbiome, particularly concerning the synchronous crosstalk between the gut and the liver, has been associated with various diseases. This study examines the gut microbiome's role in liver diseases among Egyptian patients, with a focus on the hepatitis C virus (HCV) and hepatocellular carcinoma (HCC), both of which are highly prevalent in Egypt.<br><br>METHODS: Utilizing shotgun metagenomic sequencing, we analyzed microbial gene catalogs and taxonomic profiles from 46 Egyptian patients categorized into five groups: healthy individuals, liver disease patients of different etiologies, post-HCV, treated HCV, and HCV-HCC patients.<br><br>RESULTS: Healthy and treated HCV patients exhibited distinct microbial profiles characterized by an abundance of beneficial bacteria, Faecalibacterium and Bifidobacterium (p < 0.05), associated with anti-inflammatory short-chain fatty acid production. Conversely, liver disease and HCC patients displayed increased pathogenic bacteria, Escherichia (p < 0.05), and genes linked to inflammation and oncogenesis, including lipopolysaccharide biosynthesis.<br><br>DISCUSSION: These findings suggest a dominance of Faecalibacterium in healthy Egyptians, likely attributable to traditional dietary patterns, and cytochrome P450 genes as potential HCC biomarkers, possibly connected to aflatoxin exposure. Treated HCV patients showed significant microbiome recovery, reflecting effective antiviral therapy. These findings emphasize that Egypt-specific factors, such as persistent resistance genes post-HCV due to antibiotic use and the prominence of bile acid metabolism genes, are influenced by high HCV prevalence and environmental exposures like aflatoxins. Taken together, the results highlight the need for region-specific microbiome research priorities in Egypt and underscore how local dietary, clinical, and environmental factors may shape future objectives in understanding liver disease pathogenesis and prevention.}, }
@article {pmid42131238, year = {2026}, author = {Alblaji, M}, title = {Plant-based diets for human health with implications for cardiometabolic health, gut microbiome, and nutritional adequacy.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1830797}, pmid = {42131238}, issn = {2296-861X}, abstract = {Plant-based diets have gained considerable interest in recent times due to their perceived health and environmental benefits. However, the term "plant-based diet" refers to a broad range of diets with a wide range of differences in food quality and nutritional content. This article aims to summarize the available evidence regarding the health and environmental impacts of plant-based diets, including new trends and issues. Epidemiological studies, RCTs, and life cycle assessment studies were searched in various scientific databases to investigate the relationship between plant-based diets and various health outcomes or environmental impacts. Available evidence from prospective studies and RCTs suggests that well-planned plant-based diets are associated with a lower risk of cardiometabolic diseases and beneficial alterations in the gut microbiome. Environmental studies have uniformly found lower greenhouse gas emissions, land use, and water use associated with a human diet compared with an animal-based diet; however, the extent of these positive impacts depends on the diet composition. On the other hand, nutrient adequacy such as iron, vitamin B12, omega-3 fatty acids, processing, and socio-economic factors are also important considerations. This review aims at an integrated approach in environmental sustainability viewpoints with health results, comprehensive understanding the relationship between the quality of diet and health outcomes in the context of a circular food system and research priorities in guiding future diets.}, }
@article {pmid42131305, year = {2026}, author = {Toto, F and Cardile, S and Scanu, M and Marzano, V and Petito, V and Masi, L and Puca, P and Giorgio, V and Alterio, T and Diamanti, A and De Angelis, P and Lopetuso, LR and Scaldaferri, F and Putignani, L and Del Chierico, F}, title = {Ecological patterns of the gut mycobiome and microbiome in ulcerative colitis across life stages.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1769892}, pmid = {42131305}, issn = {2235-2988}, mesh = {Humans ; *Colitis, Ulcerative/microbiology/immunology ; *Mycobiome ; *Gastrointestinal Microbiome ; Adult ; Child ; Male ; Female ; *Fungi/classification/genetics/isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; Middle Aged ; Young Adult ; Adolescent ; Dysbiosis/microbiology ; Metagenome ; Child, Preschool ; Age Factors ; Aged ; Feces/microbiology ; }, abstract = {INTRODUCTION: Age-related variations in the gut microbial communities may influence immune regulation and inflammatory processes in inflammatory bowel diseases (IBD). However, distinguishing age effects from differences in clinical characteristics remains challenging.<br><br>METHODS: We investigated life-stage-associated patterns of the gut microbiome and mycobiome while accounting for clinical heterogeneity between paediatric and adult ulcerative colitis (UC) populations. We analysed 73 targeted metagenomes of bacteria and 69 targeted metagenomes of fungi from 26 paediatric and 47 adult patients with UC. Microbial diversity metrics and multivariate analyses were applied to evaluate community variation, and mucosal immune markers were assessed by ELISA. Clinical variables, including disease activity, duration, and treatment exposure, were considered when interpreting age-related microbial differences.<br><br>RESULTS: Fungal communities exhibited higher richness in adults and formed distinct age-related clusters in beta-diversity analyses, whereas bacterial composition remained largely comparable across age groups. Children were enriched in inflammation-associated fungi (Saccharomycetes, Aureobasidium, Cladosporium) and depleted in taxa commonly linked to gut health (Clavispora, Vishniacozyma, Betamyces). Stratification by life stage identified young adults as displaying the most pronounced dysbiosis, characterised by Basidiomycota/Ascomycota and Firmicutes/Bacteroidota ratios, and reduced Faecalibacterium prausnitzii abundance. Age-associated immune patterns were observed, with lysozyme levels increasing across life stages, correlating with sIgA, and positively associating with F. prausnitzii, although declining with increasing disease severity.<br><br>DISCUSSION: Age-related variation was more evident in fungal than bacterial communities, suggesting that host developmental and immunological factors contribute to mycobiome configuration beyond clinical imbalance alone. Together, these findings indicate that life stage is linked to ecological variation of the gut mycobiome and mucosal immune responses in UC, while bacterial communities appear primarily shaped by disease-related factors. The transition from childhood to adulthood may represent a critical window of host-fungal interaction relevant for age-tailored microbiome-based strategies.}, }
@article {pmid42131426, year = {2026}, author = {Hong, HH and Kim, TH and Kim, D and Kim, J and Jo, Y and Park, Y and Jeong, E and Lee, N and Roh, H and Jang, H and Kim, SM}, title = {A pilot study on microbial dynamics in drainage fluid during trauma recovery.}, journal = {Annals of surgical treatment and research}, volume = {110}, number = {5}, pages = {347-358}, pmid = {42131426}, issn = {2288-6575}, abstract = {PURPOSE: Drainage fluid may serve as a biologically informative indicator of immune and infectious status during postsurgical recovery after trauma. However, microbiome shifts in drainage fluid associated with clinical resilience have not yet been characterized. This study aimed to investigate microbial dynamics in drainage fluid across the intensive care unit (ICU) and ward recovery phases in Korean trauma patients.<br><br>METHODS: A total of 25 drainage and 10 stool samples were collected from 10 trauma patients who underwent abdominal surgery at a regional trauma center. Microbial composition was analyzed using 16S ribosomal RNA amplicon sequencing. Alpha and beta diversity were compared between sample types and recovery stages. Linear mixed-effects models were used to identify recovery-associated taxa while adjusting for clinical variables, and predicted metabolic pathways were assessed using PICRUSt2.<br><br>RESULTS: Drainage fluid harbored distinct microbial communities independent of the intestinal microbiota. Shared taxa between drainage and stool increased significantly in patients with bowel injury, suggesting microbial translocation. Seven genera and 5 species showed significantly decreased abundance during the ward stage, with Modestobacter and Blastococcus tunisiensis demonstrating the highest discriminative ability between recovery stages (area under the curve = 0.721). Predicted metabolic pathways related to fatty acid degradation, amino acid degradation, and pro-inflammatory processes were more active during the ICU stage.<br><br>CONCLUSION: These findings provide preliminary evidence that drainage fluid microbiome profiles may reflect recovery dynamics following trauma, supporting its potential utility for microbiome-based monitoring and biomarker discovery in trauma surgery.}, }
@article {pmid42131433, year = {2026}, author = {Salamon, A and Bel Rhali, S and Szabó, A and Miklósi, &#xc1; and Andics, A and Felföldi, T and Gácsi, M and Kubinyi, E}, title = {Nasal microbiota profiles are similar at two swabbing depths in healthy awake dogs.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1795324}, pmid = {42131433}, issn = {2297-1769}, abstract = {The nasal microbiome may play an important role in dogs' olfaction, as microbial communities in the nasal cavity can directly interact with the olfactory epithelium. Previous studies have used various sampling methods and depths to examine the canine nasal microbiota and the effect of sampling depth on the detected nasal microbiota remains unclear. To address this, we investigated and compared the nasal microbiota of 81 awake family dogs, sampled at two swabbing depths (15 mm and 25 mm) of the left nostril in the same individuals. The most abundant bacterial taxa in our nasal samples belonged to Moraxella (Gammaproteobacteria), consistent with previous studies. The 15 mm samples had a higher Shannon Diversity Index compared to the 25 mm samples, indicating closer proximity to the external environment. However, we found no significant differences in richness and overall microbiota composition between the two sampling depths. These results indicate that bacterial community profiles within the anterior nasal cavity are similar at the two examined depths. Because the deeper sample was always collected first from the same nostril, potential order effects cannot be excluded. Nevertheless, based on the findings, we recommend using a sampling depth up to 15 mm when examining the nasal microbiota of healthy awake mesocephalic dogs in field settings, as it is less invasive and minimises discomfort.}, }
@article {pmid42131446, year = {2026}, author = {Heasley, CK and Stefanova, V and Funk, C and Freitas, AC and Li, G and Pell, LG and Bassani, DG and O'Callaghan, KM and Shah, PS and Shawon, J and Gaffar, SMA and Haque, R and Sarker, SA and Roth, DE}, title = {Neonatal faecal abundance of Bifidobacterium longum subspecies infantis is not associated with anthropometric outcomes up to 6 months of age in Bangladeshi infants.}, journal = {Gut microbiome (Cambridge, England)}, volume = {7}, number = {}, pages = {e5}, pmid = {42131446}, issn = {2632-2897}, abstract = {B. infantis abundance in the infant gut may be associated with growth and health outcomes. However, these relationships have not been widely studied in settings where B. infantis is a dominant early-life commensal and growth faltering is prevalent. Here, we estimated associations between neonatal B. infantis abundance and anthropometric outcomes up to 6 months of age in generally healthy infants in Dhaka, Bangladesh; diarrhoea and hospitalizations (at 1-2 and 6 months) were secondary morbidity outcomes. B. infantis stool absolute abundance was quantified by qPCR; for each infant, the primary exposure was mean abundance (0-28 days). Length-for-age, weight-for-age, and weight-for-length z-scores were derived at birth, 2, 3, and 6 months. Neonatal B. infantis abundance had a bimodal distribution, with 63% of infants having detectable B. infantis by 28 days of age. Anthropometric z-score distributions were shifted down, with means below zero. Neonatal B. infantis abundance was not associated with any anthropometric outcome at 2, 3, or 6 months of age (n = 830), or with the risks of diarrhoea or hospitalizations. The lack of association of neonatal B. infantis abundance with growth outcomes suggests that promoting early B. infantis colonization is unlikely to improve growth in populations with postnatal faltering.}, }
@article {pmid42131447, year = {2026}, author = {Chia Liu, T and Rojas-Velazquez, D and Kidwai, S and Hogenkamp, A and Garssen, J and Kraneveld, AD and Lopez-Rincon, A}, title = {Machine learning identifies differences between breast milk and formula in the gut microbiome.}, journal = {Gut microbiome (Cambridge, England)}, volume = {7}, number = {}, pages = {e7}, pmid = {42131447}, issn = {2632-2897}, abstract = {In this study, we analysed differences in the infant gut microbiome between breastfed and formula-fed infants using novel machine learning techniques. Breast milk, rich in bioactive agents, supports microbiota composition and immune development, while formulas aim to replicate its nutritional profile. We applied a methodology combining the DADA2 pipeline for 16S rRNA sequencing with the Recursive Ensemble Feature Selection (REFS) algorithm for biomarker discovery. We analysed three publicly available 16S rRNA datasets: PRJNA633365 (70 stool samples from China), PRJDB7295 (40 stool samples from the Philippines), and PRJNA562650 (40 stool samples from China). The discovery dataset (PRJNA633365) revealed 16 significant taxa out of 1,227, validated across the other two datasets. Next, we compared REFS performance with another feature selection algorithm, SelectKBest. Finally, we conducted a literature review to explore links between identified taxa and medical conditions. Additionally, we used MicrobiomeAnalyst to examine associations with diseases, diet, and lifestyle. Our results show differences in the bacterial composition between breastfed and formula-fed infants, and these findings were validated in two independent datasets. Future research should explore the functional roles of these taxa and consider regional and dietary variability to enhance understanding of microbiome dynamics and long-term health outcomes.}, }
@article {pmid42131482, year = {2026}, author = {Udobi, ME and Bella-Omunagbe, M and Afolabi, IS and Chinedu, SN}, title = {Bioactive compounds as therapeutic modulators of metabolic syndrome: targeting inflammation and gut microbiota regulation.}, journal = {Frontiers in physiology}, volume = {17}, number = {}, pages = {1766078}, pmid = {42131482}, issn = {1664-042X}, abstract = {Food bioactives, including polyphenols, flavonoids, omega-3 fatty acids, and glucosinolates, play a crucial role in preventing metabolic syndrome by modulating chronic inflammation, gut microbiota homeostasis, and metabolic processes. These compounds influence key molecular pathways implicated in metabolic dysfunction and systemic inflammation. This review explores the mechanisms through which food bioactives contribute to metabolic health, emphasizing their role in inflammation regulation, gut microbiota modulation, and insulin sensitivity. A comprehensive literature review was conducted using databases such as PubMed, Scopus, and Web of Science. Relevant peer-reviewed articles, meta-analyses, and clinical trials published in the last two decades were analyzed, focusing on bioactives' biochemical actions and therapeutic potential in Metabolic syndrome. The study showed that bioactives mitigate inflammation by inhibiting NF-κB signaling and NLRP3 inflammasome activation, reducing pro-inflammatory cytokines (TNF-α, IL-6, IL-1β). They also modulate gut microbiota, promoting beneficial bacteria (e.g., Akkermansia muciniphila) and enhancing gut barrier integrity via increased expression of tight junction proteins. Short-chain fatty acids (SCFAs) derived from microbial metabolism contribute to systemic anti-inflammatory effects. Clinical studies indicate that polyphenol-rich diets, such as the Mediterranean diet, improve metabolic syndrome parameters by lowering inflammatory markers, enhancing lipid profiles, and improving insulin sensitivity. Despite promising findings, challenges such as poor bioavailability and variability in gut microbiome responses hinder clinical application. Strategies like nanoencapsulation and microbiome-targeted nutrition may optimize bioactive efficacy. Overall, food bioactives represent a promising strategy for metabolic health. Future research should focus on enhancing bioavailability, personalized nutrition, and large-scale clinical trials to establish optimal dosing and long-term benefits.}, }
@article {pmid42131744, year = {2026}, author = {Ogedengbe, O and Hunt, J and Pang, A and Gupta, D}, title = {Silicon-mediated drought resilience mechanisms in crops: from physiology to molecular insights.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1788106}, pmid = {42131744}, issn = {1664-462X}, abstract = {Drought stress increasingly constrains crop growth, yield, and quality through reduced photosynthesis, impaired nutrient uptake, and oxidative damage, with recent occurrences causing substantial yield losses across major production regions. Silicon (Si), although not an essential nutrient, is a prevalent, non-toxic, "quasi-essential" element that can enhance crop performance under water limitation; however, Si-induced drought-mitigation mechanisms are frequently reported in isolation, based on individual studies. This review aims to provide a holistic understanding of Si's role in enhancing plant resilience to water stress by comprehensively compiling and integrating physiological to molecular mechanisms underpinning Si-mediated drought resilience, while contextualising soil Si availability, plant uptake and accumulation diversity, and agronomic delivery options. Across crops, Si fertilisation consistently improves water relations by promoting root growth, hydraulic conductance, and aquaporin regulation, enabling osmotic adjustment and modulating stomatal behaviour through hormone-reactive oxygen species interactions. Evidence is synthesised from controlled and field studies, alongside temporal trend analyses showing a shift from uptake/transport research (pre-2010) to physiological characterisation (2010-2015), and to integrative multi-omics (2020-present), including transcriptomics and metabolomics. Key research gaps include limited field validation, inconsistent experimental designs and drought imposition protocols, incomplete multi-omics-to-trait integration, and underexplored Si-microbiome interactions. Optimising the Si source, dosage, timing, and application method across different species and environments presents a practical approach to developing climate-resilient, low-input cropping systems in the face of increasing drought risk.}, }
@article {pmid42131794, year = {2026}, author = {Kalin, K and Rådholm, K and Olsson, L and Tremaroli, V and Woodward, M and Wennberg, M and Bäckhed, F and Rolandsson, O}, title = {Effects of saccharin on insulin sensitivity in adult, overweight individuals without diabetes: a real-world pilot study.}, journal = {Journal of the Endocrine Society}, volume = {10}, number = {6}, pages = {bvag096}, pmid = {42131794}, issn = {2472-1972}, abstract = {CONTEXT: It has been suggested that consumption of saccharin, a widely used artificial sweetener, decreases insulin sensitivity in rodents and humans, but studies show conflicting results.<br><br>OBJECTIVE: To investigate if saccharin affects insulin sensitivity in a proof-of-concept study in humans using hyperinsulinemic-euglycemic clamp.<br><br>METHODS: In an open-label pilot study, we recruited 14 overweight participants without diabetes who were mean 60.5 (SD 4.1) years of age and had a body mass index of 27.6 (SD 0.7). Insulin sensitivity, assessed by hyperinsulinemic-euglycemic clamp, was determined before and after consumption of 5&#x2005;mg/kg saccharin/day for 3 months. Blood was collected for analysis of diabetes-related biomarkers. Stool samples were collected before, during, and after saccharin consumption for microbiota profiling by 16S rRNA gene sequencing.<br><br>RESULTS: Thirteen of the 14 participants (6 men, 7 women) completed the study. There was no change in insulin sensitivity (mean M value difference [&#x394;M] -0.1, P = .85) or body weight (mean difference -0.1&#x2005;kg, P = .70) after consumption of saccharin. However, the mean glycated hemoglobin decreased from 38.7&#x2005;mmol/mol (SD 3.0) at visit 1 to 36.8 (SD 3.4) at visit 4 (P = .003). Overall, there was no change in composition or richness of the gut microbiota at the end of the study.<br><br>CONCLUSION: This study did not demonstrate an association between saccharin intake and impaired insulin sensitivity in adult, overweight participants without diabetes assessed by hyperinsulinemic-euglycemic clamp.}, }
@article {pmid42132027, year = {2026}, author = {Osakunor, DNM and Pfavayi, LT and Mduluza, T and Mutapi, F}, title = {Schistosomiasis and stunting: microbial and metabolic mechanisms in early childhood.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {381}, number = {1950}, pages = {}, doi = {10.1098/rstb.2025.0094}, pmid = {42132027}, issn = {1471-2970}, support = {/AMS_/Academy of Medical Sciences/United Kingdom ; //Thrasher Research Fund/ ; //British Academy/ ; //Royal Society/ ; }, mesh = {Humans ; Child, Preschool ; *Growth Disorders/parasitology/etiology/epidemiology ; *Gastrointestinal Microbiome ; Zimbabwe/epidemiology ; *Schistosomiasis haematobia/complications/drug therapy/epidemiology/parasitology ; Schistosoma haematobium/physiology ; Infant ; Praziquantel/therapeutic use ; Animals ; }, abstract = {Stunting (low height-for-age > 2 s.d. below the WHO child growth standards median) is a key indicator of chronic malnutrition and is influenced by poor nutrition, infections, chronic inflammation and impaired gut health. In sub-Saharan Africa, stunting frequently occurs in regions where schistosomiasis is endemic. Our previous research in Zimbabwean preschool children (≤ 5 years) found that Schistosoma haematobium infection alone could account for up to one-third of stunting cases. Using epidemiological, gut microbiome and metabolomic analyses, we investigated how this parasitic infection contributes to poor growth. Infected children showed significantly altered gut microbiome profiles compared to uninfected peers, indicating potential microbiome disruption linked to disease and impaired development. Metabolomic profiling revealed that S. haematobium infection elevated energy- and purine-related metabolites, reflecting metabolic stress associated with malnutrition. Early treatment with praziquantel did not significantly alter the microbiome but did restore normal metabolic profiles, aligning with observed catch-up growth. Here, we synthesize findings from our studies and others to highlight opportunities for intervention and key research gaps, supporting the inclusion of praziquantel in early health programmes and integrated strategies combining treatment with nutrition. Further research, particularly longitudinal studies, is needed to confirm causality and optimize child health outcomes in endemic areas. This article is part of the theme issue 'Biological, biomedical and environmental drivers of stunting'.}, }
@article {pmid42132029, year = {2026}, author = {Mweetwa, MN and Ashan, K and Kung, V and McNulty, NP and Besa, E and Barratt, MJ and Posma, J and Amadi, B and Gordon, JI and Kelly, P}, title = {Small intestinal microbiota in Zambian children with stunting and severe acute malnutrition.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {381}, number = {1950}, pages = {}, doi = {10.1098/rstb.20250088}, pmid = {42132029}, issn = {1471-2970}, support = {/MRC_/Medical Research Council/United Kingdom ; //Bill and Melinda Gates Foundation/ ; }, mesh = {Humans ; Zambia ; *Gastrointestinal Microbiome ; *Growth Disorders/microbiology/epidemiology ; *Severe Acute Malnutrition/microbiology/epidemiology ; Infant ; Child, Preschool ; RNA, Ribosomal, 16S/analysis ; *Bacteria/classification/isolation &amp; purification/genetics ; Male ; Female ; *Intestine, Small/microbiology ; *Duodenum/microbiology ; }, abstract = {Childhood malnutrition is linked to gut microbiome changes; however, most studies focus on faecal samples, while less is known about the small intestinal microbiome. Here, we characterized the duodenal microbiota of children in Zambia with severe acute malnutrition (SAM) and stunting and compared the microbiomes of stunted children living across the globe. To do this, duodenal aspirates from only stunted (i.e. not concurrently wasted) (n = 53) and SAM (n = 24) Zambian children were analysed by 16S rRNA gene amplicon sequencing. Associations between bacterial composition, clinical features and biomarkers of enteropathy were explored. Comparison of duodenal 16S rRNA gene datasets from malnourished children in different countries was also performed using publicly available datasets to assess the impact of age and geography on microbial diversity and composition. The duodenal microbiota in both stunted and SAM children was dominated by Streptococcus, Granulicatella, Gemella and Klebsiella. Children with SAM had lower α-diversity than stunted children. Meta-analysis revealed similarities in the bacterial composition of age-matched children in different countries, but relative abundances and their association with nutritional status differed. This study offers insight into the duodenal microbiota in children with different states of malnutrition, highlighting the potential influence of geography and age in shaping the proximal small intestine. This article is part of the theme issue 'Biological, biomedical and environmental drivers of stunting'.}, }
@article {pmid42132030, year = {2026}, author = {Mweetwa, MN and Kelly, P and Posma, J}, title = {A meta-analysis of gut microbiome research in malnourished African populations: a natural language processing approach.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {381}, number = {1950}, pages = {}, doi = {10.1098/rstb.2025.0038}, pmid = {42132030}, issn = {1471-2970}, support = {/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; *Natural Language Processing ; Africa South of the Sahara/epidemiology ; *Malnutrition/microbiology ; *Child Nutrition Disorders/microbiology ; }, abstract = {Malnutrition still affects millions of children in Africa. Changes in the gut microbiome have been implicated in malnutrition, but there has been inconsistent nomenclature of microbes. This meta-analysis reviews the microbiome literature using natural language processing (NLP) methods. We searched PubMed for gut microbiome studies of undernourished children living in low- and middle-income countries (LMICs). The primary analysis focused on continental coverage and study characteristics of microbiome research in sub-Saharan Africa (ss-Africa). We also used an NLP tool for normalizing primary data from full-text publications in ss-Africa compared with other LMICs, and between diseased and healthy children. We identified 16 studies. Most studies were conducted in Malawi and characterized the faecal microbiome using 16S rRNA sequencing. For comparison, 18 studies conducted in Bangladesh, India, Pakistan and Peru were included. With this, we identified frequently reported microbes that were distinctly identified in ss-Africa and highlighted possible signatures of an undernourished faecal microbiome across the globe. The consistent associations between elevated Pseudomonadota levels and severe acute malnutrition provide new insights into host-microbiome interactions in African contexts. However, the overlap between taxa associated with healthy and stunting underscores the need for further research to better inform potential targeted interventions in Africa. This article is part of the theme issue 'Biological, biomedical and environmental drivers of stunting'.}, }
@article {pmid42132032, year = {2026}, author = {Hlongwa, N and Rich, K and Kelly, P and Ngobeni-Nyambi, R and Stone, W and von Fintel, M and Schenck, C and Swart, R and Makhalanyane, T and Burger, R}, title = {The physiology of poverty: gut microbiome and pathways to child stunting.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {381}, number = {1950}, pages = {}, doi = {10.1098/rstb.2025.0034}, pmid = {42132032}, issn = {1471-2970}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Growth Disorders/etiology/microbiology ; *Poverty ; Hygiene ; Child, Preschool ; Child ; }, abstract = {The causes of childhood stunting remain debated, with emerging evidence highlighting the complexity of poverty-related mechanisms. While nutrition, healthcare and sanitation have traditionally been viewed as the primary drivers of stunting, new research highlights the physiological mediators linking poverty to impaired growth. Chronic exposure to unsanitary environments may lead to environmental enteric dysfunction, a subclinical gut condition that may impair the development of the gut microbiome. Stunted children frequently exhibit an immature and dysbiotic gut microbiome, which is linked to higher levels of gut inflammation, reduced nutrient assimilation and increased susceptibility to infections. Here, we examine how poverty-related factors, including poor diet and hygiene, affect gut health and early neurodevelopment, with a particular focus on the gut-brain axis. Understanding this 'physiology of poverty' reveals that effective interventions must extend beyond food provision to integrate improvements in water, sanitation, hygiene (WASH) and microbiome support (e.g. via probiotics or prebiotics). A holistic strategy targeting environmental and biological factors in early life is critical to disrupting the intergenerational cycle of stunting and poverty. We identify key evidence gaps and stress the need for multidisciplinary, context-specific approaches to mitigate stunting's long-term association with health and human capital. This article is part of the theme issue 'Biological, biomedical and environmental drivers of stunting'.}, }
@article {pmid42132035, year = {2026}, author = {Htet, MK and Nurfadilah, M and Ramsteijn, AS and Angelin, TC and Ameline, AS and Momo Kadia, B and Gabain, IL and Davies-Kershaw, H and Calvo-Urbano, B and Webster, JP and Ferguson, EL and Allen, S and Walker, AW and Fahmida, U}, title = {Exploring the diet-microbiome-growth axis among under-2-year-old children: a case-control study in East Lombok, Indonesia.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {381}, number = {1950}, pages = {}, doi = {10.1098/rstb.2025.0045}, pmid = {42132035}, issn = {1471-2970}, support = {//UK Research and Innovation/ ; }, mesh = {Humans ; Indonesia ; Infant ; *Diet ; Case-Control Studies ; *Gastrointestinal Microbiome ; Male ; Female ; RNA, Ribosomal, 16S/analysis ; *Bacteria/classification/isolation &amp; purification/genetics ; }, abstract = {Previous studies have compared the microbiota profiles of stunted and non-stunted children. However, how these profiles interact with dietary patterns is not completely understood. To assess differences in microbial diversity, composition and bacteria taxa between stunted and non-stunted children and how the consumption of food groups influence the gut microbiota of stunted children, this matched case-control study was conducted among 150 pairs of stunted and non-stunted children of between 18-23 months old in East Lombok, Indonesia. Anthropometry and dietary data were collected by trained enumerators. Microbiome data were generated by sequencing the V4 hypervariable region of the 16S rRNA gene. No between-group differences in alpha and beta diversity were observed. Exploratory analysis identified that Agathobacter, Coprococcus, Dorea, Hominimerdicola, Lawsonibacter and Ruminococcoides were more proportionally abundant among non-stunted children and Peptostreptococcus among stunted children. However, there was no association between food group consumption and abundance of these taxa. Breastfeeding significantly shaped the microbiota profiles. Future research on the association between microbiota profiles and complementary feeding should incorporate approaches such as diet modelling to capture the combined contributions of food groups and dietary components, alongside longitudinal study designs. This article is part of the theme issue 'Biological, biomedical and environmental drivers of stunting'.}, }
@article {pmid42132238, year = {2026}, author = {Roostaei, G and Riahi, T and Nikfar, S and Abdollahi, M}, title = {Harnessing the immune system in lung cancer: emerging role of the microbiome.}, journal = {Expert review of clinical immunology}, volume = {}, number = {}, pages = {}, doi = {10.1080/1744666X.2026.2661805}, pmid = {42132238}, issn = {1744-8409}, abstract = {INTRODUCTION: The microbiome has emerged as a critical regulator of tumor biology and immune response in lung cancer. Once considered sterile, the lung is now recognized to harbor a diverse microbiome that interacts with the gut - lung axis to shape inflammation, immune evasion, and therapeutic outcomes.<br><br>AREAS COVERED: This study reviews current evidence linking microbiome composition and function to lung cancer development and response to immune checkpoint inhibitors (ICIs). We explore mechanisms of microbial influence on host immunity, identify key taxa associated with treatment outcomes, and summarize therapeutic strategies such as fecal microbiota transplantation, probiotics, postbiotics, dietary changes, antibiotics, and engineered live biotherapeutics. The literature search was performed across multiple databases and sources, including PubMed, Scopus, Embase, and clinical trial registries, up to August 2025, focusing on both preclinical and clinical studies related to lung cancer, immunotherapy, and microbiome-targeted interventions.<br><br>EXPERT OPINION: Microbiome research is redefining precision oncology by presenting new biomarkers and therapeutic targets. Although early-phase trials show potential to improve ICI efficacy, implementation is limited by donor variability, methodological differences, and biosafety issues. Standardized protocols, mechanistic studies, and biomarker-driven patient selection will be crucial to incorporating microbiome modulation into routine lung cancer treatment.}, }
@article {pmid42132389, year = {2026}, author = {Hickey, E and Pradhan, A and Ma, Q and Leaves, I and Philip-Brookes, A and Duggan, S and Harvey, JA and Dambuza, IM and Cherek, P and Yuecel, R and d'Enfert, C and Gow, NAR and Brown, GD and Brown, AJP}, title = {The prebiotic inulin affects virulence factor expression in Candida albicans.}, journal = {mBio}, volume = {}, number = {}, pages = {e0385125}, doi = {10.1128/mbio.03851-25}, pmid = {42132389}, issn = {2150-7511}, abstract = {Dietary supplementation with prebiotics such as inulin has been associated with a broad range of health benefits. However, the effects of inulin on the opportunistic fungal pathogen Candida albicans, which resides as a commensal in the gut, have not been characterized. Here, RNA sequencing revealed that inulin affects the expression of C. albicans genes associated with cell wall construction, adhesion, and yeast-hypha morphogenesis. Consistent with these changes in gene expression, inulin inhibited hyphal development, increased adhesion to human Caco-2 and A431 cells, decreased the thickness of the inner layer of the C. albicans cell wall, reduced the exposure of cell wall pathogen-associated molecular patterns [β-(1,3)-glucan and chitin], and affected antifungal drug sensitivity. These changes impacted host immune recognition and cytokine responses, ultimately attenuating the virulence of C. albicans in an invertebrate infection model. Therefore, dietary supplementation with inulin is likely to influence host-fungus interactions.IMPORTANCEThe benefits of prebiotic dietary supplements, such as inulin (a natural plant dietary fiber), are thought to include a healthier gut microbiome, a reduced risk of colon cancer, and lower cholesterol levels. Unsurprisingly, prebiotic usage is increasing rapidly. However, while the effects of prebiotics upon gut bacteria have been characterized, the impacts upon Candida albicans, an opportunistic fungal pathogen that resides in the human gut, have remained obscure. We show that inulin affects the expression of virulence-related phenotypes and antifungal drug sensitivity in Candida. Furthermore, we show that inulin reduces the virulence of this fungus in an invertebrate model, consistent with the idea that inulin may lower the risk of fungal infection in healthy individuals.}, }
@article {pmid42132693, year = {2026}, author = {Martínez-Subirá, M and Cortijo Alfonso, ME and Friero, I and Macià, A and Pena, RN and Molinero, N and Moreno-Arribas, MV and Rubió-Piqué, L and Moralejo, M}, title = {Barley extrudates modulate the gut microbiome-metabolome axis in vitro through β-glucan fermentation and polyphenol biotransformation.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d6fo00601a}, pmid = {42132693}, issn = {2042-650X}, abstract = {Barley is rich in fermentable dietary fiber and phenolic compounds, both of which have recognized benefits for gut health and whose functionality is influenced by processing. Here, four barley genotypes differing in β-glucan content, type of starch, and phenolic profiles were extruded to obtain ready-to-eat products, which were then evaluated using a combined in vitro digestion-colonic fermentation model. The gastrointestinal fate of β-glucans and phenolics, short-chain fatty acids production, phenolic metabolite formation, and gut microbiota composition were assessed. After digestion, substantial amounts of β-glucans and phenolics remained in the non-bioaccessible fraction, supporting their relevance as substrates for colonic fermentation. During fermentation, the β-glucan-rich genotypes Annapurna® and Hilose® showed the strongest butyrogenic response, while the purple-grain genotype DHL-151340, characterized by a flavone- and anthocyanin-rich profile, showed an earlier and more pronounced accumulation of low-molecular-weight phenolic catabolites. Compared with the control, barley extrudates induced time-dependent shifts in microbiota composition, although community profiles tended to converge at later fermentation stages. Overall, genotype- and processing-driven differences translated into distinct fermentation and phenolic biotransformation footprints, highlighting the relevance of barley matrix composition in shaping the colonic fate of cereal bioactive compounds.}, }
@article {pmid42132952, year = {2026}, author = {Özel, &#x15e; and Lauritano, D}, title = {Oral mucosal microbiome alterations in recurrent aphthous stomatitis: a systematic review of 16 S rRNA gene sequencing studies.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {42132952}, issn = {1573-4978}, mesh = {Humans ; *Stomatitis, Aphthous/microbiology/genetics ; *Mouth Mucosa/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Dysbiosis/microbiology ; Case-Control Studies ; Saliva/microbiology ; Bacteria/genetics/classification ; Recurrence ; }, abstract = {Recurrent aphthous stomatitis (RAS) is a prevalent inflammatory disorder of the oral mucosa characterized by recurrent painful ulcerations in otherwise healthy individuals. This systematic review aimed to evaluate alterations in the oral mucosal microbiome of patients with RAS based on studies using 16 S rRNA sequencing. A systematic search of PubMed, Scopus, and Web of Science was conducted on April 14, 2026. Eligible studies included human case-control investigations evaluating oral mucosal swab samples from patients with clinically diagnosed RAS and healthy controls using 16 S rRNA sequencing. Studies based solely on saliva, culture methods, PCR-only analyses, or lacking controls were excluded. Joanna Briggs Institute Critical Appraisal Checklist for Case-Control Studies was used for the evaluation of selected articles. Six studies met the inclusion criteria. Considerable heterogeneity was observed in alpha and beta diversity outcomes. Most studies reported reduced microbial richness in RAS lesions, whereas others found increased or unchanged diversity. Ulcerated sites frequently demonstrated reduced abundance of health-associated taxa such as Streptococcus and Firmicutes, with increased levels of Proteobacteria and inflammation-associated genera including Neisseria, Haemophilus, Prevotella, and Fusobacterium. Microbial alterations were most pronounced at active ulcer sites, while non-ulcerated or healed mucosa more closely resembled healthy controls. Current evidence suggests that RAS is associated with localized, site-specific microbial dysbiosis rather than generalized oral microbiome disruption. However, methodological heterogeneity and small sample sizes limit definitive conclusions. Future standardized longitudinal studies integrating functional metagenomics are warranted to clarify the role of the microbiome in RAS pathogenesis.}, }
@article {pmid42132964, year = {2026}, author = {He, P and Stein, E}, title = {The Microbiome and Esophageal Disease: Where Are We Now?.}, journal = {Current gastroenterology reports}, volume = {28}, number = {1}, pages = {}, pmid = {42132964}, issn = {1534-312X}, mesh = {Humans ; *Esophageal Diseases/microbiology ; *Microbiota ; Gastroesophageal Reflux/microbiology ; Barrett Esophagus/microbiology ; *Esophagus/microbiology ; Dysbiosis/microbiology ; Eosinophilic Esophagitis/microbiology ; *Gastrointestinal Microbiome ; }, abstract = {PURPOSE OF REVIEW: The microbiome in the esophagus has been an area of early active investigation. In the past 5 years, advancements in next-generation sequencing and computational analysis have provided a more detailed picture of the esophageal microbiome. This review will examine the most recent advances in the past 5 years on the study of microbiome changes in healthy and diseased esophagus to better understand the link between microbiome and esophageal diseases, potentially leading to new prevention or treatment strategies.<br><br>RECENT FINDINGS: The microbiome has a key set of baseline parameters in the usual or non-diseased esophageal lumen. There are measurable changes in the baseline microbiome species of different disease phenotypes including eosinophilic esophagitis, gastroesophageal reflux disease, Barrett's esophagus and achalasia. Some studies suggest that certain microbiome features may even be associated with worse outcomes. Dysbiosis of esophageal microbiome is implicated in various esophageal disorders, including GERD, Barrett's esophagus, EoE, and achalasia. However, confounding factors such as antibiotic use, PPI use, dietary habits, and geographic location influence microbiome variability and make the standardized study of this field challenging. The next phase of research will need to include more focus on larger scale studies with reproducible parameters. As some features of the microbiome are associated with disease progression, there are multiple new avenues of intervention potentially available with an improved understanding of the human esophageal microbiome.}, }
@article {pmid42132991, year = {2026}, author = {He, WT and Xing, X and Wang, F and Li, L and Cheng, Y and Yao, G}, title = {Innovative technologies and future perspectives in tumor microbiomics.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {42132991}, issn = {1869-1889}, abstract = {Microorganisms within the tumor microenvironment represent an important but still underexplored dimension of cancer biology, influencing genomic stability, immune responses, metabolism, and therapeutic efficacy. Although recent findings underscore the significance of the tumor microbiome, distinguishing causal "drivers" from non-functional "passengers" remains a major challenge, particularly in the context of extremely low microbial biomass and high contamination risk. Advances in next-generation sequencing, single-cell genomics, and spatial transcriptomics are now transforming the field, enabling profiling that extends beyond descriptive catalogs toward functional and spatial resolution. Here, we introduce a unified, contamination-aware analytical framework tailored to the unique constraints of tumor microbiome studies, integrating standardized sampling, library construction, host-depletion strategies, and multi-layer computational analysis. We also evaluate emerging technologies that couple microbial identity with host-cell states at single-cell and spatial resolution, offering new opportunities to functionally map tumor-associated microorganisms. Furthermore, we propose that the integration of orthogonal validation strategies-combining imaging, spatial transcriptomics, in situ microbial profiling, and sequencing-is poised to define the next stage of mechanistic tumor microbiome research. Together, these perspectives outline key methodological inflection points and future directions toward a mechanistic understanding of tumor-microbe interactions and their therapeutic potential.}, }
@article {pmid42133003, year = {2026}, author = {Munir, A and Tarannum, T and Saad, N and Abdaal, M}, title = {Effectiveness of Non-Antibiotic Therapies in the Management of Recurrent Urinary Tract Infections in Women: A Systematic Review.}, journal = {International urogynecology journal}, volume = {}, number = {}, pages = {}, pmid = {42133003}, issn = {1433-3023}, abstract = {INTRODUCTION AND HYPOTHESIS: Recurrent urinary tract infections (rUTIs) are a prevalent condition in women, historically managed with continuous low-dose antibiotic prophylaxis. However, the global rise in antimicrobial resistance (AMR) necessitates the evaluation of non-antibiotic alternatives. This study was aimed at evaluating the efficacy and safety of non-antibiotic therapies, specifically D-mannose, cranberry products, probiotics, topical estrogen, methenamine hippurate, and immunoprophylaxis in preventing rUTIs in adult women.<br><br>METHODS: A systematic review was conducted in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses 2020 guidelines. We searched PubMed, Europe PMC, Science Direct, and the Cochrane Library for randomized controlled trials (RCTs) and high-quality observational studies published up to 31 January 2025. Studies were assessed for risk of bias using the Cochrane RoB 2 tool and the Newcastle-Ottawa Scale. The primary outcome was the reduction in UTI recurrence rates.<br><br>RESULTS: Twelve studies met the inclusion criteria (10 RCTs, 2 observational studies). Methenamine hippurate was found to be non-inferior to daily antibiotic prophylaxis in preventing rUTIs. Immunoprophylaxis with the sublingual vaccine MV140 significantly reduced recurrence compared with placebo, with 56-58% of women remaining UTI free in a large RCT. Vaginal estrogen proved effective for postmenopausal women, significantly reducing recurrence, despite small sample sizes in recent trials. D-mannose demonstrated efficacy equivalent to antibiotics in specialist settings, but showed no benefit over placebo in a broad primary care population. Cranberry products were generally less effective than antibiotics but prevented the development of resistant fecal flora. Probiotics significantly prolonged the time to first recurrence.<br><br>CONCLUSIONS: Non-antibiotic therapies offer viable, safe, and effective alternatives to long-term antibiotics. The evidence supports a stratified approach: methenamine hippurate and vaginal estrogen (in postmenopausal women) are supported by level 1 evidence as first-line non-antibiotic alternatives. MV140 immunoprophylaxis demonstrates high efficacy in recurrent phenotypes. D-mannose and cranberry show mixed efficacy and should be reserved for selected patient populations, particularly in specialist settings.}, }
@article {pmid42133231, year = {2026}, author = {Yiu, CH and Winardi, K and Lu, CY}, title = {Immunological Drug-Drug Interactions in Immune Checkpoint Inhibitor Therapy: Mechanisms, Clinical Evidence, and Artificial Intelligence.}, journal = {Current oncology reports}, volume = {28}, number = {1}, pages = {}, pmid = {42133231}, issn = {1534-6269}, mesh = {Humans ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology/adverse effects ; Drug Interactions ; *Artificial Intelligence ; *Neoplasms/drug therapy/immunology ; Gastrointestinal Microbiome/drug effects ; Tumor Microenvironment/drug effects/immunology ; }, abstract = {PURPOSE OF REVIEW: Immune checkpoint inhibitors (ICIs) have transformed cancer therapy, producing durable responses across multiple malignancies. However, treatment outcomes may be influenced by immunological drug-drug interactions (DDIs) arising from commonly prescribed concomitant medications. Unlike classical pharmacokinetic or pharmacodynamic DDIs, these interactions operate through systemic mechanisms that modulate anti-tumour immunity, including alterations to the gut microbiome, immune signalling pathways, and the tumour microenvironment. This review proposes a conceptual framework for "immunological DDIs" (iDDIs), extending beyond metabolic interactions toward a system-level understanding of immune regulation.<br><br>RECENT FINDINGS: We synthesise current evidence on commonly used medication classes-organised by their primary immunological mechanisms: (1) gut microbiome-mediated effects, (2) systemic immunosuppression, and (3) tumour microenvironment modulation-and their impact on ICI efficacy and safety. Meta-analyses suggest that certain medications, particularly antibiotics and proton pump inhibitors, are associated with poorer clinical outcomes, although confounding by indication and disease severity remain important limitations. Artificial intelligence (AI) is an emerging approach to detect and characterise complex DDIs using large-scale clinical and real-world data. Natural language processing, machine learning models, and large language models show potential for extracting medication exposure, predicting adverse events, and supporting clinical decision-making. Most AI applications remain at an early stage, with limited external validation and uncertain clinical utility. Future research should integrate mechanistic biology, prospective clinical studies, and explainable AI approaches to improve identification of iDDIs and optimise the safe and effective use of ICIs in oncology.}, }
@article {pmid42133449, year = {2026}, author = {Skrabulyte-Barbulescu, J and Yassin, LK and Almazrouei, S and Alkuwaiti, SH and Almarzooqi, S and Alnuaimi, F and Alketbi, S and Nakhal, MM and Rutkowska-Gauvry, P and Matar, SA and Hamad, MIK}, title = {Parental microbiome programming of early-life neurodevelopment: multi-niche contributions through the microbiome-gut-brain axis.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2673888}, doi = {10.1080/19490976.2026.2673888}, pmid = {42133449}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Female ; *Brain/growth &amp; development ; Pregnancy ; Male ; Infant ; *Brain-Gut Axis ; Animals ; Child Development ; }, abstract = {The microbiota-gut-brain axis (MGBA) is a central pathway through which gut microbial communities influence neurodevelopment via immune, metabolic, and neural signalling. Early life, spanning preconception through infancy, represents a particularly sensitive window during which parental microbiomes exert disproportionate influence on offspring gut colonization, immune education, and neurodevelopmental programming. This review synthesizes current evidence on how maternal and paternal microbiomes shape pediatric neurodevelopment through coordinated microbial, metabolic, immune, and epigenetic pathways. We examine pregnancy-associated remodeling of maternal microbiomes across gut, vaginal, oral, skin, and milk niches, highlighting how hormonal, metabolic, and immune adaptations drive site-specific microbial shifts with downstream consequences for fetal and infant brain development. Core microbial mechanisms are discussed, including short-chain fatty acids (SCFAs), tryptophan-derived metabolites, bile-acid signaling, and immune mediators that link microbial metabolism with immune and neurodevelopmental processes. These mechanisms are integrated with key transmission routes, including placental metabolite transfer, mode-of-delivery-dependent microbial seeding, breast milk-mediated signaling, and early environmental exposures that further shape the developing MGBA. We also incorporate emerging evidence on paternal microbiome contributions via preconception programming, sperm epigenetic remodeling, and germline-microbiome interactions, expanding the traditional maternal-centric view of intergenerational microbial inheritance. Finally, we evaluate modifiable factors, including diet, metabolic status, stress, antibiotic exposure, and microbiome-targeted interventions, and discuss their translational relevance. While associations between the microbiome and neurodevelopment are increasingly supported by human studies, many mechanistic insights remain derived from animal models, and causal relationships are not yet fully established. By integrating mechanistic, clinical, and systems-level perspectives, this review positions the MGBA as a promising but still evolving framework for understanding and potentially modulating early-life brain development.}, }
@article {pmid42133532, year = {2026}, author = {Bravo Iniguez, A and Sun, Q and Du, M and Zhu, MJ}, title = {Unearthing the bioactive properties of potato (Solanum tuberosum) for improving metabolic health.}, journal = {Critical reviews in food science and nutrition}, volume = {}, number = {}, pages = {1-20}, doi = {10.1080/10408398.2026.2662981}, pmid = {42133532}, issn = {1549-7852}, abstract = {Worldwide, both adults and children continue to develop metabolic diseases at an alarming rate. Metabolic syndrome (MetS) refers to a cluster of risk factors associated with an increased risk of noncommunicable diseases. The development of MetS is complex, and its mitigation requires multiple complementary strategies. One promising approach is dietary intervention with nutraceutical-rich foods that strengthen metabolic organs such as the liver and intestines against oxidative stress and inflammation. Potatoes are a widely consumed crop grown globally and are rich in macronutrients and bioactive secondary metabolites, including phenolic acids, carotenoids, and anthocyanins. They also provide resistant starch and dietary fiber that reach the colon undigested, where they positively modulate the gut microbiome, enhance short-chain fatty acid production, and reinforce the intestinal epithelial barrier. This review summarizes how different potato varieties and their chemical constituents mitigate hallmarks of MetS through both direct and indirect mechanisms. Additionally, it discusses molecular pathways induced by potato polyphenols and microbial metabolites that may underlie these effects, with particular emphasis on mediators linking metabolism to intestinal epithelial homeostasis. Current limitations and knowledge gaps are also highlighted, emphasizing the need for standardized potato-based interventions and expanded evaluation of skeletal muscle outcomes.}, }
@article {pmid42133581, year = {2026}, author = {Herrington, RTB and Lyu, Z and Raman, R and Seda, SE and Snyder, C and Bivens, NJ and Lei, Z and Islam, T and Sumner, LW and Joshi, T and Rosenfeld, CS}, title = {Disturbances of the Placenta-Brain Axis in Germ-Free Pregnant Mice.}, journal = {Biology of reproduction}, volume = {}, number = {}, pages = {}, doi = {10.1093/biolre/ioag103}, pmid = {42133581}, issn = {1529-7268}, abstract = {Maternal gut microbiota changes can profoundly shape on offspring health. The placenta may be vulnerable to maternal gut microbiota alterations. Placental disruptions can influence fetal brain development and underly risks for neurobehavioral disorders. Maternal gut microbiota disruptions might affect the placenta through alterations in bacterial short chain fatty acids (SCFA). The hypothesis tested is that depletion of maternal gut microbiota, as may occur in pregnant women treated with antibiotics and germ-free (GF) mice, impacts bacterial SCFA in her fecal samples and in placenta and fetal brain. We assessed whether transcriptomic changes would be evident in placenta and fetal brain from conceptuses derived from GF relative to multi-pathogen free (MPF) pregnant females. Maternal GF status reduced the concentrations of all measured SCFA within the stool. Surprisingly, two-methylbutanoic acid was significantly increased in male and female placenta and fetal brain samples in conceptuses from GF dams. In female and male placenta, several Prl form had altered expression in conceptuses from GF dams. In male placenta from GF dams, Hsd11b2 and Dio3 showed increased expression. Decreased expression of Sl6a2 and Slc22a3 in female fetal brain from GF dams might influence uptake of catecholamines. Results reveal depletion of maternal microbiota can lead to striking effects on the placenta-fetal brain axis. Findings raise concern as to whether maternal microbiota alterations due to other intrinsic or extrinsic factors, namely antibiotic treatment, might impact transcriptomic profiles in fetal placenta and brain. Underlying mechanisms remain uncertain but may relate to changes bacterial metabolites transferred from mother to conceptus.}, }
@article {pmid42134120, year = {2026}, author = {Liang, W and Nong, Q and Huang, H and Huang, J and Shao, J and Wang, M and Hong, P and Liu, S and Zhou, C and Zhong, S}, title = {Correlation analysis between microbial diversity in mixed-fermented shrimp juice and the synthesis pathways of characteristic flavor compounds.}, journal = {Food chemistry}, volume = {518}, number = {}, pages = {149574}, doi = {10.1016/j.foodchem.2026.149574}, pmid = {42134120}, issn = {1873-7072}, abstract = {This study elucidated flavor formation in fermented shrimp juice using metagenomics and correlation analyses. The amino acid nitrogen content peaked at 0.54 g/100 mL on the 30th day, surpassing that of traditional fish sauce. Phenolic compounds, including guaiacol and phenylacetaldehyde, were identified as key flavor contributors. The microbial community gradually developed into a stable microbiota dominated by nine genera, including Aspergillus, Lactiplantibacillus, and Meyerozyma. Metagenomic analysis demonstrated that this core microbiome governed critical metabolic pathways for carbohydrate, amino acid, and lipid metabolisms, collectively driving the efficient flavor development in the fermented product.}, }
@article {pmid42134193, year = {2026}, author = {Mao, C and Chen, D and Lai, Y and Lu, M and Wang, C}, title = {MMP1 Modulates Head and Neck Squamous Cell Carcinoma Progression and Therapeutic Response Via Tumour Microenvironment.}, journal = {International dental journal}, volume = {76}, number = {4}, pages = {109621}, doi = {10.1016/j.identj.2026.109621}, pmid = {42134193}, issn = {1875-595X}, abstract = {AIM: Head and neck squamous cell carcinoma (HNSCC) is a highly invasive malignancy driven by complex molecular interactions within the tumour microenvironment (TME). This study aimed to investigate the critical role of MMP1 in HNSCC progression, particularly its interplay with the microbiome and immune remodelling, to uncover potential therapeutic targets.<br><br>METHODS: We conducted transcriptomic analysis of HNSCC tissues and performed functional experiments in Cal-27 cells using a zebrafish tumour model, including MMP1 knockdown. The effects of TPF chemotherapy, Bifidobacterium longum, and their combination were evaluated in vitro. Additionally, we assessed macrophage recruitment, proinflammatory cytokine expression (IL-6, IL-1B, TNF-A), angiogenesis-related genes (VEGFA), zebrafish transcriptomic profiles, and gut microbiota diversity.<br><br>RESULTS: Transcriptomic profiling revealed significant gene expression differences between cancer and healthy tissues, with enrichment in metabolic, neurodegenerative, and cardiovascular pathways. MMP1 was markedly up-regulated in tumours and strongly correlated with invasion and metastasis. Functional studies demonstrated that MMP1 knockdown reduced the efficacy of TPF, B. longum, and their combination, impairing tumour growth suppression, macrophage recruitment, and proinflammatory cytokine expression. However, B. longum partially counteracted MMP1-mediated immune activation, suggesting microbial-immune crosstalk. MMP1 knockdown also retained partial inhibition of angiogenesis-related genes (eg, VEGFA), indicating a selective role in vascular remodelling. Furthermore, MMP1 knockdown attenuated the Cal-27 cell-induced reduction in zebrafish gut microbiome diversity and alterations in transcriptomic expression patterns.<br><br>CONCLUSION: Our findings establish MMP1 as a key regulator of HNSCC progression and therapeutic response, influencing microbiome-mediated immune remodelling, inflammation, and angiogenesis. These insights suggest that targeting MMP1 and modulating the microbiome could enhance therapeutic strategies for HNSCC by reshaping the TME. This study provides a foundation for further exploration of TME-targeted interventions in HNSCC treatment.}, }
@article {pmid42134220, year = {2026}, author = {Li, D and Li, Y and Chi, Y and Hou, Y and Wang, X and Pan, B}, title = {Salinization reduces microbial diversity and drives DOM-mediated community assembly along a river-lake continuum in arid Northwest China.}, journal = {Journal of environmental management}, volume = {408}, number = {}, pages = {129913}, doi = {10.1016/j.jenvman.2026.129913}, pmid = {42134220}, issn = {1095-8630}, abstract = {Hongjiannao Lake, once the largest desert freshwater lake in the arid and semi-arid regions of China, has undergone progressive salinization and ecological degradation over recent decades. During salinization, the cascade effect formed by the molecular transformation of dissolved organic matter (DOM) and the succession of microbial communities has emerged as a key mechanism for unraveling the internal processes of ecosystem degradation. In this study, we integrated hydrochemical parameters, DOM properties, and high-throughput sequencing of 16S rRNA genes to investigate microbiota differentiation and its environmental drivers along the river-lake continuum of the Hongjiannao watershed. The results showed that salinization drove molecular reconstruction of DOM, with a 37.6% decrease in humic-like components and an 84.7% increase in protein-like components. Increases in spectral slope ratio (SR) and specific UV absorbance at 254 nm (SUVA254) further indicated the breakdown of terrestrial humic substances into smaller aromatic molecules. Concurrently, the microbial community exhibited significantly suppressed alpha diversity and reduced spatial heterogeneity; the abundance of ubiquitous freshwater taxa declined, whereas salt-tolerant bacteria (e.g., certain members of Actinomycetota and Cyanobacteriota) increased. Furthermore, the number of functional annotation categories decreased, and the complexity and stability of the microbial co-occurrence network dropped sharply. Salinization drives microbial community reassembly through both direct pathways and indirect effects mediated by DOM transformation. This study reveals a cascading mechanism whereby salinization stress alters DOM bioavailability, leading to a loss of microbial diversity and functional narrowing, ultimately degrading lake ecological functions. We propose an integrated restoration strategy, including ecological water replenishment, introduction of salt-tolerant microbial consortia, and regulation of DOM inputs. This study provides a systematic, microbiome-based framework for the ecological management and restoration of salinized lakes in arid regions.}, }
@article {pmid42134306, year = {2026}, author = {Barapour, N and Cao, JZ and Wu, Y and Gupta, S and Hoopmann, MR and Qin, R and Midha, MK and Mireault, M and Juanes-Velasco, P and Hanson, C and Ahadi, S and Higgs, E and Baxter, DH and Diener, C and Dagan-Rosenfeld, O and Hornburg, D and Che, S and Edfors, F and Church, SJ and Babu, M and Thota, D and Jin, C and Chou, T and Rego, S and Avina, M and McGuire, L and Li, JW and Karathanos, T and Panyard, DJ and Acosta Parra, MA and Roberts, AK and Ranjit, AK and Rangan, E and Almagro Armenteros, JJ and Ashland, M and Castillo, KE and Traber, G and Ellenberger, M and Kellogg, R and Zhou, W and Rost, H and Kjellberg, M and Mishra, T and Kapil, C and Kusebauch, U and Patwardhan, S and Landeira-Viñuela, A and Hernandez, AP and Thomsen, ME and Mashkoor, M and Sutantiwanichkul, T and Dodig-Crnkovic, T and Bendes, A and Dahl, L and Gibbons, SM and Rangan, PV and Stensballe, A and Schwenk, JM and Unwin, RD and Fuentes, M and Sleno, L and Moritz, RL and Mahal, LK and Snyder, MP}, title = {A comparison of deep multiomics profiles across ethnicity, geography, and age.}, journal = {Cell}, volume = {189}, number = {10}, pages = {3004-3024.e35}, doi = {10.1016/j.cell.2026.04.032}, pmid = {42134306}, issn = {1097-4172}, mesh = {Humans ; Male ; *Ethnicity/genetics ; Female ; Middle Aged ; Adult ; Aged ; Geography ; Microbiota ; *Aging/genetics ; White People/genetics ; Transcriptome ; Metabolomics ; Proteomics ; Genomics/methods ; Diet ; Asian People/genetics ; Multiomics ; White ; }, abstract = {Despite extensive research, molecular differences in human populations and the influence of ancestry, age, geography, and diet are poorly understood. We performed comprehensive multiomics profiling (including genomics, transcriptomics, proteomics, metabolomics, lipidomics, metallomics, glycomics, and microbiomics) on samples from 322 healthy individuals of European, East Asian, and South Asian ancestry across multiple continents. We identified ethnicity-associated molecular features linked to host metabolism, autoimmune disease risk, drug metabolism, and neurodegenerative pathways. We uncovered ancestry- and geography-related molecular changes affecting metabolism, immune function, microbiome composition, and biological aging. Specific genetic variants and gene expression differences were associated with lipid metabolism and immune regulation. Geography influenced biological age: East Asians showed lower biological age in their ancestral regions, whereas individuals of European ancestry exhibited lower biological age in the US/Canada than in Europe. Diet-microbiome metabolism interactions displayed ethnicity-specific patterns, many related to health. This open access resource advances understanding of ethnicity-environment interactions and supports precision medicine.}, }
@article {pmid42134451, year = {2026}, author = {Vishwakarma, M and Anitha, K and Ashique, S and Mishra, N}, title = {Advances in siRNA and synbiotic therapies for colorectal cancer: a molecular and microbiota perspective.}, journal = {Drug discovery today}, volume = {}, number = {}, pages = {104697}, doi = {10.1016/j.drudis.2026.104697}, pmid = {42134451}, issn = {1878-5832}, abstract = {Colorectal cancer (CRC) remains a major global health challenge, with rising incidence and mortality despite advances in conventional therapies, often limited by recurrence, toxicity and drug resistance. siRNA-based therapeutics offer a precision approach by selectively silencing oncogenic and chemoresistance-related genes; but their clinical application is hindered by delivery, stability and off-target effects. Concurrently, synbiotics (prebiotics and probiotics) modulate gut microbiota, immune responses and inflammatory pathways involved in CRC progression. Integrating siRNA targeting with synbiotic-mediated microbiome modulation provides a complementary strategy addressing molecular and microenvironmental drivers of CRC. This review highlights key pathways, delivery strategies, co-therapeutic approaches and translational challenges, emphasizing the potential of combined RNAi and microbiome-based therapies for improved CRC management.}, }
@article {pmid42134452, year = {2026}, author = {Sharma, AK and Akhtar, MS and Orayj, K and Farooqui, S and Khan, A and Sharma, G}, title = {Microbial dysbiosis in metabolic disorders: linking epigenomic regulation and pathological mechanisms.}, journal = {Drug discovery today}, volume = {}, number = {}, pages = {104698}, doi = {10.1016/j.drudis.2026.104698}, pmid = {42134452}, issn = {1878-5832}, abstract = {Microbial dysbiosis critically contributes to metabolic disorders by altering host-microbiome interactions and disrupting metabolic homeostasis. This review highlights how dysbiosis-derived metabolites, including short-chain fatty acids (SCFA) and trimethylamine-N-oxide (TMAO), modulate epigenetic mechanisms such as DNA methylation, histone modification, and non-coding RNA expression in key metabolic tissues. These epigenomic changes impair insulin signaling, lipid metabolism, and inflammatory responses. We further explore the potential of microbial-epigenetic biomarkers for early diagnosis of metabolic disease. Moreover, we assess emerging microbiome-based therapies including prebiotics, SCFA supplementation, and fecal microbiota transplantation for their ability to reverse epigenetic dysregulation. Understanding the microbiome-epigenome-metabolism axis may enable precision diagnostics and targeted interventions for obesity, type 2 diabetes, and related disorders.}, }
@article {pmid42134481, year = {2026}, author = {Aburahma, A and Canfield, JR and Sprague, JE and Fernandez, AM}, title = {Gut Microbiome Modulation of Opioid Reinforcement in Preclinical Models: Microbial Regulation of Reward and Motivation.}, journal = {Brain research bulletin}, volume = {}, number = {}, pages = {111938}, doi = {10.1016/j.brainresbull.2026.111938}, pmid = {42134481}, issn = {1873-2747}, abstract = {Emerging evidence indicates that the gut microbiome modulates opioid-related behaviors through bidirectional communication with mesolimbic reward circuitry. Preclinical studies show that antibiotic-induced microbiome depletion, germ-free conditions, and developmental microbial disruption alter opioid reward and reinforcement in animal models. Rather than uniformly increasing or decreasing opioid responsivity, microbiome disruption produces paradigm-specific and stage-dependent effects across distinct components of reinforcement learning. Reduced microbial diversity is associated with decreased production of short-chain fatty acids (SCFAs), altered gut barrier integrity, and enhanced peripheral immune signaling. These changes converge on the ventral tegmental area (VTA) and nucleus accumbens (NAc), modifying dopaminergic transmission and transcriptional plasticity within reward-related circuits. Notably, microbiome depletion reduces morphine conditioned place preference, whereas, in separate paradigms, it increases fentanyl self-administration and motivational responding under progressive ratio schedules, revealing a dissociation between hedonic reward and reinforcement processes. SCFA supplementation can partially rescue reward-related phenotypes, supporting a mechanistic role for microbial metabolites. Across reinforcement paradigms, microbiome status emerges as a dynamic regulator of opioid reinforcement rather than a simple modulator of reward magnitude. Importantly, antibiotic exposure, which is common during infectious disease treatment of individuals with opioid use disorder (OUD), may represent a clinically relevant and underappreciated modifier of reinforcement sensitivity and relapse risk. This review uniquely integrates microbiome disruption, stress sensitivity, negative affect, and neuroimmune priming during protracted abstinence to highlight antibiotic exposure as an overlooked but actionable factor in OUD recovery.}, }
@article {pmid42134511, year = {2026}, author = {Kang, MJ and Lee, KR and Kim, MJ and Jeong, HC and Chae, YJ}, title = {Gut microbiome-related tryptophan metabolites modulate drug transporters, with prominent effects on OAT1 and OAT3.}, journal = {Toxicology and applied pharmacology}, volume = {}, number = {}, pages = {117868}, doi = {10.1016/j.taap.2026.117868}, pmid = {42134511}, issn = {1096-0333}, abstract = {The gut microbiome plays a key role in tryptophan metabolism by directly generating indole derivatives and indirectly modulating the host-driven kynurenine pathway via microbial metabolites. In this study, we examined the effects of 12 gut microbiome-related tryptophan metabolites on major drug transporters. In vitro assays using transporter-overexpressing cell lines revealed that indole-3-acrylic acid (IA), indole-3-propionic acid (IPA), kynurenic acid (KA), and xanthurenic acid (XA) inhibited organic anion transporter 1 (OAT1) and organic anion transporter 3 (OAT3) activity by up to 83.7%, with half-maximal inhibitory concentration (IC50) values ranging from 5.41 to 121 μM for OAT1 and 0.31 to 9.50 μM for OAT3. Molecular docking analysis provided qualitative support for potential interactions with OAT1. In vivo pharmacokinetic studies in rats showed that the coadministration of these metabolites significantly increased systemic exposure of furosemide, a representative OAT1/OAT3 substrate, by 1.3- to 2.9-fold and was accompanied by changes in renal excretion. In contrast, most metabolites showed minimal effects on other transporters such as organic anion transporting polypeptide 1B1/1B3 (OATP1B1/OATP1B3), organic cation transporter 2 (OCT2), multidrug and toxin extrusion 1 (MATE1), multidrug resistance protein 1 (MDR1), and breast cancer resistance protein (BCRP). These findings provide mechanistic in vitro evidence that selected gut microbiome-related tryptophan metabolites interact with OAT1/OAT3 and proof-of-concept rat pharmacokinetic data showing altered furosemide disposition after metabolite coadministration. Further studies are required to determine whether these transporter-related effects are clinically relevant in humans.}, }
@article {pmid42134583, year = {2026}, author = {Berninghaus, AE and Radniecki, TS}, title = {Influence of feedstock and operational parameters on the composition, temporal dynamics, and sensitivity of microbiomes from nineteen full-scale anaerobic municipal sludge digesters and anaerobic fat, oil, and grease co-digesters.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134877}, doi = {10.1016/j.biortech.2026.134877}, pmid = {42134583}, issn = {1873-2976}, abstract = {Anaerobic co-digestion is a key microbial-based technology in the bioeconomy. However, the effects of lipidic co-substrates on full-scale anaerobic digester microbiomes, including composition, structure and sensitivity to organic overload shocks, have yet to be fully explored. This study sequenced 12 wastewater solids mono-digesters and 7 high-strength lipidic waste co-digesters monthly for 14 months. The presence of co-substrates enriched hydrolytic bacteria, fermentative bacteria and acetoclastic methanogens, resulting in a novel co-digester core microbiome. It also decreased microbiome richness, alpha diversity, structural fluidity (i.e., mean rank shifts - MRS), and the relative abundance of sub-dominant bacterial taxa (from 45 % to 37 %). The less rich and more compositionally stable microbiomes of anaerobic co-digesters resulted in higher methane yields at lower organic shock loads (i.e., 1 mL of canola oil) compared with anaerobic mono-digesters (239.9 ± 54.6 mL CH4/mL canola oil and 87.5 ± 22.3 mL CH4/mL canola oil, respectively). However, anaerobic co-digesters had greater sensitivity to higher organic shock loads (5-20 mL of canola oil), quantified by percent reduction of methane yields, compared to anaerobic mono-digesters. A multivariate linear regression model predicting a full-scale anaerobic digester's sensitivity to organic overload shocks (Significance F = 1.99 × 10[-12]) revealed that higher operational temperature (p < 0.00) and lower bacterial richness (p < 0.00), archaeal richness (p < 0.00), bacterial MRS (p = 0.02) and archaeal MRS (p < 0.00) increased the sensitivity of anaerobic digesters to organic overloads. Thus, several co-digestion adaptations that contributed to higher methane yields at lower organic shock loads (e.g., lower bacterial richness and greater microbiome compositional stability), also led to greater sensitivity to higher organic shock loads.}, }
@article {pmid41923033, year = {2026}, author = {Guo, Z and Yu, X and Liu, Y and Hu, Q and Zhang, Z and Zhang, C and Li, J}, title = {A comparative analysis of oral microbial communities in hypertensive patients with and without chronic periodontitis.}, journal = {BMC oral health}, volume = {26}, number = {1}, pages = {}, pmid = {41923033}, issn = {1472-6831}, support = {2025A03J4171//Science and Technology Projects in Guangzhou/ ; }, abstract = {BACKGROUND: Hypertension and chronic periodontitis are both highly prevalent diseases with a well-established association. Dysbiosis of the oral microbiota, a key factor in oral health, may contribute to the mechanisms underlying their comorbidity. This study aimed to characterize the oral microbiota in hypertensive patients with and without periodontitis and explore its potential role in this disease association.<br><br>METHODS: Saliva samples from hypertensive patients without periodontitis (T, n&#x2009;=&#x2009;17), periodontitis patients without hypertension (P, n&#x2009;=&#x2009;18), comorbid patients (TP, n&#x2009;=&#x2009;16), and healthy controls (HC, n&#x2009;=&#x2009;16) underwent 16S rRNA gene (V3-V4) sequencing. Microbiota composition, diversity, differential taxa, and predicted function were analyzed.<br><br>RESULTS: Alpha diversity (Chao1/Ace indices) was significantly higher in HC versus disease groups (P&#x2009;<&#x2009;0.05), while beta diversity showed greater similarity among disease groups but marked divergence from HC (P&#x2009;<&#x2009;0.05). At genus/species levels, disease groups exhibited characteristic dysbiosis: the abundance of health-associated taxa decreased, while classic periodontal pathogens were significantly enriched. Notably, Streptococcus sp. I-G5 was uniquely enriched in the T group. Functionally, disease groups exhibited enriched lipid metabolism, immune response, and oxidative stress pathways (P&#x2009;<&#x2009;0.05), contrasting with HC group dominance in xenobiotic biodegradation and amino acid metabolism. Ten differentially abundant genera and eleven species distinguished disease states, highlighting microbiome dysbiosis and metabolic shifts in oral-systemic disease interactions.<br><br>CONCLUSION: The oral microbial community of hypertensive patients exhibited dysbiosis analogous to those observed in periodontitis, characterized by a reduced alpha diversity, an enrichment of periodontal pathogens, and activation of pro-inflammatory metabolic pathways. These findings suggest that oral microbial dysbiosis is a shared feature in hypertensive and periodontitis patients. The specific enrichment of Streptococcus sp. I-G5 in hypertension alone may indicate a potential microbial signature for this condition, contributing to a better understanding of the oral microbiome&#x2019;s role in hypertension.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12903-026-08144-6.}, }
@article {pmid42122957, year = {2026}, author = {Terry, C and Hall, LA and Halle-Smith, J and Edwards, LA and Sivakumar, S and Chapple, I and Beggs, A and Iqbal, T and Roberts, KJ}, title = {Pancreatic Cancer in the Holobiont and Therapeutic Targets: A Review.}, journal = {Journal of clinical medicine}, volume = {15}, number = {9}, pages = {}, pmid = {42122957}, issn = {2077-0383}, abstract = {Increasing evidence suggests pancreatic cancer develops within a host-microbe ecosystem in which microbial communities across anatomical niches interact with tumour biology, immune regulation, metabolism, and therapeutic response. This review examines pancreatic cancer through the lens of humans as holobionts, integrating evidence from the oral, gut, biliary, and intratumoural microbiomes. Epidemiological and sequencing studies demonstrate consistent microbial alterations across these niches in pancreatic cancer, including oral dysbiosis associated with periodontal pathogens, gut microbial shifts toward pro-inflammatory taxa, disease-specific biliary microbial signatures, and the presence of distinct intratumoural microbial communities. Mechanistic studies indicate that intestinal barrier disruption, microbial translocation, immune and metabolite signalling can influence tumour immune architecture, macrophage polarisation, T-cell infiltration, oncogenic signalling pathways, and chemotherapeutic metabolism, particularly inactivation by tumour-associated bacteria. Microbiome-driven shifts in immunometabolism can reprogramme immune-cell metabolic pathways, impairing effective T-cell activation, promoting tumour-supportive macrophage phenotypes. Emerging therapeutic strategies aim to modulate the microbiome-tumour axis, including dietary interventions, probiotics and immunonutrition, faecal microbiota transplantation, engineered microbial therapies, and microbiome-informed antibiotic strategies. While pre-clinical findings are compelling and early-phase clinical studies suggest feasibility, most evidence remains associative and heterogeneous across cohorts and methodologies. Understanding pancreatic cancer as a multi-site ecological system may help explain inter-patient variability in disease progression and treatment response. This could usher in a new era for therapeutic manipulation where future progress will depend on longitudinal, multi-omic, and interventional studies to determine whether microbiome-targeted strategies can produce clinically meaningful improvements in pancreatic cancer outcomes.}, }
@article {pmid42123280, year = {2026}, author = {Aljaraedah, T and Al-Thnaibat, S and Nawasreh, AA and Alraei, W and Al-Trad, E}, title = {A Scoping Review of Gut Dysbiosis and Malnutrition in Neurological Disorders: Implications, Indications, and Promising Therapeutic Approaches.}, journal = {Journal of clinical medicine}, volume = {15}, number = {9}, pages = {}, pmid = {42123280}, issn = {2077-0383}, abstract = {Background/Objectives: Neurological diseases are increasing worldwide, but the biological processes underlying these diseases remain poorly understood, and existing treatments have been ineffective at arresting disease progression. Emerging data indicate that dysbiosis of the microbiota-gut-brain axis and malnutrition are comorbid factors in neurological dysfunction. Methods: An extended search strategy was developed using a multifaceted approach across various databases to identify eligible studies published between January 2010 and February 2026. Results: Results showed uniform relationships among neurological conditions, loss of microbial richness, loss of short-chain fatty acid-producing bacteria, neuroinflammation, and nutritional susceptibility. The review also identifies methodological trends in microbiome profiling and nutritional assessment and suggests an integrative framework of symptom-linked microbial imbalance, malnutrition, and inflammatory processes. Conclusions: Although dietary modulation and microbiome-targeted interventions appear promising, the evidence is mostly correlational. Longitudinal and interventional studies should be well-designed to elucidate causal mechanisms and to provide effective clinical strategies.}, }
@article {pmid42123326, year = {2026}, author = {Zaman, S and Ali, N and Ullah, W and Taimur, N and Akbar, NU and Waheed, A and Muhammad, N and Khan, MS}, title = {Metagenomic Profiling Reveals Extensive Bacterial Diversity in Chicken Manure and Associated Contaminated Wastewater.}, journal = {International journal of molecular sciences}, volume = {27}, number = {9}, pages = {}, pmid = {42123326}, issn = {1422-0067}, mesh = {Animals ; Chickens/microbiology ; *Manure/microbiology ; *Wastewater/microbiology ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation &amp; purification ; Metagenome ; Microbiota/genetics ; Biodiversity ; }, abstract = {Chicken manure and its potential to contaminate water systems through the dispersal of pathogenic bacteria are major concerns in environmental and public health. In this study, a metagenomic analysis was employed to systematically identify and compare bacterial assemblages in chicken manure (CM) and in a contaminated sample of chicken manure wastewater (CMW). Whole DNA was extracted from CM and CMW, followed by whole-genome shotgun sequencing; data analysis was done using online Galaxy software (ver. 26.0.1.dev1). Metagenomic analysis reveals a complex One Health challenge. Data showed that CM and CMW are different in their microbiota, as indicated by a distinct separation of beta diversity values and limited overlapping of species between sample types. In the current study, we found a greatly significant common functional set of adapted bacterial masses, including major pathogenic bacterial groups as well as opportunistic and environmental bacterial species, indicative of a direct contamination from CM and CMW. Notably, in both CM and CMW, a plethora of opportunistic, enteric, and environmental pathogens like Escherichia coli, Salmonella enterica, and Acinetobacter baumannii were found, coupled with an indication of a direct functional flow between both ecosystems as tangled reservoirs. Chicken manure samples showed differences in taxonomic composition and inferred functional profiles at the time of sampling: CM1 was pathogen-enriched, CM2 exhibited strong nitrogen-supportive metabolism, CM3 was dominated by fiber-degrading decomposers, and CM4 showed high methane-producing potential with environmental risk. Such findings underscore the raising of chickens as a potential source of harmful bacteria for the environment. It is important to note that this study represents a preliminary investigation with certain limitations, including the absence of biological replicates, lack of temporal sampling, and limited capacity to infer dynamic ecological interactions. Yet this metagenomic report is more about describing the taxonomy and functional potential of the bacteria, rather than discussing the actual ecological processes of these microorganisms in the environment. Future studies will be required to explore these aspects.}, }
@article {pmid42123347, year = {2026}, author = {López-Tenorio, II and Constantino-Jonapa, LA and Jaimez-Alvarado, S and Hernández-Quiroz, F and Jorge-Galarza, E and Escalona-Montaño, AR and Amedei, A and Soria-García, R and Berrios-Barcenas, EA and Aguirre-García, MM}, title = {Gut-Heart Axis: Microbiome Involvement in Wild-Type Transthyretin Amyloidosis.}, journal = {International journal of molecular sciences}, volume = {27}, number = {9}, pages = {}, pmid = {42123347}, issn = {1422-0067}, support = {CBF2023-2024-734//CONAHCYT/ ; IN212422, IN219025//UNAM-DGAPA-PAPIIT/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Amyloid Neuropathies, Familial/microbiology/metabolism ; Male ; Female ; Middle Aged ; Aged ; Biomarkers/metabolism ; Dysbiosis/microbiology ; }, abstract = {Cardiac amyloidosis is a rare and progressive condition characterized by the extracellular deposition of amyloid fibrils in multiple organs. Wild-type transthyretin amyloidosis (ATTR-wt) is the most common type affecting subjects above 60 years old. Recent and growing evidence suggests a potential link between GM and cardiac amyloidosis. In this scenario, the aim of the present study is to characterize the gut microbiota (GM), related metabolites and inflammatory biomarkers in ATTR-wt patients. In the ATTR patients we identified Prevotella_9 as the core OTUs (Operational Taxonomic Unit) of this group, alongside Prevotella 7, Prevotellaceae_UCG-003 and Prevotellaceae_NK3B31. In addition, there were increased levels of long fatty acids, including tetradecanoic, hexadecanoic and octadecanoic acids, in the ATTR group. The data obtained suggest that ATTR patients have an altered gut microbiota that could be used as a potential biomarker in metabolic and cardiovascular diseases, as well as a potential predictor of adverse prognosis in ATTR patients. In addition, the intestinal dysbiosis in ATTR patients could be associated with low-grade endotoxemia promoting a pro-inflammatory state due to the translocation of bacterial components, such as LPS (lipopolysaccharide), into blood circulation.}, }
@article {pmid42123418, year = {2026}, author = {Bhoi, TK and Mahanta, DK and Samal, I and Jangra, S}, title = {Plant Defense Activation by Endophytic Metarhizium anisopliae and Beauveria bassiana Fungi Against Subterranean Termites.}, journal = {International journal of molecular sciences}, volume = {27}, number = {9}, pages = {}, pmid = {42123418}, issn = {1422-0067}, mesh = {Animals ; *Metarhizium/pathogenicity/physiology ; *Isoptera/microbiology ; *Beauveria/pathogenicity/physiology ; *Endophytes/physiology ; }, abstract = {Subterranean termites, particularly Odontotermes obesus, cause severe damage to forest nurseries and plantations in arid and semi-arid ecosystems. This study demonstrates the dual functional role of endophytic entomopathogenic fungi, Metarhizium anisopliae and Beauveria bassiana, in termite suppression and induction of plant defense responses. Laboratory bioassays revealed significantly higher virulence of M. anisopliae, with a lower LT50 (lethal time required to cause 50% mortality) of 33.1 h compared to B. bassiana (46.7 h), a steeper probit slope (5.4 ± 0.3), and strong model fit (R[2] = 0.95), indicating rapid and synchronized mortality. Endophytic colonization varied across host species and application methods, with soil incorporation consistently outperforming foliar inoculation. Maximum colonization (82.5%) was recorded in Tecomella undulata and exceeded 80% in Azadirachta indica under M. anisopliae. Biochemical analyses revealed significant increases in protein (up to 3.5 mg g[-1]), phenols (3.7 mg g[-1]), and tannins (2.7 mg g[-1]). Activity of defense enzymes was significantly enhanced, with catalase reaching 263.5 U mL[-1], while Phenylalanine ammonia-lyase and Tyrosine ammonia-lyase exceeded 170 and 198 U mL[-1], respectively, indicating activation of antioxidant and phenylpropanoid pathways. Molecular docking analysis further revealed strong interactions between fungal metabolites and termite cellulase, with Bassianin (-8.4 kcal mol[-1]) and Tenellin (-8.1 kcal mol[-1]) showing the highest binding affinities. These findings highlight the combined biochemical and molecular mechanisms underlying fungal-mediated termite suppression and plant defense induction, and future research should prioritize transcriptomic validation, rhizosphere microbiome interactions, formulation optimization, and long-term multi-location field evaluation to support sustainable termite management strategies.}, }
@article {pmid42123449, year = {2026}, author = {Toboła, M and Kuryłowicz, A}, title = {Impact of Gut Microbiota on Bone Metabolism-Present Concepts and Therapeutic Implications.}, journal = {International journal of molecular sciences}, volume = {27}, number = {9}, pages = {}, pmid = {42123449}, issn = {1422-0067}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Bone and Bones/metabolism ; Animals ; Dysbiosis/metabolism/microbiology ; Probiotics/therapeutic use ; Calcium/metabolism ; Fatty Acids, Volatile/metabolism ; Prebiotics ; }, abstract = {The gut microbiota plays a multifaceted role in calcium homeostasis and bone metabolism -acting through metabolic, immunological, and hormonal pathways that collectively constitute the gut-bone axis. The microbiota influences calcium bioavailability through several overlapping mechanisms that act in the intestine. Moreover, microbial fermentation products may directly impact the osteoblast-osteoclast interplay and, by modulating immune and endocrine functions, are crucial for bone metabolism. A healthy microbiota supports bone formation; however, intestinal dysbiosis may impair bone structure and function. This narrative review aims to present pathways linking the gut microbiota to bone metabolism, both in health and disease. First, we will discuss the influence of gut microbiota on calcium absorption. We will then outline the role that microbial metabolites, such as bile acids and short-chain fatty acids (SCFAs), play in regulating bone structure and function. In the following section, we will discuss the role of the microbiota in the immunological and hormonal modulation of bone metabolism. Finally, we will discuss how dysbiosis affects bone and how therapeutic interventions, such as probiotics, prebiotics, and postbiotics, may influence bone tissue quality.}, }
@article {pmid42123477, year = {2026}, author = {Baldo, E and Abeni, D and Agostini, G and Armato, U and Bauer, P and Belloni Fortina, A and Calza, A and Cervadoro, E and Chiarini, A and Ciprandi, G and Dal Prà, I and Faga, A and Farina, S and Geat, D and Giovannini, M and Girolomoni, G and Gisondi, P and Jousson, O and Manara, S and Mira, E and Nicoletti, G and Pagliarello, C and Pedron, R and Peroni, A and Rizzo, V and Segata, N and Tettamanti, G and Zanoni, M and Zumiani, G and Cristofolini, M}, title = {Clinical and Mechanistic Evidence for Comano Thermal Water: A Narrative Review.}, journal = {International journal of molecular sciences}, volume = {27}, number = {9}, pages = {}, pmid = {42123477}, issn = {1422-0067}, mesh = {Humans ; *Mineral Waters/therapeutic use ; Balneology/methods ; Animals ; Skin/drug effects ; }, abstract = {Comano thermal water (CTW) is a hypotonic, bicarbonate-calcium-magnesium mineral water traditionally used to manage chronic inflammatory and relapsing skin diseases. This review summarises and discusses the available clinical, experimental, and translational evidence on CTW, with a particular focus on dermatological indications. The physicochemical properties of CTW, along with the presence of a stable, non-pathogenic microbial community, are examined in relation to their potential biological activity. Clinical studies indicate that CTW-based balneotherapy, alone or in combination with narrowband Ultraviolet B (UVB) phototherapy, is associated with improvements in disease severity, symptom burden, and quality of life in patients with psoriasis and atopic dermatitis, and has a favourable safety and tolerability profile. Experimental data further suggest that CTW may exert anti-inflammatory and immunomodulatory effects, modulate keratinocyte function, support skin barrier restoration, and influence the cutaneous microenvironment, including microbiome-related pathways. The review also outlines emerging evidence for CTW in skin regeneration and in upper airway inflammatory conditions treated via inhalation-based approaches. Overall, this review suggests that CTW may serve as a biologically active therapeutic resource, warranting further investigation as a complementary approach within integrative management strategies for inflammatory and barrier-related conditions.}, }
@article {pmid42123484, year = {2026}, author = {Ahmad, A and Ahmed, MM and Akhtar, A and Liu, W and Yang, R and Sun, X and Wang, X and Bibi, S and Khan, MB and Chen, S}, title = {Unlocking Grass Stress Resistance: Fungal Endophyte-Mediated Pathogen Recognition and RNA Regulation.}, journal = {International journal of molecular sciences}, volume = {27}, number = {9}, pages = {}, pmid = {42123484}, issn = {1422-0067}, support = {32260356//National Natural Science Foundation of China/ ; (Outstanding Youth Project, Grant No. 2025DB003)//Corps Science and Technology Program/ ; (TDZKPY202607)//Tarim University of Agricultural Reclamation/ ; }, mesh = {*Endophytes/physiology ; *Stress, Physiological ; *Poaceae/microbiology/genetics/physiology ; *Host-Pathogen Interactions ; Symbiosis ; *Fungi/physiology ; Gene Expression Regulation, Plant ; Disease Resistance ; Plant Diseases/microbiology/genetics ; }, abstract = {Fungal endophytes are symbiotic microorganisms that establish strong relationships inside plant tissues, providing potential advantages, especially in grasses, by enhancing tolerance to both abiotic and biotic stresses. This review investigates the molecular mechanisms through which fungal endophytes mediate stress tolerance, targeting host-pathogen interactions. By modulating pathogen-associated molecular patterns (PAMPs), damage-associated molecular patterns (DAMPs), and effector proteins, fungal endophytes may contribute to priming the plant's immune system, enhancing its resistance to pathogen invasion. Moreover, endophyte colonization regulates core processes such as osmotic regulation, reactive oxygen species (ROS) detoxification, and secondary metabolite biosynthesis that enable plants to tolerate environmental stresses like drought, heat, and salinity. The review highlights the impact of endophytes on immune priming, systemic acquired resistance (SAR), and the regulation of non-coding RNAs that regulate host gene networks associated with stress tolerance. Furthermore, the integration of advanced multi-omics techniques genomics, transcriptomics, proteomics, metabolomics, and fluxomics has revealed emerging insights into the genetic and metabolic pathways driving these symbiotic associations. However, grass-specific molecular datasets remain limited, and the consistency of endophyte-mediated tolerance across host species and environmental conditions is not yet fully resolved. Fungal endophytes increase grass stress resilience through coordinated pathogen recognition, RNA regulation, and metabolic reprogramming while AI-assisted multi-omics approaches are emerging as tools for identifying candidate regulatory networks, although empirical validation in grass-endophyte systems remains limited. Together, these advances highlight the potential for climate-smart and sustainable crop improvement. Future research integrating functional genomics, field validation, and biosafety assessment will be essential for translating endophyte-based strategies into reliable agricultural applications.}, }
@article {pmid42123517, year = {2026}, author = {Nguyen-DeMary, K and Vascellari, S and Mastinu, M and Melis, M and Bastiaanssen, TFS and Tomassini Barbarossa, I and Tepper, BJ}, title = {Cranberry Polyphenol Extract (CPE) Oral Rinse Improves Salivary Microbiome in 6-n-Propylthiouracil (PROP) Non-Tasters and Palatability of Aronia Juice.}, journal = {International journal of molecular sciences}, volume = {27}, number = {9}, pages = {}, pmid = {42123517}, issn = {1422-0067}, support = {10180//United States Department of Agriculture/ ; }, mesh = {Humans ; *Saliva/microbiology/drug effects ; Female ; Male ; *Vaccinium macrocarpon/chemistry ; *Polyphenols/pharmacology/administration &amp; dosage/chemistry ; *Microbiota/drug effects ; Adult ; Propylthiouracil ; *Plant Extracts/pharmacology/chemistry/administration &amp; dosage ; *Photinia/chemistry ; Taste/drug effects ; *Mouthwashes/pharmacology/chemistry ; *Fruit and Vegetable Juices ; Young Adult ; }, abstract = {Sensitivity to the bitterness of 6-n-propylthiouracil (PROP) is controlled by variations in the TAS2R38 gene. This phenotype is often used as a marker for individual differences in taste perception. Previous findings show that PROP taster status is associated with differences in the salivary microbiome. It is well known that diet and environmental factors influence the risk of oral disease, but there is far less evidence showing how genetic differences play a role. Forty-seven young, healthy, PROP taster-classified adults rinsed with a cranberry polyphenol extract (CPE) oral rinse (0.75 g/L CPE powder in spring water) twice daily for 11 days. Saliva was collected pre- and post-intervention for microbiome analysis using shotgun metagenomic sequencing. At the same time points, participants evaluated two astringent juices (cranberry and aronia berry) for key attributes. At baseline, PROP taster groups differed in their salivary microbiome compositions, but post-intervention, the groups had more similar bacterial compositions. Post-intervention, non-tasters showed decreases in the relative abundance of 15 bacterial species, including a significant reduction (p = 0.037) in Eikenella corrodens, which is one bacterium, among several others, involved in oral biofilm formation. Additionally, after the intervention, sourness was reduced, and overall liking increased significantly for aronia juice. Oral dysbiosis, a risk factor for oral disease, may be controlled by bactericidal mouthwashes. Our results suggest that CPE, a natural alternative to traditional bactericidal rinses, may selectively target pathobionts while preserving salivary microbiota diversity. CPE might also provide greater benefits to non-tasters, who are at greater risk for oral disease.}, }
@article {pmid42123520, year = {2026}, author = {Yılmaz, A and Park, HJ and Ahn, EM and Bae, J}, title = {Dietary Polyphenols in Aging: A Systems-Level Perspective on Mitochondrial Quality Control and Microbiome Interactions.}, journal = {International journal of molecular sciences}, volume = {27}, number = {9}, pages = {}, pmid = {42123520}, issn = {1422-0067}, support = {RS-2026-25477916//National Research Foundation of Korea/ ; 2026-rise-15-110//Daegu Haany University Regional Innovation System &amp; Education/ ; }, mesh = {Humans ; *Polyphenols/pharmacology ; *Aging/drug effects/metabolism ; *Mitochondria/metabolism/drug effects ; Animals ; *Gastrointestinal Microbiome/drug effects ; Diet ; Signal Transduction/drug effects ; }, abstract = {Aging is a multifactorial biological process characterized by progressive functional decline and increased susceptibility to chronic diseases. Targeting the molecular mechanisms underlying aging has therefore emerged as an important strategy for promoting healthy aging. Natural polyphenols, widely present in fruits, vegetables, tea, and medical and aromatic plants, have attracted considerable attention due to their geroprotective properties. This review examines current evidence on the ability of major dietary polyphenols, including resveratrol, epigallocatechin gallate (EGCG), curcumin, and quercetin, to modulate the hallmarks of aging, with particular emphasis on mitochondrial quality control as a central regulatory mechanism. Evidence indicates that polyphenols regulate key signaling pathways involved in aging biology, including AMP-activated protein kinase (AMPK), sirtuins (SIRT), mechanistic target of rapamycin (mTOR), nuclear factor erythroid 2-related factor 2 (Nrf2), and nuclear factor-κB (NF-κB). Through coordinated modulation of these pathways, polyphenols influence mitochondrial biogenesis, mitophagy, redox homeostasis, cellular senescence, and chronic inflammation. In addition, interactions between dietary polyphenols and the gut microbiome generate bioactive metabolites, such as urolithin A, which further contribute to mitochondrial regulation. Overall, polyphenols represent promising modulators of aging-associated pathways and may support strategies aimed at improving healthspan and reducing age-related disease risk.}, }
@article {pmid42123539, year = {2026}, author = {Miranda, J and Maestre, N and Devia, M and Zapata, R and Ochoa-Díaz, MM and Annicchiarico, W}, title = {Inflammation at the Maternal-Fetal Interface: Mechanisms Linking Maternal-Fetal Immunity to Preeclampsia and Fetal Growth Restriction.}, journal = {International journal of molecular sciences}, volume = {27}, number = {9}, pages = {}, pmid = {42123539}, issn = {1422-0067}, mesh = {Humans ; Pregnancy ; Female ; *Fetal Growth Retardation/immunology/pathology/etiology ; *Pre-Eclampsia/immunology/pathology ; *Inflammation/immunology/pathology ; *Placenta/immunology ; *Maternal-Fetal Exchange/immunology ; Animals ; }, abstract = {Inflammation is a physiological and tightly regulated component of normal pregnancy, contributing to implantation, placental development, and the initiation of parturition. The placenta functions as an active immunological hub, coordinating innate and adaptive immune responses to maintain tolerance while protecting against infection. Preeclampsia and fetal growth restriction (FGR) are major causes of maternal and perinatal morbidity worldwide and represent central manifestations of placental disease. Increasing evidence indicates that these conditions share key pathophysiological mechanisms, including placental dysfunction and maladaptive maternal immune responses. When immune regulation at the maternal-fetal interface becomes disrupted, inflammatory pathways contribute to impaired placental development and vascular maladaptation. In this context, excessive immune activation-driven by inflammasome signaling, Th1/Th17 polarization, and altered natural killer and macrophage function-can compromise placental perfusion, promote antiangiogenic imbalance, and lead to systemic endothelial dysfunction. This review, therefore, focuses on how immune dysregulation contributes to placental dysfunction in preeclampsia and FGR, synthesizing current knowledge of the maternal-fetal immune interface and exploring therapeutic strategies that link pathogenic mechanisms to targeted interventions. A deeper understanding of placental immunology and inflammatory signaling is essential to develop precision therapies. Established therapies, including low-dose aspirin, low-molecular-weight heparin, and antenatal corticosteroids, aim to mitigate inflammation and optimize fetal outcomes, while adjunctive strategies target oxidative stress, nutritional deficits, and the maternal microbiome. Emerging approaches such as cytokine-targeted biologics, inflammasome inhibitors, and mesenchymal stem cell therapies show promise but require rigorous safety and efficacy evaluation. Future research should prioritize biomarker validation, pathway-specific interventions, and equitable implementation to reduce inflammation-driven pregnancy complications.}, }
@article {pmid42123569, year = {2026}, author = {Osredkar, J and Fabjan, T and Godnov, U and Jekovec-Vrhovšek, M and Osredkar, D and Finderle, P and Kumer, K and Zorec, M and Fanedl, L and Avguštin, G}, title = {Microbiome-Derived Short-Chain Fatty Acids and Tryptophan Metabolites in Children with Autism Spectrum Disorder: A Stool-Urine Multi-Omics Analysis.}, journal = {International journal of molecular sciences}, volume = {27}, number = {9}, pages = {}, pmid = {42123569}, issn = {1422-0067}, support = {This research was funded by the scientific-research program grants P3-0124 and project J3-1756//The Slovenian Research and Innovation Agency/ ; }, mesh = {Humans ; *Tryptophan/metabolism/urine ; *Autism Spectrum Disorder/metabolism/microbiology/urine ; Male ; *Fatty Acids, Volatile/metabolism/urine ; Female ; *Feces/chemistry/microbiology ; Child ; *Gastrointestinal Microbiome ; Child, Preschool ; Metabolomics/methods ; Cross-Sectional Studies ; Case-Control Studies ; Metabolome ; Multiomics ; }, abstract = {Autism spectrum disorder (ASD) has been associated with alterations in the gut microbiota and its metabolites, particularly short-chain fatty acids (SCFAs) and microbiota-derived tryptophan catabolites, which may influence neurodevelopment through immune and epigenetic mechanisms. We investigated whether stool SCFAs and tryptophan-pathway metabolites differ between children with ASD and typically developing controls, and whether these metabolites associate with ASD severity and systemic biochemical signatures. In this cross-sectional study, we analyzed stool samples from 229 children (160 with ASD, 69 controls) with complete SCFA and tryptophan-metabolite data, while urine metabolomics data were available for a subset and were used for exploratory stool-urine integration analyses. Children with ASD and controls were similar in age, but the ASD group had a higher proportion of males. Absolute concentrations of individual SCFAs, total SCFAs, and derived indices were broadly comparable between groups; nominal differences in propionate/acetate ratio and caproate did not remain significant after false discovery rate correction. Similarly, stool tryptophan-pathway metabolites reported as ng/a.u. based on the NanoDrop-derived proxy (tryptophan, kynurenine, indole-3-acetic, indole-3-lactic, indole-3-propionic, indole-3-aldehyde, N-acetyl-tryptophan, serotonin, melatonin, tryptamine) and functional ratios (kynurenine/tryptophan, indole-derived/tryptophan, serotonin/tryptophan) showed no robust ASD-control differences; N-acetyl-tryptophan was nominally higher in ASD but did not survive multiple-testing correction. In the ASD subgroup with available Childhood Autism Rating Scale (CARS) data (n = 34), SCFA and tryptophan indices showed only weak, non-significant correlations with global ASD severity. In contrast, correlation analyses revealed two coherent metabolic modules, i.e., an SCFA block with very strong internal correlations among individual SCFAs and total SCFAs and a tryptophan block with strong correlations between metabolites and their normalized ratios, while cross-module correlations were modest. These results indicate that stool SCFA and microbiota-derived tryptophan profiles do not robustly distinguish ASD from controls in this cohort, but they form stable metabolic modules compatible with microbiome-epigenome frameworks.}, }
@article {pmid42123593, year = {2026}, author = {Sibarani, JN and Iqhrammullah, M and Hidayat, AA and Alfaray, RI and Nurkolis, F and Santini, A}, title = {Multi-Axis Reprogramming of Muscle-Metabolic Crosstalk by HiLo Platinum™ Restores Strength in Prediabetes via Mitochondrial Activation and Gut Microbiome Remodeling.}, journal = {International journal of molecular sciences}, volume = {27}, number = {9}, pages = {}, pmid = {42123593}, issn = {1422-0067}, mesh = {Animals ; Male ; *Gastrointestinal Microbiome/drug effects ; Rats ; Rats, Sprague-Dawley ; *Prediabetic State/metabolism/drug therapy ; *Muscle, Skeletal/metabolism/drug effects ; *Muscle Strength/drug effects ; *Mitochondria/metabolism/drug effects ; Biomarkers/metabolism ; Dietary Supplements ; Sarcopenia/metabolism ; Disease Models, Animal ; }, abstract = {Prediabetes is increasingly recognized as a risk factor for sarcopenia, driven by chronic low-grade inflammation, insulin resistance, and impaired anabolic signaling. Nutritional interventions containing whey protein, hydroxymethylbutyrate (HMB), glucosamine, and micronutrients may offer a multi-target strategy to counteract muscle deterioration. This study aimed to evaluate the efficacy of HiLo Platinum™ supplementation in attenuating muscle strength decline in a prediabetic rat model, with integrated analysis of metabolic biomarkers and gut microbiome profiles. A randomized preclinical trial was conducted using male Sprague Dawley rats assigned to four groups: normal diet (ND), prediabetic control induced by cholesterol- and fat-enriched diet with fructose (CFEDF), and two treatment groups receiving low-dose (0.63 g/kg BW) or high-dose (1.26 g/kg BW) HiLo Platinum™. The intervention lasted six weeks. Muscle strength was assessed via a four-limb grip strength test (reverse hang time and holding impulse). Biomarkers related to inflammation, mitochondrial function, and anabolic signaling (TNF-α, IL-10, PGC-1α, IGF-1, SIRT-1, AMPK, mTOR, and myostatin), lipid profile, and blood glucose were analyzed. Gut microbiome composition and diversity were evaluated using taxonomic profiling and multivariate analyses. HiLo Platinum™ supplementation significantly improved muscle strength, evidenced by increased reverse hang time and holding impulse (p < 0.001). Both doses reduced blood glucose and improved lipid profiles, including increased HDL and decreased LDL, triglycerides, and total cholesterol. Anti-inflammatory effects were observed with reduced TNF-α and elevated IL-10 levels. Mitochondrial and metabolic regulators (PGC-1α, SIRT-1, AMPK) and anabolic mediators (IGF-1) were significantly upregulated, while mTOR levels decreased. Gut microbiome analysis revealed increased genus richness (Chao1 index) and distinct microbial shifts associated with improved metabolic and inflammatory markers. HiLo Platinum™ effectively mitigates prediabetes-induced muscle strength decline through integrated modulation of inflammatory pathways, mitochondrial function, metabolic homeostasis, and gut microbiome composition. These findings support its potential as a nutritional therapeutic strategy for preventing sarcopenia in prediabetic conditions, although further studies are needed to evaluate long-term effects and implications on muscle hypertrophy.}, }
@article {pmid42123679, year = {2026}, author = {Chu, Y and Huang, KH and Tseng, CN}, title = {Targeting the Gut-Heart Axis in Diabetic Heart Failure: Microbiota and SGLT2is as Converging Therapeutic Frontiers.}, journal = {International journal of molecular sciences}, volume = {27}, number = {9}, pages = {}, pmid = {42123679}, issn = {1422-0067}, support = {From Chang Gung Memorial Hospital, Linkou Branch, Taiwan. (CMRPG3F1831, CMRPG3F1832, CMRPG3H0991, CMRPG3H0992, CMRPG3H1801, CMRPG3K0051, CMRPG3K0052, CMRPG3K0221, CMRPG3K0222,CMRPG3K1901,CMRPG3M0121) and from National Science and Technology Council, Taiwa//Linkou Chang Gung Memorial Hospital/ ; }, mesh = {Humans ; *Sodium-Glucose Transporter 2 Inhibitors/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Heart Failure/drug therapy/metabolism/etiology/microbiology ; *Diabetes Mellitus, Type 2/drug therapy/complications/microbiology/metabolism ; Animals ; Fatty Acids, Volatile/metabolism ; }, abstract = {Emerging evidence highlights the gut microbiota as a critical modulator in the pathogenesis of heart failure (HF), particularly among patients with type 2 diabetes mellitus (T2DM). Dysbiosis contributes to systemic inflammation, endothelial dysfunction, and adverse cardiac remodeling via microbial metabolites such as trimethylamine N-oxide (TMAO) and short-chain fatty acids (SCFAs). However, the therapeutic intersection between the gut microbiota and pharmacological interventions remains insufficiently integrated. Sodium-glucose cotransporter-2 inhibitors (SGLT2is), a cornerstone of T2DM management, confer cardioprotective effects that may involve microbiota-mediated pathways. This review provides a novel synthesis of how SGLT2is influence gut ecology, specifically through altered glucose excretion and osmotic shifts, to potentially restore SCFA-producing taxa. By delineating the structural transitions from gut physiology to SGLT2i-modulated cardiac outcomes, we emphasize the gut-heart axis as a pivotal therapeutic target. This focused framework offers new insights into the triadic interplay between microbiome stability and cardiometabolic health, moving beyond traditional glucose-centric paradigms.}, }
@article {pmid42123693, year = {2026}, author = {Seifert, O and Assarsson, M and Manoharan, L and Söderman, J}, title = {Integrated Host Genetics and Skin Microbiome Profiling Suggest an HLA-C-Peptostreptococcus Axis in Psoriasis.}, journal = {International journal of molecular sciences}, volume = {27}, number = {9}, pages = {}, pmid = {42123693}, issn = {1422-0067}, support = {FUTURUM-1012326, FUTURUM-996859, and FUTURUM-1006909//Futurum - Akademin f&#xf6;r H&#xe4;lsa och V&#xe5;rd/ ; N/A//Swedish Psoriasis Association/ ; }, mesh = {Humans ; *Psoriasis/genetics/microbiology/immunology ; *Skin/microbiology ; *Microbiota/genetics ; Polymorphism, Single Nucleotide ; Male ; *HLA-C Antigens/genetics ; Female ; Genetic Predisposition to Disease ; Adult ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Genotype ; Case-Control Studies ; Skin Microbiome ; }, abstract = {Psoriasis is a chronic immune-mediated disease driven by genetic susceptibility and environmental factors, including microbial exposure. While HLA-C-linked variants represent the strongest genetic risk factors, their relationship with the cutaneous microbiome remains incompletely understood. This study aimed to investigate host-microbiome interactions in psoriasis through integrative multi-omics analysis. Skin microbiome profiling using 16S rRNA sequencing and targeted genotyping of psoriasis-associated single-nucleotide polymorphisms (SNPs) was performed in lesional and non-lesional skin from patients with plaque psoriasis and in healthy controls. Integrated analysis was conducted using supervised multivariate modeling (DIABLO) to identify coordinated genetic and microbial features associated with disease status. Combined genetic and microbial signatures differentiated lesional, non-lesional, and healthy skin. Variants within the HLA-C susceptibility region, including rs12191877, rs10484554, and rs4406273, showed contributions to group separation and demonstrated positive associations with Peptostreptococcus anaerobius. Associations involving ERAP1 variants linked antigen-processing pathways with inflammation-associated microbial taxa in lesional skin. Importantly, genotype-microbiome correlations were also detected in clinically non-lesional skin, where an increased psoriasis risk allele dosage co-varied with a higher relative abundance of P. anaerobius and Aerococcus urinae. In contrast, commensal-associated taxa were enriched in healthy controls and formed genotype-linked clusters only in non-lesional skin. These findings suggest that psoriasis is characterized by coordinated host genetic and microbial interaction patterns centered on antigen presentation pathways. The presence of a genotype-microbiome coupling in non-lesional skin may indicate that genetically determined immune configurations could shape microbial community structure prior to visible lesion development. Rather than reflecting uniform dysbiosis, psoriasis may represent a dynamic host-microbe ecosystem in which genetic susceptibility influences microbial persistence and inflammatory readiness.}, }
@article {pmid42123776, year = {2026}, author = {Wang, M and Zhu, L and Liao, J and Bao, L and Li, H and Deng, Z and Li, J and Zheng, L and Zhang, B}, title = {Human Milk Oligosaccharide LNnT Attenuates Colonic Barrier Dysfunction and Associated Cognitive Impairment via Modulating Sphingolipid Metabolism and Gut Microbiota.}, journal = {Molecules (Basel, Switzerland)}, volume = {31}, number = {9}, pages = {}, pmid = {42123776}, issn = {1420-3049}, support = {No.82560639//National Natural Science Foundation of China/ ; No.20252BAC250147//Key Project of Natural Science Foundation of Jiangxi Province/ ; }, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; Mice ; Humans ; *Sphingolipids/metabolism ; *Cognitive Dysfunction/metabolism/drug therapy ; *Milk, Human/chemistry ; *Oligosaccharides/pharmacology/chemistry ; *Colon/drug effects/metabolism/pathology ; Male ; Galactose ; Intestinal Mucosa/metabolism/drug effects ; Oxidative Stress/drug effects ; Disease Models, Animal ; Mice, Inbred C57BL ; }, abstract = {This study focuses on Lacto-N-neotetraose (LNnT), a core component of human milk oligosaccharides. Although LNnT has been demonstrated to promote early intestinal development and maintain gut homeostasis, its protective mechanism against D-galactose-induced intestinal injury and associated cognitive impairment remains unclear. This investigation systematically examined the protective effects and underlying mechanisms of LNnT against D-gal-induced colonic damage and cognitive impairment in mice. The results demonstrated that LNnT not only significantly improved systemic physiological phenotypes and upregulated the expression of colonic tight junction proteins to repair the intestinal barrier, but also effectively enhanced learning and memory abilities in mice. Concurrently, LNnT reduced serum proinflammatory factor levels, elevated the anti-inflammatory factor IL-10, and alleviated oxidative stress. Furthermore, LNnT remodeled the gut microbiome structure by increasing microbial diversity, enhancing beneficial bacteria abundance, and promoting short-chain fatty acid production. Untargeted metabolomics analysis further revealed that LNnT corrected metabolic disturbances by regulating key sphingolipid molecules (ceramide, sphingosine, S1P) and the expression of related metabolic enzymes (ACER2, SphK2). In summary, this study suggests that LNnT mitigates intestinal injury and improves cognitive function, potentially through modulation of the gut microbiota-sphingolipid metabolism axis, although further causal validation is warranted. These findings provide a mechanistic foundation for future studies exploring its potential as a functional dietary ingredient.}, }
@article {pmid42123920, year = {2026}, author = {Hachmeriyan, A and Panayotova, G and Todorova, H}, title = {From Plate to Mind: Scientific Perspectives on Foods That May Influence Anxiety and Depression.}, journal = {Nutrients}, volume = {18}, number = {9}, pages = {}, pmid = {42123920}, issn = {2072-6643}, mesh = {Humans ; *Fatty Acids, Omega-3/administration &amp; dosage ; *Depression/diet therapy ; *Anxiety/diet therapy ; Gastrointestinal Microbiome ; Micronutrients/administration &amp; dosage ; Dietary Supplements ; *Diet ; Randomized Controlled Trials as Topic ; Brain ; Probiotics/administration &amp; dosage ; Vitamins/administration &amp; dosage ; }, abstract = {Background: Nutritional psychiatry increasingly links diet quality and specific bioactive nutrients to depression and anxiety outcomes. Mechanistic evidence implicates neuroimmune activation, inflammation, altered neurotransmitter synthesis, and microbiota-derived metabolites. Objective: The objective of this study is to synthesize evidence on omega-3 polyunsaturated fatty acids (n-3 PUFAs), the microbiota-gut-brain axis, and vitamins and minerals that influence neurotransmitter synthesis, inflammation, and brain function and to translate these findings into food-based strategies. Methods: This study consisted of a focused synthesis of randomized controlled trials (RCTs), meta-analyses, and systematic reviews indexed in PubMed, Scopus and Web of Science, selected for relevance to omega-3s, probiotics/prebiotics, dietary patterns, and micronutrients (folate/B-vitamins, vitamin D, magnesium, zinc, and vitamin C/copper pathways). Results: RCT and meta-analytic evidence suggest modest benefits of omega-3 supplementation for anxiety severity and depressive symptoms, with heterogeneity by dose, EPA: DHA composition, and baseline inflammatory status. The gut-brain axis literature supports bidirectional effects of stress and microbiota, and meta-analyses of probiotics/prebiotics show small improvements in depressive and anxiety symptoms, likely dependent on strain and host phenotype. Micronutrients serve as enzymatic cofactors for monoamine and GABA synthesis and modulate immune signaling; clinical effects are the most consistent when correcting insufficiency or in biomarker-defined subgroups. A whole-diet RCT demonstrates that structured dietary improvement can reduce depressive symptoms as adjunctive therapy. Conclusions: A food-first approach emphasizing Mediterranean-style dietary patterns, omega-3-rich seafood, a diverse array of fiber, and micronutrient density is the most defensible. Supplementation may be considered selectively, guided by clinical context and nutritional status.}, }
@article {pmid42123927, year = {2026}, author = {Rodziewicz, A and Bryl, E}, title = {The Role of Microbiome and Diet on Disease Activity and Immune-Inflammatory Status in Rheumatoid Arthritis.}, journal = {Nutrients}, volume = {18}, number = {9}, pages = {}, pmid = {42123927}, issn = {2072-6643}, support = {01-10026/0010451/01/262/0/2026//Gda&#x144;sk Medical University/ ; }, mesh = {Humans ; *Arthritis, Rheumatoid/immunology/microbiology/diet therapy/prevention &amp; control ; *Gastrointestinal Microbiome ; *Diet ; Probiotics/administration &amp; dosage ; Diet, Mediterranean ; Dietary Supplements ; Inflammation ; Prebiotics ; }, abstract = {Rheumatoid arthritis (RA) is a chronic inflammatory disease of autoimmune background and unknown etiology. The importance of genetic factors in RA development is well-established. Environmental factors have also been extensively researched in relation to risk of RA and managing its symptoms. Smoking, physical activity, diet, and gut microbiota are considered to be the most essential modifiable factors in RA. Among dietary interventions, the most researched is Mediterranean diet, monounsaturated fatty acids, fish consumption, and fish oil (EPA, eicosapentaenoic acid and DHA, that is, docosahexaenoic acid). Others concerned gluten-free and vegan or vegetarian diet, salt intake, supplementation with vitamin D, antioxidants, prebiotics, and probiotics. Diet modifications can alter the gut environment, and the association between RA development or severity and the composition of gut bacteria has already been shown. This review focuses on effectiveness and usefulness of various dietary approaches and supplements in RA prevention and management, including the influence on disease activity and inflammatory status. The composition of gut microbiota and its changes in response to dietary factors are also considered. There is a great need for further research into mutual dependencies of diet, microbiome, and RA activity. The current state of knowledge provides promising evidence for future nutrition and microbial therapies.}, }
@article {pmid42123931, year = {2026}, author = {Maragno, P and Amoroso, C and Conforti, S and Michelon, M and Honcharyuk, I and Ciafardini, C and Noviello, D and Strati, F and Caprioli, F and Facciotti, F and Vecchi, M}, title = {The Assessment of Multidimensional Clinical, Biological and Patient-Reported Outcomes to Evaluate the Efficacy of Add-On Lactobacillus rhamnosus GG Supplementation in Mild Ulcerative Colitis: A Randomized Pilot Trial.}, journal = {Nutrients}, volume = {18}, number = {9}, pages = {}, pmid = {42123931}, issn = {2072-6643}, mesh = {Humans ; *Colitis, Ulcerative/therapy/drug therapy/microbiology ; Pilot Projects ; Female ; Male ; *Lacticaseibacillus rhamnosus ; Adult ; Double-Blind Method ; Middle Aged ; Mesalamine/therapeutic use/administration &amp; dosage ; *Probiotics/administration &amp; dosage/therapeutic use ; *Dietary Supplements ; Patient Reported Outcome Measures ; Quality of Life ; Gastrointestinal Microbiome/drug effects ; Treatment Outcome ; *Cholecalciferol/administration &amp; dosage/therapeutic use ; Leukocyte L1 Antigen Complex/analysis ; Feces/chemistry/microbiology ; Anti-Inflammatory Agents, Non-Steroidal/therapeutic use ; }, abstract = {Background: Ulcerative colitis (UC) is a multifactorial disease characterized by aberrant mucosal immune activation in response to intestinal dysbiosis. Contemporary management strategies aim to target inflammation and microbiome alterations while reducing relapse risk. A multidimensional assessment integrating clinical, inflammatory, immune, and microbial endpoints may better capture therapeutic effects beyond symptom control. Aims: To evaluate whether supplementation with Lactobacillus rhamnosus GG co-formulated with vitamin D3 (Dicoflor IBD Immuno) as an adjunct to optimized mesalamine (5-ASA) is associated with coordinated changes across clinical and biological domains in mild-to-moderate UC, using a multidimensional assessment framework. Methods: This single-center, randomized, double-blind, placebo-controlled pilot trial was conducted at Fondazione Ca' Granda IRCCS Policlinico di Milano between May 2022 and May 2024. Thirty-six patients with mild-to-moderate UC receiving optimized 5-ASA were randomized to LGG+VitD3 (ALD3) or placebo (AP) for 4 weeks. Clinical activity, health-related quality of life (HRQoL), fecal calprotectin, peripheral immune cell subsets, and gut microbiota composition were assessed at baseline and week 4. Results: Both 5-ASA-LGG+VitD3 (ALD3)- and 5-ASA-placebo (AP)-treated patients showed significant improvement in clinical activity and HRQoL, without between-group differences. A higher proportion of clinical responders was observed in the ALD3 group, although this was not statistically significant. LGG+VitD3-supplemented patients showed reduced fecal calprotectin levels and increased frequencies of IL-22-producing CD4[+] T cells. Microbiome analysis revealed enrichment of short-chain fatty acid-producing taxa, including Coprococcus and Fusicatenibacter, in ALD3-treated patients. Conclusions: In patients with mild UC receiving optimized 5-ASA, LGG+VitD3 supplementation does not improve short-term clinical outcomes beyond placebo but is associated with favorable modulation of inflammatory, immune, and microbial parameters, supporting the relevance of multidimensional biological endpoints in adjunctive UC management.}, }
@article {pmid42123938, year = {2026}, author = {Chiang, CK and Lai, CL and Chiu, MH and Huang, CJ}, title = {The Gut-Lung Axis in Allergic Asthma: A Narrative Review of Microbial Dysbiosis, Immune Regulation, and Nutritional Modulation.}, journal = {Nutrients}, volume = {18}, number = {9}, pages = {}, pmid = {42123938}, issn = {2072-6643}, support = {CGH-MR-B-11316//Cathay General Hospital/ ; }, mesh = {Humans ; *Dysbiosis/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; *Asthma/immunology/microbiology ; *Lung/immunology/microbiology ; Animals ; Diet ; }, abstract = {Allergic asthma is a prevalent chronic inflammatory disease of the airways whose pathogenesis has traditionally been attributed to localized immune dysfunction within the lung. However, accumulating evidence from microbiome research supports a broader system-level perspective in which cross-organ interactions contribute to disease susceptibility and progression. In particular, the gut-lung axis has emerged as a key regulatory pathway linking intestinal microbial ecology, immune development, and respiratory health. This review synthesizes current epidemiological, mechanistic, and experimental evidence supporting the role of gut microbiota dysbiosis in allergic asthma. We examine how early-life environmental and nutritional exposures and gut microbiota establishment during critical developmental windows shape long-term immune tolerance and asthma susceptibility. We then summarize characteristic features of asthma-associated gut dysbiosis and discuss how microbial-derived metabolites, including short-chain fatty acids, tryptophan metabolites, pro-allergic lipid mediators such as 12,13-dihydroxy-9Z-octadecenoic acid, and bacterial-derived histamine, modulate distal airway immune responses through epigenetic, receptor-mediated, and immune trafficking mechanisms. Particular emphasis is placed on the role of diet as a key upstream regulator of gut microbiota composition and metabolic function. Finally, we evaluate experimental and translational studies targeting the gut-lung axis, including dietary modulation, microbiome-targeted interventions such as fecal microbiota transplantation, and emerging postbiotic approaches. Collectively, current evidence indicates that gut microbial composition and metabolic function are critical determinants of respiratory immune homeostasis. Targeting the gut-lung axis through nutrition- and microbiome-based strategies offers a promising avenue for the prevention and precision treatment of allergic asthma.}, }
@article {pmid42123967, year = {2026}, author = {Blady, K and Pomianowski, B and Smółka, L and Strugała, M and Kursa, K and Stanek, A}, title = {The Therapeutic Potential of Polyphenols in Modulating Barrier Lipids, Microbiome Interactions, and Inflammatory Pathways in Atopic Dermatitis.}, journal = {Nutrients}, volume = {18}, number = {9}, pages = {}, pmid = {42123967}, issn = {2072-6643}, mesh = {Humans ; *Polyphenols/pharmacology/therapeutic use ; *Dermatitis, Atopic/drug therapy/microbiology/metabolism ; Filaggrin Proteins ; Animals ; Gastrointestinal Microbiome/drug effects ; *Anti-Inflammatory Agents/pharmacology ; Inflammation/drug therapy ; *Lipid Metabolism/drug effects ; Epidermis/drug effects/metabolism ; Signal Transduction/drug effects ; *Microbiota/drug effects ; }, abstract = {Atopic dermatitis (AD) is a chronic inflammatory skin disease with a complex pathogenesis involving epidermal barrier dysfunction, microbiome dysbiosis, and immune dysregulation. Despite significant advances in therapy, including biologics and targeted treatments, their use may be limited by adverse effects, highlighting the need for safe adjunctive strategies. Polyphenols are naturally occurring bioactive compounds that are abundant in plant-based foods and are known for their anti-inflammatory, antioxidant, and immunomodulatory properties, making them promising candidates for supportive AD management. This review integrates current evidence on the effects of polyphenols on epidermal barrier lipids, microbiome interactions, and key inflammatory pathways, including NF-κB and JAK/STAT signaling. Additionally, the role of polyphenols in modulating dendritic cell and neutrophil activity, and reducing reactive oxygen species (ROS) production and neutrophil extracellular trap (NET) formation, as well as their potential involvement in mitophagy regulation, is discussed. Polyphenols support epidermal barrier integrity by modulating the expression of key structural proteins, including filaggrin, involucrin, and loricrin, leading to a reduction in transepidermal water loss (TEWL). Furthermore, they interact bidirectionally with the gut microbiome, acting as metabolic substrates for beneficial bacteria and promoting the growth of short-chain fatty acid (SCFA)-producing species such as Lactobacillus, Bifidobacterium, and Akkermansia, while simultaneously inhibiting pathogenic strains. These findings highlight the role of polyphenols in maintaining microbiome homeostasis and supporting epidermal barrier integrity. The review encompasses findings from clinical studies, animal models, and mechanistic investigations, while also addressing limitations related to polyphenol bioavailability. Overall, polyphenols may represent a valuable adjunctive approach in AD management; however, further well-designed clinical and mechanistic studies are required to confirm their therapeutic potential.}, }
@article {pmid42124000, year = {2026}, author = {Schubert, MG and Dentand, A and Karczewski, M and Morsy, Y and Beuschlein, F and Scharl, M and Krayenbuehl, PA}, title = {Dose-Dependent Alterations of the Human Gut Microbiome During Oral Iron Supplementation: A Randomized Study in Iron-Deficient Non-Anaemic Women.}, journal = {Nutrients}, volume = {18}, number = {9}, pages = {}, pmid = {42124000}, issn = {2072-6643}, mesh = {Humans ; Female ; *Gastrointestinal Microbiome/drug effects ; Adult ; *Dietary Supplements ; *Iron/administration &amp; dosage/adverse effects ; Administration, Oral ; Dose-Response Relationship, Drug ; Feces/microbiology ; Young Adult ; RNA, Ribosomal, 16S/genetics ; Iron Deficiencies ; }, abstract = {Background/Objectives: Oral iron supplementation is widely used to treat iron deficiency but frequently causes gastro-intestinal side effects that limit treatment adherence. Unabsorbed luminal iron has been proposed to influence intestinal microbial communities, yet the effects of different oral iron doses on the human gut microbiome remain insufficiently characterized. Methods: In this randomized open-label study, 30 healthy premenopausal women with iron deficiency without anaemia received either low-dose oral iron supplementation (6 mg twice daily) administered under fasting conditions or standard-dose iron supplementation (100 mg once daily) taken with a meal for four weeks. Stool samples were collected before and after treatment and analyzed using 16S rRNA sequencing to evaluate microbiome composition. Results: Baseline characteristics, including age, body mass index, hemoglobin concentration and serum ferritin, were comparable between groups. After four weeks of treatment, distinct alterations in gut microbiome composition were observed between the low-dose and standard-dose groups. The genera Colidextribacter and GCA-900066575 decreased in the low-dose group but increased in the standard-dose group, whereas Oscillospira showed the opposite pattern. Gastrointestinal adverse events were reported by 87% of participants receiving standard-dose iron supplementation compared with 7% receiving low-dose iron supplementation (p < 0.0001). Conclusions: Oral iron supplementation induces dose-dependent changes in the intestinal microbiome and higher doses are associated with substantially increased gastrointestinal intolerance. These findings suggest that lower iron doses may reduce microbiome disruption and improve treatment tolerability.}, }
@article {pmid42124002, year = {2026}, author = {Caserta, S and Martino, EA and Skafi, M and Vigna, E and Bruzzese, A and Amodio, N and Fiorillo, M and Lucia, E and D'Arrigo, G and Olivito, V and Labanca, C and Mendicino, F and Alvaro, ME and Tripepi, G and Morabito, F and Gentile, M}, title = {The Gut Microbiota in Hematologic Malignancies: Mechanisms, Clinical Associations, and Translational Opportunities.}, journal = {Nutrients}, volume = {18}, number = {9}, pages = {}, pmid = {42124002}, issn = {2072-6643}, mesh = {Humans ; *Hematologic Neoplasms/microbiology/therapy ; *Gastrointestinal Microbiome/physiology ; Animals ; Translational Research, Biomedical ; Dysbiosis ; }, abstract = {Hematologic malignancies arise and progress within a systemic ecosystem in which the gut microbiota is an increasingly recognized, partially modifiable component. Across acute leukemias, chronic lymphocytic leukemia, plasma cell disorders, lymphomas, and clonal myeloid neoplasms, human studies consistently report reduced microbial diversity, depletion of barrier-supportive, short-chain fatty acid-producing commensals, and enrichment of Gram-negative, pro-inflammatory, or hospital-adapted taxa. These alterations are associated with pre-leukemic clonal expansion, adverse genetic and immunological features, progression from precursor conditions, and inferior outcomes after chemotherapy, immunochemotherapy, chimeric antigen receptor T-cell therapy, and allogeneic hematopoietic stem cell transplantation. Mechanistic work in animal models and ex vivo systems demonstrates that microbiota-derived signals and metabolites-including Th17/IL-17-skewing consortia and the lipopolysaccharide intermediate ADP heptose sensed by the cytosolic receptor ALPK1-can actively modulate hematopoietic stem and progenitor cell fitness, inflammatory circuits, and malignant cell survival, supporting a causal role in disease biology. At the same time, major knowledge gaps remain because most human cohorts are small, single-center, and cross-sectional, frequently rely on 16S rRNA profiling, and are vulnerable to dietary, geographic, and treatment-related confounding. Within this context, three translational domains appear particularly promising: pharmaco-microbiomics, microbiome-informed risk stratification, and rational microbiota-targeted interventions, particularly diet-based strategies and antimicrobial stewardship. Here, we provide an integrated, disease-spanning synthesis of these data, emphasizing clonal hematopoiesis and myeloid neoplasms as emerging examples of microbiota-marrow crosstalk and outlining practical priorities for embedding microbiome science into future hematologic trials. Routine microbiome profiling or empiric microbiota-directed therapies cannot yet be recommended in everyday hematology practice, but integrating microbiome science into prospective therapeutic and transplant trials offers a realistic path to improved disease modeling, biomarker development, and rational adjunctive strategies to enhance outcomes for patients with hematologic malignancies.}, }
@article {pmid42124012, year = {2026}, author = {Zeng, Y and Ahmed, M and Zhang, H}, title = {Beyond Antioxidants: The Microbial Metabolic Landscape of Anthocyanins and Their Downstream Health Implications.}, journal = {Nutrients}, volume = {18}, number = {9}, pages = {}, pmid = {42124012}, issn = {2072-6643}, support = {20243BCC31009//Key Project of Jiangxi Provincial Key Research and Development Program/ ; 32560560//National Natural Science Foundation of China/ ; }, mesh = {*Anthocyanins/metabolism/pharmacokinetics ; *Gastrointestinal Microbiome/physiology ; Humans ; *Antioxidants/metabolism ; Biological Availability ; Hydroxybenzoates/metabolism ; Animals ; Signal Transduction ; }, abstract = {BACKGROUND/OBJECTIVES: Anthocyanins are dietary pigments associated with reduced risk of chronic diseases, yet their low systemic bioavailability challenges the traditional direct antioxidant hypothesis. This review aims to reconceptualize anthocyanin bioactivity by proposing the gut microbiome as a key mediator that biotransforms these compounds into bioactive metabolites responsible for systemic health effects.<br><br>METHODS: This review synthesizes evidence on the microbial metabolism of anthocyanins and includes a structured appraisal of the literature using an evidence evaluation framework analogous to GRADE, focusing on their transit to the colon, enzymatic biotransformation by gut microbiota, and resulting production of phenolic metabolites such as protocatechuic acid (PCA). It also examines the role of specific bacterial taxa (e.g., Bifidobacterium and Lactobacillus) in enhancing bioavailability and explores the downstream cellular pathways modulated by these metabolites.<br><br>RESULTS: Gut microbiota convert anthocyanins into smaller phenolic metabolites such as PCA, syringic acid, gallic acid, and other respective metabolites, which achieve plasma concentrations up to 100-fold higher than parent compounds and can cross the blood-brain barrier. These metabolites exert systemic effects by modulating key signaling pathways (NF-&#x3ba;B and Nrf2) and restoring redox homeostasis. Additionally, beneficial gut bacteria enhance anthocyanin bioavailability and support the production of short-chain fatty acids (SCFAs).<br><br>CONCLUSIONS: Systemic health benefits of anthocyanins are largely mediated by gut microbiota through the generation of bioactive metabolites. This microbiota-driven process redefines the mechanistic understanding of anthocyanin action and highlights the microbiome as a critical determinant of their efficacy in preventing cardiometabolic and neurodegenerative diseases.}, }
@article {pmid42124014, year = {2026}, author = {Uțu, D and Nodiți-Cuc, AR and Kiș, AM and Popovici, RA and Pitic, DE and Trusculescu, LM and Marian, D and Nan, AG and Matin, AS and Cîmpian, DM and Bodo, CR and Enache, A and Olariu, I}, title = {Diet-Microbiome-Brain Axis and Mental Health: Biological Mechanisms and Nutritional Implications.}, journal = {Nutrients}, volume = {18}, number = {9}, pages = {}, pmid = {42124014}, issn = {2072-6643}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Mental Health ; *Brain/physiology ; Animals ; *Diet ; *Mental Disorders/prevention &amp; control ; Probiotics ; Prebiotics/administration &amp; dosage ; Dysbiosis ; }, abstract = {BACKGROUND/OBJECTIVES: Diet is a primary and modifiable determinant of gut microbiota composition, diversity, and metabolic activity, thereby shaping microbial-derived metabolites, immune and inflammatory signalling, neuroendocrine regulation, and neural communication with the central nervous system. Western dietary patterns, characterised by high intake of ultra-processed foods, saturated fats, and low dietary fibre, are consistently associated with gut dysbiosis, impaired intestinal barrier function, chronic low-grade inflammation, and increased risk of depression, anxiety, cognitive impairment, and neurodegenerative disorders.<br><br>METHODS: This narrative review synthesises evidence from human observational studies, randomised controlled trials, animal models, and mechanistic investigations examining interactions among diet, gut microbiota, and mental health or neurobiological outcomes. Literature searches were conducted in PubMed, Scopus, and Web of Science for articles published up to December 2025.<br><br>RESULTS: The study highlights the therapeutic potential and limitations of dietary interventions, prebiotics, probiotics, and psychobiotics, and critically evaluates them. Also facilitates an improved understanding of diet-microbiome-brain interactions, which may help the development of personalised, nutrition-based strategies integrated into mental health prevention and clinical care.<br><br>CONCLUSIONS: These findings support diet-based, microbiome-informed strategies as scalable adjuncts in mental health prevention and care.}, }
@article {pmid42124034, year = {2026}, author = {Kłosek, S and Szymczak-Paluch, M and Bernaś, A and Gawlak-Socka, S}, title = {Does Probiotic Intake Enhance the Efficacy of Oral Fungal Infection Treatment?.}, journal = {Nutrients}, volume = {18}, number = {9}, pages = {}, pmid = {42124034}, issn = {2072-6643}, support = {503/2-148-07/503-21-001//Medical University of Lodz/ ; }, mesh = {*Probiotics/therapeutic use/administration &amp; dosage ; Humans ; *Candidiasis, Oral/microbiology/therapy/drug therapy ; Antifungal Agents/therapeutic use ; Mouth/microbiology ; Microbiota ; }, abstract = {Oral candidiasis (OC) is the most frequent fungal infection among users of dental prosthetic devices, immunocompromised patients, and those who underwent chemotherapy treatment and had a complication of long-term antibiotic therapy. About 150 species of Candida fungi have been described, whereas over 80% of oral fungal infections are attributed to the opportunistic pathogen Candida albicans. Pain, dryness of oral mucosa, pathological lesions, and intermittent mucosal bleeding are the main symptoms that worsen the daily functioning of the abovementioned fungal-infected patients. A promising adjunctive strategy may involve the use of probiotic bacteria to attenuate fungal colonization in the oral cavity in order to reduce the need for conventional treatment, which carries a risk of antifungal drug resistance-a significant problem worldwide. Probiotic formulations mostly incorporate commensal bacteria that naturally inhabit oral ecosystems such as Lactobacillus spp., Bifidobacterium spp., Bacillus spp., and others. Probiotic organisms may contribute to the restoration of oral microbiome homeostasis through numerous mechanisms, such as competitive control of Candida species numbers, better adhesion to oral mucosa and production of bioactive compounds and antimicrobial metabolites. Despite many studies, the current evidence base remains heterogeneous. Well-designed studies across diverse populations are required to determine whether probiotic-based interventions can be an effective and clinically useful alternative or adjunct to standard antifungal therapy of OC.}, }
@article {pmid42124041, year = {2026}, author = {Son, JY and Do, Y and Seo, J and Choi, J}, title = {Gut-Derived Metabolic Imbalance in Autism Spectrum Disorder: Toward the Concept of a Metabolic Subtype.}, journal = {Nutrients}, volume = {18}, number = {9}, pages = {}, pmid = {42124041}, issn = {2072-6643}, support = {Ky-lin Foundation in 2024//Daegu Haany University/ ; }, mesh = {Humans ; *Autism Spectrum Disorder/metabolism/microbiology ; *Gastrointestinal Microbiome/physiology ; *Fatty Acids, Volatile/metabolism ; Dysbiosis/metabolism ; *Gastrointestinal Tract/metabolism ; Animals ; }, abstract = {Autism spectrum disorder (ASD) is highly heterogeneous in symptom onset and severity, comorbidities, and treatment responsiveness, challenging the notion of a single pathogenic mechanism. Increasing evidence indicates that some individuals with ASD exhibit prominent peripheral physiological alterations, including gastrointestinal (GI) dysfunction, gut microbial dysbiosis, immune imbalance, oxidative stress, and mitochondrial/energy metabolic vulnerability. In this context, gut-derived metabolites-particularly short-chain fatty acids (SCFAs)-have emerged as plausible modulators of the neurodevelopmental milieu through the expanded gut-immune-metabolic-brain axis. This review synthesizes: (i) SCFAs' biogenesis and physiological roles, (ii) context- and developmental stage-dependent effects, (iii) the clinical heterogeneity of reported microbiome and SCFA alterations in ASD, and (iv) propionate as a frequently discussed candidate signal and the interpretive boundaries of preclinical evidence. Human studies show substantial inter-study variability in SCFA alterations (increases, decreases, or no differences), influenced by factors such as sample type (stool vs. blood), GI symptoms, diet, medication exposure, and analytical variability. Accordingly, SCFAs should not be treated as universal ASD biomarkers but rather as context-dependent metabolic signals relevant under specific clinical and biological conditions. Building on this premise, we propose the conceptual framework of "metabolic ASD" representing a metabolically informed dimension of biological variability in which peripheral metabolic-immune perturbations may contribute to neurodevelopmental vulnerability. To avoid premature causal claims, we outline design requirements for future research, including stratified study designs, longitudinal cohorts, and integrative multi-layer analyses. Ultimately, metabolic ASD should be positioned as a testable precision medicine research framework rather than a universal etiological model.}, }
@article {pmid42124048, year = {2026}, author = {Thakur, D and Harmer, MJ}, title = {Circulating Short-Chain Fatty Acid Levels in Chronic Kidney Disease: A Systematic Review and Meta-Analysis.}, journal = {Nutrients}, volume = {18}, number = {9}, pages = {}, pmid = {42124048}, issn = {2072-6643}, mesh = {Humans ; *Fatty Acids, Volatile/blood ; *Renal Insufficiency, Chronic/blood ; Child ; Adult ; Butyrates/blood ; Female ; Male ; Propionates/blood ; }, abstract = {BACKGROUND: Chronic kidney disease (CKD) is characterised by a disrupted gut-kidney axis, wherein intestinal dysbiosis is associated with the accumulation of uraemic toxins and the potential depletion of beneficial short-chain fatty acids (SCFAs). Whilst acetate, propionate, and butyrate are known to modulate systemic inflammation and blood pressure, their precise circulating concentrations across different CKD stages and age groups remain poorly defined. This systematic review and meta-analysis aimed to quantify blood SCFA concentrations in CKD patients compared to healthy controls.<br><br>METHODS: We conducted a systematic search of Medline, EMBASE, and the Cochrane Library for clinical studies reporting blood SCFA concentrations in humans with CKD. Methodological quality was assessed using the NIH tool. Standardised mean differences (SMDs) were calculated for the quantitative meta-analysis, with subgroup analyses performed for age, CKD stage, and treatment modality (dialysis vs. transplantation).<br><br>RESULTS: Twenty-one studies encompassing 9661 participants were included. Quantitative synthesis revealed a significant and consistent systemic depletion of circulating acetate and propionate in adult CKD patients compared to healthy controls (p < 0.05). This depletion followed a stage-dependent trajectory, worsening alongside declining glomerular filtration rates. Notably, a "butyrate paradox" was identified in paediatric cohorts; whilst adults showed progressive butyrate depletion, children with CKD often maintained or exhibited elevated levels, particularly in the context of hypertension. Furthermore, whilst haemodialysis patients exhibited the most profound SCFA deficiencies, kidney transplantation appeared to partially restore these metabolites toward healthy baseline levels.<br><br>CONCLUSIONS: CKD is associated with a profound systemic reduction in acetate and propionate, supporting the model of a compromised gut-kidney axis based on converging evidence. The divergent results for butyrate in paediatric versus adult populations suggest that SCFA metabolism is influenced by age-related factors or compensatory mechanisms. These findings highlight the potential for SCFA monitoring as a candidate or emerging markers for detecting early renal damage and stratifying risk.}, }
@article {pmid42124049, year = {2026}, author = {Liu, H and Shi, CY and Fahey, JW}, title = {Sulforaphane in Cutaneous Disorders and Skin Injury: Mechanisms, Evidence, and Clinical Perspectives.}, journal = {Nutrients}, volume = {18}, number = {9}, pages = {}, pmid = {42124049}, issn = {2072-6643}, mesh = {Humans ; *Isothiocyanates/pharmacology/therapeutic use ; Sulfoxides ; *Skin Diseases/drug therapy/metabolism ; Animals ; *Skin/drug effects/metabolism/injuries ; Signal Transduction/drug effects ; Anti-Inflammatory Agents/pharmacology ; Oxidative Stress/drug effects ; Antioxidants/pharmacology ; }, abstract = {Cutaneous disorders such as atopic dermatitis, psoriasis, acne vulgaris, and rosacea, together with UV-induced skin injury and photoaging, are highly prevalent conditions that involve varying contributions from dysregulated immune responses, cutaneous inflammation, oxidative stress, barrier dysfunction, microbiome alteration, and exogenous injury. However, these conditions are biologically heterogeneous and should not be regarded as a single mechanistic class. Sulforaphane, a naturally occurring isothiocyanate found primarily in broccoli and other cruciferous vegetables, has attracted interest in dermatology because of its antioxidant, cytoprotective, and context-dependent anti-inflammatory properties. Sulforaphane exerts its biological effects by modulating key signaling pathways, particularly the Keap1/Nrf2 pathway and, in some settings, NF-κB-related signaling, thereby reducing oxidative stress and inflammation, regulating immune responses, enhancing skin barrier function, and potentially influencing the cutaneous microbiome. Preclinical studies and limited human data suggest that sulforaphane may reduce erythema, edema, and other markers of cutaneous damage in selected settings. This comprehensive review explores the role of sulforaphane across heterogeneous cutaneous conditions, with emphasis on molecular mechanisms, disease-specific differences, current evidence, and discusses key translational constraints including formulation, delivery, lack of standardized dosing, and the limitations of cell culture and animal models for predicting human efficacy. Overall, sulforaphane should presently be regarded as a promising but still early-stage translational candidate in dermatology. Robust human efficacy data remain lacking for chronic inflammatory dermatoses such as psoriasis, atopic dermatitis, acne, and rosacea, whereas the strongest current human evidence relates to UV-associated skin outcomes and photoprotection.}, }
@article {pmid42124376, year = {2026}, author = {Moltrasio, C and Marzano, AV and Romagnuolo, M}, title = {The Multifaceted Role of Keratinocytes in Hidradenitis Suppurativa Pathogenesis.}, journal = {Experimental dermatology}, volume = {35}, number = {5}, pages = {e70269}, pmid = {42124376}, issn = {1600-0625}, support = {//Italian Ministry of Health (Ricerca Corrente) of Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan (Italy)./ ; }, mesh = {Humans ; *Hidradenitis Suppurativa/immunology/etiology/physiopathology ; *Keratinocytes/physiology ; Cytokines/metabolism ; Signal Transduction ; Inflammation ; Animals ; }, abstract = {Hidradenitis suppurativa (HS) is a chronic autoinflammatory skin disorder of the pilosebaceous unit, with multiple factors contributing to its onset, activity and progression. Alongside a predisposing genetic background, hormonal and microbiome alterations, dysregulation of innate and adaptive immune response, as well as environmental/epigenetic factors contribute to its immunopathogenic landscape. In the past years, translational investigations identified several distinct inflammatory networks, not only in the chronic but also in the early stages of disease, making them potential therapeutic targets. Emerging evidence underlies the important role of keratinocytes in the pathogenesis and progression of HS, acting not only as targets of inflammatory signaling pathways but also as active producers of pro-inflammatory cytokines, chemokines and effector molecules that may influence disease onset and activity. Despite these insights, different aspects of their involvement remain underexplored, necessitating further targeted research. This review aims to highlight the experimental evidence supporting the crucial role of keratinocytes in the inflammatory response and overall pathophysiology of HS.}, }
@article {pmid42124457, year = {2026}, author = {Wang, C and Xu, Z and Ma, M and Fu, Z and Yao, K}, title = {Gallic Acid Protects Against DSS-Induced Colitis by Modulating Gut Microbiota and Suppressing the Activation of NF-κB/MAPK Signaling Pathway.}, journal = {Molecular nutrition &amp; food research}, volume = {70}, number = {9}, pages = {e70487}, doi = {10.1002/mnfr.70487}, pmid = {42124457}, issn = {1613-4133}, support = {LY22B070007//Natural Science Foundation of Zhejiang Province/ ; }, mesh = {Animals ; *Gallic Acid/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Humans ; *NF-kappa B/metabolism ; Mice, Inbred C57BL ; Caco-2 Cells ; Mice ; Dextran Sulfate/toxicity ; *MAP Kinase Signaling System/drug effects ; Male ; RAW 264.7 Cells ; *Colitis/chemically induced/prevention &amp; control/drug therapy ; Cytokines/metabolism ; Colon/pathology/drug effects ; Coculture Techniques ; }, abstract = {To investigate the protective role and mechanisms of gallic acid (GA) against ulcerative colitis (UC), C57BL/6 mice were pretreated with GA (10 or 50 mg/kg) or saline for 21 days before colitis induction with 2.5% DSS for 7 days. An in vitro Caco-2/RAW 264.7 coculture model mimicking the intestinal epithelium was used. After 24-h GA pretreatment, inflammation was induced with LPS in Caco-2/RAW 264.7 coculture cell for 4 h. GA alleviated colitis symptoms, improving body weight, preventing colon shortening, reducing histopathological damage, and lowering pro-inflammatory cytokines (IL-6, IL-22, TNF-α, IL-17α). It enhanced intestinal barrier integrity by upregulating tight junction (TJ) proteins claudin-1 and occludin. Mechanistically, GA inhibited NF-κB and MAPK pathways by suppressing phosphorylation of p65, IκB, JNK, ERK, and P38 in colon tissue. GA also favorably modulated the gut microbiome, reducing pathobionts (e.g., Desulfovibrio) and enriching beneficial genera like Enterobacteria and Prevotella. In the cell coculture model, GA suppressed LPS-induced pro-inflammatory mediators, upregulated IL-10, and restored LPS-downregulated TJ protein expression. These findings indicate that GA alleviates DSS-induced UC by restoring intestinal homeostasis, exerting anti-inflammatory effects, and providing preventive benefits upon long-term use, supporting its potential as a prophylactic agent for UC.}, }
@article {pmid42124488, year = {2026}, author = {Koynova-Tenchov, R}, title = {Molecular Dialogues in the Mitochondria-Microbiome Crosstalk: Metabolites, Signaling, and Immunity.}, journal = {Comprehensive Physiology}, volume = {16}, number = {3}, pages = {e70164}, doi = {10.1002/cph4.70164}, pmid = {42124488}, issn = {2040-4603}, mesh = {Humans ; *Mitochondria/metabolism ; Animals ; Signal Transduction/physiology ; *Microbiota/physiology ; *Gastrointestinal Microbiome/physiology ; }, abstract = {The bidirectional dialogue between mitochondria and the human microbiota-the mitochondria-microbiome axis-plays a pivotal role in regulating host metabolism, immune signaling, and overall physiological homeostasis. Growing evidence underscores the role of microbial metabolites-including short-chain fatty acids, secondary bile acids, and lipopolysaccharides-as direct modulators of mitochondrial bioenergetics, redox balance, and inflammatory cascades. Conversely, mitochondrial integrity governs the microbial landscape by regulating local oxygen tension, modulating immune-mediated selection, and secreting metabolic byproducts that shape commensal populations. Disruptions to this bidirectional crosstalk are linked to a diverse pathological spectrum. These include metabolic syndromes like obesity, type 2 diabetes, and NAFLD; neurodegenerative disorders such as Parkinson's and Alzheimer's; and systemic inflammatory conditions, notably inflammatory bowel disease and various autoimmune pathologies. Therapeutic interventions designed to modulate this axis-ranging from targeted probiotics, dietary interventions, and mitochondrial boosters-offer significant potential for reinstating physiological homeostasis. This review explores the molecular foundations of mitochondria-microbiome crosstalk, its role in disease pathogenesis, and the potential for microbiome-targeted therapies to restore mitochondrial health. Unraveling this complex dialogue may open new avenues for treating diseases rooted in metabolic and microbial dysbiosis. On the basis of a wide-ranging literature survey, the frontiers of the molecular dialogues involved in the mitochondria-microbiome communications are evaluated. By analyzing publication trends, we identify nascent perspectives and transformative concepts, mapping the mitochondria-microbiome axis research, aiming to bridge the gap between basic science and translational applications. This synthesis offers a fresh lens for treating diseases rooted in this intricate biological interplay.}, }
@article {pmid42124590, year = {2026}, author = {Schell, LD and Liow, YJ and Carmody, RN}, title = {Fasting and re-feeding independently alter mouse gut microbiota during intermittent fasting.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.02.25.707984}, pmid = {42124590}, issn = {2692-8205}, abstract = {Intermittent fasting (IF) elicits metabolic benefits that are partially driven by the gut microbiome. Studies have focused on endpoint IF-induced changes in the gut microbiome but have not explored whether the oscillating nature of IF elicits day-to-day microbiome changes that could independently affect health. To discriminate the long-term and short-term effects of IF on the gut microbiota, we fasted mice every other day (IF1:1) or every two days (IF1:2), measuring daily changes in body mass and composition, food intake, and gut microbiota composition. We show that short-term effects of fasting and re-feeding on gut microbiota composition outweigh longer-term effects of IF treatment, with composition responding differently to re-feeding and fasting. Re-feeding specifically promoted rapid expansion of Lactobacillus , a bacterial genus linked mechanistically to the metabolic benefits of IF. Our results highlight the plasticity of the gut microbiota, especially re-feeding effects, as a potential contributor to microbiome-mediated metabolic benefits of IF.}, }
@article {pmid42124632, year = {2026}, author = {Adade, EE and Wang, R and Henneberry, CM and Lemus, AA and Stevick, RJ and Perez-Pascual, D and Audrain, B and Orsino, AJ and Farnsworth, DR and Ghigo, JM and Valm, AM}, title = {Cross hybridization Inference for Phylogenetic Resolution (CIPHR)-FISH enables microbiome imaging with strain level taxonomic resolution.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.02.26.708344}, pmid = {42124632}, issn = {2692-8205}, abstract = {The spatial organization of microbial communities is a critical determinant of host-microbe interactions, yet species-level mapping remains challenging due to high 16S rRNA sequence homology and spectral crosstalk in multiplexed fluorescence in situ hybridization (FISH). To address this challenge, we developed Cross-hybridization Inference for Phylogenetic Resolution (CIPHR)-FISH, a pipeline that integrates strategic probe design with supervised machine learning. CIPHR-FISH transforms probe cross-hybridization and spectral overlap, traditionally viewed as experimental noise, into informative molecular signatures. Using a gnotobiotic zebrafish model colonized with a defined mix of 10 zebrafish bacterial strains, we trained a support vector machine (SVM) on empirical hybridization patterns from pure bacterial cultures. CIPHR-FISH achieved 99.2 % macro-averaged accuracy, significantly outperforming standard linear unmixing (62.5 %), and successfully discriminated strains with 99.7% sequence homology. Applying this tool to gnotobiotic zebrafish larvae revealed distinct biogeographies: the intestinal bulb hosted highly structured, multi-layered polymicrobial aggregates, while the skin exhibited sparse, uniformly dispersed individual bacterial cells. Notably, we observed significant inter-individual variation in spatial community structure that was obscured by traditional bulk 16S rRNA sequencing. CIPHR-FISH provides a robust, scalable framework for high-resolution spatial biology by converting the limitations of molecular labeling into a rich data source for taxonomic classification. This approach enables the quantification of micro-scale ecological and stochastic forces that shape the microbiome across hosts.}, }
@article {pmid42124675, year = {2026}, author = {Badenoch, AJ and Pang, Z and Chung, CH and Robida, A and Badenoch, B and Natesan, R and Kakish, L and Li, J and Chandrasekaran, S}, title = {Modeling Microbiome Modulation of Tumor Metabolic Networks to Predict Synergistic Therapies.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.02.25.707963}, pmid = {42124675}, issn = {2692-8205}, abstract = {Differences in microbiome composition profoundly influence drug response, yet methods to model the metabolic interplay between tumors, microbes, and therapeutics remain limited. We present a generalizable framework combining machine-learning and genome-scale metabolic modeling to prioritize combination therapies for colorectal cancer (CRC) in the presence of Fusobacterium nucleatum (Fn) and other pathogenic, probiotic, and commensal microbes. Trained on 6,514 drug combinations in microbe-free CRC cell lines, the model predicted synergistic combinations in both microbe-free and microbe-associated contexts and generalized to immunotherapy-associated conditions. Predictions were validated using an asymmetric co-culture system that mimics the colon's normoxic-anaerobic gradient, confirming synergistic combinations in HCT116 cells with Fn , including drugs not typically used in CRC therapy. Mechanistic analysis and targeted pharmacological perturbations revealed phospho-inositol metabolism and cysteine transport as key determinants of Fn -dependent drug synergy. Together, this work introduces a scalable, microbiome-aware framework to enable discovery of context-specific combination therapies.}, }
@article {pmid42124729, year = {2026}, author = {Cho, B and Kostic, AD and Tierney, BT and Patel, CJ}, title = {The Oral Microbiome Is a Population-Scale Readout of the Exposome, Age, and Systemic Health.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.02.23.707541}, pmid = {42124729}, issn = {2692-8205}, abstract = {The oral microbiome interfaces humans and the environment and is implicated in diseases from caries to cardiovascular conditions. Yet, few studies systematically interrogate oral taxa associations with the host phenome and exposome in diverse populations. We developed a comprehensive oral microbiome atlas, deploying a Microbiome Association Study (MAS) evaluating relationships between host features including exposome, disease, and physiology and the microbiome in a 10,000-person representative US population. Evaluating demographics, 133 phenotypes, 473 exposures, and 20 disease outcomes across 1,349 taxa yielded >800k relationships and 45,757 FDR-significant associations. Age emerged as a major organizing axis, with genera following non-linear life-course patterns. Oral disease, smoking, and dietary sugar correlated with aciduric and anaerobic taxa, whereas oral health featured oxygen-tolerant Proteobacteria . The exposome and cardiovascular/respiratory disease linked to diverse taxa. These results establish the oral microbiome as a sensitive, population-scale indicator of the exposome, phenome, and systemic health.}, }
@article {pmid42125129, year = {2026}, author = {Khantsi, M and Babalola, OO}, title = {Influence of Cowpea Plants on Soil Bacterial Community and Soil Quality: Effects of the Rhizosphere.}, journal = {Plant-environment interactions (Hoboken, N.J.)}, volume = {7}, number = {}, pages = {e70157}, pmid = {42125129}, issn = {2575-6265}, abstract = {Cowpea (Vigna Unguiculata), a vital legume for suitable agriculture and food security in sub-Saharan Africa, plays a crucial role in improving soil health through intricate plant-microbe interactions in the rhizosphere. This review synthesizes current knowledge on the microbial interactions in the rhizosphere, focusing on soil health, microbial diversity, and their contributions to nutrient cycling and plant growth. Cowpea roots foster a diverse microbial consortium, including nitrogen-fixing rhizobia, phosphate-solubilizing bacteria and organic matter decomposers, which enhance soil fertility and structure. The microbial community in the cowpea rhizosphere is shaped by complex soil physiochemical properties, such as potential of hydrogen (pH), nutrient availability, and salinity, which significantly influence plant-microbe interactions. However, contradictions persist regarding pH's effect on microbial diversity, with unresolved questions about how specific environmental conditions regulate microbial taxa. Advanced techniques, including metagenomic analyses, have provided deeper insights into the taxonomic and functional composition of rhizosphere microbiomes, uncovering both abundant and rare microbial taxa involved in these processes. Despite these advancements, gaps remain in understanding the dynamic responses of microbial communities to environmental stresses. Bridging these gaps through integrative multi-omics approaches will enable the development of microbiome-informed strategies to improve cowpea productivity and promote sustainable agricultural practices, ensuring resilience in the face of climate variability.}, }
@article {pmid42125405, year = {2026}, author = {Li, Q and Li, Z and Zeng, G and Zhang, M and Wang, F and Chen, P and Yan, S}, title = {Geographical and seasonal variations of soil microbiomes and metabolomes in the core production area of Jiang-flavor Baijiu: a multi-omics characterization.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1816391}, pmid = {42125405}, issn = {1664-302X}, abstract = {The unique flavor of Chinese Jiang-flavor Baijiu is hypothesized to be influenced by the regional environment. However, the specific contributions of soil microbiomes and metabolomes remain poorly characterized. This study systematically analyzed soil phenotypes, microbiomes, and metabolomes at five sampling sites near the Moutai production area across spring and autumn. Using high-throughput sequencing, untargeted metabolomics, and multi-omics integration, we explored the impacts of geographical location and seasonal changes. Results revealed significant differences in soil microbial biomass, dominant taxa, and differential metabolites among sites. Region-specific marker microorganisms and metabolic pathways were identified. Seasonal variations, particularly in Region A, strongly affected metabolite profiles. Multi-omics correlation analysis revealed that Ascomycota abundance was positively associated with flavor precursor metabolites including phenylpropanoids, organosulfur compounds, and nucleosides, which are known precursors of aromatic compounds found in Baijiu. This study characterizes the distinct ecological profiles of soils in the core production area, providing a foundational dataset for understanding the regional environmental context of Jiang-flavor Baijiu. These findings offer insights for protecting the regional ecological integrity associated with production areas.}, }
@article {pmid42125496, year = {2026}, author = {Cho, MY and Eom, JH and Kim, JW and Kim, Y and Park, JA and Kim, HJ and Lee, JY and Han, HL and Ko, SJ and Her, SB and Ko, DY and Kim, HS and Baek, H}, title = {Oral microbiome profiles by periodontitis stage in a Korean population.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1809787}, pmid = {42125496}, issn = {2235-2988}, mesh = {Humans ; *Microbiota/genetics ; Male ; Female ; Middle Aged ; Cross-Sectional Studies ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; Adult ; *Periodontitis/microbiology ; Republic of Korea/epidemiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Pilot Projects ; *Mouth/microbiology ; DNA, Bacterial/genetics ; Dysbiosis/microbiology ; Biodiversity ; Aged ; }, abstract = {BACKGROUND: Periodontitis is a chronic inflammatory disease driven by oral microbial dysbiosis. Although the oral microbiome has been characterized in diverse populations, comprehensive profiling across periodontal disease stages defined by the 2018 AAP/EFP classification remains limited in Korean adults.<br><br>METHODS: In this pilot prospective cross-sectional study, oral microbiome profiles were characterized in 74 participants classified into three groups: healthy controls (n = 24), Stage I-II periodontitis (n = 12), and Stage III-IV periodontitis (n = 38). Mouthwash samples were collected and subjected to 16S rRNA gene sequencing of the V3-V4 hypervariable region. Alpha diversity, beta diversity (PERMANOVA with sequential covariate adjustment for age, sex, and smoking), differential abundance (MaAsLin2), and core microbiome analyses were performed.<br><br>RESULTS: Stage III-IV periodontitis was associated with significantly higher Shannon diversity, Simpson diversity, and Pielou's evenness compared to both healthy and Stage I-II groups, indicating increased evenness rather than species richness. Beta diversity analyses revealed significant community-level separation across groups after adjustment for demographic confounders (allp = 0.001). Differential abundance analysis identified 14 genera significantly associated with disease status. Twelve genera were enriched in Stage III-IV, including established periodontal pathogens Tannerella and Treponema, as well as emerging pathobionts Filifactor and Fretibacterium. Rothia and Kingella were enriched in periodontal health, consistent with their roles in nitrate reduction and maintenance of a health-compatible oral environment. Core microbiome analysis identified 40 universally present genera, with Anaeroglobus detected exclusively in Stage III-IV at 100% prevalence.<br><br>CONCLUSION: These findings support the polymicrobial synergy and dysbiosis model of periodontitis pathogenesis and provide a foundation for developing microbiome-based diagnostic tools for periodontal disease assessment in Korean populations.}, }
@article {pmid42125498, year = {2026}, author = {Huang, Y and Tang, Y and Huang, Y and Wang, Y}, title = {Commentary: Gut and oral microbiome profiles in patients with obesity and ischemic heart disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1834415}, pmid = {42125498}, issn = {2235-2988}, }
@article {pmid42125597, year = {2026}, author = {Pasaribu, B and Herawati, T and Purba, NP and Lewaru, MW and Sofyana, NT and Dilens, CVM and Dewanti, LP and Alina, DN and Agung, MUK}, title = {Shotgun metagenomic dataset of microbial communities in the water column of the Flores Sea, Indonesia.}, journal = {Data in brief}, volume = {66}, number = {}, pages = {112791}, pmid = {42125597}, issn = {2352-3409}, abstract = {The Flores Sea is a crucial component of the Indonesian Throughflow (ITF) pathway, which influences the transport of carbon, oxygen, and nutrients that support marine ecosystems. Here, we present the first dataset of microbial communities from the Flores Sea, Indonesia, generated using shotgun metagenomic sequencing of water column samples. Taxonomic analysis revealed that Proteobacteria (86%) was the most abundant phylum. In the dataset, the most abundant taxa identified through metagenomic analysis demonstrated Pseudoalteromonas lipolytica, Chromohalobacter salexigens, Marinobacter nauticus, Halopseudomonas aestusnigri, Pseudomonas mendocina, Flavobacterium beibuense, and Flavobacterium rakeshii, respectively. Functional annotation indicated that metabolism was major functional category in the microbial community. This metagenomic dataset provides valuable baseline information on microbial communities that may support future ocean monitoring and conservation strategies in the Flores Sea.}, }
@article {pmid42125670, year = {2026}, author = {Lim, JN and Oh, Y and Han, K and Mun, S and Lee, JY}, title = {Evaluation of digital colorimetric analysis as an objective indicator representing microbial diversity and biological succession of dental plaque.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2670840}, pmid = {42125670}, issn = {2000-2297}, abstract = {BACKGROUND: Visual assessment of dental plaque is limited by subjectivity and variability in imaging conditions.<br><br>OBJECTIVE: This study aimed to objectively quantify plaque maturation using CIE L*a*b*-based color difference (&#x394;E*) and evaluate its association with microbial community structure and pathogenicity.<br><br>DESIGN: Dental images were obtained from 30 participants after application of a plaque-disclosing agent. Plaque color was quantified as &#x394;E* relative to unstained tooth surfaces and classified into Low-&#x394;E* and High-&#x394;E* groups. Saliva and supragingival plaque samples from Low-&#x394;E* and High-&#x394;E* sites were collected, and full-length 16S rRNA gene sequencing was performed using the PacBio Sequel IIe platform.<br><br>RESULTS: Saliva showed significantly higher microbial diversity than plaque samples. The Low-&#x394;E* group was dominated by early colonizers, including Streptococcus sanguinis, whereas the High-&#x394;E* group showed enrichment of anaerobic and periodontal disease-associated taxa, including Prevotella, Treponema, Selenomonas, Campylobacter, and Porphyromonas endodontalis. The lightness value (L*) was negatively correlated with periodontal pathogens, including Treponema denticola and Tannerella forsythia. PICRUSt2 analysis indicated upregulation of inflammatory pathways, including NOD-like receptor signaling and apoptosis, in the High-&#x394;E* group.<br><br>CONCLUSIONS: &#x394;E*-based colorimetric analysis may serve as an objective indicator of dental plaque maturation and pathogenic potential, supporting personalized oral hygiene feedback.}, }
@article {pmid42125834, year = {2026}, author = {de Souza, LHN and da Silva, GF and Dos Santos Ferreira, MCA and Mello, PL and Ferreira, LEN}, title = {Candida albicans, HIV And Immune System in a Holobiont Perspective.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {134}, number = {5}, pages = {e70224}, doi = {10.1111/apm.70224}, pmid = {42125834}, issn = {1600-0463}, mesh = {Humans ; *Candida albicans/immunology/physiology/pathogenicity ; *HIV-1/immunology/physiology ; *HIV Infections/immunology/microbiology/virology ; Host-Pathogen Interactions/immunology ; CD4-Positive T-Lymphocytes/virology/immunology ; }, abstract = {Holobiont describes all types of relationships between hosts and their associated microbial communities, which can also attenuate the virulence of pathogens by the host microbiome. The cross-kingdom interactions between HIV, Candida albicans, and the human immune system have presented intriguing biological aspects. The human immunodeficiency 1 (HIV-1) virus is responsible for causing the acquired immune deficiency syndrome (AIDS) by infecting CD4[+] cells. HIV-1 internalization also depends on binding to coreceptors in the cell membrane, such as CCR5 and CXCR4. The expression of these chemokine receptors, as well as their ligands, can be modulated by the presence of Candida albicans PAMPs. Thus, this review discusses the inflammatory response mechanism activated by the commensal fungi Candida albicans that can modify the rate of immune cell infection by HIV-1. Despite the possibility of this crosstalk modulation, future research must validate the clinical significance of this holobiont interaction.}, }
@article {pmid42126047, year = {2026}, author = {Asszonyi, J}, title = {Wheat Dwarf Virus as a Modulator of Multi-Stress Responses in Wheat.}, journal = {Physiologia plantarum}, volume = {178}, number = {3}, pages = {e70931}, pmid = {42126047}, issn = {1399-3054}, support = {IGA26-AF-IP-010//Mendelova Univerzita v Brn&#x11b;/ ; QL24010142//Mendelova Univerzita v Brn&#x11b;/ ; }, mesh = {*Triticum/virology/physiology ; *Plant Diseases/virology ; *Stress, Physiological ; *Geminiviridae/physiology ; Plant Growth Regulators/metabolism ; }, abstract = {Wheat dwarf virus (WDV) is an emerging constraint to cereal production whose epidemiological significance has intensified under climate change. Rising temperatures, extended vector activity, and the expansion of Psammotettix alienus into new regions have increased both the frequency and severity of WDV outbreaks. Beyond its direct effects on plant development, WDV acts as a powerful regulator of host physiology, functioning as a host signalling hub that reprograms hormonal signalling, alters source-sink relationships, disrupts redox homeostasis, and modulates responses to both abiotic and biotic stress. Recent molecular studies have revealed how viral proteins manipulate the cell cycle, transcriptional machinery, and RNA silencing pathways to optimise viral replication while attenuating defence responses. These processes intersect with core stress-response networks, particularly those governed by abscisic acid, gibberellins, cytokinins, and auxin, positioning WDV as a model system for investigating hormonal crosstalk under combined stress. Despite advances in genomics, transcriptomics, and vector biology, major knowledge gaps persist regarding WDV interactions with co-occurring fungal pathogens, its impact on the plant microbiome, and its role in shaping cereal resilience under drought, heat, or nutrient limitations. This review synthesises current understanding of WDV biology from the molecular to the ecological scale, highlights mechanisms underpinning stress integration, and outlines future research priorities essential for developing sustainable management strategies in a changing climate.}, }
@article {pmid42126821, year = {2026}, author = {Prasad, A and Shuler, MS and Flanagan, R and Dayal, V and Lithander, FE}, title = {Dietary supplements for Parkinson's disease: State of the science.}, journal = {Journal of Parkinson's disease}, volume = {}, number = {}, pages = {1877718X261446386}, doi = {10.1177/1877718X261446386}, pmid = {42126821}, issn = {1877-718X}, abstract = {Parkinson's disease (PD) is the fastest growing neurological condition worldwide with its prevalence set to double by 2050. With no cure in sight, management has turned to lifestyle modification, in particular to diet and exercise. The disease-modifying potential of dietary approaches has been of recent interest, particularly given emerging links between diet and reductions in systemic inflammation, oxidative stress, and alterations in the gut microbiome composition, all of which may modulate neurodegeneration. This review summarises the current 'state of the science' of dietary supplements in modifying disease progression through a lens of the pathophysiological hallmarks of PD. Biomarkers and clinical outcomes that serve as proxy measurements for disease modification are examined, whilst looking ahead at which dietary supplements show the most promise and should be the focus of future research.}, }
@article {pmid42126887, year = {2026}, author = {Guo, Y and Li, J and Nishio, S and Hattori, H and Nochi, T and Matsuda, T and Toda, M}, title = {Long-term antibiotic treatment attenuates the development of food allergy in a murine model.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1093/bbb/zbag069}, pmid = {42126887}, issn = {1347-6947}, abstract = {While short-term antibiotic exposure has been reported to exacerbate the development of allergies, the effects of long-term administration remain less understood. This study addressed the influences of prolonged antibiotic administration in a murine model of food allergy. Mice received a broad-spectrum antibiotic cocktail (ABX) for six weeks from pre-sensitization through allergen challenge. ABX reduced allergic reactions, serum IgE levels, and intestinal mast cell counts. Production of Th2 cytokine, but not of Th1 and Th17 cytokines, was lowered in allergen-stimulated splenocytes of ABX-treated allergic mice, whereas the levels of these cytokines in their intestines decreased. ABX did not significantly alter the levels of regulatory cytokine IL-10 in intestines and regulatory T cells in spleens. ABX reduced gut bacterial amount, though Lactobacillus, Lactococcus, and Streptococcus remained detectable. Collectively, the long-term ABX suppresses allergic reaction by modulating Th2-mediated events dominantly, providing insights into the complex role of antibiotics in allergy models.}, }
@article {pmid42127027, year = {2026}, author = {Morikawa, Y and Kato, H and Umemura, T and Hirai, J and Shibata, Y and Hagihara, M and Asai, N and Mikamo, H and Iwamoto, T}, title = {Multicenter retrospective observational study on the clinical effectiveness of butyrate-producing Clostridium butyricum containing probiotics in patients with COVID-19.}, journal = {Virulence}, volume = {}, number = {}, pages = {2673650}, doi = {10.1080/21505594.2026.2673650}, pmid = {42127027}, issn = {2150-5608}, abstract = {Butyrate-producing bacteria, which are components of the gut microbiome, activate host defense mechanisms against several types of infections, including respiratory viral infections. However, the clinical effectiveness of butyrate-producing Clostridium butyricum (CB)-containing probiotics in patients with coronavirus disease 2019 (COVID-19) remains unclear. We investigated the in-hospital mortality, period of mechanical ventilation, and incidence of secondary bacterial pneumonia in patients with COVID-19 from 2020 to 2021. The patients were divided into the probiotic (27) and non-probiotic (256) groups. The two groups did not show a significant difference in the SOFA scores (probiotic vs. non-probiotic, 2.1 ± 2.3 vs. 2.1 ± 2.9). Additionally, all patients received antiviral agents to treat COVID-19; however, the two groups did not show significant difference in their distribution. However, patients receiving CB preparations showed the shorter periods of mechanical ventilation (1.1 ± 2.5 days vs. 3.9 ± 9.4 days). Although not statistically significant, they also showed lower incidence of secondary bacterial pneumonia (7.4% vs. 15.6%) and the lower in-hospital mortality (3.7% vs. 15.2%) compared to the non-probiotic group. This retrospective clinical study revealed that the administrations of CB preparations might attenuate clinical symptoms related to COVID-19 and improve mortality. However, further clinical and basic studies are required to validate our findings.}, }
@article {pmid42127284, year = {2026}, author = {He, M and Zhao, N}, title = {A mixed effect similarity matrix regression model (SMRmix) for integrating multiple microbiome datasets at the community level.}, journal = {Biometrics}, volume = {82}, number = {2}, pages = {}, doi = {10.1093/biomtc/ujag077}, pmid = {42127284}, issn = {1541-0420}, support = {R21AI154236/GF/NIH HHS/United States ; R01GM147162/GF/NIH HHS/United States ; U24OD023382/GF/NIH HHS/United States ; }, mesh = {Humans ; *Microbiota ; Computer Simulation ; Colorectal Neoplasms/microbiology ; Regression Analysis ; *Models, Statistical ; Dysbiosis/microbiology ; HIV Infections/microbiology ; Gastrointestinal Microbiome ; }, abstract = {Recent studies have highlighted the importance of the human microbiota in health and disease. However, in many areas of research, individual microbiome studies often provide inconsistent results due to limited sample sizes and the heterogeneity in study populations and experimental procedures. This inconsistency underscores the need for integrative analysis of multiple microbiome datasets. Despite the critical need, statistical methods that incorporate multiple microbiome datasets and account for study heterogeneity are not available in the literature. To address this, we propose a mixed effect similarity matrix regression (SMRmix) approach for identifying community-level microbiome shifts associated with outcomes. SMRmix has a close connection with the microbiome kernel association test, one of the most popular approaches for such a task, but it is only applicable when we have a single study. SMRmix enables researchers to consolidate findings from diverse microbiome studies. Through extensive simulations, we show that SMRmix maintains well-controlled Type I error rates and achieves higher power than competing methods. We further demonstrate its utility on two real-world datasets-17 HIV gut dysbiosis studies and 11 colorectal cancer studies-showing that SMRmix provides consistent results on community-level shifts in both applications.}, }
@article {pmid42127330, year = {2026}, author = {Weinberg, J and Crandall, WJ and Jarrell, ZR and Lim, G and Liu, K and Lee, HY and Patel, S and Gacasan, CA and Go, YM and Jones, DP}, title = {Structural Diversity and Analytical Characterization of Acylhomocarnitines.}, journal = {Journal of proteome research}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jproteome.5c01255}, pmid = {42127330}, issn = {1535-3907}, abstract = {Homocarnitine is a five-carbon analog of carnitine produced in mammals through hydroxylation of the microbiome-derived metabolite δ-valerobetaine. Here, we describe liquid chromatography-mass spectrometry methods for the measurement of fatty acyl-homocarnitines, a previously uncharacterized family of mammalian metabolites. These acyl-homocarnitines are homologs of acyl-carnitines, in which the fatty acid is extended by one carbon. We show that short-chain fatty acyl-CoAs are converted to corresponding acyl-homocarnitines by carnitine acetyltransferase and that these enzyme-generated standards exhibit retention times and ion dissociation patterns identical to acyl-homocarnitines produced by mammalian cells. In vitro [13]C3-homocarnitine isotope tracer studies showed that mammalian cells produce short-, medium-, and long-chain acyl-homocarnitines. Ion dissociation analyses established diagnostic product ions to distinguish acyl-homocarnitines from isomeric acyl-carnitines. Sample preparation and chromatographic methods are provided to separate and analyze isomers in extracts of mouse tissues. These findings expand knowledge of carnitine analogs and establish analytical strategies to differentiate acyl-homocarnitines from isomeric acyl-carnitines.}, }
@article {pmid42127415, year = {2026}, author = {Ge, M and Maeda, T and Li, J and De Mares, MC and Kifaro, EG and Gidamo, GH and Shiroguchi, K and Moeller, AH and Zhang, Z and Jin, J}, title = {Standardized and batch effect-independent technologies enable global collaboration in microbiome research.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag122}, pmid = {42127415}, issn = {1751-7370}, }
@article {pmid42127418, year = {2026}, author = {Parizadeh, M and Laforest-Lapointe, I and Serrano-Vázquez, A and Morán-Silva, P and Rojas-Velázquez, L and Torres, J and Ximénez-García, C and Arrieta, MC}, title = {Impact of Maternal, Infant, and Household Factors on Early-life Gut Microbiome Development in a Rural Setting.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag124}, pmid = {42127418}, issn = {1751-7370}, abstract = {Early-life gut microbiome development is influenced by host, microbial, environmental, and social factors. Rural infants typically exhibit greater microbial diversity than their urban counterparts, yet microbiome maturation patterns in less industrialized settings remain underexplored. Additionally, though microbial eukaryotes are integral to gut ecology, most studies to date have focused predominantly on bacterial communities. Using shallow shotgun metagenomics and 18S rRNA gene sequencing, we characterized eukaryotic and bacterial gut microbiomes in an intensively sampled longitudinal cohort of ten infants from a rural community in Morelos, Mexico, each followed monthly from the first to the 18th month, providing an unusually detailed view of early-life microbiome development in a low-resource setting. Although both bacterial and eukaryotic alpha diversity increased over time, they showed distinct colonization trajectories. Age, delivery mode, and environmental exposures, such as animal contact and household factors, influenced bacterial and eukaryotic community compositions, as well as bacterial metabolic composition. Inter-kingdom microbial networks varied with age, with a reduction in taxonomic diversity after the first year of life. Age and mode of birth also influenced changes in the overall community structure and connectivity of microbial co-occurrence patterns, but did not impact the associations among specific microbial taxa. Functional profiling revealed that bacterial metabolic potential diversified with age, whereas the mode of birth had a minimal impact on functional variation. These findings highlight the dynamic nature of bacterial and eukaryotic microbiota in early life and underscore the need to explore how rural environmental exposures shape microbial maturation, with potential implications for immune development and long-term health.}, }
@article {pmid42127598, year = {2026}, author = {Wang, X and Duan, Y and Wang, H and Zhao, R and Wang, F and Tang, T and Wang, Q and You, J}, title = {Fritillaria hupehensis cultivated under the canopy of Magnolia officinalis demonstrated superior anti-inflammatory and expectorant effects.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {156}, number = {}, pages = {158261}, doi = {10.1016/j.phymed.2026.158261}, pmid = {42127598}, issn = {1618-095X}, abstract = {BACKGROUND: Fritillaria hupehensis is a medicinal plant used for treating cough and inflammation. Its cultivation under the canopy of Magnolia officinalis (U-F. hupehensis) increases alkaloid content compared to traditionally field-grown cultivation (T-F. hupehensis).<br><br>PURPOSE: This study aims to evaluate the superior therapeutic efficacy of U-F. hupehensis against cough and inflammation and to elucidate the role of its rhizosphere bacterial community in enhancing the accumulatio of key bioactive compounds.<br><br>METHODS: The anti-inflammatory and expectorant efficacy of U-F. hupehensis was evaluated in animal models (ammonia-induced cough, phenol red excretion, and LPS-induced bronchitis). Network pharmacology and cellular experiments identified the key bioactive compounds. Soil physicochemical properties and 16S rRNA sequencing were used to analyze the rhizosphere bacterial community. The relationship between the rhizosphere microbiome and bioactive compound accumulation was analyzed using structural equation modeling.<br><br>RESULTS: U-F. hupehensis exhibited significantly stronger anti-inflammatory and expectorant effects than T-F. hupehensis. Hupehenine, peimine, and sipeimine were validated as the primary active components responsible for this enhanced efficacy. Understory cultivation increased rhizosphere microbial diversity. A specific keystone microbial module (Module 1) was identified and shown to directly mediate the accumulation of the bioactive compounds.<br><br>CONCLUSION: The superior anti-inflammatory and expectorant efficacy of understory-cultivated F. hupehensis is driven by a marked increase in the key bioactive alkaloids (hupehenine, peimine, and sipeimine). Our study identifies a specific rhizosphere microbial community as the pivotal mediator of this enhanced alkaloid accumulation. These results provide a pharmacologically relevant mechanism that explains the differential therapeutic potential of F. hupehensis from distinct cultivation sources.}, }
@article {pmid42127772, year = {2026}, author = {Dejong, T and Bhatt, K and Rodrigues, A and Massenet, T and Lievens, S and Focant, JF and Stefanuto, PH}, title = {Comparative development of volatile-oriented multi-SPME and derivatisation-based GC×GC-TOFMS workflows for non-targeted faecal metabolomics.}, journal = {Talanta}, volume = {308}, number = {}, pages = {129954}, doi = {10.1016/j.talanta.2026.129954}, pmid = {42127772}, issn = {1873-3573}, abstract = {Gas chromatography-mass spectrometry (GC-MS) remains a key technique in metabolomics, yet most workflows rely on chemical derivatisation to enable the analysis of non-volatile metabolites. Although derivatisation broadens metabolite coverage, it increases sample preparation time and may introduce additional analytical variabilities. In contrast, solid-phase microextraction (SPME) enables rapid, solvent-free sampling of volatile and semi-volatile compounds, representing an attractive alternative for non-targeted studies. However, methodological developments integrating SPME with comprehensive two-dimensional gas chromatography (GC × GC-MS) remain limited. In this study, a simultaneous multi-SPME GC × GC-TOFMS workflow was developed for the non-targeted screening of faecal samples. Three identical fibres were used simultaneously to generate technical replicates from a single biological sample resulting strong performances in terms of relative standard deviation (10%). Dedicated fibre storage containers and optimised storage conditions were also developed to preserve analyte stability between sampling and injection. In parallel, commonly used GC × GC column configurations were evaluated. The optimised workflow was applied to stool reference materials generated within an interlaboratory metabolomics study coordinated by the National Institute of Standards and Technology (NIST), investigating the effects of diet (vegan vs. omnivore) and sample preservation (aqueous vs. lyophilised) to develop the more adequate stool reference material. SPME results were compared with derivatisation-based metabolomic and lipidomic workflows. Multivariate analysis revealed clear discrimination between diets and storage conditions, while data-fusion analysis highlighted the complementary nature of volatile, metabolomic, and lipidomic profiles. This work provides practical guidance for developing robust GC × GC-MS workflows for complex biological matrices, highlighting the need of multi-extraction approaches for comprehensive analytical coverage.}, }
@article {pmid42127813, year = {2026}, author = {De Sordi, L}, title = {Making room for gut prophages in human health.}, journal = {Cell host &amp; microbe}, volume = {34}, number = {5}, pages = {766-769}, doi = {10.1016/j.chom.2026.03.018}, pmid = {42127813}, issn = {1934-6069}, mesh = {Humans ; *Prophages/physiology/genetics ; *Gastrointestinal Microbiome/physiology ; *Bacteria/virology/genetics ; *Host Microbial Interactions ; *Gastrointestinal Tract/microbiology/virology ; }, abstract = {Prophages are pervasive in the human gut yet largely overlooked in microbiome research, despite substantial functional potential. Emerging evidence indicates that prophages regulate bacterial fitness, community structure, and microbe-host interactions. Here, I argue that integrating prophage biology is important to understand microbiota-driven functions in human health and disease.}, }
@article {pmid42127814, year = {2026}, author = {Jin, Y and Zhao, J and Zuo, T}, title = {Potential impacts of antivirals on the virome.}, journal = {Cell host &amp; microbe}, volume = {34}, number = {5}, pages = {770-774}, doi = {10.1016/j.chom.2026.04.005}, pmid = {42127814}, issn = {1934-6069}, mesh = {*Antiviral Agents/pharmacology/therapeutic use ; *Virome/drug effects ; Humans ; Animals ; *Virus Diseases/drug therapy/virology ; *Microbiota/drug effects ; *Viruses/drug effects ; Gastrointestinal Microbiome/drug effects ; }, abstract = {The use of antivirals has transformed viral infection management and reduced mortality. However, the effect of antivirals on the commensal virome, a crucial player in microbiome homeostasis and mammalian health, is largely unclear. This Forum delves into this nascent area and discusses the potential impacts of antivirals on the virome.}, }
@article {pmid42127816, year = {2026}, author = {Che, Y and Kong, HH}, title = {The human skin virome: Ecological dynamics, aberrant profiles, and therapeutic opportunities.}, journal = {Cell host &amp; microbe}, volume = {34}, number = {5}, pages = {790-807}, doi = {10.1016/j.chom.2026.04.008}, pmid = {42127816}, issn = {1934-6069}, mesh = {Humans ; *Virome ; *Skin/virology/microbiology/immunology ; Microbiota ; Bacteriophages/physiology ; Bacteria/virology ; *Viruses/classification/genetics/isolation &amp; purification ; Immunity, Innate ; Adaptive Immunity ; }, abstract = {Human skin harbors a complex microbial ecosystem in which viruses, including eukaryotic viruses, bacteriophages, and endogenous retroviruses, are integral yet comparatively understudied. Shaped by host physiology, genetics, and environmental exposures across the lifespan, the cutaneous virome interacts closely with resident bacteria, fungi, and immune cells. In this review, we synthesize current knowledge of virome composition, biogeography, and dynamics, with an emphasis on how bacteriophages influence bacterial ecology, gene flow, and antimicrobial resistance on the skin. We further discuss how human-tropic viruses engage innate and adaptive immunity to support homeostasis while also contributing to inflammatory, infectious, and neoplastic skin diseases. Finally, we highlight methodological advances and persisting technical challenges in virome detection and functional annotation, and we outline emerging translational opportunities, including bacteriophage-based therapeutics, microbiome-targeted interventions, and immunomodulatory strategies.}, }
@article {pmid42127821, year = {2026}, author = {Li, XT and Feng, J}, title = {Diversity recruits resilience via metabolite signaling.}, journal = {Cell host &amp; microbe}, volume = {34}, number = {5}, pages = {820-822}, doi = {10.1016/j.chom.2026.03.022}, pmid = {42127821}, issn = {1934-6069}, mesh = {*Microbiota ; *Signal Transduction ; Rhizosphere ; *Glycine max/microbiology/physiology/metabolism ; Stress, Physiological ; Droughts ; Soil Microbiology ; Plant Roots/microbiology ; Biodiversity ; Adaptation, Physiological ; }, abstract = {The rhizosphere microbiome drives plant stress resilience. In this issue of Cell Host &amp; Microbe, Chen et al. show that microbial diversity programs drought adaptation in soybeans by linking community complexity to host metabolism and microbiome assembly, with outcomes shaped by diversity-dependent metabolite signaling and selective recruitment of beneficial taxa.}, }
@article {pmid42127855, year = {2026}, author = {Mei, Z and Zhou, H and Liu, K and Gao, C and Du, H and Sheng, Z and Gong, Y}, title = {Traditional Chinese medicine improves performance and intestinal health in laying hens under acute and chronic heat stress by modulating ileal metabolic functions.}, journal = {Poultry science}, volume = {105}, number = {8}, pages = {107056}, doi = {10.1016/j.psj.2026.107056}, pmid = {42127855}, issn = {1525-3171}, abstract = {Heat stress (HS) represents a significant challenge in poultry production, impairing thermoregulation, intestinal function, and productive performance. This study utilized acute (6 h) and chronic (14 d) HS models at 36°C in laying hens to characterize stage-dependent responses and evaluate the protective effects of a ten-ingredient traditional Chinese medicine (TCM) formulation. Both acute and chronic HS significantly increased rectal temperature and respiratory rate. Egg production declined by approximately 18% following acute HS and was further compromised under chronic exposure, along with reduced eggshell strength and weight. Dietary TCM supplementation (0.5%) alleviated physiological stress and partially restored laying performance, with more pronounced recovery observed under chronic HS. Serum analysis and histopathology indicated that TCM attenuated HS-induced impairment of ileal barrier function. Metabolomic profiling revealed stage-dependent responses: acute HS primarily disturbed redox balance, whereas chronic HS induced broader remodeling related to energy and nutrient utilization. TCM supplementation modulated metabolic functions to support immediate stress buffering under acute HS while stabilizing long-term energy support and intestinal capacity under chronic HS. Metagenomic analysis indicated that TCM selectively promoted microbial groups related to intestinal metabolism and nutrient utilization, aligning with metabolomic findings. Correlation analyses linked these TCM-associated microbial and metabolic signatures with improved thermoregulatory responses, oxidative status, and intestinal barrier indicators. Collectively, these results demonstrate that TCM supplementation enhances heat resilience in laying hens through stage-dependent modulation of the gut microbiota-metabolome axis, supporting its application as a nutritional strategy to maintain productivity under thermal challenge.}, }
@article {pmid41959837, year = {2026}, author = {Irajizad, E and Fahrmann, JF and Katayama, H and Strati, P and Nair, R and Chihara, D and Ahmed, S and Iyer, SP and Locke, FL and Davila, M and Flowers, CR and Shpall, E and Jenq, R and Neelapu, SS and Hanash, S and Westin, J and Jain, MD and John, TM and Saini, NY}, title = {Pre-infusion plasma proteomics identifies an endothelial-immune priming signature predictive of severe cytokine release syndrome and neurotoxicity following CAR T-cell therapy in relapsed/refractory lymphoma.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.29.26349664}, pmid = {41959837}, abstract = {BACKGROUND: Severe cytokine release syndrome (CRS) and immune effector cell-associated neurotoxicity syndrome (ICANS) remain frequent, life-threatening complications of CD19 chimeric antigen receptor (CAR) T-cell therapy and constrain its safety, scalability, and outpatient adoption. Existing predictive models lack sufficient external validation for routine clinical use, and pre-infusion biomarkers that capture host susceptibility before infusion are urgently needed.<br><br>METHODS: We applied unbiased mass-spectrometry-based proteomics to pre-infusion biofluids from 98 prospectively-followed adults with relapsed/refractory (r/r) lymphoma at two academic centers (MD Anderson Cancer Center, n = 39, plasma; Moffitt Cancer Center, n = 59, serum). Logistic regression with backward feature selection on the MD Anderson cohort yielded panels for severe (Grade &#x2265; 2) CRS and ICANS that were locked and tested without refitting on the Moffitt cohort. Patients were stratified into low-, intermediate-, and high-risk tertiles. Ingenuity Pathway Analysis defined upstream regulators and canonical pathways. The 17 CRS-associated and 21 ICANS-associated consensus proteins were classified into mechanistic themes for biological interpretation.<br><br>RESULTS: A 5-marker CRS panel (SCRIB, MYL6, MTHFD1L, HSP90B1, MMP2) achieved AUCs of 0.85 (95% CI 0.72-0.98) and 0.76 (0.63-0.89) in the discovery and validation cohorts, respectively. An expanded 8-marker ICANS panel (the CRS panel plus SPOCK2, SLC3A2, CD84) achieved AUCs of 0.91 (0.81-1.00) and 0.67 (0.51-0.84). In the combined dataset, high-risk-tertile patients were 13.84-fold (95% CI 4.21-56.26) and 8.59-fold (2.87-29.09) more likely to develop Grade &#x2265; 2 CRS and ICANS, respectively. Pathway analysis converged on AKT-driven inflammation and endothelial activation. Functional clustering of the consensus proteins partitioned into mechanistically coherent themes consistent with a dual-anatomy model: severe CRS reflected peripheral macrophage priming and endothelial activation with surplus complement amplification (HSP90B1&#x25b4;, CSF1&#x25b4;, MMP2&#x25b4;, HEG1&#x25b4;, C3&#x25b4;) and endotheliopathic coagulation (PROC&#x25be;, F7&#x25be;), whereas severe ICANS reflected cerebrovascular junction and basement-membrane stripping (CDH5&#x25be;, ITGB1&#x25be;, FN1&#x25be;, brain-enriched SPOCK2&#x25be;), hepatic synthetic suppression (TTR&#x25be;, APOA2&#x25be;, IGFBP3&#x25be;), compromised plasma antioxidant capacity (GPX3&#x25be;, PON1&#x25be;), and inflammasome dis-restraint via DPP9&#x25be;. PGLYRP2 and SCRIB depletion were shared by both signatures and identified a common upstream priming substrate.<br><br>CONCLUSIONS: Externally validated, pre-infusion proteomic panels predict severe CRS and ICANS following CAR T-cell therapy and define a coherent pre-infusion endothelial-immune priming axis (HSP90B1, MMP2, AKT) with mechanistically interpretable, druggable nodes. The dual-anatomy framework distinguishes peripheral CRS-biased from cerebrovascular ICANS-biased phenotypes downstream of a shared microbiome-host barrier priming substrate, providing a foundation for biomarker-guided risk stratification and cluster-matched prophylactic intervention to enhance the safety and outpatient feasibility of CAR T-cell therapy.}, }
@article {pmid42112445, year = {2026}, author = {Furuya, R and Nishikawa, Y and Ota, Y and Prah, I and Mahazu, S and Kifushi, M and Yoshida, M and Suzuki, M and Hoshino, Y and Suzuki, T and Takeyama, H and Ablordey, A and Saito, R}, title = {Single-cell genomic profiling of antimicrobial resistance in Escherichia coli from the Densu River, Ghana.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1797725}, pmid = {42112445}, issn = {1664-302X}, abstract = {INTRODUCTION: River water serves as a natural reservoir for antimicrobial resistance (AMR) factors. Although environmental AMR poses a global threat to public health as it spreads to local communities through the microbiome in aquatic environments, the actual situation remains unclear, especially in developing countries. In this study, we sought microbiome data, including AMR information, for multiple bacterial strains from river water samples using a single-cell genomics platform.<br><br>METHODS AND RESULTS: After antimicrobial selection of samples from the Densu River in Ghana, 16S rRNA amplicon sequencing revealed a high proportion of the genus Escherichia-Shigella with ampicillin and sulbactam selection. Single-cell genomic analysis revealed differences in AMR and virulence factor profiles among the same species of Escherichia coli, including the CTX-M-15 extended-spectrum &#x3b2;-lactamase-producing ones. Pan-genome analysis predicted 4,814 gene clusters, of which 2,264 were accessory, including 605 singletons. Phylogenetic tree analysis using the maximum likelihood method showed the heterogeneity of single-cell amplified genomes (SAGs), and cluster of orthologous gene analysis for each SAG confirmed the difference in the ratio of each functional group.<br><br>CONCLUSION: This study demonstrates the potential of single-cell genomics using the single-cell amplified genome in gel method to enhance environmental AMR surveillance with high resolution and accuracy. It also represents the first application of this approach to aquatic environments in Ghana, thereby contributing to the development of microbial ecology and genomic resources.}, }
@article {pmid42112609, year = {2026}, author = {Cao, Y and Xu, H and Xu, C and Zu, M and Sun, J and Xiong, D and Ye, J and Han, K and Gao, Q and Shi, X and Li, L and Li, B and Shahbazi, MA and Cribbs, AP and Chai, J and Reis, RL and Kundu, SC and Liu, Y and Nie, G and Xiao, B}, title = {Zwitterionic Lipid Nanotherapeutics from Mulberry for Oral Treatment of Diabetic Colitis.}, journal = {ACS nano}, volume = {}, number = {}, pages = {}, doi = {10.1021/acsnano.5c17183}, pmid = {42112609}, issn = {1936-086X}, abstract = {Diabetic colitis is a severe gastrointestinal complication of type 2 diabetes, which presents the key pathophysiological hallmarks of hyperglycemia, intestinal barrier disruption, immune dysregulation, and microbial metabolic imbalance, posing significant therapeutic challenges in clinical practice. Here, we leveraged artificial intelligence to identify the therapeutic potential of 1-deoxynojirimycin (DNJ) for addressing diabetic colitis. To improve its bioavailability and efficacy, we developed a mulberry-derived nanotherapeutic with surface functionalization of zwitterionic polymer (PpC) for DNJ encapsulation. Following oral administration, the resultant nanotherapeutics, PpC@DNJ-LNPs, efficiently traversed the gastrointestinal tract, enabling controlled DNJ release while inhibiting the α-glucosidase activity to regulate glucose homeostasis. Concurrently, they orchestrated colonic mucosa-microbiome interaction, promoting intestinal immune balance and microbiota remodeling. These synergistic effects collectively confer hypoglycemic, anti-inflammatory, antioxidant, and epithelial barrier-restoring effects, ultimately reshaping the glucose level and intestinal microecology. Our study demonstrates the translational potential of PpC@DNJ-LNPs as a safe and effective oral therapeutic platform for diabetic colitis.}, }
@article {pmid42112774, year = {2026}, author = {Jourdain, L and Rossi, P and Charpagne, A and Chevalier, E and Praz, V and Marquis, J and Weber, J and Gu, W}, title = {A Scalable and Cost-Effective In-Line Barcoding Strategy for Standardized 16S rRNA Gene Amplicon Sequencing: Performance Evaluation and Bias Assessment.}, journal = {Molecular ecology resources}, volume = {26}, number = {4}, pages = {e70138}, pmid = {42112774}, issn = {1755-0998}, support = {200021_219222//Swiss National Science Fundation (SNF)/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *DNA Barcoding, Taxonomic/methods/economics ; *Bacteria/genetics/classification ; *Archaea/genetics/classification ; DNA Primers/genetics ; Cost-Benefit Analysis ; High-Throughput Nucleotide Sequencing/methods ; DNA, Bacterial/genetics/chemistry ; Sequence Analysis, DNA/methods ; }, abstract = {In-line barcoding offers a streamlined and scalable alternative to two-step PCR library preparation for 16S rRNA gene amplicon sequencing, enabling cost-effective, high-throughput profiling of microbial communities. Here, we tested 136 and 156 in-line barcoded primer pairs for bacterial and archaeal communities for their performance across environmental samples and a mock standard community. The primers were designed by combining widely used universal 16S rRNA gene primers with existing barcode sets from Illumina kits. The designed primer pairs produced efficient and consistent amplification with minimal dropout and no systematic taxonomic bias. Through clustering and performance-based filtering, we selected final sets of 96 pairs for both bacterial and archaeal communities that work efficiently and well together for direct further use. This in-line tagging strategy is easy to adopt with fewer processing steps and PCR-associated artefacts, allows straightforward sample tracking, and supports reliable large-scale microbiome studies. We also present a framework for evaluating barcode- or primer-induced biases. More broadly, the proposed in-line barcoding strategy can be adapted to any amplicon-sequencing application, as well as targeted sequencing, highlighting its relevance beyond 16S rRNA gene surveys. All validation datasets, open-source processing scripts, and barcode design resources are provided to promote reproducibility and community-wide adoption.}, }
@article {pmid42112809, year = {2026}, author = {Coates, LC and Storms, DH and Spearman, SS and Shahab-Ferdows, S and Christensen, SH and Lewis, JI and Mølgaard, C and Michaelsen, KF and Allen, LH and Lemay, DG and Kable, ME}, title = {Stool microbial composition is associated with recent and future diarrhea and fever events in breastfed Danish infants.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0013426}, doi = {10.1128/msystems.00134-26}, pmid = {42112809}, issn = {2379-5077}, abstract = {UNLABELLED: Gastroenteritis is an important cause of ailment among infants in high-income countries, including Denmark. There are many cases of diarrhea among Danish children for which no etiological agent is detected. This study investigated the associations between gastroenteritis-related morbidities (diarrhea, fever, and vomiting) and gut microbial community in well-nourished, breastfeeding Danish infants. Infant stool samples, morbidity questionnaires, and diet/breastfeeding questionnaires were collected at three time points during the first 8.5 months of life. The V4-V5 region of the 16S rRNA gene was amplified from stool DNA extracts, sequenced with Illumina MiSeq, and analyzed using QIIME2. PERMANOVA, linear mixed-effects modeling, and ANCOM-BC2 were used to identify associations between infant gut microbiome and gastroenteritis-related morbidities across all visits. Logistic regression and random forest models were employed to determine whether early gut microbial alpha diversity or abundance, respectively, could predict morbidity later in infancy. Alpha diversity was negatively associated with diarrhea. Granulicatella abundance was positively associated with diarrhea. From 3.5 to 6 months of age, Bacteroidales abundance was negatively associated with fever. Faith's phylogenetic diversity, Staphylococcales abundance, and Haemophilus abundance during 3.5 months of life were positively associated with future diarrhea during ages 3.5-8.5 months. Pielou's evenness and Actinobacteriota abundance within 3.5 months of life had negative and positive associations, respectively, with fever during ages 3.5-8.5 months. This study reveals diarrhea is associated with stool Granulicatella in well-nourished, breastfeeding Danish infants, as it is in children from low-income countries, and that the early gut microbiome may contribute to risks of diarrhea and fever morbidities later in infancy.CLINICAL TRIALSThis trial was registered at ClinicalTrials.gov as NCT03254329.<br><br>IMPORTANCE: Gastroenteritis continues to cause much morbidity among infants in high-income countries, and the relationship with the gut microbiome is not fully understood, especially for well-nourished and breastfeeding infants. In the study presented here, infant stool Staphylococcales abundance (comprised of Staphylococcus and Gemella) and Haemophilus abundance during the first few months of life were positively associated with later diarrhea in well-nourished and breastfeeding Danish infants. Meanwhile, the abundance of Granulicatella (a facultative anaerobe with pathogenic potential) was greater in stool from infants who had recent diarrhea, suggesting further research is needed to determine its possible role in diarrhea and recovery from diarrhea. Fever usually did not co-occur with diarrhea or vomiting. Early life Actinobacteriota abundance was positively associated with later fever. This phylum was represented here by both pathobionts (Actinomyces) and mutualists (bifidobacteria), which may have contributed to fever differently-pathobionts through infection and mutualists through promotion of effective immune response to infection.}, }
@article {pmid42112827, year = {2026}, author = {Cao, TTT and Herckes, P and Straub, D and Sarkar, S and Garcia-Pichel, F}, title = {Growth and formaldehyde degradation of photoheterotrophic Methylobacterium within radiation fogs.}, journal = {mBio}, volume = {}, number = {}, pages = {e0046326}, doi = {10.1128/mbio.00463-26}, pmid = {42112827}, issn = {2150-7511}, abstract = {UNLABELLED: The atmosphere contains thousands to millions of bacterial cells per cubic meter. However, it remains unclear if microbes are at all active or growing in situ or whether they are merely being transported in an inactive state. Based on the analyses of 32 overland radiation fog events over a 2-year period, we show that fog waters, with bacterial concentrations similar to those in continental or marine bodies of water, contain microbiomes well differentiated in composition from those in the dry aerosol microbiomes that occur locally before, during, or after fog events. They are consistently and strongly enriched in photoheterotrophic Methylobacterium species, suggesting that fog populations may be metabolizing volatile C1 compounds in situ, although phototrophy seems much less important. Indeed, metabolically active bacteria in the fog, and representative isolates of the main field populations, can degrade formaldehyde at unprecedently high rates; most of this activity seems to play a detoxification role. The increase in bacterial aerobiome counts upon intervening fog events, the dependence of microbial concentration on ambient temperature, the increases in cell size and frequency of dividing cells in fog water with respect to cells in interstitial aerosols of fogs, in addition to their metabolic capacity, all suggest that the fog water microbiome is actually growing. Consequently, droplets of atmospheric water should be considered a potential aquatic microhabitat. Our results highlight the fog microbiome's role in atmospheric chemistry and have implications for fog harvesting as a source of fresh water for human use.<br><br>IMPORTANCE: While bacteria are common in the atmosphere, their activity in situ has remained unclear. Using stagnant radiation fogs as new study systems where sampling is optimal, the dynamics, composition, cellular characteristics, and metabolic rates of fog water microbiomes, dominated by Methylobacterium sp., show that they are a hub of active detoxification of atmospheric formaldehyde and likely growing in situ on the basis of heterotrophic or photoheterotrophic metabolism of volatile C1 compounds, with implications for atmospheric chemistry and fog harvesting as sources of freshwater.}, }
@article {pmid42112889, year = {2026}, author = {Amechatte, G and Radouane, N and El Mouttaqi, A and Licastro, D and Hirich, A and Mohamed, H and Ahmed, B}, title = {Deterministic abiotic filtering and halophilic core microbiomes shape bacterial community assembly in coastal salt flats (sabkha) of southern Morocco.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0006126}, doi = {10.1128/aem.00061-26}, pmid = {42112889}, issn = {1098-5336}, abstract = {Coastal salt flats, locally known as sabkhas, are hypersaline, alkaline desert ecosystems that impose extreme abiotic stress on microbial and plant life. Despite their ecological significance, plant-associated microbiomes in these habitats remain poorly characterized. In this study, we investigated the bacterial communities of native halophytes across three sabkha sites in southern Morocco using an integrated culture-independent and culture-dependent framework. Soil physicochemical analyses revealed strong gradients in salinity and ionic composition, along with consistent alkaline pH across sites. These conditions strongly structured bacterial assemblage: alpha diversity declined progressively from bulk soil to rhizosphere soil, root, and shoot; and beta diversity showed clear compartmental separation driven by environmental factors. Canonical correspondence analysis identified electrical conductivity (EC), Na2O, K2O, and carbonate fractions as the main abiotic drivers. Across plant species, bacterial communities converged toward a stable halophilic core microbiome dominated by Halomonas, Kushneria, and Marinococcus, with 66% of amplicon sequencing variants (ASVs) shared across compartments. Host identity played a secondary role as environmental filtering overshadowed host-specific associations. Culture-dependent isolation recovered 19 halophilic and halotolerant bacterial strains, including representatives of Halomonas, Idiomarina, Marinobacter, Psychrobacter, Planomicrobium, and Bacillus. These isolates exhibited robust growth on saline Marine Agar medium, indicating strong salt tolerance consistent with their occurrence in hypersaline environments. The strong concordance between cultured isolates and metabarcoding profile confirms that dominant halophilic lineages are both ecologically robust and readily culturable. Together, these findings demonstrate that sabkha plant microbiomes are primarily shaped by deterministic abiotic filtering and harbor resilient, stress-adapted bacterial communities. Sabkhas thus represent promising reservoirs of halophilic microbes with potential applications in saline agriculture and improving crop resilience under extreme environmental conditions.IMPORTANCECoastal salt flats (sabkhas) are among the most extreme terrestrial environments, characterized by high salinity, alkalinity, and limited water availability. As soil salinization expands worldwide, understanding how life persists in such habitats is increasingly important for sustainable agriculture. This study shows that sabkha ecosystems impose strong environmental filtering on plant-associated bacterial communities, leading to highly structured microbiomes across soil, root, and shoot compartments. Despite differences among sites and plant species, bacterial communities converged toward a shared halophilic core microbiome, dominated by salt-adapted genera that are resilient to extreme ionic stress. Importantly, many of these dominant bacteria were readily culturable, highlighting sabkhas as accessible reservoirs of stress-tolerant microbes. Our findings demonstrate that abiotic conditions outweigh plant identity in shaping microbiome assembly under extreme stress and reveal sabkha halophytes as valuable natural models for discovering microbes with potential applications in saline agriculture, soil restoration, and crop resilience in salt-affected environments.}, }
@article {pmid42112933, year = {2026}, author = {Gee, M and Sharp, C}, title = {Bacterial weaponry and the ecological factors of competitive success.}, journal = {Essays in biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1042/EBC20250028}, pmid = {42112933}, issn = {1744-1358}, support = {N/A//University of Reading (UoR)/ ; }, abstract = {Bacteria have evolved complex protein systems known as bacterial weapons to inhibit or kill their competitors. These bacterial weapons are a remarkably diverse arsenal that influence the composition and function of important microbial communities such as the human microbiome. In turn, the spatial constraints, nutrient availability, environmental stressors, and the presence of competitors determine not only whether weapons are expressed, but which weapons provide the greatest advantage. While bacterial weaponry is widespread, the types, mechanisms, and abundance of these systems vary between, and even within, species. Recent research has highlighted the importance of bacterial weaponry in community invasion and pathogenicity. Their potency and narrow killing spectrum have also generated interest in exploiting bacterial weapons to engineer microbial communities or develop therapeutics that avoid the disruption of broad-spectrum antibiotics. Understanding how ecological context affects weapon efficacy could reveal new virulence mechanisms used by pathogens and inform the design of novel treatments and microbiome-based therapies. This review outlines three of the best-studied bacterial weapon systems (protein bacteriocins, the type VI secretion system, and contact-dependent inhibition), highlighting their roles in microbial ecology, pathogenicity and their potential as therapeutics.}, }
@article {pmid42113072, year = {2026}, author = {Csikó, G and Palócz, O and Várhidi, Z and Sátorhelyi, P and Erdélyi, B and Jurkovich, V}, title = {Evaluation of the local tolerance and systemic safety of a novel intravaginal probiotic product in cows.}, journal = {Veterinary research communications}, volume = {50}, number = {4}, pages = {}, pmid = {42113072}, issn = {1573-7446}, mesh = {Animals ; *Probiotics/administration &amp; dosage/adverse effects ; Female ; Cattle ; Administration, Intravaginal ; Vagina/microbiology/drug effects ; }, abstract = {Since its discovery, the microbiota has been increasingly recognised for its role in maintaining health and contributing to various disease conditions. In the reproductive tract, microbial populations can significantly influence endometrial health, internal homeostasis, and fertility. The preservation or restoration of a balanced microbiota through appropriate probiotic products may support reproductive health; in addition, candidate probiotics must be demonstrated to be safe for use. The aim of this study was to assess the local tolerance and systemic safety of a novel intravaginal probiotic product in cows. Twenty-four animals were enrolled and assigned to four groups: single-dose, three-, and five-fold dose of the test product, and a placebo group receiving excipients only. Physical examination and evaluation of the vaginal mucosa were conducted prior to each treatment, one day after and one and two weeks after the final probiotic administration. Blood and urine samples were collected before treatment and following treatment: one day after the last administration of intravaginal probiotic and again two weeks post-treatment. Blood haptoglobin, serum amyloid A, glucose, non-esterified fatty acids, and beta-hydroxybutyrate were measured to assess inflammatory and metabolic responses, and differences over time and between groups were statistically analysed. No dose-dependent systemic changes were observed; however, transient, time-related alterations were noted across all groups, including controls. The investigational probiotic product was well tolerated both locally and systemically, with tolerability comparable across all groups, including the placebo. These data establish a safety profile in healthy cows and support further investigation of this product in studies focusing on efficacy and microbiome modulation.}, }
@article {pmid42114033, year = {2026}, author = {Pavitra, SP and Tan, KK and Tan, TK and Er, YX and Vinnie-Siow, WY and Ya'cob, Z and Low, VL and Lim, YAL}, title = {Microbial communities of the Southeast Asian black flies (Diptera: Simuliidae) based on multiple hypervariable regions of 16S rRNA.}, journal = {Journal of medical entomology}, volume = {63}, number = {3}, pages = {}, doi = {10.1093/jme/tjag051}, pmid = {42114033}, issn = {1938-2928}, support = {//Ministry of Higher Education, Malaysia/ ; MO002-2019//Higher Institution Centre of Excellence (HICoE)/ ; TIDREC-2023//Higher Institution Centre of Excellence (HICoE)/ ; }, mesh = {Animals ; RNA, Ribosomal, 16S/analysis/genetics ; *Simuliidae/microbiology ; Male ; Female ; *Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification ; Malaysia ; High-Throughput Nucleotide Sequencing ; RNA, Bacterial/analysis ; }, abstract = {Black flies (Diptera: Simuliidae) are important vectors of disease-causing agents, but little is known about their microbiome in Southeast Asia, highlighting the need for further investigation. In Malaysia, Simulium cheongi, Simulium jeffreyi, and Simulium vanluni are among the most abundant black fly species and are of potential medical importance, making them suitable representatives for microbiome studies. In this study, their bacterial communities were characterized using next-generation sequencing (NGS) targeting seven hypervariable regions (V2, V3, V4, V6 to V7, V8, and V9) of the 16S rRNA gene to enable comprehensive community profiling. The alpha diversity of the bacterial community showed the highest values of Shannon and Simpson indices in S. jeffreyi and increased values of observed species and Chao1 indices in S. cheongi. Males showed greater microbial diversity than females in the alpha diversity analysis, with all alpha rarefaction plots reaching a plateau. Moreover, the beta diversity of the microbial communities measured by Bray-Curtis distance indices revealed three PCs coordinates with 63.75% of the total variance. However, no significant differences in alpha and beta diversity indexes were found among the three species. The bacterial composition included six phyla, 15 classes, 37 orders, 78 families, 143 genera, and 216 bacterial species, with the V3 region having the highest taxonomic identification. The V9 region had the least detection at all taxonomic levels, emphasizing the importance of selecting appropriate hypervariable regions to accurately assess the diversity of black fly bacterial communities.}, }
@article {pmid42114284, year = {2026}, author = {Abd El-Hack, ME and Ashour, EA and Khafaga, AF and Khaleel, HK and Kamal, M and Taha, AE and Alfifi, AE and Al-Rasheed, M and Khan, MMH}, title = {Functional effects of rosmarinic acid on gut health and epigenetic regulation in antibiotic-free poultry diets.}, journal = {Poultry science}, volume = {105}, number = {8}, pages = {106943}, doi = {10.1016/j.psj.2026.106943}, pmid = {42114284}, issn = {1525-3171}, abstract = {Rosmarinic acid (RA), a bioactive polyphenol found in Salvia officinalis and other Lamiaceae herbs, has attracted attention for its functional feed application in animal nutrition. RA supplementation positively influences growth efficiency, liver antioxidant status, and serum biochemical indices in broilers. Its antimicrobial and immunomodulatory effects promote health and productivity. Studies suggest benefits for gut health and meat quality; however, epigenetic regulation of RA in poultry is considered a minor future perspective, being mostly based on mammalian studies. Hypothesized impacts of RA on chronic disease prevention and as a microbiome-engineering agent require further investigation. This review explores the regulatory effects of RA on DNA methylation, non-coding RNAs (ncRNAs), and histone modifications, which influence gut microbiome structure, nutrient absorption, and immune function in poultry. It emphasizes RA's potential as a functional food for gastrointestinal health, metabolic regulation, and chronic disease prevention, alongside its use in antibiotic-free poultry feed for microbiome engineering. The review also discusses RA's effects on lipid metabolism and oxidative stress, highlighting its role in maintaining intestinal barrier health. Nevertheless, certain limitations must be acknowledged, as successful nutritional interventions depend on understanding individual variability, including genetics, metabolism, age, and health status. Tailored methodologies, such as micronutrition and genomic nutrition, can improve diet quality, promote nutrient absorption, and enhance overall animal health. A tailored feeding regimen focuses on selecting nutrients with proven benefits for key health outcomes, such as omega-3 fatty acids, which scientific evidence shows promote brain and heart health while reducing inflammation.}, }
@article {pmid42114326, year = {2026}, author = {Esen, S}, title = {An update on heat stress impacts on rumen microbiome composition, fermentation parameters, and mitigation approaches in ruminants.}, journal = {Journal of thermal biology}, volume = {139}, number = {}, pages = {104480}, doi = {10.1016/j.jtherbio.2026.104480}, pmid = {42114326}, issn = {0306-4565}, abstract = {Over the past decade, there has been an increasing amount of literature on heat stress (HS) effects on ruminant production systems, yet much uncertainty still exists about the relationship between HS and rumen microbial ecology across species. This narrative review synthesizes peer-reviewed evidence from 2020 to 2025, with the aim of providing a critical appraisal of HS effects on rumen microbiome composition and fermentation parameters in cattle, buffalo, sheep, and goats. A convergent pattern emerges from the available data: HS consistently reduces cellulolytic bacteria (Fibrobacter, Ruminococcus) while increasing lactate-producing and starch-fermenting taxa. Acetate proportions declined by 29-33% in buffalo and beef cattle, whereas total VFA in sheep increased during mild HS, reflecting species-dependent fermentation responses. A strong relationship between breed-level heat tolerance and rumen microbiome diversity has been reported in several recent studies, providing converging evidence that heat tolerance may be characterized as a holobiont phenotype. It has been demonstrated that HS extends beyond classical VFA changes to disrupt B-vitamin synthesis, amino acid metabolism, biogenic amine homeostasis, and bile acid biotransformation. Nutritional interventions, including probiotics, chromium, herbal supplements, and rumen-protected amino acids, have been shown to partially restore microbial balance, although responses vary with HS severity and host genotype. Notwithstanding these findings, the generalisability of much published research on this topic is limited by methodological heterogeneity across studies. Taken together, these findings highlight the need for standardized experimental protocols, multi-omics integration, and microbiome-targeted intervention strategies.}, }
@article {pmid42114574, year = {2026}, author = {Li, X and Cheng, S and Wang, X and Gu, X and Xu, X and Duan, X and Xue, G and Oleskowicz-Popiel, P and Xu, J and Liu, B and Liu, Z and Zhou, A and Makinia, J}, title = {Intrinsic waste component synergy: calcium-rich eggshell waste modulates fungal-bacterial microbiome toward selectively medium-chain fatty acid production.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134795}, doi = {10.1016/j.biortech.2026.134795}, pmid = {42114574}, issn = {1873-2976}, abstract = {The valorization of waste streams into medium-chain fatty acids (MCFAs) through fungi-bacteria synergy is often hindered by substrate competition and distinct ecological niches. This study demonstrates that eggshell waste acts as a bioregulator to optimize this interaction for caproate production. At a 20 g/L dosage, eggshells facilitated high caproate production (22.3 ± 1.3 gCOD/L) driven by in-situ ethanol supply (11.3 ± 1.9 gCOD/L). The amendment established stable micro-niches, significantly enriching yeasts (Wickerhamomyces, Candida, and Issatchenkia, 69.2%) and chain-elongating bacteria (CEB, Caproiciproducens, and Clostridium_sensu_stricto_12, 10.2%), while metagenomics confirmed upregulated glycolysis and reverse β-oxidation pathways. Additionally, yeast synergy with CEB via ethanol cross-feeding in a sugar-rich environment can be disrupted under the sugar-depleted phase. The coculture experiments unveiled that 8 g/L Ca[2+] alleviates fungi-bacteria conflict and promotes CEB functionality. This study presents a waste valorization strategy, leveraging intrinsic waste synergies to optimize fungal-bacterial interactions and drive endogenous ethanol-based caproate production.}, }
@article {pmid42114665, year = {2026}, author = {Moerdijk, AS and van Genuchten, WJ and Duijnhouwer, AL and Snoeren, MMM and Hirsch, A and van den Berg, LEM and Boersma, E and Kauling, RM and van den Bosch, AE and Udink Ten Cate, FEA and Helbing, WA and Bartelds, B}, title = {Evaluation of high intensity interval training in patients with a right ventricle to pulmonary artery conduit in a randomized controlled trial - Rationale and design of the 'Right HIIT' study.}, journal = {American heart journal}, volume = {}, number = {}, pages = {107477}, doi = {10.1016/j.ahj.2026.107477}, pmid = {42114665}, issn = {1097-6744}, abstract = {BACKGROUND: Exercise training is a promising, relatively low cost strategy to optimize exercise capacity, primarily studied in patients with tetralogy of Fallot and Fontan physiology. However, rare and complex biventricular disorders are understudied. High intensity interval training (HIIT) is a time-efficient alternative to the more commonly studied aerobic training. Despite group level improvements in exercise capacity, individual variation suggests the existence of responders and non-responders to exercise training. We therefore designed a HIIT intervention trial for patients with complex outflow tract disorders aimed to test efficacy and identify predictors of response.<br><br>METHODS: The Right HIIT study is a multicenter, randomized controlled trial aiming to enroll 38 patients aged 12 to 45 years with a right ventricle to pulmonary artery conduit. Participants will be randomized to a 12-week home-based HIIT program (intervention) or standard of care (SoC) group. The primary endpoint is change in peak oxygen consumption from baseline to 12 weeks. Secondary endpoints include other cardiopulmonary exercise testing and imaging parameters, blood biomarkers, gut microbiome composition, quality of life and physical activity levels. After the randomized phase, the SoC group will receive the HIIT program, with repeated data collection after 12 weeks. Thus, pre-post HIIT data will be available in all patients, for the purpose of supportive analyses and identifying predictors of response.<br><br>CONCLUSION: The Right HIIT study will analyze whether a HIIT program improves exercise capacity in patients with a right ventricle to pulmonary artery conduit and which factors are associated with the ability to improve exercise capacity.}, }
@article {pmid42114750, year = {2026}, author = {Saedi, N and Zhang, S and Sahana, G and Villumsen, TM and Stephansen, RB and Lund, MS and Cai, Z and Karaman, E}, title = {Comparison of 16S rRNA Sequencing and Shotgun Metagenome Sequencing for Estimating Genotypic and Phenotypic Parameters of Enteric Methane Emission in Dairy Cattle.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2025-28157}, pmid = {42114750}, issn = {1525-3198}, abstract = {Methane emissions from ruminants significantly contribute to greenhouse gases, making it crucial for sustainable livestock breeding to understand how both genetic and microbial factors influence methane production. We compared the heritability and microbiability for enteric methane in cows using microbial features derived from 16S rRNA amplicon data and shotgun metagenomics data, together with genome-wide marker data. The features derived from 16S rRNA data were 16s genus (16s-G), 16s species (16s-S), 16s Predicted microbial genes (16s-PMG) and 16s Predicted metabolic pathways (16s-PMP). The features derived from metagenomics data were metagenomic species (M-S) and metagenomic genus (M-G) considering 3 different databases (MGnify, GTDB, and NCBI). The heritability of methane ranged from 0.08 to 0.14. The 16s-G explained 28% of phenotypic variation in methane, and contributed the most to the heritability estimate for methane among other features. For the same feature data sets, we estimated the heritability of each microbial feature. Most microbial features had low heritability, while a subset had high values (up to 0.8). The highest heritabilities were observed for M-S MGnify feature RUG592 sp902767285 (0.95) and M-G NCBI genus feature Leadbettera (0.98). We found that the microbiota in the rumen is primarily determined by environmental factors, whereas host genetics has a significant impact on the abundance of certain functionally important microbes. To the best of our knowledge, this study presents the first comparison of methane heritability in dairy cattle incorporating microbial data (1) from multiple techniques such as 16S rRNA amplicon sequencing and shotgun metagenomic sequencing, and (2) from multiple levels of microbial features such as 16s-G, 16s-S, 16s-PMG, 16s-PMP, and M-S and M-G. Our results highlight heritable microbial species/genus as potential targets for microbiome-informed breeding strategies to reduce methane emissions in dairy cattle.}, }
@article {pmid42114808, year = {2026}, author = {Reynolds, GK and Dowling, MR and Valencia-Klug, J and Teh, BW and Anderson, MA and Vanguru, V and Harrison, SJ and Ho, PJ and Slavin, MA and Thursky, K}, title = {Infections in the first 30-days after CAR-T therapy in Patients Not Receiving Fluoroquinolone Prophylaxis.}, journal = {Transplantation and cellular therapy}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jtct.2026.03.040}, pmid = {42114808}, issn = {2666-6367}, abstract = {BACKGROUND: Routine fluoroquinolone (FQ) prophylaxis may increase the risk of antimicrobial resistance, microbiome disruption, and Clostridioides difficile infection in patients receiving chimeric antigen receptor T-cell (CAR-T) therapy for haematological malignancy. In Australia, FQ prophylaxis is not routinely used. We evaluated the aetiology of early fever following CAR-T to better understand the incidence of infections, particularly bloodstream infections, in a cohort not receiving FQ prophylaxis.<br><br>METHODS: This bicentric Australian retrospective study included adults receiving standard-of-care CD19 CAR-T therapy for DLBCL (2019-2023). The primary outcome was the cause of sustained fever (&#x2265;38.0&#xb0;C on &#x2265;1 days) from infusion to day 30. Recurrent fever required &#x2265;72 hours afebrile before a new fever. Infections were classified as microbiologically-confirmed, clinically-defined, or fever syndrome per consensus criteria.<br><br>RESULTS: 204 adults (median age 64 years, IQR:57-71) received tisagenlecleucel (50%) and axicabtagene (50%), after a median of 3 prior therapies (IQR:3-4). Sustained fever occurred in 131/204 patients (64%), comprising 161 episodes. Of these, 36 (21%, 28pts) were microbiologically-confirmed infections, 14 (9%, 14pts) were clinically-defined infections, and 110 (69%, 108pts) were fevers of unknown origin. Bacteremia occurred in 7/204 patients (3.4%; 9 events), with one fatal polymicrobial bacteremia. Other microbiologically-confirmed infections included C. difficile (7/36), URTI (13/36) and invasive fungal infection (5/36). Risk factors for early microbiologically-confirmed infection in univariate analysis included axicabtagene product (HR=2.5, p=0.019), grade &#x2265;3 ICANS (HR=3.4, p=0.012), and prolonged neutropenia (ANC &#x2264; 0.5&#x202f;&#xd7;&#x202f;10&#x2079;/L for &#x2265;14 days; HR=3.7, p=0.014).<br><br>CONCLUSION: Early bacteremia rates remain low without routine FQ prophylaxis. Initial sustained fevers are predominantly non-infectious. Our data do not support universal fluoroquinolone prophylaxis in CAR-T therapy.}, }
@article {pmid42115049, year = {2026}, author = {Ha, S and Zhang, X and Li, L and Yu, J}, title = {MASLD and MASLD-associated HCC: emerging biomarkers and therapeutic avenues.}, journal = {Science bulletin}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.scib.2026.04.048}, pmid = {42115049}, issn = {2095-9281}, abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is a leading chronic liver disease on a global scale. With its increasing incidence and advances in research technologies, our understanding of the mechanisms, non-invasive diagnostic strategies and therapeutic approaches for MASLD and its more advanced forms, including metabolic dysfunction-associated steatohepatitis (MASH) and hepatocellular carcinoma (HCC), has substantially expanded. This article reviews the pathophysiological mechanisms underlying MASLD and its transition to more severe forms, evolving from well-established mechanisms including insulin resistance, abnormalities in lipid metabolism and inflammation, to recently explored novel mechanisms, such as immune regulation, RNA modification and gut microbiome. Additionally, emerging biomarkers for diagnosis and prognosis, such as non-invasive serum markers and genetic variants are highlighted. This review evaluates contemporary therapeutic strategies, with particular emphasis on the recent FDA approval of resmetirom and semaglutide, alongside other pharmacological agents currently in phase 3 clinical trials. It also discusses innovative interventions aimed at improving the management of MASLD and MASLD-HCC, specifically in the context of gut modulation and enhancing the efficacy of immunotherapy. The necessity for strategies aimed at early detection and multifactorial treatment approaches is critical to address the rising burden of MASLD and its complications, with a call for further research into personalised medicine and innovative multidisciplinary therapeutic targets.}, }
@article {pmid42115134, year = {2026}, author = {van der Meulen, LWJ and Bergmans, ME and Assil, S and Abdisalaam, I and Rijneveld, R and Klaassen, ES and Tibboel, AJ and Brach, T and Herpers, BL and Frieling, J and Freyee, B and Platenkamp, K and van Poelgeest, ME and Rissmann, R and van Doorn, MBA and Niemeyer-van der Kolk, T}, title = {Lack of improvement after short-term topical antistaphylococcal endolysin SA.100 therapy in patients with mild-to-moderate atopic dermatitis: Results from a randomized, vehicle-controlled trial.}, journal = {British journal of clinical pharmacology}, volume = {}, number = {}, pages = {}, doi = {10.1002/bcp.70608}, pmid = {42115134}, issn = {1365-2125}, support = {//Micreos Human Health B.V./ ; }, abstract = {Atopic dermatitis (AD) is a chronic immune-mediated inflammatory skin disease. An overgrowth of Staphylococcus aureus (S. aureus) and decreased microbial diversity is apparent in 70%-90% of AD patients. SA.100 is a recombinant endolysin targeting S. aureus that might be a novel treatment for patients with mild-to-moderate AD. To test safety, pharmacodynamics and efficacy of SA.100 a double-blind, randomized, vehicle-controlled trial in 53 subjects with mild-to-moderate AD was performed. Patients were randomized equally to topical SA.100 or vehicle with stratification for S. aureus positivity. SA.100 was safe and well tolerated. No reduction of S. aureus and no changes in microbiome features were seen after 2 weeks of treatment. Additionally, no statistically significant changes in clinical or patient-reported outcomes were observed compared to vehicle. In conclusion, topical SA.100 was safe and well tolerated in patients with mild-to-moderate AD, but our findings do not support short-term clinical use.}, }
@article {pmid42115189, year = {2026}, author = {Wojciechowska, AW and Wojciechowski, JW and Zielinska, K and Soeding, J and Kosciolek, T and Kotulska, M}, title = {Aggregation in gut: on the link between neurodegeneration and bacterial functional amyloids.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01005-8}, pmid = {42115189}, issn = {2055-5008}, support = {2019/35/B/NZ2/03997//Narodowe Centrum Nauki/ ; 2023/05/Y/NZ2/00080//Narodowe Centrum Nauki/ ; 2019/35/B/NZ2/03997//Narodowe Centrum Nauki/ ; }, abstract = {Amyloids are insoluble protein aggregates with a cross-beta structure, which are traditionally associated with neurodegeneration. Similar structures, named functional amyloids, expressed mostly by microorganisms, play important physiological roles, e.g., bacterial biofilm stabilization. Using a bioinformatics approach, we identify gut microbiome functional amyloids and analyze their potential impact on human health via the gut-brain axis. The results point to taxonomically diverse sources of functional amyloids and their frequent presence in the extracellular space. The retrieved interactions between gut microbiome functional amyloids and human proteins indicate their potential to trigger inflammation, affect transport and signaling processes; pathways typically affected by host-microbiome interactions. We also find a greater relative abundance of bacterial functional amyloids in patients diagnosed with Parkinson's disease in two out of three analyzed datasets. Our results generate hypotheses on a tentative link between neurodegeneration and gut bacterial functional amyloids, which require further experimental validation.}, }
@article {pmid42115298, year = {2026}, author = {Park, SH and Park, J and Kim, J and Choi, H and Kim, IG and Chung, EJ and Na, KJ}, title = {Analysis of unmapped RNA-seq data from cancer spatial transcriptome toward characterizing cancer microbiome.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-52324-x}, pmid = {42115298}, issn = {2045-2322}, support = {RS-2024-00357094//National Research Foundation of Korea/ ; 2020R1C1C1007105//National Research Foundation of Korea/ ; 2620210050//Seoul National University Bundang Hospital/ ; }, abstract = {Spatial characterization of microbial-like signals in tumor tissues remains challenging, particularly in direct Visium data, where microbial reads are sparse and may not be fully retained in standard count matrices. Here, we present an extended unmapped-read analysis as a proof-of-concept workflow for summarizing microbial-like 16S rRNA signals in four direct Visium specimens from colorectal cancer (CRC), oral squamous cell carcinoma (OSCC), and head and neck squamous cell carcinoma (HNSC). The workflow uses a custom reference containing four selected 16S rRNA sequences and computes a per-spot mismatch ratio to quantify sequence-level dissimilarity relative to each reference. Compared with PathSeq, the workflow yielded different spatial signal patterns and mismatch summaries across the analyzed specimens. Among the four tested references, the CRC specimen showed lower mismatch ratios relative to the E. coli reference than the other analyzed specimens, an observation compatible with the intestinal context but not definitive evidence of species-level presence or evolutionary proximity. Given the small sample set, restricted reference panel, and lack of dedicated negative controls, these findings should be interpreted as hypothesis-generating. This study provides a complementary proof-of-concept framework for exploring microbial-like signals in direct Visium data.}, }
@article {pmid42115377, year = {2026}, author = {Catani, G and O'Connor, JM and Spinelli, A and Perea, J}, title = {Early-onset colorectal cancer: a comprehensive review reframing hypotheses and defining research priorities.}, journal = {International journal of colorectal disease}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00384-026-05145-3}, pmid = {42115377}, issn = {1432-1262}, abstract = {PURPOSE: Early-onset colorectal cancer (EOCRC), defined as colorectal cancer diagnosed before the age of 50 years, is increasing worldwide and represents a growing clinical and public health challenge. Whether EOCRC constitutes a biologically distinct entity remains uncertain, and current diagnostic and therapeutic strategies are largely extrapolated from late-onset disease.<br><br>METHODS: This narrative review summarizes recent evidence on EOCRC biology, diagnosis, and management, focusing on molecular and genomic features, tumor microenvironment, exposome-related factors, diagnostic pathways, treatment paradigms, and emerging strategies for early detection. We critically examine the gap between biological insights and real-world clinical practice and outline priorities for future research.<br><br>RESULTS: EOCRC displays a heterogeneous molecular landscape that substantially overlaps with late-onset colorectal cancer. Although advances in multiomics profiling, liquid biopsy, and microbiome research have improved biological understanding, these findings have not yet translated into EOCRC-specific diagnostic or therapeutic approaches. Diagnosis remains delayed due to age-based screening paradigms and symptom misattribution, resulting in advanced-stage presentation. Younger patients frequently receive intensified treatment despite limited age-specific evidence and insufficient attention to long-term toxicity, fertility, and survivorship.<br><br>CONCLUSION: EOCRC underdiagnosis is likely multifactorial. While limitations in biological knowledge and diagnostic tools may play a role, the discrepancy between current paradigms and the age-specific risk profiles of younger patients likely represents an important contributing factor. Progress will require biology-informed, risk-adapted screening strategies and EOCRC-focused clinical research.}, }
@article {pmid42115408, year = {2026}, author = {Cheng, B and Gong, L and Xu, H and Wang, Z and Huang, H and Guan, X and Wu, P}, title = {The microbiome across the prostate disease continuum: from health and BPH to prostatitis/CPPS and cancer.}, journal = {Oncogene}, volume = {}, number = {}, pages = {}, pmid = {42115408}, issn = {1476-5594}, abstract = {Microbial contributions to prostate health and disease extend beyond the mere detection of organisms in urine or tissue. Rather than acting as stable colonisers, microbial influences on the prostate are better conceptualised as converging fluxes: systemically circulating gut-derived metabolites, immune education occurring in distal lymphoid compartments, and intermittent exposure to microbial products from the lower urinary tract. These inputs converge on a limited set of conserved mediator-receptor axes-including short-chain fatty acids, bile acids and indole derivatives-that calibrate epithelial barrier integrity, inflammatory thresholds, antigen-presentation capacity and myeloid cell fate. Crucially, the biological relevance of these axes is stage-dependent. In benign prostatic hyperplasia and chronic prostatitis/chronic pelvic pain syndrome, metabolite tone shapes inflammatory activation thresholds and barrier resilience. In localized prostate cancer, these same pathways intersect with antigen-processing machinery and immune exclusion. In castration-resistant disease, tumour-intrinsic metabolic plasticity and redox balance predominate, with microbial and host-derived metabolites assuming relevance when they modulate lipid remodelling and ferroptotic vulnerability. Interpretation is constrained by the intrinsically low biomass of urine and prostate tissue. Robust inference therefore requires quantitative anchoring, orthogonal validation and explicit separation of association from causality. Translational progress is most likely to emerge from calibrated measurement and stage-aware modulation rather than indiscriminate ecological manipulation. By integrating mechanistic, spatial and clinical evidence, this Review proposes a stage-aware framework for the gut-urinary-prostatic axis and delineates when microbial and metabolite signalling meaningfully conditions prostate disease biology-and when it does not.}, }
@article {pmid42115470, year = {2026}, author = {Fragkou, PC and Moschopoulos, CD and Marová, D and Alahmad, B and Skevaki, C and , }, title = {Climate change-associated heat extremes and immune dysregulation: emerging links with autoimmunity, allergy, and infectious diseases.}, journal = {Seminars in immunopathology}, volume = {48}, number = {1}, pages = {}, pmid = {42115470}, issn = {1863-2300}, mesh = {Humans ; *Climate Change ; *Hypersensitivity/etiology/immunology/epidemiology/metabolism ; *Communicable Diseases/etiology/immunology/epidemiology ; Animals ; *Autoimmunity ; *Hot Temperature/adverse effects ; Disease Susceptibility ; *Autoimmune Diseases/etiology ; Environmental Exposure/adverse effects ; }, abstract = {Climate extremes are increasingly shaping both environmental and human health outcomes. Global warming has led to a rise in the frequency, duration, and intensity of extreme temperature events, with heatwaves emerging as one of the most hazardous weather-related threats. Beyond their well-recognized cardiovascular and respiratory effects, heat extremes are now understood to influence immune function. Growing evidence indicates that heat extremes along with air pollution, wildfires, humidity shifts, and ecosystem disruption can impair epithelial barrier integrity and disturb immune regulation. These stressors may promote chronic inflammation, alter adaptive immune responses, and compromise host defense mechanisms. Experimental and epidemiological data suggest that heat stress can reduce effective B-cell responses, modify antigen presentation, and increase inflammatory signaling, while combined exposures to heat and pollutants may further increase susceptibility to infectious, allergic, and autoimmune diseases. Although the physical drivers of climate change are well established, the biological pathways linking environmental stressors to immune dysregulation remain incompletely defined. This review synthesizes current evidence on the mechanisms by which extreme heat events influence immune tolerance and disease risk. We discuss implications for allergy, autoimmunity, and infectious diseases, highlight vulnerable populations, and outline key research priorities needed to inform clinical and public health adaptation.}, }
@article {pmid42115547, year = {2026}, author = {Chung, CS and Kherallah, K and Ashina, N and Beraja, GE and Budhiraja, A and Dienes, S and Goldberg, M and Xiong, G and Alhusayen, R and Goldberg, S and Gonzalez, T and Hsiao, JL and Lev-Tov, H and Sibbald, C and Piguet, V and Porter, M}, title = {Symposium on Hidradenitis Suppurativa Advances 2025 Proceedings.}, journal = {Dermatology and therapy}, volume = {}, number = {}, pages = {}, pmid = {42115547}, issn = {2193-8210}, }
@article {pmid42115794, year = {2026}, author = {Chen, J and Chen, S and Sun, H and Wang, Y}, title = {Lower airway microbiome and metabolomic profiles of recurrent wheezing in infants: a case-control study.}, journal = {Allergologia et immunopathologia}, volume = {54}, number = {3}, pages = {49-80}, pmid = {42115794}, issn = {1578-1267}, mesh = {Humans ; Male ; Female ; Infant ; *Respiratory Sounds/etiology ; *Microbiota ; Case-Control Studies ; RNA, Ribosomal, 16S/genetics ; Bronchoalveolar Lavage Fluid/microbiology ; Metabolome ; Metabolomics ; Recurrence ; DNA, Bacterial/genetics ; Bacteria ; }, abstract = {OBJECTIVES: To characterize the microbiome shifts and subsequent metabolite alterations associated with recurrent wheezing (RW) in infants.<br><br>METHODS: A total of 33 subjects were enrolled in this study, including 18 infants diagnosed with RW, and 15 normal infants as controls. Bronchoalveolar lavage (BAL) fluid was collected from all the subjects. Bacterial DNA was then isolated and analyzed by 16S ribosomal RNA sequencing. In addition, the metabolomic profile of BAL fluid samples was analyzed with mass spectrometry using complementary chromatographic methods. Spearman's rank correlation analysis was conducted to explore associations between microbial taxa and metabolites.<br><br>RESULTS: The study had 21 (63.6%) boys and 12 (36.4%) girls. The mean age was 26.8 &#xb1; 4.9 months. Haemophilus (P = 0.003) and Porphyromonas (P = 0.007) genera showed significant difference between the two groups. The metabolites of "starch and sucrose metabolism pathway" and "pentose phosphate pathway" showed significant correlations with the two bacterial genera. For starch and sucrose metabolism pathway, glucose-6-phosphate showed significant positive correlations with Haemophilus (r = 0.44 and P = 0.009) and Porphyromonas (r = 0.45 and P = 0.008). For pentose phosphate pathway, Sedoheptulose 7-phosphate, an intermediate in the pentose phosphate pathway, showed significantly positive correlations with Haemophilus (r = 0.42 and P = 0.02) and Porphyromonas (r = 0.43 and P = 0.01).<br><br>CONCLUSIONS: Our study provided new evidence that alteration in respiratory tract microbiome could be associated with RW in infants. By elucidating the microbiome and metabolite profile, we identified novel biomarkers potentially useful for personalized management of RW in infants. The future studies should validate the underlying mechanisms in longitudinal cohorts and explore interventions targeting metabolic-microbial crosstalk.}, }
@article {pmid42115865, year = {2026}, author = {Huang, J and Chen, Z and Chen, M and Zeng, Z and Zhuang, X}, title = {Specific alterations in the gut microbiome and metabolome across disease locations of Crohn's disease: a systematic review.}, journal = {BMC gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12876-026-04898-z}, pmid = {42115865}, issn = {1471-230X}, support = {82200605//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Crohn's disease (CD) exhibits substantial heterogeneity in disease behavior and therapeutic outcomes across distinct disease locations. Specific alterations in the gut microbiota and metabolites may drive this variation. This review aims to characterize the distinctive microbial and metabolic signatures across CD phenotypes based on disease location.<br><br>METHODS: Electronic databases were searched from inception to December 2025 for studies that observed alterations in gut microbiota and metabolites in CD patients with different disease locations.<br><br>RESULTS: Forty-eight studies including 3,577 CD patients and 2,916 healthy controls (HCs) were analyzed. Ileal Crohn's disease (ICD) was characterized by significant dysbiosis compared with HCs, featuring enrichment of Enterobacteriaceae (especially adherent-invasive Escherichia coli [AIEC]), Fusobacterium and Shigella, alongside depletion of Faecalibacterium prausnitzii, Roseburia and Coprococcus. Patients with colonic Crohn's disease (CCD) exhibited increased levels of Proteobacteria, pro-inflammatory families (Actinomycetaceae, Micrococcaceae) and opportunistic pathogens (Streptococcus, Klebsiella). In contrast, a decrease in short-chain fatty acid (SCFA)-producing families (Lachnospiraceae, Ruminococcaceae) and F. prausnitzii was observed in CCD. Ileocolonic Crohn's disease (ICCD) displayed features combining ICD and CCD elements, with specific depletion in Alistipes communis and enrichment of Shigella flexneri. More pro-inflammatory bacteria were observed in ICD compared with CCD. In terms of metabolic alterations, ICD showed impaired enterohepatic bile acid circulation with excessive fecal loss of conjugated bile acids, while CCD exhibited defective conversion of primary to secondary bile acids. ICCD exhibited both impaired ileal reabsorption and defective colonic transformation.<br><br>CONCLUSIONS: Our results identified disease location-specific alterations in the microbiome and metabolome of CD, which might be associated with the clinical manifestations and prognosis of different phenotypes.}, }
@article {pmid42115921, year = {2026}, author = {Bulfoni, M and De Martino, M and Gualandi, N and Marzinotto, S and Vesca, G and Krpan, B and Marcon, B and Bertoni, M and Tascini, C and Pipan, C and Curcio, F}, title = {Gut microbiota profiling of the population residing in Friuli-Venezia Giulia through next-generation sequencing.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05117-1}, pmid = {42115921}, issn = {1471-2180}, abstract = {The gut microbiota is an ecological community of symbiotic and commensal microorganisms that play crucial roles in nutrient metabolism, maintaining the structural integrity of the intestinal mucosal barrier, immunomodulation, and pathogen protection. The composition of the gut microbiota varies with age, ethnicity, lifestyle, and dietary habits. Given the microbiota's growing role as a modulator of various physiological and pathological conditions, our study aimed to investigate the genetic profile of the microbiome individuals residing in the Friuli-Venezia Giulia region. We analyzed fecal swab samples from 109 individuals belonging to a general population cohort. The hypervariable V3-V4 regions of bacterial 16 S rRNA were analyzed using Next Generation Sequencing (NGS) on the MiSeq system (Illumina). The relative abundance of phyla, classes, orders, families, and species was defined using the BaseSpace 16s metagenomics app (Illumina). Firmicutes was the most represented phylum (51.1%), followed by Bacteroidetes (38.3%) and Actinobacteria (3%). At the class level, Clostridia (45.2%) and Bacteroidia (37.7%) were predominant, while Clostridiales (46.9%), Bacteroidales (26.6%), and Anaeroplasmatales (12.6%) were notable orders. Lachnospiraceae (21.9%) and Ruminococcaceae (16.2%) were the most frequent families, with Faecalibacterium prausnitzii (10.3%), Bacteroides vulgatus (4.6%), and Bacteroides dorei (3.5%) being prominent species. Each participant's taxa were analyzed to identify genera associated with alterations in gut microbial composition. Significant associations emerged between specific taxa of microorganisms and age, gender, anti-inflammatory drugs, tobacco consumption, and allergies. This study provides valuable insights into gut microbiota composition in a population-based cohort. The characterization of the microbiota in the Friuli-Venezia Giulia (FVG) region lays the foundation for future research into regional variations in microbiota composition and its impact on health.}, }
@article {pmid42115936, year = {2026}, author = {Dalgic, A and Yet, I}, title = {Identifying gut microbiome signatures of type 1 diabetes using machine learning and evolutionary feature selection.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05113-5}, pmid = {42115936}, issn = {1471-2180}, abstract = {BACKGROUND: Type 1 Diabetes Mellitus (T1D) has been increasingly associated with alterations in the gut microbiome. However, the impact of taxonomic resolution, feature selection strategies, and machine learning methods on microbiome-based prediction remains incompletely understood.<br><br>METHODS: We analyzed publicly available 16S rRNA gene sequencing datasets from two geographic cohorts to evaluate microbiome-based prediction of T1D. Microbial features were constructed at multiple taxonomic levels and as full hierarchical taxonomic paths preserving phylogenetic structure. Machine learning models were trained using stratified cross-validation and cross-cohort validation frameworks. Feature selection was performed using Binary Particle Swarm Optimization (BPSO) to identify compact and predictive microbial signatures. Model performance was evaluated using AUC, Accuracy, F1 score, and Matthews Correlation Coefficient. Differential abundance analysis using the LinDA framework was used to support biological interpretation of selected taxa.<br><br>RESULTS: Tree-based models, particularly Random Forest and XGBoost, achieved the strongest predictive performance across taxonomic representations. Taxonomic resolution influenced model behavior, with family-level features providing strong performance with compact feature sets, while higher-resolution representations did not consistently improve performance despite increased complexity. BPSO identified consistently selected taxa across validation frameworks, suggesting stable predictive signatures. Several of these taxa have been linked to inflammatory or metabolically altered gut environments. Cross-cohort validation showed reduced performance compared with within-study models, highlighting challenges in generalization.<br><br>CONCLUSION: Machine learning combined with BPSO-based feature selection provides an effective framework for identifying predictive microbial signatures associated with T1D. Our findings highlight the importance of taxonomic resolution, feature stability, and cross-cohort validation in microbiome-based predictive modeling. Integrating evolutionary feature selection with machine learning and biological validation may improve the robustness and interpretability of candidate microbial signatures.}, }
@article {pmid42116047, year = {2026}, author = {Choi, JW and Kim, H and Ham, SH and Han, YJ and Kim, SE and Sung, MK}, title = {Probiotic Bifidobacterium bifidum BGN4 supplementation modulates gut microbiome composition and reduces circulating zonulin, TNFα, and insulin in adults with excess adiposity: a randomized, double-blind, placebo-controlled trial.}, journal = {Nutrition &amp; metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12986-026-01124-1}, pmid = {42116047}, issn = {1743-7075}, support = {2023R1A2C1005313//National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT)/ ; 2022R1A2C1004626//National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT)/ ; }, abstract = {BACKGROUND: Obesity, characterized by excess body fat accumulation, is closely linked to the alteration of gut microbiota, which contribute to systemic inflammation. Probiotics intervention has emerged as a promising strategy favorably modulating gut microbiota composition in obese individuals accompanied by improvements in metabolic parameters. The objective of this study was to evaluate whether supplementation with Bifidobacterium bifidum BGN4 alters gut microbiota composition and to assess its associated effects on circulating zonulin, a marker of intestinal permeability, as well as metabolic parameters in individuals with excess adiposity.<br><br>METHODS: This randomized, double-blind, placebo-controlled trial involved 60 adults with excess body fat (body fat percentage&#x2009;&#x2265;&#x2009;20% for males and&#x2009;&#x2265;&#x2009;28% for females). A total of 60 adults were enrolled, and sex- and age-stratified randomization allocated 30 participants to each group. Participants received one capsule of B. bifidum BGN4 (9&#x2009;&#xd7;&#x2009;10[9] colony forming unit) or matched placebo for 8&#xa0;weeks. Blood samples were analyzed for zonulin, TNF&#x3b1;, hs-CRP, glucose, insulin, lipid profiles, and total antioxidant capacity. Fecal samples were analyzed to determine alterations in gut microbiota composition.<br><br>RESULTS: A total of 58 participants, with 29 individuals in each group, successfully completed the 8-week intervention. Supplementation with B. bifidum BGN4 did not result in significant changes in BMI, body fat percentage, or the primary outcome, hs-CRP. In contrast, significant improvements were observed in serum zonulin (between-group differences: -1.61&#x2009;&#xb1;&#x2009;2.69&#xa0;ng/mL), TNF&#x3b1; (between-group differences: -0.17&#x2009;&#xb1;&#x2009;0.26&#xa0;pg/mL), and fasting insulin (between-group differences: -3.52&#x2009;&#xb1;&#x2009;10.25 &#x3bc;IU/mL). The probiotic intervention modulated the enrichment of several taxa, including Bacteroides coprocola, Bifidobacterium catenulatum group, Lactiplantibacillus plantarum group, and Prevotella stercorea. In addition, several microbial taxa demonstrated correlations with metabolic and inflammatory parameters. No adverse effects were observed, as indicated by stable liver enzyme concentrations, blood pressure, and gastrointestinal symptoms.<br><br>CONCLUSION: The results indicate that B. bifidum BGN4 may serve as a preventive strategy for metabolic disorders in individuals with excess adiposity through the maintenance of gut microbial balance and intestinal barrier integrity thereby potentially mitigating inflammation and metabolic stress.<br><br>TRIAL REGISTRATION: Clinical trial registration number: KCT0010817. Date of registration: July 28, 2025.}, }
@article {pmid42116157, year = {2026}, author = {Li, S and Lin, L and Zhang, M and Liu, J and Lu, E and Cao, Z}, title = {Nanoengineered bile acid-mediated orchestration of versatile immuno-microbial cues for treating periodontitis.}, journal = {Journal of nanobiotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12951-026-04495-y}, pmid = {42116157}, issn = {1477-3155}, support = {82401198//National Science Foundation of China/ ; 52171075//National Science Foundation of China/ ; 22575146//National Science Foundation of China/ ; 2022M710748//China Postdoctoral Science Foundation/ ; 22YF1439400//the Youth Science and Technology Talents-the Sailing program of Shanghai/ ; 25ZR1401224//Natural Science Foundation of Shanghai/ ; }, abstract = {Periodontitis, a globally prevalent inflammatory disease, is propelled by a vicious cycle involving microbial dysbiosis, hyperactive host immune responses, excessive oxidative stresses, and chronic inflammations. Current treatments largely focus on reducing microbial pathogens, yielding limited therapeutic efficacy. Here, we report a polydopamine-based taurolithocholic acid (TLCA) nanotherapeutic (PDCA) that reprograms versatile immuno-microbial cues to ameliorate periodontal inflammation and restore tissue homeostasis. Leveraging the dual function of polydopamine in drug delivery and redox capacity, after cellular uptake, PDCA scavenges reactive oxidation species, and releases TLCA to interact with its nuclear receptors in various target cells, exerting multifaceted regulatory effects. In inflamed human gingival fibroblasts, PDCA reduces the oxidative stress and enriches intracellular accumulation of TLCA to assist its interaction with vitamin D receptor, thus attenuating the expression of pro-inflammatory cytokines. Furthermore, PDCA modulates hyperactive immune responses, including suppressing the maturation of dendritic cells, inhibiting osteoclast differentiation of monocytes, downregulating pro-inflammatory CD4[+] lymphocytes, and upregulating regulatory T cells. Concomitantly, this immunomodulation is associated with the restoration of periodontal microbiome homeostasis, contributing to a reduction in pathogens and an enrichment of beneficial flora. In addition, PDCA not only rescues inflammatory tissue destructions in both therapeutic and prophylactic mouse models of periodontitis, but also elicits robust decrement in pro-inflammatory cytokine production in ex vivo human periodontitis tissues. This work highlights polydopamine-based bile acid nanomedicine as a microenvironment-targeting platform for immuno-microbial rebalance, offering a transformative strategy to treat oral inflammatory diseases.}, }
@article {pmid42116193, year = {2026}, author = {Tamang, A and Kumar, A and Thakur, A and Kumar, R and Kumar, D and Hallan, V and Pandey, SS}, title = {Unravelling the fungal endomicrobiome of Picrorhiza kurrooa for increasing in-planta picroside biosynthesis using endophytic Trichoderma harzianum PKRF1.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00909-4}, pmid = {42116193}, issn = {2524-6372}, support = {MLP-201, MLP-207 and MLP-171//Council of Scientific and Industrial Research, India/ ; MLP-201, MLP-207 and MLP-171//Council of Scientific and Industrial Research, India/ ; }, abstract = {BACKGROUND: Endophytic fungi form an integral part of plant microbiomes, influencing host physiology, stress resilience, and secondary metabolism. While next-generation sequencing (NGS) has greatly advanced the identification of endophytes, it often falls short of assigning functional roles, necessitating integration with culture-based approaches for downstream applications. Picrorhiza kurrooa, a critically endangered Himalayan medicinal herb valued for its hepatoprotective picrosides, suffers from reduced metabolite content in tissue culture-derived plants, likely due to microbiome loss in the course of aseptic in-vitro practices. Moreover, the diversity and functional role of fungal endomicrobiome in P. kurrooa remain unexplored.<br><br>METHODS: Internal transcribed spacer (ITS)-based amplicon sequencing was performed to assess and compare the endophytic fungal communities of wild-type (Wt) and in-vitro propagated (Tc) P. kurrooa. Fungal taxa unique to Wt-plants were identified and cross-referenced with culturable isolates. A dominant isolate present only in Wt-plants, Trichoderma harzianum PKRF1, was reintroduced into Tc-plants to evaluate its effect on plant growth and picroside biosynthesis. Whole-genome sequencing and comparative genomics of PKRF1 were also conducted to elucidate its functional capabilities and possible candidates for its endophytic nature.<br><br>RESULTS: Metagenomic analysis revealed a significant reduction in fungal diversity in Tc plants, with several taxa, including Trichoderma, Cyphellophora, and Preussia, exclusively associated with Wt-plants. Inoculation of Tc-plants with PKRF1 led to successful root colonization, enhanced photosynthetic efficiency, biomass, and significantly higher levels of picrosides. Transcript profiling confirmed upregulation of key biosynthetic genes. Genomic analysis of PKRF1 revealed genes associated with multiple plant-beneficial traits, including nutrient acquisition, phytohormone production, stress tolerance, plant colonization, and competitive interactions, distinguishing it from non-endophytic Trichoderma isolates.<br><br>CONCLUSIONS: These findings provide the first comprehensive insight into changes in endophytic fungal diversity of P. kurrooa associated with in-vitro cultivation. Furthermore, the application of cultivated endophytes from wild plants demonstrated the potential to restore microbial functions lost during in-vitro propagation and enhance secondary metabolite production in cultivated plants. Overall, this approach offers a promising strategy to integrate metagenomic information into beneficial plant-microbe interactions for practical applications.}, }
@article {pmid42116194, year = {2026}, author = {Buetas, E and Conde-Pérez, K and Concha, &#xc1; and Celeiro, C and Noguera, JF and Bou, G and Pardiñas-López, S and Vallejo, JA and Poza, M and Carda-Diéguez, M and Mira, A}, title = {Metatranscriptomic analysis of the microbiota of tumor tissue in colon cancer.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02372-2}, pmid = {42116194}, issn = {2049-2618}, abstract = {BACKGROUND: Colorectal cancer (CRC) is the second leading cause of cancer-related deaths, accounting for more than 900,000 deaths a year worldwide. Microbial dysbiosis, including the presence of oral bacteria in the gut, has been linked to CRC. Some mechanisms by which specific microorganisms potentially drive tumorigenesis have been described, but there is a lack of studies elucidating whole microbiota activity in the tumor and their implication for the development of the disease. Here, the metatranscriptomic data of tumor and control tissue-associated microbiota (n = 18 pairs), as well as from subgingival sulcus (n = 15) of CRC patients, was analyzed.<br><br>RESULTS: We confirmed that Fusobacterium nucleatum was more active in the tumor tissue than in the control gut mucosa. In addition, the activity of this species was positively correlated with other oral bacteria in the tumors, including Parvimonas micra, Peptostreptococcus stomatis, and Granulicatella adiacens, along with gut bacteria like Hungatella hathewayi, suggesting a potential relationship among them. Regarding bacterial gene expression, a change in the functional profile was observed, including a higher expression of genes associated with carbon metabolism in control in contrast to an increase of amino acid-related genes in tumor. Furthermore, genes implicated in the biosynthesis and transport of lipopolysaccharide were increased in tumors. Interestingly, a significantly higher expression in tumor than control tissue of potential virulence factors from F. nucleatum was found, supporting their relevance in niche colonization and tumorigenesis. Correlation analysis of the bacterial activity with the host transcriptional profile showed significant correlations of the Fusobacterium-Peptostreptotoccus-Hungatella cluster with human genes involved in inflammation and metastasis, confirming the association of this microbial consortium with tumor development. For the first time, the gene expression profiles of oral bacteria in the gut and the oral cavity were compared. The cluster of co-active bacteria identified in tumors was partially found in the oral samples, suggesting a stable interaction and potential synergy. Although there were thousands of differentially expressed genes between subgingival sulcus and tumor tissue, the expression of key virulence factors was not significantly different.<br><br>CONCLUSIONS: In short, this study discovered new traits about tumor microbial-associated composition and activity and its connection with the oral composition that would be essential to unravel the translocation, colonization, and tumorigenesis of the CRC.}, }
@article {pmid42116227, year = {2026}, author = {Hron, BM and Zhang, YJ and Golden, C and Chalmers, C and Nemec, G and Delaney, E and Ozcan, E and Kim, M and Jalali, L and Solari, T and Brezsny-Feldman, J and Alm, EJ and Bry, L and Rosen, R}, title = {Association between blenderized tube feeds and differential oropharynx, stomach, and stool microbiome signatures relative to conventional formula feeds in children fed via enteral tube: A cross-sectional study.}, journal = {JPEN. Journal of parenteral and enteral nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1002/jpen.70097}, pmid = {42116227}, issn = {1941-2444}, support = {//Supported by National Institutes of Health R01 DK097112 (PI: Rosen) and K23 DK133679 (PI: Hron), NASPGHAN Astra- Zeneca Research Award (PI: Hron), NIH K12 5K12HD052896 (PI: Fleisher, awarded to Zhang); NASPGHAN Foundation/Reckitt/Mead Johnson Nutrition Young Investigator Development Award (PI: Zhang); AGA Research Scholar Award (PI: Zhang); Harvard Digestive Diseases Center Grants P30 DK034854 (NIH) and Massachusetts Life Sciences Center Capital Grant./ ; }, abstract = {BACKGROUND: Blenderized gastrostomy tube feeds are associated with reduced gastrointestinal symptoms. We hypothesize that patients receiving blenderized tube feeds, compared with standard formula, will have less gastric-oropharyngeal microbial overlap, a possible biomarker of less gastroesophageal refluxate, and differences in beta diversity in the oropharynx, stomach, and stool.<br><br>METHODS: Children requiring enteral tube feeds for >3 months were prospectively recruited to provide saliva via posterior tongue swabs, gastric aspirates, and stool samples. Exclusion criteria were history of cystic fibrosis or solid organ transplant or antibiotic treatment course within 4 weeks. The primary exposure was diet category (formula vs. blenderized feeds). The primary outcome was Jaccard similarity between the gastric and oral microbiomes. Relationships of diet to Jaccard and relative bacterial abundance were analyzed by multivariate linear regression models adjusting for age, sex and proton pump inhibitor use.<br><br>RESULTS: Sixty (60.6%) children received blenderized tube feeds and 39 (39.4%) received formula. Beta diversity in the oral and rectal samples differed significantly between patients on blenderized versus formula feeds. Importantly, gastric and tongue microbiomes had significantly less overlap (by Jaccard distance) in patients receiving blenderized feeds, adjusting for covariates. Several key oral, gastric and stool commensal organisms were present in higher relative abundance in the blenderized versus formula group.<br><br>CONCLUSION: Oropharyngeal microbiomes are more distinct from the gastric microbiomes in patients receiving blenderized feeds, and the oropharyngeal and stool microbiomes demonstrated differential bacterial abundance compared with formula. Overall, these findings suggest a highly favorable microbial profile with blenderized feeds.}, }
@article {pmid42116335, year = {2026}, author = {Nie, Y and Lin, X}, title = {Analysis of oral microbiome characteristics and their correlation with oral health diseases.}, journal = {Medicine}, volume = {105}, number = {19}, pages = {e48600}, pmid = {42116335}, issn = {1536-5964}, mesh = {Humans ; Female ; Male ; Cross-Sectional Studies ; *Microbiota ; Middle Aged ; *Oral Health ; *Mouth Diseases/microbiology/epidemiology ; Adult ; *Mouth/microbiology ; Aged ; }, abstract = {To investigate the relationship between oral microbiome characteristics and oral health status, examining microbial diversity and the prevalence of specific bacterial genera. We conducted a cross-sectional study of 154 patients who underwent oral examinations at our hospital from January 2023 to December 2023. Based on routine oral examinations and medical history inquiries, patients were divided into oral health group (n = 71) and oral health disease group (n = 83). Oral samples were collected and analyzed using next-generation sequencing and bioinformatics to assess microbial diversity and abundance. Key demographic and behavioral factors were recorded, and statistical analyses determined oral microbiome characteristics with oral health. The oral health disease group had significantly higher average age, smoking rates, body mass index, alcohol use, family history of oral diseases, and worse oral health indicators (e.g., plaque, gum inflammation, calculus, periodontal status, decayed/missing teeth, and decayed, missing, and filled teeth scores). They also showed lower microbial diversity (Shannon, Chao1, and evenness indices) and reduced levels of protective bacteria (Streptococcus and Actinomyces). In contrast, the oral health group had higher flossing rates, more caries-free individuals, and greater microbial diversity. The Shannon, Chao1, and evenness indices were inversely linked to oral disease, while the Simpson Index (measuring dominance) was positively correlated. Protective bacteria were negatively linked to disease, whereas harmful bacteria (Fusobacterium and Prevotella) were positively correlated. Our findings highlight decreased microbial diversity as a significant factor in oral diseases, suggesting that maintaining a diverse oral microbiome was crucial for oral health.}, }
@article {pmid42116339, year = {2026}, author = {Han, GY and Wang, ZJ and Wang, DX and Wang, CY and Yang, MQ}, title = {Forging new insights in forensic microbiome studies: A 2000 to 2024 bibliometric analysis redefining the landscape.}, journal = {Medicine}, volume = {105}, number = {19}, pages = {e48661}, pmid = {42116339}, issn = {1536-5964}, mesh = {*Bibliometrics ; Humans ; *Microbiota ; *Forensic Sciences ; *Forensic Medicine ; RNA, Ribosomal, 16S ; Machine Learning ; }, abstract = {BACKGROUND: Microbial diversity has been extensively studied across various fields, including medicine and therapeutics. Its application in forensics is rapidly expanding due to its effectiveness. This study aimed to conduct a comprehensive bibliometric analysis of global research on forensic microbiome, providing a foundational knowledge framework for this emerging field.<br><br>METHODS: A comprehensive literature search was performed using the Web of Science Core Collection database to identify publications related to the forensic microbiome. Annual publication output, research collaborations, research hotspots, and developmental trends in this field were analyzed using bibliometric software (VOSviewer and CiteSpace).<br><br>RESULTS: In total, 709 articles published between 2000 and 2024 were selected. The first study in this field was published in 2000. Recently, the number of publications and citations has grown significantly. Cooperation network analysis revealed that the United States of America contributes the most to forensic microbiome research, with the highest publication volume. Michigan State University emerged as the most prolific institution. Forensic Science International is the most productive journal in this field. Carter David O. contributed the most to the articles and is the most co-cited authors. Keywords cluster analysis identified 4 major research clusters: bacteria, forensic medicine, 16s ribosomal ribonucleic acid, and machine learning. Machine learning, human microbiome, and forensic microbiology have attracted increasing attention from researchers.<br><br>CONCLUSION: This bibliometric analysis provides a data-driven and objective overview of forensic microbiome research currently, offering readers a valuable reference for future research. Our review provides insights into contemporary trends, global patterns of collaboration, fundamental knowledge, high-interest research areas, and emerging frontiers in the forensic microbiome.}, }
@article {pmid42116498, year = {2026}, author = {Wang, L and Liang, C and Yu, J and Zhang, Y and Li, H and Hu, Y and Liu, W and Qu, X and Xie, W and Wang, X and Yuan, H}, title = {Timing matters in type 2 diabetes: Early high-Fiber nutrition enhances glycemic control and reshapes gut microbiota.}, journal = {Food research international (Ottawa, Ont.)}, volume = {236}, number = {}, pages = {119257}, doi = {10.1016/j.foodres.2026.119257}, pmid = {42116498}, issn = {1873-7145}, mesh = {Humans ; *Diabetes Mellitus, Type 2/diet therapy/microbiology/blood ; *Dietary Fiber/administration &amp; dosage ; *Gastrointestinal Microbiome ; Male ; Female ; Cross-Over Studies ; Middle Aged ; *Glycemic Control/methods ; Blood Glucose/metabolism ; Glycated Hemoglobin/metabolism/analysis ; Aged ; Obesity/diet therapy ; Time Factors ; Adult ; Overweight/diet therapy ; }, abstract = {Early, intensive dietary intervention may open a therapeutic window for type 2 diabetes (T2D) remission. We conducted a randomized, 2:1 crossover trial in 34 newly diagnosed overweight or obese patients with T2D. Participants were assigned to receive either high-fiber nutritional therapy (HFNT)-a 7-day very-low-calorie, high-fiber diet followed by a 23-day standard diabetes diet-or conventional diabetes treatment (control condition). Each treatment was administered for 90 days before crossover. Compared with the control condition, early HFNT led to greater reductions in HbA1c [-9.45% (-18.04, -4.63) vs 1.44% (-7.73, 3.08); P = 0.010] and fasting plasma glucose [-12.70% (-24.51, -6.01) vs 3.46% (-8.14, 0.94); P = 0.005], while changes in BMI and HOMA-IR were not significant (P > 0.05). Gut microbiome profiling revealed enrichment of short-chain fatty acid-producing taxa (Eubacterium ruminantium group, Blautia, Roseburia, Akkermansia muciniphila, Oscillospira) and depletion of pathogenic genera (Escherichia-Shigella) after HFNT, with compositional shifts correlating with improved glycemic control. Notably, glycemic benefits in participants receiving HFNT first persisted after crossover, whereas participants receiving conventional care first did not achieve full metabolic recovery after switching. These findings suggest that in newly diagnosed T2D, early, fiber-enriched, intermittent energy restriction can induce durable glycemic improvements, potentially mediated by gut microbiota remodeling. This trial highlights a narrow but impactful nutritional intervention window that may alter the trajectory of T2D progression.}, }
@article {pmid42116511, year = {2026}, author = {Xu, H and Kong, W and Tang, Q and Fan, K and Liu, M and Mo, K and Xu, Z and Zhang, W}, title = {Analysis of microbiome succession and metabolome dynamics in Jiupei during Chinese strong-flavor Baijiu fermentation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {236}, number = {}, pages = {119274}, doi = {10.1016/j.foodres.2026.119274}, pmid = {42116511}, issn = {1873-7145}, mesh = {*Fermentation ; *Microbiota ; *Metabolome ; Food Microbiology ; Taste ; Volatile Organic Compounds/analysis ; Bacteria/metabolism/classification/genetics ; *Wine/microbiology/analysis ; Fungi/metabolism/classification ; Metabolomics ; Flavoring Agents ; China ; }, abstract = {Microbial successions during Jiupei fermentation are critical for the flavor synthesis of strong-flavor Baijiu, but their dynamics and associated metabolites across different vertical Jiupei layers have not yet been characterized in detail. This study employed metagenomic sequencing combined with metabolomic techniques to investigate the complex relationship between microbial succession and metabolite formation in Jiupei of strong-favor Baijiu fermentation. Results demonstrated that a total of 2940 compounds were identified and classified into 13 classes; of which over 94.7% of amino acids and derivatives, 57.5% of organic acids, and certain sugar alcohols increased during fermentation, whereas more than 81.8% of flavonoids decreased, particularly in the lower Jiupei layer. The volatile compounds, including ethyl caproate and ethyl lactate, showed a significant increase. Meanwhile, microbial diversity and richness dropped sharply from day 0 to day 30, with a recovery by day 60 in the middle and lower layers. The early stage of fermentation is characterized by the fungi Paecilomyces variotii, Lichtheimia ramosa, Rhizopus arrhizus, and Aspergillus chevalieri, as well as the bacteria Saccharopolyspora rectivirgula, Lactiplantibacillus plantarum, Leuconostoc citreum, and Weissella confusa, which secrete amylases and glycosylases to hydrolyze starch into sugars via enrichment of carbohydrate-related pathways, such as starch and sucrose metabolism, glycolysis/gluconeogenesis, and fructose and mannose metabolism. Acetilactobacillus jinshanensis, Lentilactobacillus diolivorans, and Philodulcilactobacillus myokoensis sharply increased in the later stage of fermentation, alongside enriched pathways for fatty acid and secondary metabolite biosynthesis. Acetilactobacillus jinshanensis ‌might synergistically accumulate characteristic flavor compounds through transferase and ligase reactions. These findings reveal the stage-specific microbial metabolic characteristics and synergistic mechanisms in flavor formation, providing a scientific basis for optimizing Baijiu fermentation processes to enhance Baijiu quality.}, }
@article {pmid42116975, year = {2026}, author = {Latt, TS and Aye, TT and Ko, K and Win, SS and Chit, TT and Myint, KNS}, title = {Restructuring the Obesity Paradigm: Molecular Etiologies, Clinical Complexities, and the Future of Precision Intervention.}, journal = {Cureus}, volume = {18}, number = {4}, pages = {e106767}, pmid = {42116975}, issn = {2168-8184}, abstract = {Obesity is a complex, chronic, and relapsing disease affecting adults globally and continues to rise across all age and socioeconomic groups. Once regarded as a lifestyle issue, obesity is now recognized as a multifactorial condition influenced by multiple factors. This review consolidates current evidence on the dynamic pathophysiology of obesity, highlighting advances in understanding its genetic foundations, hormonal imbalances, gut microbiome disruptions, and the influence of early-life exposures, and emphasizing the systemic impact of obesity through its associations with cardiometabolic diseases, certain cancers, and mental health disorders. Emerging treatment paradigms include glucagon-like peptide-1 and dual agonists, endoscopic and surgical interventions, and microbiota-directed therapies. Advances in artificial intelligence and precision medicine are also redefining individualized care. Despite these developments, obesity remains underdiagnosed and undertreated in many healthcare systems. In high-income regions, the uptake of advanced therapies is limited by fragmented care pathways, in which obesity management is spread across multiple uncoordinated providers, and by affordability barriers due to high costs. In low-resource settings, constrained infrastructure and competing health priorities continue to hinder timely diagnosis and treatment. A shift toward holistic, patient-centered, and equity-driven models of care is essential for effectively addressing the global burden of obesity and improving long-term health outcomes.}, }
@article {pmid42117346, year = {2026}, author = {Nguyen, HKD and Jones, PJ and Kendal, D and Powell, SM and Raspin, K and Dickinson, J and Flies, EJ}, title = {A Comparison of the Gut Microbiome of Two Sympatric Macropods Along an Urbanisation Gradient in Tasmania.}, journal = {Environmental microbiology reports}, volume = {18}, number = {3}, pages = {e70359}, pmid = {42117346}, issn = {1758-2229}, support = {//Holsworth Wildlife Research Endowment/ ; }, mesh = {*Gastrointestinal Microbiome/genetics ; Tasmania ; *Macropodidae/microbiology ; Urbanization ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification ; Sympatry ; Feces/microbiology ; Parks, Recreational ; Cities ; Animals ; }, abstract = {This study investigates the gut flora of the red-necked wallaby (Notamacropus rufogriseus rufogriseus) and the Tasmanian pademelon (Thylogale billardierii) in the small city of Hobart, Tasmania, Australia. Faecal samples were collected from greenspaces across the Greater Hobart region. These greenspaces were chosen in areas with different human population densities. DNA was extracted from these samples, and targeted sequencing of the bacterial 16S ribosomal RNA gene was performed to understand the bacterial community. Our results showed that despite the many shared ecological traits between the two species, their gut microbiome displayed different responses to urban living. Alpha and beta diversity were significantly different across the urban gradient for Bennett's wallaby, but not for Tasmanian pademelon. Relative composition for both species was different across the urbanisation gradient. Some bacterial taxa associated with nutrient processing showed the clearest changes. The conclusion of this research is that living in cities can affect the gut microbiome of these two marsupial herbivores. More studies are needed to determine whether this has implications for the health of these species.}, }
@article {pmid42117437, year = {2026}, author = {Tumelty, M and Patel, K and Petersen, H and Delaney, C and Lappin, D and Gibson, J and Ramage, G and van der Gast, C and Smith, A and Nile, CJ}, title = {Investigations into the aetiopathogenesis of orofacial granulomatosis using multiple omics technologies reveal a potential role for B cells.}, journal = {Clinical and translational medicine}, volume = {16}, number = {5}, pages = {e70689}, doi = {10.1002/ctm2.70689}, pmid = {42117437}, issn = {2001-1326}, support = {//Royal College of Surgeons of England/ ; //Royal College of Physicians and Surgeons of Glasgow/ ; //Tenovus Scotland/ ; //University College London Hospitals Biomedical Research Centre/ ; //NIHR Newcastle Biomedical Research Centre/ ; }, }
@article {pmid42117804, year = {2026}, author = {Zalila-Kolsi, I and Al-Barazie, R}, title = {Probiotics and the Human Microbiome: Classical Functions, Emerging Systemic Roles, and Future Therapeutic Frontiers.}, journal = {Biology}, volume = {15}, number = {9}, pages = {}, doi = {10.3390/biology15090665}, pmid = {42117804}, issn = {2079-7737}, abstract = {Probiotics, live microorganisms that confer health benefits when administered in adequate amounts, are increasingly recognized as modulators of interconnected microbiome-host networks that extend beyond gastrointestinal function. This review synthesizes evidence on classical probiotic roles in maintaining gut homeostasis, immune regulation, and infection prevention, while integrating emerging systemic effects across the gut-brain, gut-skin, gut-oral, and metabolic axes. Rather than presenting isolated outcomes, we adopt a systems-level framework that links probiotic actions to shared mechanisms, including microbial metabolite signaling (e.g., SCFAs), competitive exclusion of pathobionts, barrier reinforcement, and immune-neuroendocrine pathway modulation. We further discuss translational advances that enable rational probiotic design, including targeted delivery platforms (encapsulation and protective matrices), engineered/next-generation strains, and postbiotic-inspired strategies, alongside sustainability considerations and regulatory/labeling challenges. Finally, we outline future directions emphasizing precision microbiome-centered interventions, synthetic biology, and AI-assisted multi-omics analysis to support strain- and context-specific probiotic strategies. Collectively, this review provides an integrated, systems-oriented synthesis to guide future research and accelerate safe clinical and industrial applications of probiotics.}, }
@article {pmid42117816, year = {2026}, author = {Chen, H and Wang, W and Ye, X and Feng, L and Wang, M and Xie, T and Ren, D and Song, Y and Chen, S and Zhang, C and Zhu, W}, title = {Gut Microbiota Assembly and Host Phenotypic Variation: Core Adaptive Strategies of Triplophysa yarkandensis (Cypriniformes: Nemacheilidae) to Saline-Alkaline Stress.}, journal = {Biology}, volume = {15}, number = {9}, pages = {}, doi = {10.3390/biology15090677}, pmid = {42117816}, issn = {2079-7737}, support = {32541125//National Natural Science Foundation of China/ ; TDZKBS202534//The President's Fund of Tarim University/ ; TDZKBS202543//The President's Fund of Tarim University/ ; 525307003//"Tianchiyingcai" Introduction Project/ ; 525307006//"Tianchiyingcai" Introduction Project/ ; }, abstract = {Triplophysa yarkandensis (Cypriniformes: Nemacheilidae), a rare endemic fish in the Tarim River Basin, Xinjiang, China, plays a pivotal role in maintaining the stability of plateau saline-alkaline aquatic ecosystems, yet its survival is increasingly threatened by habitat salinization. However, the multi-dimensional synergistic adaptation mechanisms linking its phenotypic variation, intestinal structure, and associated microbial communities to extreme saline-alkaline stress remain poorly understood. In this study, we innovatively integrated morphological/intestinal histological characterization, 16S rRNA gene sequencing, and microbial ecological analyses (co-occurrence networks and assembly processes) to systematically decode its adaptive strategies. Results revealed that T. yarkandensis exhibits a streamlined body shape, morphological variability, and elongated intestinal villi that may support locomotion and nutrient/ion uptake under osmotic stress. Its gut exerts a stringent selective filter, driving distinct differentiation between water and gut microbial communities-with gut-enriched core taxa (Aurantimicrobium and Aestuariivirga) and functional pathways (unsaturated fatty acid biosynthesis and ABC transporters) specialized for osmoregulation. Notably, the water microbial assembly is dominated by stochastic processes, while the gut assembly relies on host-driven deterministic selection, forming a habitat-specific adaptive pattern. These findings uncover the synergistic adaptation system of host phenotype and gut microbiota for survival in extreme saline-alkaline habitats, advancing our understanding of fish-microbe co-evolution in extreme ecosystems and providing critical theoretical support for the conservation of rare plateau fish, as well as guidance for the utilization of saline-alkaline water resources in aquaculture.}, }
@article {pmid42117850, year = {2026}, author = {Asylbekkyzy, L and Kossalbayev, BD and Ahmad, F and Wang, J and Sadvakasova, AK and Bauenova, MO and Abseyt, AA and Zaletova, DE}, title = {Environmental Filtering of Bacterial Communities Driven by Pesticide Residue Profiles in the Almaty Region, Kazakhstan.}, journal = {Biology}, volume = {15}, number = {9}, pages = {}, doi = {10.3390/biology15090712}, pmid = {42117850}, issn = {2079-7737}, abstract = {Soil contamination by complex pesticide mixtures poses a systemic threat to ecosystem health, yet the mechanisms of microbial community assembly under the coexistence of legacy and modern pollutants remain insufficiently understood. This study evaluated the influence of legacy organochlorine pesticides (OCPs) versus current-use agrochemicals on the structure and inferred functional potential of soil bacterial communities in the Almaty Region, Kazakhstan, using high-throughput 16S rRNA gene sequencing and GC-MS/MS analysis of 217 compounds. Results revealed a clear contrast between contamination regimes: modern organophosphate insecticides and herbicides, such as simazine (up to 32.3 mg kg[-1] at the Amangeldy site), were associated with lower alpha diversity (Shannon ≈ 3.03) and enrichment of copiotrophic taxa such as Pseudomonas and Sphingobium. In contrast, persistent OCP residues, such as p,p'-DDE (up to 1.43 mg kg[-1] at the Kyzylkairat site), were associated with higher diversity (Shannon ≈ 5.46) and enrichment of more stress-tolerant oligotrophic lineages, including Acidobacteria and Vicinamibacteraceae. Procrustes analysis supported significant concordance between pesticide profiles and taxonomic structure (M[2] = 0.286, p < 0.001), indicating that pesticide residue composition was strongly associated with bacterial community structure across the studied soils. The observed shift in community balance, particularly the relative increase in Pseudomonas versus Acidobacteria, is proposed as a candidate compositional indicator of ecosystem instability in semi-arid agricultural soils and may inform future remediation-oriented studies.}, }
@article {pmid42117863, year = {2026}, author = {Li, D and Deng, Y and Zhao, X and Liao, Q and Chen, J and Li, C and Liao, H}, title = {Soil pH and Nitrogen Content Drive the Succession of RubisCO-Harboring Microbial Communities Across Picea asperata Plantation Ages.}, journal = {Biology}, volume = {15}, number = {9}, pages = {}, doi = {10.3390/biology15090725}, pmid = {42117863}, issn = {2079-7737}, support = {2024NSFSC0849&#xff1b;2025ZNSFSC1221//Sichuan Science and Technology Program/ ; SCJJ24ZD68//the historical study of ancient and famous trees along the Shu Dao Roads: a case study of Cuiyun Corridor in Zitong/ ; }, abstract = {Autotrophic carbon-fixing microbes can assimilate atmospheric carbon dioxide into biomass via the Calvin-Benson-Bassham (CBB) cycle (their primary carbon fixation pathway), thereby reinforcing soil carbon sequestration in the plantation ecosystem; however, the succession of RubisCO-harboring microbial communities across stand ages remains poorly understood. Here, we investigated the community succession of microbes carrying the gene encoding RubisCO, a key enzyme in the CBB cycle, across a stand-age chronosequence in a Picea asperata plantation ecosystem. Our results revealed a progressive decrease in microbial α-diversity and a significant restructuring of community composition with increasing stand age, characterized by an enrichment of Proteobacteria and a concomitant depletion of Actinobacteria. While the Shannon-Wiener index was most strongly correlated with soil total nitrogen content, redundancy analysis identified soil pH as the predominant environmental driver of community turnover, a relationship that was found to be threshold-dependent, with substantial community shifts occurring in response to pH variations of 0.5 to 1.0 units. These findings suggest that sustaining the diversity of RubisCO-harboring microbes in older stands-a process potentially enhanced by soil nitrogen management-provides a viable strategy for augmenting the carbon sequestration capacity of managed forests through targeted microbiome regulation.}, }
@article {pmid42118059, year = {2026}, author = {Vaishnav, A and Jansa, J}, title = {Arbuscular mycorrhizal fungi- linked microbial processes in soil nitrogen cycling.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag050}, pmid = {42118059}, issn = {1574-6941}, abstract = {Arbuscular mycorrhizal fungi (AMF) create an extended plant-soil interface (referred to as mycorrhizal hyphosphere) where specific microbial interactions shape key steps of the nitrogen (N) cycle. Extraradical hyphae of the AMF host diverse microbes that help mineralize organic substrates, regulate ammonium and nitrate transformations, and enhance N retention. These processes allow plants to access both inorganic N and the N released from complex organic compounds. This review synthesizes current evidence for AMF-microbe interactions in relation to mineralization, nitrification, denitrification, and (di)nitrogen fixation. It also highlights unresolved questions, such as when AMF transition from facilitating to competing for N, how they access stabilized organic N pools, and how the carbon:nitrogen:phosphorus (C:N:P) nutrient stoichiometry of the soil environment constrain AMF-mediated N transfer to plants. Furthermore, we discuss how AMF-centered pathways can contribute to more circular N flows in agroecosystems by promoting tighter internal N cycling through microbial immobilization, turnover, and subsequent transfer to plants via AMF hyphae. By integrating spatial, microbial, and stoichiometric perspectives, this review provides a mechanistic framework for understanding AMF-driven N dynamics and their potential role in enhancing N use efficiency in managed and natural systems.}, }
@article {pmid42118196, year = {2026}, author = {Stewart, J and Ockert, LE and Hawke, T and Power, M and Bino, G}, title = {First insights into the Drivers of the Cloacal Microbiome of the Wild Platypus (Ornithorhynchus anatinus).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02788-1}, pmid = {42118196}, issn = {1432-184X}, abstract = {The host microbiome plays a critical role in wildlife health, reproduction, and environmental responses. The platypus (Ornithorhynchus anatinus), a semi-aquatic monotreme endemic to eastern Australia, has remained microbiologically understudied despite conservation concern. Here, we present the first characterisation of the wild platypus cloacal microbiome using 16 S rRNA amplicon sequencing of samples collected across its eastern range, including sites recently affected by drought and bushfire. We found that region, and environmental disturbances such as bushfire and drought were significant drivers of bacterial community structure and composition, with influence from sex and breeding season also. Bushfire and drought both disrupted microbial community structure. The microbiome partially recovered following low-severity fires, but not after severe fire or prolonged drought, suggesting that microbiome resilience is linked to disturbance intensity. These findings suggest that the platypus microbiome is sensitive to environmental pressures and may offer a minimally invasive indicator of individual and ecosystem health. In addition to these ecologically important findings, across all sampled regions the platypus cloacal microbiome was consistently dominated by Campylobacterota and Fusobacteriota, with Pseudomonadota and Bacillota also prominent in the core microbiomes. Our results provide a critical baseline for integrating microbial health into conservation planning for this unique mammal.}, }
@article {pmid42118217, year = {2026}, author = {Thakur, S and Chaitanya, MVNL and Singh, SK and Khurana, N and Selvaraj, J and M, AL and Mazumder, A and Sengupta, P}, title = {Urolithin A: A Novel Postbiotic for inflammation, aging, and cancer: A Journey from Dietary ellagitannins to clinical use.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {42118217}, issn = {1573-4978}, mesh = {Humans ; *Coumarins/pharmacology/therapeutic use/metabolism ; *Neoplasms/drug therapy/metabolism ; *Inflammation/drug therapy/metabolism ; *Aging/drug effects ; Gastrointestinal Microbiome/drug effects ; *Hydrolyzable Tannins/metabolism/pharmacology ; Animals ; }, abstract = {BACKGROUND: Urolithin A (UA) is synthesized when the body metabolizes ellagic acid and ellagitannins. UA has been a widely recognized physiologically active compound throughout the previous decade. The gut microbiota affects metabolic regulators AMPK and sirtuins, initiates autophagy, and activates mitochondrial quality control, which is essential for infection resistance, intestinal health, and inflammation reduction.<br><br>METHODS: A preclinical study indicates that UA alters cancer cell metabolism, fortifies the intestinal barrier, safeguards the brain, and supports skeletal muscle health. UA enhances muscle endurance, mitochondrial function indicators, and cardiometabolic health without side effects or adverse reactions in preliminary human trials, primarily including the elderly and sedentary individuals. UA production exhibits significant variability due to the heterogeneity of gut flora. The existing classifications of A, B, and O kinds, absence of longitudinal data, limited trial sizes, and inconsistency between results and real-world outcomes impede the pharmaceutical advancement of UA.<br><br>RESULTS: This review commenced with an examination of UA's origins, chemical properties, gastrointestinal metabolism, absorption, molecular functions, and therapeutic potential. The literature's validity, applicability, and knowledge gaps indicate that UA is a postbiotic treatment that influences the gut microbiome's impact on mitochondrial pathways affecting various bodily systems, considering the intricate connections among inflammation, aging, and cancer. Comprehensive clinical trials are required to validate the optimal composition, dosage, and therapeutic efficacy.}, }
@article {pmid42118429, year = {2026}, author = {Tekin, B and Gurbanov, R}, title = {Taxonomic and functional remodeling of the gut microbiota during aging and implications for microbiota-derived biomarkers.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {6}, pages = {}, pmid = {42118429}, issn = {1573-0972}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Aging/physiology ; Biomarkers/analysis ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Animals ; Host Microbial Interactions ; Fatty Acids, Volatile/metabolism ; }, abstract = {The gut microbiota represents a complex microbial ecosystem that contributes to host metabolic regulation, immune homeostasis, and intestinal barrier function. Across the lifespan, gut microbial communities exhibit marked taxonomic and functional variation driven by environmental exposures, dietary patterns, medication use, and age-associated immune alterations. These differences are closely linked to chronic inflammatory states and immune dysregulation that accompany aging. This review synthesizes current evidence on age-associated differences in gut microbiota composition and functional capacity, with a focus on microbial traits and metabolic pathways relevant to host-microbe interactions. Pathological aging is frequently associated with reduced microbial diversity, loss of short-chain fatty acid-producing commensal bacteria, and enrichment of opportunistic or pro-inflammatory taxa. In contrast, healthy aging and longevity are commonly associated with more stable, resilient, and metabolically adaptable microbial communities. At the functional level, recurrent alterations in short-chain fatty acid biosynthesis, bile acid transformation, and tryptophan- and choline-related metabolic pathways define conserved features across aging-associated microbial profiles. Across neurodegenerative, metabolic, and cardiovascular conditions, overlapping taxonomic and functional patterns indicate shared microbiota-associated signatures linked to inflammatory states. Advances in metagenomic sequencing, functional annotation, and microbiome-focused biotechnological approaches now enable integrated analysis of microbial structure and metabolic potential. These developments provide a robust framework for identifying reproducible microbiome-based indicators relevant to aging-associated physiological changes and for translating microbiome research into biotechnology-driven applications.}, }
@article {pmid42118552, year = {2026}, author = {Palacios, S and Martin, J and Hernandez, I and Orozco, R}, title = {Estradiol loss, the "estrobolome," and midlife symptoms: what the gut microbiome adds to menopause care.}, journal = {Menopause (New York, N.Y.)}, volume = {}, number = {}, pages = {}, pmid = {42118552}, issn = {1530-0374}, abstract = {IMPORTANCE AND OBJECTIVE: Menopause is characterized by sustained estradiol decline affecting vasomotor, metabolic, skeletal, and neurobehavioral systems. Emerging evidence suggests that the gut microbiome may interact with endocrine pathways during this life stage.<br><br>METHODS: Narrative review of literature examining relationships between menopause, estradiol signaling, gut microbiome composition, and symptom domains. Artificial intelligence (AI) disclosure: artificial intelligence tools were used for language editing and to assist in the preliminary creation of a conceptual illustration. All scientific content, literature interpretation, and final manuscript preparation were performed and reviewed by the authors. The authors take full responsibility for the accuracy, integrity, and originality of the work.<br><br>DISCUSSION AND CONCLUSION: Current evidence indicates menopause is associated with shifts in gut microbial diversity and metabolic function. However, most human evidence remains observational and associative, and causal mechanisms remain to be established.}, }
@article {pmid42118590, year = {2026}, author = {Qu, P and Ding, S and Zhang, Y and Zhao, Y and Song, E and Hu, L and Ding, R and Cao, W and Hou, Y and Qi, J and Zhao, J and Duan, C and Liu, S and Shen, C and Zhao, Y and Guo, Y and Zheng, Z and Luo, S and Hu, H and Bai, L and Zhao, S and Wang, B and He, S and Wu, Y and Xiong, X and Wu, Q and Gu, W and Rom, O and Xu, A and Zheng, L and Zhang, J and Liu, E and Chen, YE}, title = {Metabolic dysfunction-associated steatohepatitis exacerbated by Clostridium perfringens-derived ammonia is attenuated by tripeptide DT-109.}, journal = {The Journal of clinical investigation}, volume = {}, number = {}, pages = {}, doi = {10.1172/JCI200522}, pmid = {42118590}, issn = {1558-8238}, abstract = {The global prevalence of metabolic dysfunction-associated steatohepatitis (MASH) is rising, driven by a complex interplay of metabolic disturbances, inflammation, and fibrosis, yet effective treatment options remain limited. This study examined the relationships among intestinal microbial dysbiosis, ammonia production, and hepatic CD8+ T cell activity in MASH, and assessed the therapeutic potential of DT-109, a glycine-based tripeptide. We investigated the gut-liver axis across human cohorts and both non-human primate and mouse MASH models. Multi-omics approaches were used to characterize ileal microbiota, ammonia levels, and hepatic immune and metabolic pathways. Causality was verified through microbiota transplantation, C. perfringens NirA-knockout mutants, and functional validation in vitro and in vivo. The efficacy of DT-109 was evaluated in non-human primates and mice. Our results revealed a significant increase in the ammonia-producing gut bacterium C. perfringens, which led to elevated intestinal ammonia and disruption of the intestinal barrier in MASH. Elevated ammonia levels triggered FosB-mediated upregulation of chemokine C-C motif ligand 5 (CCL5) in CD8+ T cells, which in turn drove T cell cytotoxicity in the liver. Notably, DT-109 effectively lowered C. perfringens abundance, reduced intestinal ammonia, restored intestinal barrier integrity, and alleviated CD8+ T cell dysregulation in MASH. These results identify a distinct mechanism in which gut-derived ammonia drives CD8+ T cell-mediated MASH and demonstrate that DT-109 effectively targets this axis by inhibiting C. perfringens and reducing ammonia, ultimately ameliorating MASH.}, }
@article {pmid42118793, year = {2026}, author = {Kawashima, M and Aoki, T and Hamada, H and Watanabe, C and Oyanagi, E and Kono, T and Yamagata, T and West, NP and Yano, H}, title = {Continuous high-fat high-sugar diet overrides the therapeutic potential of fecal microbiota transplantation from exercised and/or inulin-conditioned donors in obese mice.}, journal = {PloS one}, volume = {21}, number = {5}, pages = {e0349286}, doi = {10.1371/journal.pone.0349286}, pmid = {42118793}, issn = {1932-6203}, mesh = {Animals ; *Fecal Microbiota Transplantation/methods ; *Inulin/pharmacology/administration &amp; dosage ; Male ; *Diet, High-Fat/adverse effects ; *Obesity/therapy/etiology/microbiology/metabolism ; Mice ; Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; *Physical Conditioning, Animal ; Fatty Acids, Volatile/metabolism ; Mice, Obese ; Feces/microbiology ; }, abstract = {Fecal microbiota transplantation (FMT) is a promising therapeutic strategy for obesity and related metabolic disorders. Exercise and dietary fiber intake, such as inulin supplementation, have been shown to differentially modulate the gut microbiota and synergistically improve metabolic health. The present study aimed to investigate whether FMT from lean donor mice subjected to voluntary exercise and/or inulin supplementation could ameliorate metabolic dysfunction in high-fat high-sugar diet (HFHSD)-induced obese mice. Four-week-old male C57BL/6J mice were fed HFHSD throughout the experimental period and assigned to one of five groups: sham FMT, FMT from sedentary donors, from exercised donors, from inulin-supplemented donors, or from donors receiving both interventions. Following 12 weeks of obesity induction, mice were treated with antibiotics and then underwent a 4-week FMT protocol. Physical and metabolic parameters, gut microbial composition, and cecal short-chain fatty acid (SCFA) levels were examined in both donors and recipients. The results demonstrated that FMT from exercised and/or inulin-supplemented donors failed to improve obesity-related phenotypes or glucose intolerance in recipients. These outcomes were accompanied by only partial alterations in gut microbiota and SCFA profiles. Collectively, our findings suggest that persistent HFHSD exposure compromises the colonization and function of beneficial microbes, limiting the metabolic benefits of FMT. Successful application of FMT in severe obesity may require prior optimization of the host intestinal environment through dietary interventions or microbiome-targeted strategies.}, }
@article {pmid42118940, year = {2026}, author = {Zhang, H and Stackpole, K and Iglesia, CB}, title = {Femtech Revolution for Pelvic Floor Disorders and Sexual Health.}, journal = {Urogynecology (Philadelphia, Pa.)}, volume = {}, number = {}, pages = {}, pmid = {42118940}, issn = {2771-1897}, abstract = {IMPORTANCE: Consumer-directed female technology ("femtech") is rapidly expanding into pelvic floor and sexual health, yet clinicians have limited guidance on the safety, efficacy, and appropriate use of these products.<br><br>OBJECTIVES: The objective of this review is to summarize currently marketed female technology products relevant to pelvic floor disorders, sexual function, and vaginal health, and to highlight key evidence, limitations, and implications for clinical practice.<br><br>STUDY DESIGN: This is a narrative review of commercially available technologies for urinary incontinence, sexual dysfunction, and vaginal health. Product categories include external and intravaginal pelvic floor muscle training devices, vibrators, and dilators for sexual function and pain, regenerative medicine interventions such as platelet-rich plasma injections, sexual wellness applications, and direct-to-consumer vaginal microbiome testing platforms.<br><br>RESULTS: Pelvic floor devices and in-office energy therapies offer nonsurgical options for urinary incontinence, but high-quality, independent long-term data are scarce, and costs are often substantial. Sexual wellness devices, including vibrators and dilators, are increasingly recognized as therapeutic tools but are variably supported by clinical research. Early studies of platelet-rich plasma suggest potential benefit for sexual function, yet protocols and outcomes remain heterogeneous. Digital applications and microbiome tests expand access and patient engagement but frequently lack rigorous validation and may raise concerns regarding privacy, equity, and interpretation of results.<br><br>CONCLUSIONS: Female technology offers novel opportunities to address pelvic floor and sexual health outside traditional care pathways. Urogynecologists should be familiar with these products, provide balanced counseling on benefits, risks, and cost, and advocate for independent trials to define their role within evidence-based care.}, }
@article {pmid42119038, year = {2026}, author = {López Tacoaman, YF and Alcivar, M and Alujević, K and Bakewell, L and Curlis, JD and Gonzalez, A and Gripshover, ND and Gulati, S and Pirani, RM and Ratia, N and Romero, D and Wuthrich, KL and Cox, CL and Logan, ML and McMillan, WO and Fontaine, SS and Williams, CE}, title = {Host and Environmental Drivers of Gut Microbiome Variation in Wild Anolis Lizards.}, journal = {Molecular ecology}, volume = {35}, number = {9}, pages = {e70358}, doi = {10.1111/mec.70358}, pmid = {42119038}, issn = {1365-294X}, support = {DEB-2024157//National Science Foundation/ ; DEB-2024179//National Science Foundation/ ; DEB-2024109//National Science Foundation/ ; //Smithsonian Tropical Research Institute/ ; }, mesh = {Animals ; *Lizards/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; Panama ; RNA, Ribosomal, 16S/genetics ; Environment ; Symbiosis ; }, abstract = {Animals maintain close associations with diverse microbiota that inhabit their digestive tracts, and these associations can profoundly affect host physiology and fitness. Gut microbiome composition is shaped by both host traits and environmental factors, yet the relative importance of these forces remains unclear in many taxa, including squamate reptiles (lizards and snakes). To address this gap, we analysed the gut microbiomes of seven species of Anolis lizards in the lowland tropical rainforest of central Panama. We sought to determine how environmental and host species characteristics shaped gut microbiome composition. Specifically, we examined (1) interspecific variation in the anole gut microbiome, (2) the relative roles of environment and host species in shaping gut microbiomes across two study locations, and (3) patterns of phylosymbiosis. We found that host-related factors (species identity, body size, and phylogenetic distance) were significant predictors of the composition of Anolis gut microbiomes. However, environmental factors, including locality and year of sampling (associated with temperature, humidity, and precipitation), also exerted significant effects. We detected evidence of phylosymbiosis, but this pattern was moderate, possibly due to the strong effect of environmental variation. Our work contributes to the growing body of literature on lizard gut microbiomes by using comparative observations across habitats and species to identify the factors that shape these communities in the wild.}, }
@article {pmid42119192, year = {2026}, author = {Stemen, EL and Radka, CD}, title = {Lactobacillus iners at the nexus of microbiota, immunity, and pregnancy.}, journal = {Journal of reproductive immunology}, volume = {175}, number = {}, pages = {104909}, doi = {10.1016/j.jri.2026.104909}, pmid = {42119192}, issn = {1872-7603}, abstract = {Pregnancy induces a dynamic reconfiguration of the vaginal microbiome, typically marked by increased dominance of Lactobacillus species and reduced microbial diversity. Among these bacteria, Lactobacillus iners stands out for its unique genomic traits, controversial associations with vaginal health, and frequent presence across all stages of gestation. This review synthesizes current literature on the maternal microbiome with a focus on L. iners, exploring its strain-level diversity, metabolic idiosyncrasies, and inflammatory potential. We discuss how host factors such as ethnicity, sexual activity, maternal age, and especially obesity, influence microbial composition, and evaluate conflicting data surrounding L. iners in contexts like in vitro fertilization, preterm birth, and postpartum recovery. Emerging evidence suggests that L. iners may act as a transitional species, whose effect on pregnancy outcomes depends on its abundance, genetic features, and interactions with the host immune system. We also assess limitations of current animal models and propose future directions for understanding this enigmatic bacterium. Unraveling the role of L. iners will be essential to predicting, preventing, and managing adverse pregnancy outcomes in diverse populations.}, }
@article {pmid42119272, year = {2026}, author = {Amico, MD and Skowron, M and Centkowska, K and Mikolaszek, B and Rappa, F and Baranska-Rybak, W and Ruchala, J and Cal, K and Rzeszutek, I and Górska-Ponikowska, M}, title = {Lactobacillus-derived extracellular vesicles as postbiotic modulators of redox signalling and cellular senescence in skin homeostasis.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {199}, number = {}, pages = {119457}, doi = {10.1016/j.biopha.2026.119457}, pmid = {42119272}, issn = {1950-6007}, abstract = {The skin acts as a dynamic barrier-combining physical, chemical, and immunological defences-while hosting a diverse microbiome essential for cutaneous homeostasis. Dysbiosis and impaired redox balance are linked to various inflammatory conditions; however, the mechanisms by which microbial signals regulate skin cell senescence remain unclear. This study evaluated the effects of Lactobacillus-derived extracellular vesicles (EVs) on human keratinocytes (HaCaTs) and dermal fibroblasts (HDFs) under both physiological and stress-induced premature senescence (SIPS) conditions. SEM analysis confirmed the presence of spherical membrane-bound structures consistent with EV morphology, providing a qualitative characterisation. Functional assays indicate that low concentrations of EVs (1.25-2.5% v/v) increase the metabolic activity of HaCaT cells; however, only the 1.25% v/v concentration significantly promotes early wound closure, whereas the 2.5% v/v concentration induces a decoupling between metabolism and motility. In HDFs, EVs significantly reduced basal intracellular reactive oxygen species (ROS) levels, demonstrating an inherent capacity to modulate redox homeostasis. Furthermore, immunofluorescence analysis revealed that EVs exert cell-specific and context-dependent modulatory effects on the DNA damage response (DDR) and senescence-associated secretory phenotype (SASP). While EVs significantly regulated p21, 53BP1, and MMP-3 expression across both cell types under both basal and SIPS conditions, a specific modulation of COX-2 was observed exclusively in fibroblasts following SIPS induction. These results indicate that Lactobacillus-derived EVs support epidermal regeneration and protect dermal cells from molecular senescence by modulating redox-sensitive pathways. Our findings highlight the potential of these vesicles as multifunctional postbiotic regulators-providing a mechanistic basis for future strategies aimed at maintaining skin homeostasis and mitigating cellular ageing.}, }
@article {pmid42119275, year = {2026}, author = {Tuniyazi, M and Gao, R and Song, H and Zhao, L and Reheman, A and Qi, M}, title = {Methylated tirilazad alleviates DSS-induced colitis in mice through reciprocal microbiome-metabolome.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {199}, number = {}, pages = {119468}, doi = {10.1016/j.biopha.2026.119468}, pmid = {42119275}, issn = {1950-6007}, abstract = {Ulcerative colitis (UC) pathogenesis involves complex interactions between inflammatory reactions, gut dysbiosis, metabolic disruption, and barrier dysfunction. Current therapies primarily target inflammation but fail to correct the underlying dysbiotic ecosystem. We hypothesized that methylated tirilazad (MT), a synthetic 21-aminosteroid with the antioxidant properties of tirilazad, would alleviate colitis by orchestrating a beneficial restructuring of the gut microbiome and its metabolic output. Using a DSS-induced murine colitis model in C57BL/6 mice, we evaluated MT via integrated multi-omics approaches, including 16S rRNA gene sequencing and untargeted metabolomics, coupled with correlation network analysis. In vitro experiments using human intestinal Caco-2 cells were further performed to verify the direct anti-inflammatory effects of MT. MT treatment ameliorated clinical severity, suppressed systemic and colonic inflammation (reducing IL-6, TNF-α; elevating IL-10), restored gut barrier integrity (increasing Occludin, ZO-1), and mitigated oxidative stress. 16S rRNA sequencing revealed that MT reversed DSS-induced dysbiosis, uniquely enriching for the probiotic species Lactobacillus johnsonii (8.4-fold) while suppressing pathobionts like Desulfovibrio fairfieldensis (13.3-fold reduction). Metabolomic analysis showed that MT normalized colitis-associated metabolic disturbances, specifically downregulating the pro-inflammatory eicosanoid 12R-HETE and upregulating barrier-supportive dipeptides (e.g., Gly-Tyr). Integrated correlation analysis established 12R-HETE as a key node, positively linked to pathogenic bacteria and inflammation, and negatively to barrier proteins. In vitro cell experiments confirmed that MT directly inhibited LPS-induced pro-inflammatory cytokine expression in Caco-2 cells. Our findings demonstrate that MT alleviates colitis not merely through direct anti-inflammatory action, but via a reciprocal microbiome-metabolome reprogramming loop, wherein microbial restructuring drives metabolome correction, which in turn reinforces barrier integrity and immune homeostasis. This positions MT as a novel microbiota-metabolome-directed therapeutic candidate that addresses both the symptomatic and root causes of UC.}, }
@article {pmid42119288, year = {2026}, author = {Yuan, T and Yang, S and Hu, A and Cui, J}, title = {Attapulgite-supported nanoscale zero-valent iron promotes iron cycling and microbial synergy for the simultaneous remediation of cadmium and arsenic in paddy soils.}, journal = {Journal of hazardous materials}, volume = {512}, number = {}, pages = {142275}, doi = {10.1016/j.jhazmat.2026.142275}, pmid = {42119288}, issn = {1873-3336}, abstract = {The antagonistic environmental geochemical behaviors of cadmium (Cd) and arsenic (As) present a critical challenge for the simultaneous remediation of contaminated paddy soils. Here, we report the synthesis of attapulgite-supported nanoscale zero-valent iron (ATP-nZVI), and its remediation performance was systematically investigated. Batch adsorption kinetics studies showed that ATP-nZVI material exhibits superior adsorption capacity performance for Cd and As compared with its individual components. Importantly, the pot experiment demonstrated that ATP-nZVI application significantly increased soil pH and iron content, while concurrently enriching the soil microbiome, especially iron- and arsenic-reducing bacteria. This synergistic Fe-microbe interaction stimulated iron cycling, effectively reducing the bioavailability of Cd and As and promoting the formation of iron plaques in rice roots. Consequently, ATP-nZVI treatment decreased Cd and As accumulation in rice grains by 86.49% and 19.15%, respectively, while enhancing grain yield and essential micronutrient profiles (Zn, Mn, Cu, Fe and Mg). This work offers a cost-effective, eco-friendly and sustainable remediation strategy for the integrated management of multi-heavy metal contaminated agricultural soils.}, }
@article {pmid42119367, year = {2026}, author = {Hasavci, D and Blank, T}, title = {Rogue gut microbes derail memory.}, journal = {Immunity}, volume = {59}, number = {5}, pages = {1177-1179}, doi = {10.1016/j.immuni.2026.04.008}, pmid = {42119367}, issn = {1097-4180}, mesh = {*Gastrointestinal Microbiome/immunology ; Humans ; Animals ; *Memory/physiology ; Hippocampus ; Myeloid Cells/immunology ; Inflammation/immunology ; Fatty Acids/metabolism ; Mice ; }, abstract = {The gut microbiome contributes to age-related cognitive decline, but signaling mechanisms remain unclear. In a recent issue of Nature, Cox et al. show that P. goldsteinii-derived fatty acids activate myeloid cells, thus inducing inflammation that disrupts vagal signaling and hippocampal memory encoding.}, }
@article {pmid42119379, year = {2026}, author = {Su, W and Liu, J and Liu, Y and Zhao, J and Liu, Y and Wang, J and Yu, W and Jin, G and Li, L and Yan, R and Li, A and Zhao, H}, title = {Characterizing the impact of the environmental exposome on the oral microbiome and its role in mortality: An exposome-wide association study.}, journal = {Ecotoxicology and environmental safety}, volume = {318}, number = {}, pages = {120226}, doi = {10.1016/j.ecoenv.2026.120226}, pmid = {42119379}, issn = {1090-2414}, abstract = {BACKGROUND: The oral microbiome is a critical interface between environmental influences and human health, but its response to the cumulative exposome remains poorly characterized. We investigated the associations among the environmental exposome, the oral microbiome, and all-cause mortality.<br><br>METHODS: Among 6901 nationally representative U.S. adults, we implemented an Exposome-Wide Association Study (ExWAS) framework and the Deletion/Substitution/Addition algorithm to assess associations of 100 environmental chemical exposures with oral microbial diversity and taxa using survey-weighted linear regression models. Survey-weighted Cox proportional hazards models assessed associations between exposures and all-cause mortality. Multiple comparisons were controlled using the Benjamini-Hochberg false discovery rate. Mediation analysis explored the potential role of the oral microbiome in the exposure-mortality associations.<br><br>RESULTS: Tobacco-related exposures, including volatile organic compound metabolites (2,5-dimethylfuran and furan), polycyclic aromatic hydrocarbons (PAHs; 2-hydroxyfluorene and 3-hydroxyfluorene), and nicotine metabolites, showed the strongest associations with oral microbiome composition. These patterns were marked by depletion of commensal genera such as Alloprevotella, Peptostreptococcus and Neisseria, and the enrichment of stress-tolerant taxa including Bifidobacterium and Lactobacillus. Most of these exposures, particularly PAHs, were nominally associated with higher all-cause mortality. Exploratory mediation analyses suggested that overall community structure and specific taxa (e.g., Bifidobacterium, Haemophilus) represent a potential mediation pathway in the associations of cadmium, furan, PAHs, and nicotine metabolites with mortality.<br><br>CONCLUSIONS: The oral microbiome may serve as a sensitive biosensor of the chemical exposome and a potential intermediate factor linking environmental exposures to mortality risk. These hypothesis-generating findings highlight the oral cavity as a key arena for environmental health impacts.}, }
@article {pmid42119408, year = {2026}, author = {Singh, AK and Choi, J and Ramirez, GA and Guan, J and Singh, P and Tolstorukov, I and Oakley, BB and Kim, WK}, title = {Effects of Aspergillus sp. supplementation with or without xylanase on growth performance, nutrient digestibility, and the gastrointestinal microbiome of broilers.}, journal = {Poultry science}, volume = {105}, number = {8}, pages = {106978}, doi = {10.1016/j.psj.2026.106978}, pmid = {42119408}, issn = {1525-3171}, abstract = {This study aimed to evaluate the in vivo enzyme activity of Aspergillus sp. in the presence and absence of supplemental xylanase enzyme and determine its effect on the growth performance, nutrient digestibility, and microbiome of broilers. A total of 120 male Cobb® 500 broilers were randomly assigned to 12 replicate cages across 4 treatments (n = 3 per treatment) and raised till 21 days. The dietary treatments were arranged in a 2 × 2 factorial design with xylanase and Aspergillus sp. addition as the main factors. The xylanase was included at 520 U/kg and Aspergillus sp. was supplemented as conidiospores at 6.4 × 10[7] CFU/ kg of the basal diet by replacing sand. The total feed intake and the total body weight per cage were recorded weekly. The total feed intake and total excreta output were recorded on d 20 to calculate apparent metabolizable energy (AME) and nitrogen-corrected AME (AMEn). The jejunum, ileum, and ceca were collected on d 14 and d 21 for quantitative PCR and microbiome analyses. The growth performance and nutrient digestibility data were analyzed by two-way ANOVA in a completely randomized design using SAS 9.4 (SAS Inc., Cary, NC) with statistical significance declared at P < 0.05. The treatments did not have a significant effect on the nutrient digestibility and growth performance of the broilers. However, a trend was observed for the interaction between xylanase and Aspergillus sp. on the average daily gain (ADG) and the final body weight gain (FBWG) of broilers during d 0-21 (P = 0.099). Microbiome analysis revealed no major shifts in overall community structure, although several taxa exhibited small but statistically significant differences in response to dietary supplementation with xylanase and/or Aspergillus spores. AI-enabled genome and literature searches indicated that taxa enriched under enzymatic treatments commonly possess metabolic functions related to the fermentation of complex carbohydrates for the production of short-chain fatty acids. The results indicate that the effects of Aspergillus sp. on nutrient digestibility and utilization by broilers are influenced by the presence of exogenous enzymes and dietary substrates and are further modulated by the gut microbiome. Supplemental Aspergillus sp. conidiospores provided similar and numerically greater improvements in FBWG and exerted significant effects on the select members of the gastrointestinal microbiome.}, }
@article {pmid42119567, year = {2026}, author = {Chen, C and Xing, Y and Xing, G and Zeng, F and Zheng, N and Sha, S and Zhao, L and Zhang, Y and Ling, Y and Yao, X and Liu, C and Zhang, Y and Mei, T and Guo, R and Kang, J and Cheng, L and Fan, S and Sun, W and Li, S and Yan, Q and Yao, X and Kong, X and Ma, W}, title = {Multi-faceted characterization of the gut microbiome and metabolome in patients with primary Sjögren syndrome.}, journal = {Cell reports. Medicine}, volume = {}, number = {}, pages = {102777}, doi = {10.1016/j.xcrm.2026.102777}, pmid = {42119567}, issn = {2666-3791}, abstract = {The gut microbiome and its metabolomic potential in primary Sjögren syndrome (pSS) remain largely unexplored. Here, we perform whole-metagenome shotgun sequencing of fecal samples from 206 pSS patients and 355 non-pSS controls, integrating compositional and functional profiling with serum and fecal metabolomes. pSS is associated with extensive multi-kingdom alterations, including 49 bacterial (e.g., Streptococcus parasanguinis, Ligilactobacillus salivarius, and Veillonella parvula), 19 fungal (notably Candida albicans), and 1,323 viral species. These signatures form robust inter-kingdom correlations and achieve high diagnostic accuracy in an independent validation cohort. Functional and metabolomic analyses reveal enrichment of toxin-related and aromatic pathways and depletion of protective metabolites in patients. pSS-enriched bacteria harbor abundant immunogenic epitopes, virulence factors, and antimicrobial resistance genes, and induce proinflammatory responses ex vivo. Together, these findings outline a multi-faceted microbial framework for pSS and suggest mechanistic links between gut dysbiosis and immune dysregulation.}, }
@article {pmid42119619, year = {2026}, author = {Zeng, Y and Yang, F and Li, Z and Wang, Q and Zhang, K}, title = {Overlooked role of Species-Specific earthworm mucus in antibiotic resistance gene suppression during vermicomposting.}, journal = {Bioresource technology}, volume = {455}, number = {}, pages = {134842}, doi = {10.1016/j.biortech.2026.134842}, pmid = {42119619}, issn = {1873-2976}, abstract = {Antibiotic resistance genes (ARGs) from livestock manure pose a significant threat to both environmental and public health. Vermicomposting mitigates ARG dissemination, yet the species-dependent differences in earthworm mucus's contribution remain poorly understood. This study examined how mucus from three earthworm species (Eisenia fetida, Eudrilus eugeniae, Perionyx excavatus) differentially reduced ARGs in cow manure. Untargeted metabolomics revealed species-specific mucus profiles. All three types of mucus lowered ARG abundance albeit through distinct ecological patterns. E. fetida mucus promoted co-elimination of ARGs and mobile genetic elements (MGEs) alongside host bacteria. E. eugeniae mucus selectively suppressed key host bacteria, effectively decoupling ARG-MGE associations in a pattern of host-associated decoupling. By contrast, P. excavatus mucus induced a composite suppression mode that incorporated both patterns. Each mucus uniquely reshaped the manure microbiome and its functional interaction network, demonstrating species-specific reprogramming of the ecosystem. These findings highlight that earthworm mucus is a critical yet overlooked regulator of ARG fate, and its species-specific composition underlies divergent ecological trajectories. This offers new insights into targeted biological interventions in waste management.}, }
@article {pmid42119786, year = {2026}, author = {Khetan, R and Donnellan, L and Collins, K and Kamath, S and Ariaee, A and Rajapaksha, W and Wignall, A and Young, C and Hoffman, P and Subramaniam, S and Joyce, P}, title = {The gut microbiota regulates the protein corona formation, biodistribution, and cellular uptake of lipid nanoparticles.}, journal = {Journal of controlled release : official journal of the Controlled Release Society}, volume = {395}, number = {}, pages = {114995}, doi = {10.1016/j.jconrel.2026.114995}, pmid = {42119786}, issn = {1873-4995}, abstract = {Nanomedicines promise to transform oncology by improving pharmacokinetics, enhancing tumor targeting, and reducing systemic toxicities relative to conventional chemotherapies. However, clinical outcomes remain inconsistent, with marked inter-patient variability in biodistribution and therapeutic response. This variability is thought to arise from heterogeneity in "bio-nano" interactions, yet the upstream drivers of these interactions are poorly defined. We propose that the gut microbiota is a clinically relevant regulator of nanomedicine behavior, given its established influence on host immunity, metabolism, and proteome composition - all key determinants of bio-nano interactions. To test this, rats underwent a 14-day microbiota modulation using a prebiotic, broad-spectrum antibiotics, or control treatment. PEGylated liposomes were then intravenously administered to assess the impact of microbiota composition on (i) protein corona formation, (ii) nanoparticle biodistribution, and (iii) in vitro anti-cancer efficacy of doxorubicin-loaded liposomes following exposure to plasma from each group. Microbiota modulation produced distinct protein coronas, characterized by increased protein adsorption and unique proteomic profiles enriched in complement factors, apolipoproteins, and immunoglobulins. These corona differences were associated with altered biodistribution profiles, affecting both the magnitude and organ-level partitioning of nanoparticle-associated signal. Antibiotic treatment increased total systemic signal consistent with altered retention and/or clearance, whereas prebiotic supplementation was associated with reduced overall signal and decreased proportional partitioning into mononuclear phagocyte system organs, with a corresponding shift in distribution balance toward peripheral tissues including the heart, kidney, and brain. Notably, the prebiotic-derived corona markedly enhanced liposomal uptake and cytotoxicity in A549 and ES-2 cancer cells, linking protein adsorption and corona composition with bio-nano cellular interactions. Collectively, these findings provide experimental evidence that microbiota modulation influences nanoparticle behavior by altering bio-nano interactions, revealing an emerging "gut-nano axis" as a potentially controllable source of nanomedicine variability.}, }
@article {pmid42119819, year = {2026}, author = {Varghese, RT and Akurati, S}, title = {Sleep, lipids, and metabolic health in the Indian obesity epidemic: an integrative review of mechanisms, burden, and breakthroughs.}, journal = {Diabetes research and clinical practice}, volume = {}, number = {}, pages = {113319}, doi = {10.1016/j.diabres.2026.113319}, pmid = {42119819}, issn = {1872-8227}, abstract = {BACKGROUND: India faces a growing obesity epidemic within the context of persistent undernutrition, creating a dual burden with major cardiometabolic consequences. This population is particularly vulnerable to metabolic disease because of the "Asian Indian phenotype," characterized by increased visceral adiposity and higher metabolic risk at lower body mass index thresholds.<br><br>OBJECTIVE: To review current evidence on the relationship between sleep health, lipid dysregulation, and metabolic dysfunction in the obesity epidemic in India, with emphasis on epidemiology, biologic mechanisms, and implementation relevance.<br><br>METHODS: PubMed-indexed literature published from 2015 through February 2026 was reviewed, prioritizing India-specific epidemiologic studies, national reports, and policy-relevant publications. International mechanistic studies were included when relevant to biologic plausibility and translational understanding.<br><br>RESULTS: Obesity in India shows substantial regional and urban-rural variation, while dyslipidemia remains highly prevalent and inadequately controlled, particularly in people with type 2 diabetes mellitus. Sleep disturbances, including short sleep duration, circadian misalignment, shift work, and obstructive sleep apnea, are increasingly recognized as contributors to metabolic dysfunction. Mechanistic evidence suggests that sleep disruption may impair metabolic health through clock gene dysregulation, bile acid-lipid desynchronization, microbiome-derived short-chain fatty acid signaling, inflammation, and neuroendocrine stress pathways. However, India-specific lipidomic, longitudinal, and sleep-focused interventional data remain limited.<br><br>CONCLUSIONS: Sleep health disturbances appear to be important and potentially modifiable contributors to metabolic dysfunction in India. Improving access to obstructive sleep apnea diagnosis and continuous positive airway pressure therapy, strengthening dyslipidemia management, and integrating sleep health into broader noncommunicable disease frameworks may improve prevention and care in high-risk Indian populations.}, }
@article {pmid42119851, year = {2026}, author = {Xiong, HL and Zhao, Q and Liu, SQ and Chen, LL and Nie, MT and Hong, XL and Ding, CH and Huang, R and Jiang, N and Chen, F and Song, YH and Zhang, X and Wang, KQ and Zhu, CP and Xie, WF}, title = {Rifaximin ameliorates cirrhotic portal hypertension through suppression of microbiome-derived deoxycholic acid.}, journal = {Journal of hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jhep.2026.05.001}, pmid = {42119851}, issn = {1600-0641}, abstract = {BACKGROUND &amp; AIMS: Microbiome-derived deoxycholic acid (DCA) elevates serum 5-hydroxytryptamine (5-HT), a mediator of portal hypertension (PH). Rifaximin, a non-absorbable antibiotic, is known to reduce DCA levels. We aimed to elucidate the role of DCA in cirrhotic PH and the therapeutic potential of rifaximin.<br><br>METHODS: PH was induced in mice by thioacetamide (TAA) injection or bile duct ligation (BDL). Mice were treated with antibiotics (ABX) or rifaximin, with or without exogenous DCA replenishment. A cohort of 51 cirrhotic patients and 19 healthy controls was analyzed to validate the correlations among DCA, 5-HT, and hepatic venous pressure gradient (HVPG). Mice with tissue-specific knockout of gut epithelial Tph1 (Tph1[VKO]), vascular smooth muscle cell Htr1a (Htr1a[&#x394;VSMC]), or Kcnj9 (Kcnj9[&#x394;VSMC]) were employed for mechanistic studies.<br><br>RESULTS: Fecal DCA positively correlated with portal pressure (PP) in TAA-induced PH mice (r = 0.631, P < 0.001) and with HVPG in patients (r = 0.5874, P < 0.001). ABX reduced fecal DCA, serum 5-HT, and PP in TAA- or BDL-induced PH mice. Exogenous DCA reversed the ABX-induced reductions in serum 5-HT and PP, an effect abolished in Tph1[VKO] mice. GIRK3 (encoded by Kcnj9) was upregulated in portal veins from PH mice and patients. VSMC-specific Kcnj9 deletion attenuated PH and prevented 5-HT-induced PP elevation. Mechanistically, 5-HT triggers PVSMC contraction via the HTR1A-GIRK3-Ca[2+]-MLC2 pathway. Rifaximin alleviated PH by reducing DCA in wild-type mice but showed no additional PP reduction in Tph1[VKO], Htr1a[&#x394;VSMC], or Kcnj9[&#x394;VSMC] mice.<br><br>CONCLUSIONS: Microbiome-derived DCA exacerbates PH by enhancing TPH1-dependent 5-HT biosynthesis, which activates PVSMC contraction via HTR1A-GIRK3 signaling. Rifaximin alleviates cirrhotic PH by reducing DCA levels, highlighting a potential therapeutic strategy for clinical PH management.<br><br>IMPACT AND IMPLICATIONS: Portal hypertension is a key driver of cirrhosis-related complications, yet current therapies exhibit suboptimal efficacy. Herein, we elucidate the role of the gut microbial metabolite DCA in the pathophysiology of cirrhotic portal hypertension through the TPH1-5-HT/HTR1A-GIRK3 axis and provide preclinical evidence that rifaximin ameliorates cirrhotic portal hypertension by reducing DCA. These insights may open a new avenue for the clinical management of cirrhotic portal hypertension.}, }
@article {pmid42119931, year = {2026}, author = {Zhai, C and Li, Y and Han, H and Ma, B}, title = {Acute ammonia exposure induces hepatic lipid metabolism disorders in wild burbot (lota lota) via the gut-liver axis: New insight into conservation of threatened species.}, journal = {Comparative biochemistry and physiology. Toxicology &amp; pharmacology : CBP}, volume = {307}, number = {}, pages = {110559}, doi = {10.1016/j.cbpc.2026.110559}, pmid = {42119931}, issn = {1532-0456}, abstract = {Accumulating evidence indicates that exogenous toxins can induce lipid metabolic disorders by influencing the gut microbiome. However, the effects of ammonia nitrogen on the gut microbiota and hepatic lipid metabolism of the burbot (lota lota) remain unknown. Therefore, we integrated biochemical measurements, 16S rDNA sequencing, and transcriptomic analysis to evaluate the impact of 96 h of ammonia nitrogen exposure on oxidative stress, the immune response, lipid metabolism, and gut microbiota in the liver and intestine of lota lota. In this study, lota lota exhibited oxidative damage and immunosuppression following ammonia nitrogen exposure, as evidenced by decreased antioxidant and immune enzyme activities and a concomitant increase in malondialdehyde (MDA) content. Furthermore, ammonia nitrogen exposure altered gut microbial diversity: the abundance of Proteobacteria decreased, whereas that of Bacteroidota and Firmicutes increased. In addition, transcriptomic analysis revealed that the expression of genes related to fatty acid metabolism (fabp, elovl6, pltp) and gut barrier dysfunction (collagen, ecm) was altered. Notably, lipopolysaccharide (LPS) was identified as a key microbial-derived signal triggered by ammonia nitrogen, as demonstrated by ELISA. The translocation of LPS from gut to liver, resulting from compromised intestinal barrier integrity, activated the gut-liver axis and contributed to hepatic lipid metabolic disorders. Overall, the current study elucidates the gut-liver axis-mediated mechanism of ammonia nitrogen toxicity and provides valuable information for understanding the toxic effects of ammonia nitrogen on lota lota and conserving this threatened cold-water species.}, }
@article {pmid42119964, year = {2026}, author = {Greenshields, J and Beale, DJ and Bissett, A and Anastasi, A and Irving, AD and Andrews, E and Capper, A}, title = {Seagrass Under Siege? Investigating the Effects of Microplastics on Eelgrass (Zostera muelleri) in a Laboratory-Controlled Mesocosm Study.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128321}, doi = {10.1016/j.envpol.2026.128321}, pmid = {42119964}, issn = {1873-6424}, abstract = {Seagrass meadows are critical coastal ecosystems that are increasingly recognised for their potential to form microplastic sinks. This study investigated the impacts of microplastic contamination on Eelgrass (Zostera muelleri), a dominant seagrass in the Indo-Pacific. Through a 90-day mesocosm experiment, Z. muelleri was exposed to three escalating microplastic concentrations (885, 3,540, and 8,850 particles.kg[-1] sediment) to evaluate morphological, photosynthetic (pulse amplitude modulation fluorometry), bacterial microbiome (16S rRNA gene amplicon sequencing), and leachate (LC-QToF-MS/MS) responses. Relative to controls (0 particles.kg[-1]), no significant morphological effects were detected at current environmental concentrations (885 particles.kg[-1] sediment), but significant declines in biomass (72-86%), rhizome length (110-190%), and leaf count (8-10 fewer leaves) under elevated microplastic loads. Photosynthetic (Y-Yield) efficiency was not affected, and sediment microbiomes exhibited resilience, with no significant shifts in diversity. Chemical analyses identified 82 leachates in sediments, including ten unique to treatments spiked with microplastics, suggesting leachate toxicity may be related to observed biological impacts. These findings suggest that Z. muelleri may be resilient to microplastic pollution at current observed concentrations but are likely to be negatively affected if microplastic pollution continues to rise. Research on leachate-specific effects is required for targeted mitigation strategies to help conserve these vital ecosystems.}, }
@article {pmid42119966, year = {2026}, author = {Athira, AS and Sreejith, VN and Megha, C and Athira, PS and Reshmi, K and Murugadas, V and Joseph, TC}, title = {Metagenomic Characterization of Bacterial Communities on Beach Macroplastics: Insights into Antimicrobial Resistance and Virulence.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128213}, doi = {10.1016/j.envpol.2026.128213}, pmid = {42119966}, issn = {1873-6424}, abstract = {Macroplastic debris in coastal environments provides stable substrates for microbial colonization, yet comparative assessments with natural substrates remain limited. This study investigated bacterial communities associated with beach macroplastics collected from four sites along the Kochi coast, Kerala, India (Fort Kochi, Cherai, Puthenthode, and Puthuvypin) during the pre-monsoon season, and compared them with those colonizing natural inanimate substrates (driftwood, seaweed, and shells). Composite sampling across multiple transects was employed, and shotgun metagenomic sequencing was used to characterize taxonomic composition, functional pathways, antimicrobial resistance genes (ARGs), and virulence factors. Across all samples, Pseudomonadota (average ∼64.8%) dominated, followed by Bacillota, Actinomycetota, and Bacteroidota. Plastic-associated communities showed greater dominance of specific genera, including Vibrio, Alteromonas, and Pseudoalteromonas, whereas natural substrates exhibited more evenly distributed taxa (Streptomyces, Marinobacter, Sulfitobacter etc). Functional annotation revealed the presence of core metabolic pathways across all samples, while xenobiotic degradation and lipid metabolism pathways were more prominently represented in plastic-associated communities, particularly at urban-influenced sites. A total of 42 ARGs belonging to eight antibiotic classes were identified, with β-lactam resistance genes constituting ∼42% of detected ARGs. Plastic-associated samples showed broader ARG profiles, including blaTEM-116, tetM, and sul1. A total of 73 virulence genes were identified, with plastic samples showing higher abundance of β-lactamase (blaTEM-116, tetM) and adhesion-associated genes (pilA, ompA). In addition, 1,264-2,046 virulence-related gene hits per site were detected, with consistently higher counts observed in plastic-associated communities. Overall, the findings demonstrate that macroplastics support distinct microbial assemblages and functional gene distributions compared to natural substrates, highlighting their role as microbial habitats in human-impacted coastal environments.}, }
@article {pmid42119968, year = {2026}, author = {Son, JS and Chang, GD and Jang, S and Lee, S and Sim, Y and Song, JH and Jeong, J and Ryu, CM}, title = {Polyethylene and polystyrene oxidation by host and microbial oxidoreductases in Zophobas atratus.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2026.05.024}, pmid = {42119968}, issn = {2090-1224}, abstract = {INTRODUCTION: Insect-mediated oxidation is a promising strategy for degrading hydrocarbon-based plastics. There is evidence for better long-term ingestion and sustained intestinal oxidation of polyethylene (PE) and polystyrene (PS) in the plastivore Zophobas atratus than in Galleria mellonella. However, the mechanisms underlying intestinal oxidation of PE and PS remain unclear.<br><br>OBJECTIVES: Host and microbial enzymes that mediate intestinal PE and PS oxidation in Z. atratus were evaluated.<br><br>METHODS: Long-term feeding assays were performed using G. mellonella and Z. atratus to compare PE and PS ingestion and oxidation activities. Germ-free Z. atratus larvae were generated using antibiotic treatment to evaluate host-derived oxidation. Transcriptome-based reverse genetics with heterologous expression in Pichia pastoris was used to identify candidate intestinal PE-oxidizing enzymes. The Z. atratus gut microbiome was enriched in media containing PE or PS as the sole carbon source and plastic-oxidizing bacteria were isolated. Candidate microbial enzymes were screened using a single-gene mutant library of a phylogenetic neighbor and validated by heterologous expression in Escherichia coli.<br><br>RESULTS: Z. atratus exhibited higher ingestion and intestinal oxidation of PE and PS than G. mellonella. Antibiotic treatment significantly reduced PE and PS oxidation in Z. atratus; however, the residual activity indicated contributions from both gut microbes and host-derived enzymes. Transcriptome-based reverse genetics using P. pastoris expression identified CYP6k1-ZP10 as a host PE-oxidizing enzyme, which was validated by RNA interference. Host enzymes involved in PS oxidation were not detected. Instead, Klebsiella variicola was isolated as the dominant gut bacterium capable of oxidizing both plastics. Functional screening revealed an FMN-dependent monooxygenase responsible for PE and PS oxidation.<br><br>CONCLUSION: These findings demonstrate the dual contribution of host- and microbe-derived oxidoreductases to PE and PS oxidation in Z. atratus.}, }
@article {pmid42120003, year = {2026}, author = {Feidenhansl, C and Schweinshaut, K and Rruci, E and Nguyen, MT and Poehlein, A and Brüggemann, H}, title = {Engraftment of staphylococcal strains on human skin can competitively displace native staphylococci.}, journal = {Beneficial microbes}, volume = {}, number = {}, pages = {1-14}, doi = {10.1163/18762891-bja00119}, pmid = {42120003}, issn = {1876-2891}, abstract = {Topical probiotic formulations containing live bacteria are being explored as treatments for skin disorders such as atopic dermatitis and acne vulgaris. Certain bacterial strains with antimicrobial and/or anti-inflammatory properties show promise as bacterial therapeutics that could improve these conditions and serve as alternatives to antibiotics, which are increasingly compromised by rising antimicrobial resistance. However, little is known about the engraftment efficacy of such bacterial strains or their impact on the native skin microbiome. In this study, we applied two different coagulase-negative staphylococcal strains, one with antimicrobial activity (Staphylococcus epidermidis 2C-5) and one lacking any activity (Staphylococcus hominis H2-S92), on human back skin of 14 healthy volunteers. Engraftment was assessed using strain-specific PCR and three amplicon-based sequencing approaches at 7 and 30 days after application. Microbial profiles shifted modestly, showing a relative increase in staphylococci and a decrease in Cutibacterium spp. S. epidermidis 2C-5 drastically increased from 0.8% pre-application to 46.9% and 12.1% at days 7 and 30, respectively. S. hominis H2-S92 showed a relative rise from 1.4% to 35.8% at day 7, declining to 2.4% by day 30. Interestingly, Staphylococcus capitis relative abundance decreased by 50-60% at the application sites. These findings indicate that both strains can temporarily engraft and competitively displace native staphylococci. S. epidermidis 2C-5 appeared to colonize more effectively, possibly due to its bacteriocin production. Neither strain affected the phylotype composition of Cutibacterium acnes, suggesting lack of reach to sebaceous follicles, C. acnes' primary niche. This study supports the potential of staphylococcal probiotics for modulating the skin microbiome. While they may be effective for conditions involving staphylococcal dysbiosis, such as atopic dermatitis, they appear less suited for treating disorders like acne vulgaris, which are associated with C. acnes imbalance.}, }
@article {pmid42120207, year = {2026}, author = {Miao, Y and Sun, X and Wang, W and Shen, Q and Zhang, R}, title = {Dynamical model-guided SynCom design for sustainable agriculture.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2026.04.008}, pmid = {42120207}, issn = {1878-4380}, abstract = {Synthetic microbial communities (SynComs) are emerging as promising alternatives to single-strain inoculants in agriculture, offering greater functional robustness and environmental adaptability. However, transforming conceptual studies into engineerable and scalable agricultural practices remains challenging. In this opinion article, we synthesize current research on plant SynComs through a framework that moves from strain-centered assembly toward system-level design, linking the identification of truly stable coexisting communities in natural microbiomes to the elucidation of plant-microbe-soil interaction mechanisms, the development of dynamical models, and the integration of these models into platform-based design and production pipelines. We focus on recent advances that integrate generalized Lotka-Volterra and consumer-resource models with multi-omics data and other system-level constraints, with the aim of introducing model-driven concepts of SynCom design and promoting their large-scale application in agriculture.}, }
@article {pmid42120244, year = {2026}, author = {Waqas, M and Yaning, C and White, JC and Berg, G and Geilfus, CM}, title = {Nano-selenium coordinates plant-microbiome redox for sustainable crops.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2026.04.023}, pmid = {42120244}, issn = {1878-4372}, abstract = {Foliar selenium nanomaterials act as redox-active coordinators linking photosynthesis, root carbon allocation, and rhizosphere microbiomes. By enhancing photosynthesis, nitrogen cycling, and microbial function, they improve 'nitrogen use efficiency, crop quality, profitability, and greenhouse gas mitigation' under reduced fertilizer inputs. This framework highlights nano-enabled pathways toward sustainable agriculture.}, }
@article {pmid42120383, year = {2026}, author = {Tingley, JP and Andersen, TO and Mihalynuk, LG and Xing, X and Low, KE and Whiteside, DP and Altshuler, I and Jujihara, N and Shearer, AY and Klassen, L and Serin, S and Smith, E and Reintjes, G and Patel, TR and Boraston, AB and Hagen, LH and Pope, PB and Abbott, DW}, title = {Distribution of microbial carrageenan foraging pathways reveals a widespread latent trait within the ruminant intestinal microbiome.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42120383}, issn = {2041-1723}, support = {J-002817; J-003135//Gouvernement du Canada | Agriculture and Agri-Food Canada (Agriculture et Agroalimentaire Canada)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics/physiology ; *Carrageenan/metabolism ; *Ruminants/microbiology ; Rumen/microbiology ; Glycoside Hydrolases/metabolism/genetics ; Feces/microbiology ; Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Seaweed/metabolism ; Bacteroides/metabolism/genetics/isolation &amp; purification ; Metagenomics ; Phylogeny ; }, abstract = {Seaweeds represent a promising source of sustainable, alternative feeds for livestock. Despite their increasing popularity in agriculture, the dietary fate of seaweed polysaccharides, such as carrageenan, is unknown. Here, we apply functional microbiome analyses of ruminant gastrointestinal tract microbiomes to discover catabolic enzymes specific for carrageenan digestion from the red seaweed Mazzaella japonica. M. japonica preferentially increased Bacteroides abundance within the feces over the rumen, and bacterial isolates have the capacity to use carrageenans as a sole carbon source. We identify carrageenan-active polysaccharide utilization loci (CarPULs) and characterize recombinant GH16 subfamily 17 carrageenases, informing previously uncharacterized substrate specificities for the subfamily, and providing insights into pathway specialization of divergent CarPULs. Selective enrichment and metagenomic mining reveals that carrageenan catabolism is widespread among geographically and taxonomically distinct ruminants, suggesting it is a latent trait widely distributed in the Order Artiodactyla and carried within their microbiomes as part of the microbial "dark matter". These pathways are structurally distinct from those found in marine bacteria, highlighting a complex and ancient evolutionary history of CarPULs in ruminant microbiomes.}, }
@article {pmid42120518, year = {2026}, author = {Han, Q and Shi, Y and Yi, X and Ai, Z and Wu, M and He, T and Jing, X and Wang, Z and Xiang, Z}, title = {Dynamic microbiome-host interactions and their associations with systemic metabolism and radiological characteristics during early lung adenocarcinoma.}, journal = {NPJ precision oncology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41698-026-01471-5}, pmid = {42120518}, issn = {2397-768X}, support = {2022YFA1304300//National Key Research and Development Program of China/ ; 82495200//National Natural Science Foundation of China/ ; 82171931//National Natural Science Foundation of China/ ; GZNL2023A02001//Major Project of Guangzhou National Laboratory/ ; }, abstract = {Lung adenocarcinoma (LUAD) accounts for approximately 40% of non-small cell lung cancer. Although the microbiome may play a role in LUAD, a comprehensive understanding of its ecological landscape and interactions with the tumor host, particularly during early development of LUAD, remains lacking. Here we employed a multi-omic approach to assess the dynamics of the tumor microbiota-host interaction across stages of early LUAD, including benign nodules, adenocarcinoma in situ (AIS), minimally invasive adenocarcinoma (MIA), and invasive adenocarcinoma (IAC). We found a strong and intricate interaction between the microbiome and host immune and metabolic pathways in AIS, while microbiome-host interactions substantially diminish in MIA and IAC. Serum metabolites and CT-based radiological features, such as atropaldehyde, sterculic acid, nodule morphology and maximum nodule diameter, were closely associated with the microbiome-host interaction network, suggesting they could be non-invasive markers indicating tumor ecological and pathological changes. Multi-omic integration revealed an optimal performance in classifying individual LUAD stages, particularly between AIS and MIA that was otherwise challenging to differentiate using a single data type. Our results highlight the dynamic interaction between microbiome and host during early LUAD, which can be partially reflected in systemic metabolic and radiological manifestations, providing a novel framework for understanding early-stage LUAD.}, }
@article {pmid42120611, year = {2026}, author = {Hudson, J and Akhand, A and Nwe, MT and Coffey, MJ and van Dorst, J and Chuang, S and Ooi, CY}, title = {Obstructive sleep apnea and primary snoring in children are associated with oropharyngeal dysbiosis and a mild compositional imbalance in the gastrointestinal tract.}, journal = {Journal of clinical sleep medicine : JCSM : official publication of the American Academy of Sleep Medicine}, volume = {22}, number = {1}, pages = {}, pmid = {42120611}, issn = {1550-9397}, support = {2020/GNT1194358//National Health and Medical Research Council/ ; }, mesh = {Humans ; *Dysbiosis/microbiology/complications ; Male ; *Sleep Apnea, Obstructive/microbiology/complications ; Female ; *Snoring/microbiology/complications ; Child ; *Oropharynx/microbiology ; *Gastrointestinal Microbiome ; Cohort Studies ; Feces/microbiology/chemistry ; Child, Preschool ; *Gastrointestinal Tract/microbiology ; }, abstract = {BACKGROUND: Obstructive sleep apnea (OSA) and primary snoring (PS) represent a spectrum of sleep-related breathing conditions. Emerging evidence links OSA to perturbations in the oropharyngeal and gut microbiomes and the pathogenesis of OSA-related comorbidities. However, the microbiome composition and factors driving dysbiosis in children remain unresolved.<br><br>METHODS: Two pediatric cohorts were examined to assess the microbiome associated with sleep-disordered breathing in the airway (Cohort A) and gut (Cohort B) using 16S rRNA gene profiling. Oropharyngeal swabs were collected from participants with OSA, PS, and healthy controls (HC) (n&#x2009;=&#x2009;60). Cohort B participants (OSA and HC, n&#x2009;=&#x2009;46) provided stool samples for microbiome and fecal calprotectin measurements and completed a dietary survey.<br><br>RESULTS: Oropharyngeal microbial diversity differed between OSA and HC, characterized by an increase in gastrointestinal specific taxa and reduced oral commensals. Similar shifts were observed between PS and HC, with few taxa differing between OSA and PS. In the gut, children with OSA showed an imbalance marked by an increase in opportunistic pathogens and reduced beneficial organisms. However, diversity assessments did not show any indication of dysbiosis or inflammation, and there were no overall differences in dietary intake.<br><br>CONCLUSIONS: Dysbiosis in the oropharyngeal microbiomes of OSA and PS points to shared pathophysiological factors (e.g., snoring) as possible drivers of microbiome disruption across the spectrum of sleep-disordered breathing. The gastrointestinal microbiome of children with OSA indicates a mild microbial imbalance that may elicit harmful outcomes or manifest as dysbiosis if left untreated. Together, these findings support a role of the microbiome as a possible mediator of comorbidities across the spectrum of sleep-disordered breathing. Current knowledge/study rationale:&#xa0;Obstructive sleep apnea (OSA) and primary snoring (PS) represent a continuum of sleep-related breathing disorders. While adult and animal studies suggest OSA-induced microbiome disruptions contribute to the onset of comorbidities, the factors driving dysbiosis in children remain unresolved. This study investigated the airway and gut microbiomes in pediatric OSA, PS, and healthy controls to identify microbial alterations linked to these conditions. Study impact:&#xa0;This study revealed that children with obstructive sleep apnea and primary snoring exhibit similar altered oropharyngeal microbiomes, distinct from that of healthy controls, suggesting common underlying pathophysiological factors.}, }
@article {pmid42120908, year = {2026}, author = {Yakabe, K and Inoue, Y and Yanagisawa, Y and Imai, S and Suwa, S and Ando, M and Wu, Y and Kurokawa, R and Tanakorn, S and Haneda, T and Miki, T and Ito, M and Hirayama, A and Kurashima, Y and Fukuda, S and Hase, K and Suda, W and Takeyama, H and Hori, S and Kim, YG}, title = {Acarbose redirects gut microbiome utilization of dietary carbohydrates to suppress anaphylaxis in mice.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {42120908}, issn = {2058-5276}, support = {JP23K27409//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP23K18223//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 22H03541//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 19gm6010004h0004//Japan Agency for Medical Research and Development (AMED)/ ; JP223fa627003//Japan Agency for Medical Research and Development (AMED)/ ; JP23gm1010009//Japan Agency for Medical Research and Development (AMED)/ ; JPMJER1902//MEXT | JST | Exploratory Research for Advanced Technology (ERATO)/ ; FOREST Program JPMJFR2354//MEXT | JST | Core Research for Evolutional Science and Technology (CREST)/ ; JPMJCR22N1//MEXT | JST | Core Research for Evolutional Science and Technology (CREST)/ ; }, abstract = {Microbiota-accessible carbohydrates modulate host immunity by shaping gut microbial composition and metabolism. However, their role in modulating the microbiota to influence allergic responses is unclear. Here we show that a widely used antidiabetic agent, the α-glucosidase inhibitor acarbose, redirects dietary carbohydrate utilization by gut bacteria to suppress mast-cell-dependent anaphylaxis in mice, independently of adaptive immune responses. Enhanced carbohydrate availability promoted the proliferation of Parabacteroides distasonis in the mouse gut, leading to increased succinate abundance and intracellular NAD[+] levels, and reduced reliance on b-type cytochrome-dependent anaerobic respiration. Direct administration of succinate suppressed systemic anaphylaxis and mast cell degranulation in vitro, implicating succinate as a key effector. A human cohort analysis revealed that patients treated with α-glucosidase inhibitors showed a lower incidence of anaphylaxis than untreated individuals. These findings uncover a previously unrecognized gut-microbiota-mediated pathway linking dietary carbohydrate metabolism to systemic immune regulation.}, }
@article {pmid42121018, year = {2026}, author = {Uzoigwe, C}, title = {Schizophrenia and Doxycycline: Microbiome Mediator?.}, journal = {The American journal of psychiatry}, volume = {}, number = {}, pages = {appiajp20251193}, doi = {10.1176/appi.ajp.20251193}, pmid = {42121018}, issn = {1535-7228}, }
@article {pmid42121025, year = {2026}, author = {Guo, S and Liu, M and Liu, Z and Chen, K and He, M and Li, Y and Luo, X and Shangguan, Y and Zeng, X and Liu, Y and Ouyang, Y and Zhou, Z and Qin, Y}, title = {Balanced NPK fertilization enhances maize yield and shapes rhizosphere bacterial communities in purple soil: evidence from a ten-year field experiment.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05142-0}, pmid = {42121025}, issn = {1471-2180}, support = {2023YFD2301902//National Key R&amp;D Program of China/ ; 5+1QYGG002//"5+1" Agricultural Cutting-edge Technologies Special Project of the Sichuan Academy of Agricultural Sciences/ ; 2025ZSSFGH08//Scientific and Technological Achievement Transformation Project of the Sichuan Academy of Agricultural Sciences/ ; 2025YFHZ0251//Sichuan Science and Technology Program/ ; SCCXTD-2024-SD-18//Sichuan innovation team of national modern agricultural industry technology system/ ; }, abstract = {Balanced fertilization with nitrogen (N), phosphorus (P), and potassium (K) plays a pivotal role in sustaining maize productivity and shaping soil-microbe interactions. However, the integrated effects of long-term fertilization on crop performance, soil nutrient dynamics, and rhizosphere bacterial communities in purple soils remain unclear. In a 10-year field experiment in purple soil, conducted under a randomized complete block design (RCBD) with three blocks, we evaluated the effects of different fertilization regimes on maize growth and yield, soil physicochemical properties, and bacterial community composition using 16 S rRNA gene sequencing. Nitrogen-containing fertilizer treatments (NPK, NK, NP) markedly enhanced grain yield, shoot and root biomass, and root morphological traits compared with unfertilized (CK) and PK treatments, with balanced NPK fertilization delivering the highest performance. Fertilization significantly influenced soil nutrient availability, with NPK maintaining more stable nutrient levels over time. Microbial analyses revealed that rhizosphere communities were more responsive to fertilization than bulk soil communities, with N availability driving diversity shifts and community separation. Key taxa, including Variovorax, Microscillaceae, Lysobacter, and Dyadobacter, were enriched in N-fertilized soils and positively correlated with grain yield and N uptake. Collectively, these findings demonstrate that balanced NPK fertilization, particularly nitrogen input, enhances maize productivity by simultaneously improving soil fertility and fostering beneficial rhizosphere microbial assemblages, offering a basis of sustainable nutrient and microbiome management in purple soil.}, }
@article {pmid42121042, year = {2026}, author = {Hwengwere, K and Gregson, BH and Salter, SJ and Bolton, E and Alqahtani, L and Rofael, S and Teixeira, VH and McHugh, TD and January, GG and Peck, LS and Upton, M and Clark, MS}, title = {The effects of feeding guild, seasonality, and warming on the gut microbiomes of Antarctic echinoderms.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05114-4}, pmid = {42121042}, issn = {1471-2180}, support = {NE/S007334/1//Natural Environment Research Council/ ; }, abstract = {BACKGROUND: Antarctic marine food webs are expected to be significantly impacted by future climate change. In particular, the recent rapid regional warming in the West Antarctic Peninsula has, and will continue to have, a negative impact on endemic marine biodiversity. However, despite the growing recognition of the role microbial symbionts play in mediating responses to environmental change, microbiome characterisation has been conducted for only a small fraction of the marine invertebrates in the Southern Ocean. Our study examined the effects of feeding guild, seasonality, and experimental warming (6 months at + 2 °C) on the gut microbiome of six species of near-shore marine Antarctic echinoderms sampled from waters off Rothera Research Station, Antarctica. Our study used 16 S rRNA amplicon sequencing of the V3-V4 region, with analyses including measurements of alpha and beta-diversity alongside co-occurrence network analyses.<br><br>RESULTS: Of the six invertebrate species sampled in winter, peak species diversity values in gut microbiomes were observed in the omnivores, Ophionotus victoriae and Sterechinus neumayeri, with lower values in the scavenger/predator, Odontaster validus, and the suspension feeders, Cucumaria georgiana, Echinopsolus charcoti, and Heterocucumis steineni. In the seasonal experiment, H. steineni bacterial gut species diversity doubled from winter to early summer yet decreased by a similar magnitude during the same period in O. victoriae. Despite these opposing diversity trends, both species displayed similar increases in the relative abundances of Bacteroidota and Bacillota in winter and early summer in their gut microbiomes. Bacterial diversity in the gut microbiome of the sea cucumbers E. charcoti and H. steineni, was not impacted by six-months at +&#x2009;2 &#x2da;C above ambient, although C. georgiana displayed a decrease in observed ASVs following this treatment.<br><br>CONCLUSIONS: These results suggest a strong influence of feeding guild and seasonality on the gut microbiomes of these invertebrates. There appeared to be little effect of warming (+&#x2009;2&#xa0;&#xb0;C) on the taxonomic composition of the gut microbiomes of the three holothurians. This highlights the need to examine the functional significance of experimental warming treatments using metabolomics and transcriptomics alongside microbial species diversity analyses to understand whether gut microbiomes can aid resilience under future climate change.}, }
@article {pmid42121077, year = {2026}, author = {Song, C and Li, Y and Deng, Y and He, D and Fan, X}, title = {Gut microbiota profiles associated with temporal lobe epilepsy and psychiatric comorbidities: a family-matched case-control 16S rRNA study.}, journal = {BMC neurology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12883-026-04958-7}, pmid = {42121077}, issn = {1471-2377}, abstract = {We investigated alterations in the intestinal microbiota of patients with temporal lobe epilepsy (TLE) and their associations with drug resistance and psychiatric comorbidities. Thirty TLE patients and 30 family-matched healthy controls sharing the same household diet were recruited, and fecal samples were analyzed by high-throughput 16S rDNA sequencing on the Illumina MiSeq [Formula: see text] bp platform. Differential abundance was assessed using Metastats and LEfSe with Benjamini-Hochberg false-discovery-rate correction, and independently validated using ANCOM-BC to account for the compositional nature of microbiome data. Community α- and β-diversity indices showed no significant differences between groups; however, ANCOM-BC identified species-level signatures in drug-resistant epilepsy, including significant depletion of Bacteroides plebeius and Coprococcus comes. Among psychiatric subgroups, Ruminococcus was significantly reduced in patients with comorbid depression, while Bilophila was enriched in those with comorbid anxiety and depression. Bacteroides stercoris distinguished the anxiety-plus-depression subgroup from the depression-only subgroup with robust support from both ANCOM and ANCOM-BC. Given the modest overall sample size ([Formula: see text] per arm) and small psychiatric and drug-resistance subgroups, these findings should be regarded as exploratory and hypothesis-generating associations rather than definitive biomarkers. They identify candidate microbial taxa warranting validation in larger, longitudinal cohorts combined with metagenomic and metabolomic approaches.}, }
@article {pmid42121222, year = {2026}, author = {Sanon, A and De Coninck, L and Wang, L and Badolo, A and Matthijnssens, J and Trappeniers, K and Delang, L}, title = {Convergent enrichment of Gammaproteobacteria along Aedes aegypti development across different breeding sites.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00578-1}, pmid = {42121222}, issn = {2524-4671}, support = {Global Minds scholarship//KU Leuven/ ; C14/20/108//KU Leuven/ ; 11L1325N//Fonds Wetenschappelijk Onderzoek/ ; }, abstract = {BACKGROUND: Aedes aegypti mosquitoes are the main vector of pathogens like dengue virus and chikungunya virus. The immature life stages of mosquitoes share the same habitat with a variety of microorganisms in aquatic environments. To better understand the microbial diversity in field-derived Ae. aegypti, we analysed simultaneously collected larvae, pupae, and freshly emerged adults from Burkina Faso together with their breeding water via 16S rRNA gene sequencing.<br><br>RESULTS: We observed a decrease in bacterial diversity and load across the mosquito life stages. At the phylum level, a strong increase in relative abundance of Proteobacteria was found along the mosquito stages. The same 40 amplicon sequence variants were consistently found as most abundant in the adults, regardless of the sample collection site, and all belonged to the Gammaproteobacteria. Our data suggest that these bacteria were not randomly derived by chance from the environment in the mosquito but rather deposited by a female mosquito during oviposition, a transmission route recently coined as "diagonal transmission". Indeed, our results indicated that there is a selection of Gammaproteobacteria from the breeding water and that these bacterial members are further maintained from larvae to adults.<br><br>CONCLUSION: This study provided new data on the microbiome composition of field-collected Ae. aegypti, contributing to an enhanced understanding of the origin and colonization route of the mosquito microbiome, potentially via a diagonal transmission route.}, }
@article {pmid42121259, year = {2026}, author = {Tang, Q and Zhen, R and Yang, B and Miao, Z and Wei, Y and Ruan, S and He, Y and Xiong, Y and Wu, Q and Wang, L and Jiang, Z and Yi, H}, title = {Butyrate combined with niacin enhances intestinal barrier function repair in weaned piglets infected with ETEC by promoting colonic metabolism and antimicrobial peptide expression.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42121259}, issn = {1674-9782}, support = {2024YFD1300805//National Key Research and Development Program of China/ ; 31902199//National Natural Science Foundation of China/ ; CAR-35//China Agriculture Research System/ ; 2024TQ08N106//Special Support Plan of Guangdong/ ; NYQS202628//Special Funding for the Construction of the High-Level Academy of Agricultural Sciences/ ; }, abstract = {BACKGROUND: Weaning piglets are highly susceptible to enterotoxigenic Escherichia coli (ETEC) infections, which can cause intestinal barrier function dysfunction and death. However, there is still a lack of efficient, economical, and safe nutritional interventions. This study aimed to investigate the effects of combining butyrate with niacin on intestinal barrier function repair and resistance to ETEC infection in weaned piglets. In this study, two 14-d animal experiments were designed to observe the optimal butyrate-to-niacin ratio and assess their responses to the ETEC challenge.<br><br>RESULTS: Supplementation with butyrate and niacin at a ratio of 100:2 (2,000&#xa0;mg/kg butyrate and 40&#xa0;mg/kg niacin, BN2) increased the average daily gain (ADG) and reduced the diarrhea incidence. We also observed an increase in the levels of nicotinamide adenine dinucleotide (NAD) in the colon of weaned piglets. Notably, BN2 promoted amino acid anabolism in the colon and enhanced glycolysis and the tricarboxylic acid (TCA) cycle by increasing the acetylation of key enzymes in the TCA. Furthermore, BN2 enhanced the expression of indispensable genes for the colonic mucosal barrier, including antimicrobial peptides such as&#xa0;porcine &#x3b2; defensin 1 (pBD1), porcine &#x3b2; defensin 2 (pBD2), and proline-arginine rich 39-amino acid peptide (PR39), tight junction proteins, and improved colonic microbiome composition. Based on these findings, we found that BN2 alleviated growth restriction and diarrhea, and modulated the expression of antimicrobial peptides, tight junction proteins, and cytokines to reduce colonic barrier function dysfunction in weaned piglets challenged with ETEC. Mechanistically, we confirmed that BN2 elevated the protein expression of acetylation of histone 3 lysin 27 (H3K27ac) and enhanced the binding of acH3K27 to the promoter regions of pBD1 and PR39.<br><br>CONCLUSIONS: Supplementation with BN2 improved growth performance, supported colonic barrier function repair, and enhanced disease resistance in weaned piglets challenged with ETEC. This offers new insights into nutritional strategies for intestinal barrier function repair of piglets infected with ETEC.}, }
@article {pmid42121260, year = {2026}, author = {Zhou, Z and Lamanna, A and Halder, R and Pansart, E and Narayanasamy, S and Boussoufa, B and Kerkour, T and Wilmes, P and Williams, E}, title = {Integrative analysis of the mouse cecal microbiome across diet, age, and weight in the diverse BXD population.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02369-x}, pmid = {42121260}, issn = {2049-2618}, support = {PRIDE21/16749720/NEXTIMMUNE2//Luxembourg National Research Fund/ ; }, abstract = {BACKGROUND: The gut microbiota adapts to and shapes the host's metabolic state through affecting circulating metabolites and consequent gene regulatory networks, resulting in systemic influences in diverse organs via connections such as the gut-liver axis. Numerous variables such as diet, age, and host genetics modulate the composition of the gut microbiome, but their interactions and specific associative and mechanistic links to host molecular phenotypes remain incompletely unannotated. Integrated multi-omics approaches in genetically diverse populations offer an opportunity to dissect these interactions and identify predictive microbial signatures for host phenotypes, such as body weight and molecular associations with gene expression pathways in gut and liver.<br><br>RESULTS: We sequenced, aligned, and integrated the cecal metagenome, metatranscriptome, and host transcriptome from 232 mice across 175 distinct cohorts according to a low-fat chow diet (CD) or a high-fat diet (HF), four adult ages (between roughly 180 to 730&#xa0;days of age), and 43 distinct genotypes (inbred BXD strains). Genetics and diet exerted the strongest influence on microbiota abundance and activity, followed by age. HF feeding significantly reduced diversity across all ages and all genotypes, altering&#x2009;>&#x2009;300 species. Machine learning models based on microbial profiles reliably predicted body weight within dietary group (AUC&#x2009;=&#x2009;0.84 for CD, 0.79 for HF) and chronological age (AUC&#x2009;=&#x2009;0.84), with model performance of age prediction rising to 0.95 when integrating top microbial features with liver proteomics. Network analyses of expression data revealed links between genes, pathways, and specific microbes, including a negative association between cecal Ido1 expression and short-chain fatty acid (SCFA)-producing Lachnospiraceae, suggesting dietary fat may modulate host tryptophan metabolism through microbiota shifts.<br><br>CONCLUSIONS: Whole metagenome and metatranscriptome sequencing approaches have massively expanded the landscape of microbiome analysis compared to earlier short-read 16S analyses. The resulting datasets quantify hundreds of uniquely identifiable microbes, which can be used to create sets of highly predictive microbial biomarkers for aging and obesity. When trained on controlled mouse populations, these results demonstrate that microbiome profiling can achieve high predictive capacity (AUC&#x2009;=&#x2009;0.95 with multi-omics integration) for complex readouts such as age and body weight (AUC&#x2009;=&#x2009;0.84), even considering genetic and dietary variation, establishing a framework for biomarker development. While at present many bacteria are still functionally unannotated at the species level, multi-omics approaches - including gene expression from the host tissues - provide insights into the functional associations of specific taxa in the microbiome. Video Abstract.}, }
@article {pmid42121284, year = {2026}, author = {Burkhart Colorado, AS and Nusbacher, NM and O'Connor, J and Marden, T and Higgins, J and Neff, CP and Fiorillo, S and Campbell, TB and Borok, M and Boyd, K and Sterrett, J and Palmer, BE and Lozupone, C}, title = {The impact of western versus agrarian diet consumption on gut microbiome composition and immune dysfunction in people living with HIV in rural and urban Zimbabwe.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02410-z}, pmid = {42121284}, issn = {2049-2618}, support = {R01 DK108366/DK/NIDDK NIH HHS/United States ; T15LM009451//U.S. National Library of Medicine/ ; }, abstract = {BACKGROUND: People living with HIV (PLWH) suffer from chronic inflammation even with effective antiretroviral therapy (ART). A high-fat, low-fiber western-type diet has been linked with inflammation, in part through gut microbiome changes. In sub-Saharan Africa (SSA), a region with high HIV burden, urbanization has been linked with a shift from traditional agrarian towards westernized diets, and with changes in food security. To explore the relationship between diet, inflammation, and the gut microbiome in PLWH, we enrolled 1) ART Naïve PLWH who provided samples before and after 24 weeks of ART, 2) PLWH on ART at both timepoints and 3) HIV-seronegative controls. Individuals were evenly recruited from rural and urban Zimbabwe. Using a food frequency survey designed to measure intake of agrarian versus western-type food items in Zimbabwe, we determined how diet differs with urbanization, HIV-infection and treatment, and is related to inflammation and the gut microbiome.<br><br>RESULTS: Individuals residing in a rural area of Zimbabwe less frequently consumed high-fat, low-fiber western type food items and had lower consumption of diverse food items overall, except for sadza, a subsistence staple, processed from home-grown grains. Consumption of a more western-type diet correlated with lower CD4&#x2009;+&#x2009;T cell percentage in untreated and treated PLWH and increased T cell exhaustion in PLWH on ART. PLWH on ART at time of enrollment also consumed diverse food items at a lower frequency and more often were underweight. Low food consumption correlated with muted improvements in T cell exhaustion after 24&#xa0;weeks of ART. Individuals residing in the rural area had more Prevotella-rich/Bacteroides-poor microbiomes, but this was not significantly mediated by diet. Carbohydrate substrate degradation capabilities in the microbiome, based on predictions made using metagenomic polysaccharide utilization loci, correlated with dietary intake patterns.<br><br>CONCLUSIONS: Taken together, this work supports that consumption of more high-fat/low-fiber type food items has the potential to exacerbate HIV pathogenesis in a sub-Saharan setting where HIV burden is high and reinforces the importance of nutritional support for promoting immunologic response to ART in PLWH in SSA. Video Abstract.}, }
@article {pmid42121732, year = {2026}, author = {Fang, Q and Ke, L and Bian, L and Li, S and Chi, H and Chen, Y and Qiu, X and Shi, S and Chen, S}, title = {Dietary Modulation of Gut Microbiota and Metabolome Shapes Growth Performance in Thamnaconus septentrionalis.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {9}, pages = {}, doi = {10.3390/ani16091312}, pmid = {42121732}, issn = {2076-2615}, support = {2023R1082//Fujian Provincial Department of Science and Technology/ ; FJHYF-L-2025-6//Fujian Ocean and Fisheries Department/ ; 2024S0039//Fujian Provincial Department of Science and Technology/ ; }, abstract = {Thamnaconus septentrionalis is an economically important marine aquaculture species in China. However, the acceptance rate of formulated feeds in commercial farming is only 30-40%, substantially lower than the 80-90% achieved with fresh feeds, which severely constrains the intensive development of this industry. The gut microbiota-mediated regulatory mechanisms underlying the effects of different feed types on growth performance remain unclear, limiting the precise development of efficient formulated feeds. This study established four feed types (commercial pellet feed K, custom-formulated feed P, frozen shrimp X, and fresh fish meat Y) through a 60-day feeding trial. Growth performance data, 16S rRNA sequencing, and untargeted metabolomics were analyzed. Random Forest-Partial Least Squares Regression models were employed to identify key microbial-metabolite features. Results indicated that the Y group exhibited the optimal feed conversion ratio (1.14), with intestinal Firmicutes abundance (45.3%) significantly higher than the K group (28.5%). Short-chain fatty acid levels increased by more than 350-fold, enriching short-chain fatty acid-producing bacteria such as Lactobacillus and Faecalibacterium. The P group, formulated with high fishmeal content (40%), achieved performance levels comparable to the Y group across most indicators. Machine learning models identified key microbial-metabolite features predicting growth performance, providing a multi-omics framework for developing efficient formulated feeds for marine carnivorous fish.}, }
@article {pmid42121765, year = {2026}, author = {Piuzana, LG and Tomich, TR and Rotta, PP and Carvalho, D and Amorim, WPF and Silva, LHR and Vieira, JVF and Ribeiro, EF and Silva, ALD}, title = {Effects of Sodium Monensin and a Tannin-Yeast Blend on Intake, Milk Yield, and Methane Emissions in Lactating Holstein Cows.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {9}, pages = {}, doi = {10.3390/ani16091345}, pmid = {42121765}, issn = {2076-2615}, support = {001//Coordena&#xe7;&#xe3;o de Aperfeicoamento de Pessoal de N&#xed;vel Superior/ ; 085/2022//American Nutrients of Brazil LTDA/ ; 425168/2025-5//Instituto Nacional de Ci&#xea;ncia e Tecnologia de Ci&#xea;ncia Animal/ ; APQ-08688-25//Instituto Nacional de Ci&#xea;ncia e Tecnologia de Ci&#xea;ncia Animal/ ; APQ-05448-24//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; }, abstract = {This study evaluated the effects of sodium monensin or a blend containing condensed tannins and yeast products on intake, digestibility, performance, and methane emissions in lactating Holstein cows. Nine cows (three rumen-fistulated and six non-fistulated) were assigned to three 3 × 3 Latin squares. The treatments were: a control (CON), sodium monensin (MON; 12 mg/kg of dry matter [DM]), condensed Acacia tannins and Saccharomyces cerevisiae yeast blend (SUP; 2 g/kg of DM). The trial lasted 84 days, with three 28-day periods. Neutral detergent fiber (NDF) intake was higher in CON and SUP (p = 0.029). Milk yield, energy-corrected milk, and milk composition did not differ (p > 0.05). The total methane emissions were not affected by treatments (p > 0.05). Methane yield/Kg of DM intake (DMI), organic matter intake (OMI), and digestible OM tended to be lower in SUP (p = 0.091, p = 0.093, p = 0.086). SUP increased the DM, crude protein (CP), and NDF ingestion rates (p = 0.049, p = 0.028, p = 0.013) and decreased the CP rumen pool (p = 0.014). Rumen pH tended to be higher in SUP (p = 0.067). The potentially digestible NDF digestion rate decreased in MON (p = 0.007). Finally, SUP-treated animals showed a tendency to reduce their methane yield relative to DMI, OMI, and digestible OM. Further studies should investigate the long-term impacts of supplementation, rumen microbiome changes, and underlying mechanisms driving methane mitigation.}, }
@article {pmid42121808, year = {2026}, author = {Wu, H and Chen, L and Huang, T and Liu, Y and Luo, L and Kong, L and Sun, Y and Zhang, W and Guo, Z and He, Z and Luo, Y and Xiao, J and Lu, Y}, title = {Identification of Association Between Mucus Microbiota and Gene Expression in the Gill of a Streptococcus agalactiae-Resistant Nile Tilapia Strain Though Multi-Omics Analyses.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {9}, pages = {}, doi = {10.3390/ani16091389}, pmid = {42121808}, issn = {2076-2615}, support = {GXKEYLA20230109//Ministry of Agriculture and Rural Affairs/ ; CARS-46//China Agriculture Research System/ ; 2022YFD2400804//National Key Research and Development Program of China/ ; }, abstract = {Streptococcus agalactiae infections severely threaten global tilapia aquaculture, causing substantial mortality and economic damage. The "Zhuangluo 1" (ZL) strain, derived from the fast-growing GIFT Nile tilapia and refined through multiple generations of selection, uniquely combines robust resistance to S. agalactiae with improved growth traits. This study examined gene expression and regulation of gill mucus microbiota in ZL during experimental S. agalactiae challenge. 16S rRNA sequencing revealed Flavobacterium, Vogesella, Hydrogenophaga, Acidovorax, Rheinheimera, and Deinococcus as prominent genera in the gill mucus microbiome of ZL across time points. Transcriptome time-course analysis identified differentially expressed genes in gills of ZL that were predominantly enriched in cytoskeleton in muscle cells and motor protein pathways. Abundances of the dominant genera Flavobacterium and Hydrogenophaga showed significant correlations with genes regulating mucus secretion, mucin glycosylation, immune modulation, and oxidative stress response in ZL. Untargeted metabolomics of gill mucus revealed substantially higher levels of metabolites potentially linked to microbial metabolism and host-microbiota interactions in ZL. A complementary genome-wide association study for resistance in ZL further localized genes underlying these expression-microbiota associations. These findings elucidated microbiota-host interactions between ZL and gill mucus microbiota, and provide more insights into the role of mucus regulation in disease resistance.}, }
@article {pmid42121833, year = {2026}, author = {Pelenė, U and Šiukščius, A and Nainienė, R and Merkelytė, I and Šveistienė, R}, title = {The Equine Reproductive Microbiota: Composition, Dynamics, Dysbiosis, and Implications for Fertility in Mares and Stallions.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {9}, pages = {}, doi = {10.3390/ani16091414}, pmid = {42121833}, issn = {2076-2615}, abstract = {The equine reproductive microbiota has emerged as an important factor influencing reproductive health and fertility in both mares and stallions. Traditionally, the equine uterus was considered sterile, and microbial presence was interpreted primarily in the context of infection. However, sequencing-based studies have demonstrated that the reproductive tract, including the uterus and semen, contains detectable microbial communities or microbial DNA signatures, challenging this traditional paradigm. In mares, the vaginal microbiota is consistently dominated by Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria, whereas the uterine environment represents a low-biomass niche in which interpretation is complicated by contamination risk and the inability of sequencing-based methods to distinguish viable from nonviable microorganisms. Culture-based studies consistently identify opportunistic pathogens such as Streptococcus equi subsp. zooepidemicus, Escherichia coli, and Pseudomonas aeruginosa in association with endometritis and persistent breeding-induced endometritis, while sequencing-based studies suggest broader community-level dysbiosis rather than simple pathogen presence. In stallions, semen is not sterile and commonly contains taxa such as Porphyromonas, Corynebacterium, Peptoniphilus, and other opportunistic bacteria that may influence sperm quality and microbial transmission to mares during breeding. However, most reported associations remain correlative, and direct longitudinal evidence for persistent stallion-to-mare microbial transmission is limited. This review synthesizes current evidence on microbial composition, hormonal influences, dysbiosis, and reproductive implications of the equine reproductive microbiota, integrating culture-based and sequencing-based findings while emphasizing methodological limitations associated with low-biomass samples. Improved understanding of these microbial ecosystems may support more evidence-based reproductive diagnostics and microbiome-informed fertility management in horses.}, }
@article {pmid42121870, year = {2026}, author = {Yim, CD and Kwon, H and Park, JJ and Lee, SJ and Seo, JH and Hah, YS and Ahn, SK}, title = {Rediscovering the Gut-Mito-Ear Axis: A Systems-Biology Framework for Ototoxic Vulnerability and Microbiome-Targeted Prevention.}, journal = {Cells}, volume = {15}, number = {9}, pages = {}, doi = {10.3390/cells15090769}, pmid = {42121870}, issn = {2073-4409}, support = {GNUHBRIF&#x2011;2024&#x2011;0001//Gyeongsang National University Hospital/ ; GNUHBRIF-2023-0001//Gyeongsang National University Hospital/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Animals ; *Systems Biology ; *Ototoxicity/prevention &amp; control/microbiology ; *Mitochondria/metabolism ; *Cochlea/drug effects ; *Ear, Inner ; }, abstract = {Ototoxicity is traditionally viewed as a local cochlear adverse effect of indispensable therapies such as cisplatin and aminoglycosides. However, emerging evidence suggests that cochlear vulnerability is shaped by systemic physiology, including inflammatory tone, vascular barrier integrity, and metabolic state. In this Review, we propose a Gut-Mito-Ear axis in which gut ecosystem function influences circulating mediator modules that converge on two cochlear mediator nodes: blood-labyrinth barrier (BLB) gating and mitochondrial stress tolerance. We synthesize evidence showing that gut perturbation can alter cochlear outcomes in vivo, that at least one microbiota-derived metabolite signal can directly protect hearing in experimental settings, and that BLB dysfunction and inflammatory trafficking are mechanistically relevant to cisplatin- and aminoglycoside-induced injury. We further organize the literature using an evidence-weighted framework that distinguishes direct cochlear causality from mechanistic plausibility and explicitly retains negative studies as boundary-setting evidence. Finally, we outline a translational roadmap in which microbiome-targeted prevention is pursued through mediator-anchored, non-interference-aware strategies and evaluated across linked state variables spanning exposure context, gut function, defined mediator modules, BLB gating, mitochondrial stress tolerance, and auditory phenotype. The Gut-Mito-Ear axis is not considered an established mechanism. We present it as a falsifiable systems-biology model that organizes the current evidence. Within this model, we define the minimum and ideal standards for A-tier causal evidence, explicit criteria for interpreting boundary-setting negative (A-) studies, and a set of testable predictions for causal validation.}, }
@article {pmid42122017, year = {2026}, author = {Sado, A and Tomaszewska, M and Wójcik, S and Rulkiewicz, A}, title = {Skin as a Metabolic Organ: Dermatologic Markers of Morbid Obesity and Their Role in Risk Stratification and Treatment Monitoring.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {16}, number = {9}, pages = {}, doi = {10.3390/diagnostics16091314}, pmid = {42122017}, issn = {2075-4418}, abstract = {Morbid obesity is a chronic condition characterized by metabolic disorders and low-grade chronic inflammation, both of which are closely linked to insulin resistance and adipokine dysregulation. In addition to its systemic effects, obesity also leads to structural and functional changes in the skin, supporting its role as an active metabolic and immunological organ. This study analyzed skin lesions occurring in individuals with morbid obesity and explored their potential relevance in the context of metabolic risk and treatment response rather than establishing clinically validated tools. The focus was on how excess adipose tissue affects the skin through metabolic, hormonal and mechanical mechanisms. Although this review focuses on morbid obesity, many of the included studies examine general obesity without separating its severity. Therefore, the findings may not fully reflect patients with BMI ≥ 40 kg/m[2] and should be interpreted with caution. Three main areas were considered: the pathophysiological mechanisms underlying obesity-related skin lesions, selected dermatological manifestations as potential markers associated with metabolic risk, and changes in these manifestations during pharmacological, surgical, and lifestyle interventions. Available studies show that acanthosis nigricans and multiple acrochordons are consistently associated with insulin resistance, metabolic syndrome, and metabolic dysfunction-associated steatotic liver disease. An increase in BMI is also associated with impairment of the epidermal barrier, changes in the composition of skin lipids, and modifications of the skin microbiome, while biomechanical factors promote the development of chronic inflammation in the intertriginous areas. It has been shown that normalization of metabolic parameters achieved through GLP-1-based pharmacotherapy, bariatric surgery, or lifestyle changes can improve some skin manifestations, especially acanthosis nigricans. However, it should be emphasized that most available data are based on cross-sectional or observational studies, and validated composite dermatological indices are still unavailable. Skin changes in patients with morbid obesity often reflect underlying metabolic and hormonal disturbances. They may have potential as additional, non-invasive clinical clues, but they should not be treated as independent tools for risk assessment or treatment monitoring. At present, most evidence shows associations only, and it is unclear whether these findings add meaningful predictive value beyond standard metabolic markers. More prospective studies are needed to confirm their clinical usefulness and to define their role in assessing metabolic risk and monitoring treatment over time.}, }
@article {pmid42122090, year = {2026}, author = {Hamod, A and Popovici, R and Oancea, M and Grigore, M and Lazăr, T and Vasilache, IA and Pristavu, A and Gafițanu, D and Cristofor, A and Tănase, A and Mandici, C and Grigore, AM and Strat, L and Bucșineanu, C and Ciocoiu, M}, title = {Vaginal Microbiota Composition and HPV Genotype-Specific CIN2+ Risk: A Cross-Sectional Study.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {16}, number = {9}, pages = {}, doi = {10.3390/diagnostics16091387}, pmid = {42122090}, issn = {2075-4418}, abstract = {Background/Objectives: Emerging evidence links vaginal microbiome dysbiosis with HPV persistence and CIN progression, but whether microbiome markers provide incremental prognostic value beyond molecular triage assays remains unclear. This study aimed to evaluate whether Lactobacillus depletion and Shannon diversity improve prediction of biopsy-confirmed CIN2+ and CIN3+ outcomes beyond CINtec and HPV-16 genotyping. Methods: This was a secondary analysis of a cross-sectional study including 82 women undergoing cervical screening or follow-up for abnormal cytology. Associations with CIN2+, CIN3+, and CINtec positivity were estimated using modified Poisson regression. Multiplicative interaction between HPV-16 and Lactobacillus depletion was formally tested. Incremental discriminative performance was assessed using area under the receiver operating characteristic curve (AUC), DeLong's test, net reclassification improvement (NRI), and integrated discrimination improvement (IDI). Results: HPV-16 was the strongest predictor of CIN2+ (PR = 6.08, p < 0.001) and CIN3+ (PR = 5.53, p = 0.001). A significant sub-multiplicative interaction indicated that Lactobacillus depletion carried its strongest prognostic signal in HPV-16-negative women (CIN3+: PR_interaction = 0.04, p = 0.003). Adding microbiome markers to CINtec + HPV-16 significantly improved CIN2+ discrimination (ΔAUC = 0.034, p = 0.031), driven by correct downward reclassification of non-events (NRI_non-events = 0.833). When added to HPV-16 + age, IDI for CIN2+ reached 0.092 (p = 0.004). Conclusions: Vaginal microbiome markers, particularly Lactobacillus depletion, provide statistically significant incremental discriminative value for CIN2+ beyond CINtec p16/Ki-67 dual staining and HPV-16 genotyping. Microbiome-based triage may be most impactful in HPV-16-negative women.}, }
@article {pmid42122249, year = {2026}, author = {Dragomir, RD and Saftescu, S and Sandu, DL and Dulan, A and Croitoru-Cazacu, IM and Croitoru, AE and Croitoru, VM and Vornicu, V and Nagy, DE and Perva, IT and Sirca, D and Popovici, DI}, title = {Artificial Intelligence-Guided Personalized Gut Microbiome Modulation for Persistent Secondary Gastrointestinal Symptoms in Oncology Patients: Clinical Efficacy and Biological Correlates from a Prospective Validation Study.}, journal = {Cancers}, volume = {18}, number = {9}, pages = {}, doi = {10.3390/cancers18091453}, pmid = {42122249}, issn = {2072-6694}, support = {No Grant Number//Victor Babe&#x219; University of Medicine and Pharmacy Timi&#x219;oara/ ; }, abstract = {Background/Objectives: Persistent gastrointestinal (GI) symptoms following oncologic treatment represent a major unmet need in survivorship care, often managed symptomatically without addressing underlying biological mechanisms. This study aimed to evaluate the clinical efficacy and biological correlates of an artificial intelligence (AI)-guided, personalized microbiome modulation strategy in oncology patients with chronic secondary GI dysfunction. Methods: We conducted a prospective, single-arm, open-label validation study including 29 adult female oncology patients with persistent GI symptoms lasting ≥3 months. Participants underwent baseline multidimensional assessment integrating shotgun metagenomic sequencing, inflammatory and nutritional biomarkers, and clinical symptom profiling. An AI-guided platform generated individualized dietary, supplement, and lifestyle recommendations. Outcomes were assessed at baseline and after a 3-month intervention, focusing on intra-individual changes in stool frequency (primary endpoint), self-reported energy, microbiome composition, and metabolic biomarkers. Paired statistical analyses, correlation testing, and multivariable regression were performed. Results: After three months, stool frequency significantly decreased (4.69 ± 2.41 to 2.07 ± 1.19 episodes/day; p < 0.0001), accompanied by a marked increase in energy levels (4.00 ± 1.04 to 7.24 ± 1.12; p < 0.0001). Microbiome analysis revealed consistent enrichment of butyrate-producing and barrier-supportive taxa, including Faecalibacterium prausnitzii, Eubacterium rectale, Roseburia intestinalis, Akkermansia muciniphila, and Bifidobacterium longum. Butyrate-related biomarkers and vitamin-associated parameters (B-complex, vitamin D) showed significant improvement, while lactate levels normalized. Changes in Bifidobacterium longum were independently associated with stool frequency reduction (β = -0.783, p = 0.0082). Conclusions: AI-guided personalized microbiome modulation was associated with significant clinical improvement and biologically coherent microbial and metabolic shifts in oncology patients with persistent GI symptoms. These findings support a precision supportive-care approach targeting microbiome restoration, warranting further validation in randomized controlled trials.}, }
@article {pmid42122815, year = {2026}, author = {Boutafda, A and Kounbach, S and Zourif, A and Benhida, R and Danouche, M}, title = {Silicon at the Soil-Plant-Microbiome Interface: Rhizospheric Reconfiguration and Crop Resilience to Environmental Stresses.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {9}, pages = {}, doi = {10.3390/plants15091320}, pmid = {42122815}, issn = {2223-7747}, support = {AS-FN-36//OCP Group (Morocco)/ ; }, abstract = {Silicon is increasingly applied in agriculture to improve plant productivity under both abiotic and biotic stress constraints. Nevertheless, its mechanisms of action are often studied separately at the soil, plant, or microbiome levels, limiting a comprehensive understanding of its overall impact on agroecosystem functioning. This review proposes an integrated perspective of the soil-plant-microbiome continuum, linking silicon chemistry in soil solutions with the effects of silicon amendments on soil properties and the processes of uptake, transport, and deposition in the plants. We show that silicon bioavailability depends on maintaining a pool of dissolved silicon dominated by orthosilicic acid, regulated by mineral weathering, adsorption-desorption dynamics, polymerization, pH, iron and aluminum oxides, and organic matter. In soils, silicon inputs can improve structure, modulate acidity and cation exchange balances, influence nutrient availability, and reduce the mobility of certain metals. They may also affect enzymatic activities and microbial community composition. In plants, silicon uptake and transport, mediated by specific transporters, contribute to tissue silicification, the maintenance of leaf architecture, and the regulation of water, ionic, and redox homeostasis. These processes provide a basis for enhanced tolerance to drought, salinity, and metal toxicity, as well as biotic stress caused by pathogens and pests. Finally, we discuss key limitations to the agronomic application of silicon, including the diagnosis of the silicic status of soils, the choice of source and mode of application, and the genotypic variability of acquisition, as well as the need for multi-site tests and more robust mechanistic validations. This synthesis provides a coherent mechanistic framework to better define the conditions under which silicon can serve as a reliable tool for sustainable crop management under climate change.}, }
@article {pmid42108288, year = {2026}, author = {Yan, C and Zhang, F and Long, C and Yin, Y and Wang, L}, title = {A Brief Review of Microbial Omics: Methods and Perspectives.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3033}, number = {}, pages = {1-20}, pmid = {42108288}, issn = {1940-6029}, mesh = {*Genomics/methods ; *Metabolomics/methods ; *Proteomics/methods ; *Microbiota/genetics ; *Computational Biology/methods ; Single-Cell Analysis/methods ; Artificial Intelligence ; Transcriptome ; Metagenomics/methods ; }, abstract = {Microbial omics has progressed from isolated genomic analyses into a comprehensive, integrated multi-omics framework, profoundly advancing our understanding of microbial complexity and functionality. This mini-review systematically outlines the core technologies within microbial omics-including genomics, transcriptomics, proteomics, and metabolomics-by introducing their fundamental principles, common experimental workflows, and state-of-the-art bioinformatic strategies. We particularly highlight the emergence of single-cell microbial omics as a transformative methodology that resolves molecular and functional heterogeneity within communities, enabling the identification of rare taxa, strain-level microdiversity, and specialized functional roles that are obscured in bulk analyses. Furthermore, we discuss how artificial intelligence (AI)-driven tools are revolutionizing the interpretation of high-dimensional omics data, uncovering latent biological patterns, improving predictive modeling of microbial behavior, and facilitating the translation of microbiome insights into clinical and environmental applications. The review concludes by comparing the strengths, limitations, and optimal use cases of each omics layer and single-cell approach while also addressing ongoing technical challenges and future directions in the field.}, }
@article {pmid42108289, year = {2026}, author = {Li, B and Zhao, T and Xu, J and Meng, Q and Yin, Q and Zou, Y}, title = {Standardized Protocols for Environmental Sample Collection: Minimizing Contamination and Preserving Microbial Community Integrity.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3033}, number = {}, pages = {21-42}, pmid = {42108289}, issn = {1940-6029}, mesh = {*Specimen Handling/methods/standards ; Humans ; *Microbiota ; *Environmental Microbiology ; Soil Microbiology ; *Environmental Monitoring/methods ; Water Microbiology ; }, abstract = {Accurate microbial community assessment begins with reliable sample collection. Environmental matrices, such as soil, water, and human-associated habitats, each present unique challenges that can introduce contamination or alternative microbial structures in samples. This chapter provides an overview of standardized sampling strategies for these environments, emphasizing principles for minimizing external contamination and preserving the integrity of microbial communities. Key considerations in field practice, sample handling, preservation, and transport are summarized, along with common pitfalls and practical solutions.}, }
@article {pmid42108291, year = {2026}, author = {Li, B and Yang, X and Zhao, T and Xu, J and Meng, Q and Yin, Q and Zou, Y}, title = {Metagenomic Assembly and Gene Prediction.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3033}, number = {}, pages = {63-89}, pmid = {42108291}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *Metagenome ; *Computational Biology/methods ; Molecular Sequence Annotation ; Contig Mapping/methods ; Software ; Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; }, abstract = {Metagenomic assembly and gene prediction connect quality-controlled reads to downstream microbiome analyses. This chapter outlines core assembly strategies, including per-sample versus co-assembly and short-read versus hybrid approaches, and highlights key parameters and metrics for evaluating assembly quality. Gene prediction from contigs and the construction of nonredundant gene catalogs are introduced as fundamental steps for representing community coding potential. The resulting contigs and gene sets provide essential input for metagenome-assembled genome (MAG) reconstruction, as well as taxonomic and functional annotation in subsequent chapters.}, }
@article {pmid42108292, year = {2026}, author = {Guo, JX and Gao, YZ}, title = {Absolute Quantification of Bacteria in the Microbiome and Its Application.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3033}, number = {}, pages = {91-103}, pmid = {42108292}, issn = {1940-6029}, mesh = {*Microbiota/genetics ; *Bacteria/genetics/isolation &amp; purification/classification ; High-Throughput Nucleotide Sequencing/methods ; Humans ; DNA, Bacterial/genetics ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; }, abstract = {The advent of genomics and deep sequencing technologies has facilitated the development of absolute quantification techniques, which offer researchers more objective and precise sequencing outcomes. Unlike traditional relative quantification methods, which provide comparative data, absolute quantification delivers definitive measurements of genes or taxa. This analytical approach mitigates the potential for extraneous influences when comparing disparate samples, thereby reducing analytical errors. The implementation of absolute quantification techniques enhances our comprehension of microbial community structures, ecological dynamics, and their associations with host health or disease conditions. This chapter emphasizes a straightforward and broadly applicable method for genomic quantification, which necessitates the incorporation of a specified amount of internal standard DNA into the samples, eliminating the need for subsequent adjustments during library construction and sequencing. By assessing the proportion of internal standard DNA across various samples, sequencing data can be transformed into absolute quantification metrics. The internal standard method for absolute quantification is versatile and can be effectively utilized across multiple domains, including disease diagnosis, microbial ecology research, the fermentation industry, and environmental monitoring. Overall, absolute quantification methods furnish a more accurate and holistic perspective for microbiome research.}, }
@article {pmid42108293, year = {2026}, author = {Liu, J and Li, Y and Huang, T}, title = {Network Analysis in Microbiome Research: Methods, Tools, and Applications.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3033}, number = {}, pages = {105-115}, pmid = {42108293}, issn = {1940-6029}, mesh = {Humans ; *Microbiota ; *Computational Biology/methods ; Algorithms ; }, abstract = {The human microbiome operates as a complex, interconnected ecosystem where microbial interactions dictate community stability, host health, and disease progression. Understanding these dynamics requires moving beyond simple taxonomic catalogs to systems-level network analyses. This chapter reviews network methodologies in microbiome research, progressing from traditional correlation-based approaches to advanced artificial intelligence techniques. We systematically cover co-occurrence, protein-protein interaction, metabolic, multi-omics integrated, and evolutionary transmission networks. Computational tools-spanning general platforms and specialized pipelines-are compared alongside topology metrics and community detection algorithms. Furthermore, we highlight the integration of graph neural networks and protein language models, discussing current challenges in data standardization, model interpretability, and the merging of mechanistic and data-driven paradigms.}, }
@article {pmid42108295, year = {2026}, author = {Peng, B and Chang, X}, title = {Omics Approaches to Unraveling the Complexity of the Gut-Lung Axis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3033}, number = {}, pages = {147-164}, pmid = {42108295}, issn = {1940-6029}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Lung/metabolism ; *Metabolomics/methods ; Lung Diseases/metabolism/microbiology ; Metagenomics/methods ; Dysbiosis ; Animals ; *Genomics/methods ; Proteomics/methods ; }, abstract = {The complex, bidirectional communication between the gut and the lungs, known as the "gut-lung axis," profoundly influences host immune homeostasis and the pathogenesis of respiratory diseases. In recent years, multi-omics approaches, including metagenomics, metabolomics, and metatranscriptomics, have emerged as the core driving force for unraveling the complexity of this interorgan cross talk network. This review aims to systematically summarize the current omics-based evidence in the field of the gut-lung axis. We highlight key communication mechanisms discovered through multi-omics integration, particularly how gut microbiota-derived metabolites, exemplified by short-chain fatty acids (SCFAs), mediate distal immune regulation. Concurrently, we consolidate omics evidence from the contexts of respiratory infectious diseases, chronic lung disorders, and aging, systematically delineating the impact of gut dysbiosis on pulmonary pathophysiology via the gut-lung axis and emphasizing the feasibility of disease management in patients with lung diseases by modulating the gut microbiota. Although omics technologies have significantly advanced our understanding of this field, the challenge of effectively integrating vast, heterogeneous data and transitioning from "correlation" to "causation" remains a primary hurdle. By reviewing and discussing the current omics evidence in the gut-lung axis, this paper aims to provide new perspectives for future mechanistic explorations and clinical translation strategies.}, }
@article {pmid42108298, year = {2026}, author = {Song, Q}, title = {Infection-Associated Microecology and Hepatocellular Carcinoma.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3033}, number = {}, pages = {209-215}, pmid = {42108298}, issn = {1940-6029}, mesh = {*Carcinoma, Hepatocellular/etiology/microbiology/pathology ; *Liver Neoplasms/etiology/microbiology/pathology ; Humans ; *Gastrointestinal Microbiome ; *Hepatitis B, Chronic/complications/virology ; Animals ; Aflatoxins ; }, abstract = {Hepatocellular carcinoma (HCC) is the second leading cause of cancer-related mortality worldwide and remains one of the few malignancies with steadily increasing incidence and death rates over recent years. Globally, major etiological drivers of HCC include chronic hepatitis B virus (HBV) and hepatitis C virus (HCV) infections, consumption of aflatoxin-contaminated food, heavy alcohol intake, obesity, cigarette smoking, and type 2 diabetes mellitus. In China, however, the exceptionally high burden of HCC is primarily attributable to chronic HBV infection and aflatoxin exposure, with approximately 80% of Chinese HCC patients testing positive for HBV. The natural history of the disease generally progresses from chronic hepatitis to liver cirrhosis and ultimately to HCC. Throughout this trajectory, the infection-associated microecological environment exerts a crucial influence on hepatocarcinogenesis. This chapter will examine the role and mechanistic underpinnings of infection-related microecology-particularly the gut microbiome-in the development of HCC and highlight the clinical relevance of infection-associated microbial components in liver cancer treatment.}, }
@article {pmid42108392, year = {2026}, author = {Kou, R and Zheng, J and Hou, S and Qiao, L and Liu, X}, title = {The Effect of SO2 Pulse on Synergistic Interaction of Postharvest Quality and Fungal Community During Thin-Skinned Grape Storage.}, journal = {Journal of food science}, volume = {91}, number = {5}, pages = {e71021}, doi = {10.1111/1750-3841.71021}, pmid = {42108392}, issn = {1750-3841}, support = {2024YFD2100800//China Rural Technology Development Center/ ; 32402194//National Natural Science Foundation of China/ ; 6202512184//Agriculture and Rural Affairs Bureau of Dabancheng District, Urumqi/ ; }, mesh = {*Vitis/microbiology/drug effects ; *Sulfur Dioxide/pharmacology ; Food Storage ; Fruit/microbiology/drug effects ; *Fungi/drug effects/classification ; *Food Preservation/methods ; Catechol Oxidase/metabolism ; }, abstract = {SO2 is commonly used to control postharvest grape mold, but the technology of low-residue usage and the regulatory effects on the grape microbial community are still to be explored. In this research, slow-release SO2 pads (SR) and intermittent high SO2 pluses (IHP) were adopted to treat Daqing grapes during low-temperature storage. The results showed that IHP maintained the best appearance, grape-skin integrity, and reduced the SO2 residue by 49.9% compared to SR group. Meanwhile, the grapes of IHP significantly reduced the decay, inhibited the browning and weight loss, and maintained higher firmness than the control. To explain the reason, the activities of enzymes associated with the immune resistance system, including superoxide dismutase (SOD), peroxidase (POD), phenylalanine ammonia (PAL), and polyphenol oxidase (PPO) were found a higher level in IHP during storage. More importantly, changes in fungi communities were analyzed using internal transcribed spacer (ITS) in the IHP and control groups. The changes in fungal communities showed that IHP preserved the richness of OTU and diversity of fungi communities, effectively inhibiting the relative quantity of the primary pathogens: B. cinerea, C. chasmanthicola, and A. alternata. Furthermore, correlation analysis suggested that microbial communities and immune resistance independently regulate grape postharvest quality while being interrelated, collectively influencing the postharvest quality of Daqing grapes and forming "short-term stress-grape immune resistance (the postharvest quality)-the postharvest grape surface microbiome" a novel interaction system. Thus, we inferred that IHP could induce grape resistance, inhibit surface pathogens, modify surface microbiome, and maintain the postharvest quality of the grapes.}, }
@article {pmid42108513, year = {2026}, author = {Huang, Q and Wen, C and Gu, S and Jie, Y and Li, G and Yan, Y and Wu, G and Yang, N}, title = {Gut microbiota and their metabolites contribute to the heterosis of breast muscle yield in broilers.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42108513}, issn = {1674-9782}, support = {2022YFF1000204//the National Key Research and Development Program of China/ ; ZDYF2023XDNY036//the Key Research and Development Program of Hainan province/ ; GK AA23062049//the Guangxi Science and Technology Major Program/ ; 6262015//Beijing Natural Science Foundation/ ; }, abstract = {BACKGROUND: Breast muscle yield is a key economic trait in broilers, directly affecting carcass value and profitability, and has been significantly improved by intensive selection and exploiting heterosis through crossbreeding. Our previous work showed that synergy between the gut microbiota and host genome underlies breast muscle heterosis in crossbred progeny (CR) derived from Cornish (CC) and White Plymouth Rock (RR) lines. However, the molecular mechanisms by which the gut microbiota contributes to heterosis in breast muscle yield remain poorly understood. Here, we integrated cecal microbiome, metabolome, and transcriptome data from 266 birds at 42 days of age to elucidate the potential gut microbiota-mediated molecular mechanisms underlying breast muscle yield heterosis.<br><br>RESULTS: To assess whether heterosis extends beyond productive traits to the gut microbiota and their metabolites in broilers, we compared the cecal microbial and metabolic profiles of CR with those of their parental lines. The gut microbiota of CR were clearly distinct from those of both parental lines and exhibited heterosis characteristics, with 88 genera displaying heterotic patterns that collectively accounted for approximately 85% of the total microbial abundance. Heterosis was also evident in the cecal metabolites of CR birds. Differential abundance analysis across groups identified 868 cecal metabolites, and abundance-pattern classification showed that approximately 75% exhibited nonadditive patterns in the crossbred progeny. These nonadditive metabolites were predominantly host-microbiota co-metabolites and were mainly enriched in amino acid and lipid metabolic pathways. Importantly, seven of the nine genera previously identified in association with breast muscle yield exhibited heterosis in the crossbred progeny. At the metabolomic level, yield-associated genera were linked to a distinct set of 35 cecal metabolites, dominated by sphingolipids, ether-linked phospholipids, and acyl-homoserine lactones. These metabolites formed coordinated associations with the expression of 269 host genes, which were functionally enriched in MAPK signaling and focal adhesion pathways.<br><br>CONCLUSIONS: These findings suggest that heterosis exists not only in productive traits but also in gut microbiota and their metabolites, the latter in turn contributed to breast muscle yield, which offers valuable guidance for elucidating the molecular basis of heterosis in animals.}, }
@article {pmid42108623, year = {2026}, author = {Kashkouli, M and Fathipour, Y}, title = {Cross-kingdom signaling manipulation by insect-associated microbial symbionts: Linking molecular mechanisms to pest management strategies.}, journal = {Pest management science}, volume = {}, number = {}, pages = {}, doi = {10.1002/ps.70885}, pmid = {42108623}, issn = {1526-4998}, abstract = {Microbial symbionts associated with herbivorous insects can modulate plant hormone networks and reconfigure induced defenses during feeding. This review synthesizes current knowledge on how symbiont effectors converge on conserved jasmonic acid (JA)/salicylic acid (SA)/ethylene (ET) signaling hubs to suppress or reprogram plant immunity. These microbial partners secrete a diverse arsenal of bioactive molecules, including effector proteins (e.g., the histidine-rich Ca[2+]-binding protein ApHRC from Serratia symbiotica in pea aphids), enzymes (e.g., gut microbiome-derived proteases in Anticarsia gemmatalis larvae), and host metabolite mimics (e.g., cytokinin production induced by Wolbachia in the apple leaf-mining moth). Through these mechanisms, symbionts selectively manipulate plant hormonal pathways, a form of molecular interference that often enhances herbivore performance by increasing feeding efficiency, fecundity, and host plant range, thereby increasing plant susceptibility to biotic stress. These physiological alterations trigger cascading ecological effects, reshaping multitrophic interactions: symbiont-mediated changes in herbivore-induced plant volatiles (HIPVs) and secondary metabolites influence the behavior of natural enemies, alter competitive outcomes among herbivores, and disrupt plant-insect communication. Consequently, microbial symbionts act as hidden ecological engineers, driving community dynamics and evolutionary trajectories. By integrating molecular, ecological, and evolutionary perspectives, we propose a unified framework that explicitly links symbiont effector function to plant immune modulation and its ecosystem-level consequences. Ultimately, this synthesis underscores the potential of targeting insect-microbe partnerships through approaches such as effector blocking, microbiome augmentation, or symbiont disruption, for developing sustainable pest management strategies and advancing the field of plant defense ecology. © 2026 Society of Chemical Industry.}, }
@article {pmid42108649, year = {2026}, author = {Hermanson, JB and Tolba, SA and Gazi, MA and Chrisler, EA and Kaur, M and Sidebottom, AM and Liu, Y and Martinez-Boggio, G and Lucas, LN and Amador-Noguez, D and Rey, FE and Leone, VA}, title = {Gut microbes mediate the synergistic effects of dietary cholesterol and saturated fat in driving fibrosing MASH.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2668121}, doi = {10.1080/19490976.2026.2668121}, pmid = {42108649}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Cholesterol, Dietary/adverse effects/metabolism ; Mice ; Humans ; Diet, High-Fat/adverse effects ; Male ; *Dietary Fats/adverse effects/metabolism ; *Fatty Acids/metabolism/adverse effects ; Mice, Inbred C57BL ; Bile Acids and Salts/metabolism ; *Fatty Liver/microbiology/metabolism/pathology ; Specific Pathogen-Free Organisms ; *Liver Cirrhosis/microbiology ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Hepatic Stellate Cells/metabolism ; Liver/pathology ; Germ-Free Life ; Non-alcoholic Fatty Liver Disease ; }, abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) affects approximately one-third of the global population and can progress to metabolic dysfunction-associated steatohepatitis (MASH) with fibrosis, increasing the risk of cirrhosis, hepatocellular carcinoma, and mortality. Gut microbes driven by diets high in saturated fat, simple sugar, and cholesterol contribute to disease progression, yet the underlying mechanisms remain undefined. We explored the independent and synergistic effects of dietary saturated fat and cholesterol on MASH development using specific pathogen-free (SPF) and germ-free (GF) mice. We demonstrate that (1) both dietary cholesterol and saturated fat are required to induce fibrosing MASH in SPF mice, whereas GF mice are protected, (2) saturated fat and cholesterol individually alter gut microbial membership, potentially via altered bile acid metabolism, while their combination promotes a distinct composition, including an increase in Parasutterella spp. which correlates with hepatic fibrosis, and (3) diluted cecal contents from SPF, but not GF, mice fed high-fat, high-cholesterol diets are enriched in deoxycholic acid and activate human hepatic stellate cells in vitro, suggesting a mechanistic link between dietary lipid-induced microbiota and liver fibrogenesis. These findings reveal how specific Western dietary components shape the gut microbiota and contribute to hepatic fibrosis via stellate cell activation, offering potential targets for therapeutic interventions against MASLD/MASH.}, }
@article {pmid42108651, year = {2026}, author = {Xu, Z and Mu, L and Su, H and Zhang, X and Shang, H and Li, Z and Tak Vai Chan, M and Ka Kei Wu, W and Chen, H}, title = {Probiotics in colorectal cancer: mechanisms, biomarkers, and adjunct strategies.}, journal = {Cancer biology &amp; medicine}, volume = {}, number = {}, pages = {}, doi = {10.20892/j.issn.2095-3941.2026.0133}, pmid = {42108651}, issn = {2095-3941}, support = {24103225//RGC-GRF Hong Kong/ ; 14104924//RGC-GRF Hong Kong/ ; C4008-23W//RGC-CRF Hong Kong/ ; C4042-24GF//RGC-CRF Hong Kong/ ; 82573882//National Natural Science Foundation of China [NSFC]/ ; 82272989//National Natural Science Foundation of China [NSFC]/ ; 22210032//Health and Medical Research Fund [HMRF]/ ; 2025.090//CUHK Direct Grant for Research/ ; }, abstract = {Colorectal cancer (CRC) is among the most common malignant tumors and remains a leading cause of cancer-related mortality worldwide. The gut microbiota and metabolites, which are modulated by host genetics and environmental exposures, have emerged as key contributors to the pathogenesis of CRC. A key feature of gut dysbiosis in CRC is the enrichment of pathogenic bacteria alongside the depletion of beneficial commensals. Probiotic supplementation has been shown to counteract this imbalance and suppress tumor progression. Mechanistically, probiotics suppress CRC development through multifaceted actions, including directly inhibiting tumor cell growth, reducing inflammation, reinforcing the intestinal barrier, and reprogramming host immunity. This review summarizes evidence on the inhibitory role of probiotics in CRC, evaluates the potential of probiotics as predictive biomarkers, and discusses microbiome-modulation strategies designed to enhance immunotherapy and chemotherapy, thereby offering a complementary paradigm for CRC prevention and treatment.}, }
@article {pmid42108693, year = {2026}, author = {van Heule, M and Heil, B and Norris, JK and Gedye, K and Lin, X and De Spiegelaere, W and Daels, P and Dini, P}, title = {Vaginal host-microbe signatures linked to placental outcomes in mares.}, journal = {Equine veterinary journal}, volume = {}, number = {}, pages = {}, doi = {10.1002/evj.70185}, pmid = {42108693}, issn = {2042-3306}, support = {//Special Research Fund at the University of Ghent (BOF)/ ; //New Zealand Equine Research Foundation/ ; //John P. Hughes Endowment/ ; }, abstract = {BACKGROUND: Ascending placentitis is a leading cause of late-term pregnancy loss in mares. Although pathogens are presumed to ascend from the caudal reproductive tract, the association between the vaginal microbiome and placentitis has not been systematically examined.<br><br>OBJECTIVES: To characterise microbial and host gene expression in the equine vagina during gestation and to identify taxa or transcripts that were associated with the presence of an abnormal placenta at birth.<br><br>STUDY DESIGN: Prospective, paired observational study.<br><br>METHODS: Vaginal wall swabs were collected from 49 multiparous Thoroughbred mares at days&#x2009;42-46 and 118-133 of gestation (first and second trimester). Pregnancies were monitored to term, and placentas were classified as normal (healthy) or abnormal. Complete data was available for 37 mares, and 13 were included in this study: normal (n&#x2009;=&#x2009;6), abnormal (n&#x2009;=&#x2009;5), and ascending placentitis (n&#x2009;=&#x2009;2). Total RNA underwent deep dual RNA-sequencing. Alpha- and beta-diversity metrics, differential expression, and microbe-host correlation analyses were performed.<br><br>RESULTS: Global vaginal microbial diversity did not differ between mares with healthy or abnormal placentas. Several microbes from the phyla Actinomycetota and Pseudomonadota showed altered activity in mares with abnormal placentas. Vaginal transcriptome showed a subtle inflammatory response in the second trimester in the abnormal placenta group in the absence of clinical signs. Correlation analysis suggested an interaction between bacterial survival and virulence genes and host inflammation and apoptosis genes.<br><br>MAIN LIMITATIONS: Samples were obtained from clinical cases, limiting the availability of a complete history.<br><br>CONCLUSIONS: Although overall vaginal microbial diversity was similar between outcome groups, distinct host vaginal transcriptional and microbial activity signatures distinguished mares with an abnormal placenta at birth. These findings warrant targeted investigation of the vaginal immune response and bacterial virulence factors as early biomarkers and therapeutic targets.}, }
@article {pmid42108760, year = {2026}, author = {Pereira, EC and Bell, CA}, title = {Observing the invisible: X-ray CT for plant-microbe interactions.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71252}, pmid = {42108760}, issn = {1469-8137}, support = {BB/X009823/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Plant-microbe interactions are inherently spatial, yet the physical structure of the soil and rhizosphere is rarely treated as a mechanistic variable in experimental design. X-ray computed tomography (X-ray CT) enables nondestructive, three-dimensional, and time-resolved imaging of intact root-soil systems, providing direct access to the structural context in which plant-microbe interactions occur. Rather than a secondary imaging technique, X-ray CT can offer a wealth of data as a primary experimental platform for future plant-microbe research. Here, we highlight key structural traits that X-ray CT can quantify and discuss how they may shape microbial behaviour, plant immune responses, and disease outcomes. We expand on how X-ray CT could be employed in future to provide a framework to disentangle direct microbial effects from indirect, structure-mediated feedbacks. For breeding and management, it could enable selection for root traits and soil practices that engineer favourable microhabitats rather than targeting organisms in isolation. Despite this potential, broader adoption will require overcoming current limitations related to access to instrumentation, analytical expertise, and the integration of structural data with biological measurements. Overall, we suggest that resolving these issues will enable the integration of X-ray CT-derived structure with molecular, microbiome, and modelling approaches to enable the development of digital rhizospheres, offering a pathway from descriptive observations to predictive, structure-aware in silico frameworks in plant-microbe research.}, }
@article {pmid42108828, year = {2026}, author = {Pylro, VS and Morais, DK}, title = {Rethinking Alpha Diversity in Marker-Gene Microbiome Studies: Dominance Matters More Than Richness.}, journal = {Environmental microbiology}, volume = {28}, number = {5}, pages = {e70325}, doi = {10.1111/1462-2920.70325}, pmid = {42108828}, issn = {1462-2920}, support = {441346/2023-5//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 406658/2022-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; Finance Code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; RED-00181-23//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; RED-00330-16//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; APQ-04011-24//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; APQ-08335-25//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; APD-01038-25//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; 2649/22//FINEP/ ; }, mesh = {*Microbiota/genetics ; *Biodiversity ; *Bacteria/genetics/classification ; Genetic Markers ; }, abstract = {In the era of widespread marker-gene sequencing, alpha diversity metrics are increasingly used to infer ecological responses and biodiversity patterns in microbial communities. We highlight key conceptual and methodological limitations underlying these metrics, particularly the open-ended nature of microbial richness and the uneven detectability of taxa. We argue that, in marker-gene-based studies, alpha diversity often reflects shifts in dominance rather than true richness. We discuss why common assumptions fail, outline the risks of misinterpretation and propose a dominance-centred perspective to improve ecological inference in microbiome research.}, }
@article {pmid42108955, year = {2026}, author = {Yoon, EC and Seok, J and Kim, YK and Yoon, HY}, title = {A harmonized respiratory-gut microbiome cohort framework for idiopathic pulmonary fibrosis.}, journal = {Tuberculosis and respiratory diseases}, volume = {}, number = {}, pages = {}, doi = {10.4046/trd.2026.0032}, pmid = {42108955}, issn = {1738-3536}, }
@article {pmid42109051, year = {2026}, author = {Zhang, L and Che, X and Zhang, X and Sun, X and Wang, Y and Zhang, R}, title = {Fabricating Blackened Jujube Polysaccharide-Zn (II) Complex to Enhance its Anti-Inflammatory Effect: Structural Characterization and Biological Evaluation.}, journal = {Journal of food science}, volume = {91}, number = {5}, pages = {e71128}, doi = {10.1111/1750-3841.71128}, pmid = {42109051}, issn = {1750-3841}, support = {//Central Government Guiding Local Science and Technology Development Fund of Shandong Province, China (YDZX2025029)/ ; //Science &amp; Technology Cooperation Program of Shandong (2025KJHZ017)/ ; //Taishan Industrial Experts Program (TSCY20241184)/ ; //Haoxiangni Health Food Co.,Ltd. Horizontal Research Project (SSH20250428)/ ; //The grants from Key R&amp;D Program of Shandong Province, China (2024TZXD064, CJZBCZGQXTHG02, 2024TZXD015, 2024TZXD007)/ ; }, mesh = {*Polysaccharides/chemistry/pharmacology ; Animals ; *Anti-Inflammatory Agents/chemistry/pharmacology ; *Zinc/chemistry/pharmacology ; Mice ; Gastrointestinal Microbiome/drug effects ; *Ziziphus/chemistry ; Colitis/drug therapy/chemically induced ; Male ; Dextran Sulfate/adverse effects ; *Plant Extracts/chemistry/pharmacology ; Mice, Inbred C57BL ; Disease Models, Animal ; }, abstract = {Polysaccharides extracted from blackened jujubes (BP) demonstrate remarkable pharmacological activities. Chelation with zinc ions represents an effective strategy for enhancing their biological functions. In this study, a novel polysaccharide-Zn (II) complex derived from blackened jujube (BP-Zn) was successfully synthesized, and its structural characteristics as well as anti-inflammatory effects were comprehensively evaluated in a dextran sulfate sodium (DSS)‑induced colitis model. The results indicated that -OH and -COOH groups in BP interacted with zinc ions through ligand bonds. Zinc chelation enhances the structural stability and molecular properties of BP. The BP-Zn complex demonstrated significant anti-inflammatory properties by a reduction in body weight loss, an increased thymus index, and the restoration of intestinal barrier integrity. Furthermore, microbiome analysis revealed that the BP-Zn complex modulated the gut microbiota, boosting beneficial bacteria while inhibiting pathogenic species. Metabolomic profiling demonstrated that BP-Zn modulated key metabolic pathways involved in inflammation and immune regulation, particularly amino acid and flavonoid metabolism. These results suggested that BP-Zn complex has strong potential as natural anti-inflammatory agents.}, }
@article {pmid42109217, year = {2026}, author = {Tsaousis, AD and Gentekaki, E and Al, FD}, title = {Blastocystis and chronic urticaria: the evidence reviewed does not justify routine testing or treatment.}, journal = {Journal of medical microbiology}, volume = {75}, number = {5}, pages = {}, pmid = {42109217}, issn = {1473-5644}, mesh = {Humans ; *Chronic Urticaria/parasitology/diagnosis/drug therapy ; *Blastocystis Infections/diagnosis/drug therapy/complications/parasitology ; *Blastocystis/isolation &amp; purification ; Diagnostic Tests, Routine ; Feces/parasitology ; Prevalence ; }, abstract = {Ulusan Bagci et al. propose Blastocystis spp. as a hidden cause of chronic urticaria and suggest routine stool testing and treatment in positive cases. We argue that this conclusion is not supported by the current evidence, which is dominated by heterogeneous diagnostics, cross-sectional prevalence comparisons prone to misclassification and non-randomized treatment-response reports lacking clearance-linked endpoints. We outline minimum standards for interpretable inference, including quantitative detection, longitudinal sampling and trials linking confirmed clearance vs. persistence to validated urticaria outcomes.}, }
@article {pmid42109313, year = {2026}, author = {Duval, H and Knox, K and Fairfield, H and Chai, RC and Corr, AP and Qiang, YW and Belknap, K and Abayomi, K and Schimelman, A and Nestor, B and Karam, M and Jachimowicz, E and Stohn, PJ and Guan, X and Lynes, MD and Hamidi, H and Croucher, PI and Ryzhov, S and Reagan, MR}, title = {Microenvironmentally derived fatty acid-binding proteins 4 and 5 are novel therapeutic vulnerabilities in multiple myeloma.}, journal = {Blood neoplasia}, volume = {3}, number = {2}, pages = {100229}, pmid = {42109313}, issn = {2950-3280}, abstract = {Multiple myeloma (MM) is an incurable cancer of monoclonal plasma cells. Despite its dependency on the bone marrow (BM), therapies targeting the BM microenvironment are lacking, barring immunotherapies. Obesity is associated with worse outcomes in MM, and although antiobesity treatments may benefit patients with MM, this is not yet known. Moreover, those treatments have side effects, and their specific mechanisms of action are elusive because of the interconnectedness of obesity, metabolic syndrome, diet, fiber intake, gut microbiome, inflammation, and the immune system. Fatty acid-binding proteins (FABPs) play a role in obesity and other diseases, but no studies of microenvironmentally derived FABPs' effects on cancer progression exist. Therefore, we tested the hypothesis that microenvironmentally derived FABPs support MM progression using single-cell sequencing data, in vivo models, and MM Research Foundation Relating Clinical Outcomes in MM to Personal Assessment of Genetic Profile data. We found that global Fabp4/Fabp5 double-knockout (Fabp4/5 [dKO]) mice have modifications in body composition, immune cells, and skeletal parameters. Murine myeloma cell (Vk12598) engraftment and growth (tumor incidence) were higher in wild-type (WT) vs Fabp4/5 [dKO] mice. High-fat diet-fed Fabp4/5 [dKO] mice were further protected from metabolic and skeletal diseases, and tumor incidence was reduced, whereas survival was increased in Fabp4/5 [dKO] vs WT mice. Finally, low FABP5 expression in granulocyte-monocyte progenitors, typically considered immunosuppressive, is associated with improved survival of patients with MM, implicating reduced immunosuppression and improved immune-mediated tumor eradication as one mechanism of action. Overall, the data suggest that tumor-extrinsic FABP4/5 support MM progression, which, combined with previous myeloma cell-intrinsic findings, suggests targeting FABP4/5 may cause a 2-pronged attack in MM.}, }
@article {pmid42109325, year = {2026}, author = {Murella, S and Kaur, H and Gunti, V and Polakala, T and Kanani, R and Juttu, GK}, title = {Breaking the habit: Evidence-based approaches to smoking cessation.}, journal = {Bioinformation}, volume = {22}, number = {2}, pages = {800-805}, pmid = {42109325}, issn = {0973-2063}, abstract = {Smoking is a major public health concern that significantly impacts the oral cavity, the primary site of exposure. Tobacco consumption has been linked to conditions such as leukoplakia, oral cancer and impaired wound healing and severe periodontal disease. At the same time, vaping disrupts the oral microbiome and compromises implant stability, both influenced by social, economic, behavioral and political determinants. Evidence suggests that multicomponent interventions, including dental-based programs combined with community initiatives, behavioral strategies such as Motivational Interviewing and the 5Rs framework and pharmacotherapies such as varenicline, bupropion or NRTs are essential for improving cessation outcomes and reducing tobacco-related oral health risks. Thus, we show the consequences of conventional smoking and vaping on oral tissues, periodontal structures, sensory perception, dental implants and saliva.}, }
@article {pmid42109673, year = {2026}, author = {Srivastava, K and Srivastava, R}, title = {Explainable deep learning approaches and clinical insights for cancer biomarker identification.}, journal = {Frontiers in oncology}, volume = {16}, number = {}, pages = {1810793}, pmid = {42109673}, issn = {2234-943X}, abstract = {Biomarkers play a pivotal role in contemporary cancer immunotherapy by guiding diagnosis, patient stratification, therapeutic decision-making, and longitudinal assessment of treatment responses. Despite the transformative impact of immune checkpoint inhibitors, adoptive cell therapies, and neoantigen-based vaccines, durable clinical benefit is achieved in only a subset of patients, highlighting the critical need for accurate predictive and prognostic biomarkers. Technological advances are rapidly expanding the biomarker repertoire through high-resolution approaches such as single-cell and spatial omics, circulating tumor DNA analysis, immune-related gene expression signatures, and microbiome profiling. These platforms enable deeper characterization of immune dynamics, resistance mechanisms, and therapeutic responsiveness. Recent advances in artificial intelligence, machine learning, and deep learning have fundamentally reshaped immunotherapy biomarker discovery by enabling the integration of complex, high-dimensional multiomics, radiomic, and clinical datasets into unified predictive frameworks. Deep learning models have demonstrated superior performance in predicting immune checkpoint inhibitor responses, immune-related adverse events, and mechanisms of therapeutic resistance across multiple cancer types. The incorporation of explainable AI approaches further enhances clinical interpretability by linking algorithmic predictions to biologically validated immune processes. Future progress will depend on multimodal biomarker integration, analytical standardization, and rigorous prospective validation, alongside addressing regulatory, economic, and implementation challenges to advance precision cancer immunotherapy.}, }
@article {pmid42109721, year = {2026}, author = {Zhu, Y and Li, Y}, title = {Gut microbiota in perimenopausal atherosclerosis: the estrogen-gut-vascular axis and personalized cardiovascular prevention.}, journal = {Frontiers in endocrinology}, volume = {17}, number = {}, pages = {1815352}, pmid = {42109721}, issn = {1664-2392}, mesh = {Humans ; *Perimenopause/metabolism ; *Gastrointestinal Microbiome/physiology ; Female ; *Estrogens/metabolism ; *Atherosclerosis/prevention &amp; control/microbiology/metabolism ; Precision Medicine ; *Cardiovascular Diseases/prevention &amp; control ; }, abstract = {The risk of atherosclerosis rises markedly in perimenopausal women. The observed discrepancy between the traditional "estrogen cardioprotection hypothesis" and the complex effects of hormone replacement therapy in clinical practice suggests the existence of intermediary mechanisms that are not yet fully understood. Recent research indicates that the gut microbiota may play a pivotal role in this "estrogen paradox". By integrating current evidence, this review systematically elucidates the core driving function of the "estrogen-gut-vascular axis" in disease progression: declining estrogen levels lead to intestinal barrier dysfunction and associated imbalances in microbial metabolites (e.g. reduced short-chain fatty acids and increased pro-inflammatory metabolites), collectively accelerating atherogenesis. Targeting this axis through dietary modification, microbial therapeutics, and precision hormone interventions may break this pathological cycle. Notably, effective nutritional strategies must consider food matrix, individual microbial metabolic capacity, and timing of intervention. Furthermore, building on extensive research into age-related shifts in gut microbiota, this review proposes the novel concept of 'gut microbial age' based on functional metabolic profiles, to quantify the functional state of host-microbiome interactions. This concept aims to provide new perspectives and tools for personalized cardiovascular risk assessment and precise intervention in perimenopausal women.}, }
@article {pmid42110058, year = {2026}, author = {Gomez, AM and Palencia, CJ}, title = {Granulomatosis With Polyangiitis Unmasked by COVID-19 Infection: A Case Report.}, journal = {Cureus}, volume = {18}, number = {4}, pages = {e106729}, pmid = {42110058}, issn = {2168-8184}, abstract = {Granulomatosis with polyangiitis (GPA) is a type of anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV), in which small- to medium-sized vessels are targeted. The incidence increases with age, and the most commonly affected systems include the sinonasal tract, lungs, and kidneys. Etiology remains unclear, although exposure to environmental triggers, including infections, has been hypothesized to initiate or unmask autoimmunity in genetically predisposed individuals. The nasal microbiome is also hypothesized to play a role in the disease process, although research is still ongoing. In this report, we present a case of a 65-year-old female with a long history of nonspecific musculoskeletal, sinus, and gastrointestinal complaints, who developed multifocal pneumonia with hemoptysis and progressive pulmonary disease shortly after COVID-19 infection.}, }
@article {pmid42110391, year = {2026}, author = {Mazic de Sonis, A and Granger, C}, title = {Non-pharmacological pain treatments as neuro-epigenetic revalidation strategies: integrating chronobiology, acupuncture, and pharmaco-nutrition.}, journal = {Frontiers in pain research (Lausanne, Switzerland)}, volume = {7}, number = {}, pages = {1786367}, pmid = {42110391}, issn = {2673-561X}, abstract = {BACKGROUND: Chronic pain is increasingly conceptualized as a disorder of maladaptive neural plasticity sustained by central sensitization, neuroinflammation signalling, disrupted biological rhythms, metabolic dysregulation and environmentally mediated epigenetic modulation, and altered gut-brain interactions. While pharmacological approaches remain central to pain management, their long-term efficacy is limited by tolerance, adverse effects, opioid-induced hyperalgesia, and inter-individual variability. Growing evidence suggests that non-pharmacological interventions may modulate pain not only symptomatically, but through deeper neurobiological and epigenetic mechanisms.<br><br>HYPOTHESIS: We propose that selected non-pharmacological pain treatments, particularly chronobiology-informed acupuncture and targeted pharmaco-nutrition, may be considered as neuro-epigenetic revalidation strategies. These interventions may restore adaptive gene expression profiles and neural, immune, metabolic and circadian regulation disrupted in chronic pain, thereby reducing nociceptive sensitization and improving treatment responsiveness.<br><br>RATIONALE: Acupuncture has been shown to modulate central pain networks, including prefrontal, limbic, and sensorimotor regions, with effects distinct from sham procedures. Chronobiological regulation of sleep-wake cycles, hormonal rhythms, and feeding timing influences inflammatory pathways and epigenetic regulation. In parallel, the gut-brain axis, through intestinal barrier integrity, microbiome composition, and immune-glial signalling, plays a critical role in pain chronification and drug metabolism. Nutritional and nutraceutical interventions can influence these pathways and have been associated with changes in inflammatory tone, opioid tolerance, and neuroimmune interactions.<br><br>TESTABLE PREDICTIONS: This framework generates testable predictions linking multimodal interventions to dynamic modulation of epigenetic signatures (DNA methylation, microRNA expression), chronobiological and sleep parameters, inflammatory mediators, gut-brain markers and clinically meaningful outcomes. Longitudinal, multimodal study designs are required to evaluate association between regulatory recalibration and sustained clinical improvement.<br><br>CONCLUSION: Viewing non-pharmacological pain treatments within a neuro-epigenetic revalidation model provides a coherent system-level perspective model that bridges neuroscience, chronobiology, epigenetics, and integrative pain medicine. This integrative model supports the development of personalized, mechanism-based strategies for chronic pain management while encouraging biomarker-informed translational research.}, }
@article {pmid42110445, year = {2026}, author = {Carrouel, F and Kanoute, A and Faye, D and Rhanoui, M and Lan, R and Bourgeois, D}, title = {Oral prophylaxis for the reduction of interdental dysbiosis-associated red complex pathogens during pregnancy: a randomized clinical trial.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1798508}, pmid = {42110445}, issn = {2296-858X}, abstract = {INTRODUCTION: Periodontal disease during pregnancy is associated with adverse outcomes such as preterm birth, low birth weight, and preeclampsia. Socransky's red complex pathogens including Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola, are key risk factors for these complications. This study aims to evaluate whether daily use of calibrated interdental brushes, in addition to conventional tooth brushing, reduces the bacterial load these pathogens in pregnant women.<br><br>METHODS: A randomized controlled trial was conducted in six obstetric clinics in Senegal between March 2022 and January 2023. One hundred pregnant women, aged 18-40 and in their third month of pregnancy, were randomized into a test group using interdental brushes plus tooth brushing and a control group using tooth brushing alone. The outcome was the change in bacterial load from the third to eighth month of pregnancy, quantified using real-time polymerase chain reaction techniques.<br><br>RESULTS: By the eighth month, the test group demonstrated a statistically significant reduction in total bacterial load compared to the control group, with a mean reduction of 36.6% (95% CI: 31.2-41.1%, p&#x202f;<&#x202f;0.001). Notably, T. denticola load decreased by 92.1% (95% CI: 87.1-95.6%, p&#x202f;<&#x202f;0.001) in the test group, while it increased in the control group. Reductions were also observed for P. gingivalis and T. forsythia, although these differences were not statistically significant (p&#x202f;=&#x202f;0.061 and p&#x202f;=&#x202f;0.148, respectively).<br><br>DISCUSSION: These findings suggest that adding calibrated interdental brushes to a conventional tooth brushing routine is more effective in lowering the bacterial load of harmful red complex pathogens in pregnant women.<br><br>CONCLUSION: The results support the inclusion of interdental cleaning in prenatal oral health care guidelines as a strategy for managing periodontal risk during pregnancy.}, }
@article {pmid42110460, year = {2026}, author = {Wu, F and Chen, Y and Ni, X and Yi, T and Tan, S}, title = {The oral-gut-liver axis: linking periodontal microbiota to the pathogenesis of liver diseases.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1810114}, pmid = {42110460}, issn = {2296-858X}, abstract = {Oral microbiota plays a critical role in linking oral and systemic health, with dysbiosis closely associated with the onset and progression of chronic liver diseases. This review systematically examines the central role of the "oral-gut-liver axis" in hepatic pathophysiology. Epidemiological evidence has identified periodontitis and specific oral pathogens, such as Fusobacterium nucleatum (F. nucleatum), as independent risk factors for the progression of non-alcoholic fatty liver disease (NAFLD), development of cirrhosis, and incidence of hepatocellular carcinoma (HCC). The underlying mechanisms primarily involve four interrelated pathways: (1) direct bacterial translocation, where pathogens such as F. nucleatum colonize the liver via bacteremia and activate oncogenic pathways; (2) systemic dissemination of bacterial metabolites, such as lipopolysaccharides (LPS), driving hepatic inflammation, oxidative stress, and fibrosis via Toll-like receptor 4 (TLR4) signaling and reactive oxygen species (ROS)-mediated pathways; (3) systemic immune inflammation, wherein periodontitis acts as a chronic inflammatory focus that continuously releases pro-inflammatory mediators into the circulation; and (4) indirect effects mediated by gut microbiota dysbiosis, whereby oral bacteria compromise the intestinal barrier, facilitating the influx of gut-derived toxins into the liver. These findings underscore the significant impact of oral health on hepatic status. In the short term, oral microbial profiles represent promising noninvasive diagnostic and prognostic biomarkers. Preliminary clinical trials indicate that periodontal therapy can improve metabolic parameters in patients with NAFLD. In the long term, promoting interdisciplinary collaboration between hepatology and oral medicine and strategically integrating oral health interventions into the comprehensive management framework for liver diseases hold significant public health potential for mitigating the global burden of hepatic disorders.}, }
@article {pmid42110505, year = {2026}, author = {Li, J and Zhang, H and Zhang, P and Hu, J}, title = {Potential Benefits of Gut Microbiota Modulation in Chronic Obstructive Pulmonary Disease.}, journal = {International journal of chronic obstructive pulmonary disease}, volume = {21}, number = {}, pages = {594405}, pmid = {42110505}, issn = {1178-2005}, mesh = {*Gastrointestinal Microbiome/drug effects ; *Pulmonary Disease, Chronic Obstructive/microbiology/therapy/physiopathology/metabolism ; Animals ; Humans ; *Dysbiosis/therapy ; Disease Models, Animal ; *Lung/physiopathology/microbiology/metabolism/pathology ; *Fecal Microbiota Transplantation ; Male ; Mice, Inbred C57BL ; Metabolomics/methods ; Anti-Bacterial Agents ; Female ; *Bacteria/genetics/metabolism/drug effects/growth &amp; development/classification ; Middle Aged ; Ribotyping ; Aged ; Case-Control Studies ; Mice ; RNA, Ribosomal, 16S/genetics ; T-Lymphocytes, Regulatory/immunology/metabolism ; }, abstract = {BACKGROUND: The gut-lung axis is increasingly recognized. This study aimed to find out whether and how the gut microbiome involved in the pathogenesis of chronic obstructive pulmonary disease (COPD).<br><br>METHODS: Gut microbiota was characterized via 16S rRNA gene sequencing in COPD patients and a smoking-induced mouse model. Gut dysbiosis was induced by antibiotic cocktail (ABX) and restored by fecal microbiota transplantation (FMT). Plasma metabolomics was conducted using liquid chromatography-mass spectrometry (LC-MS), and pathway analysis was performed with MetaboAnalyst 5.0. Differentially expressed genes were identified by RNA sequencing and functionally interpreted through gene set enrichment analysis (GSEA).<br><br>RESULTS: Both COPD patients and mice showed altered gut microbiota, characterized by a unique microbial composition and reduced diversity. ABX induced gut dysbiosis exacerbated pathological lung changes, impaired lung function, and promoted Treg cell exhaustion in COPD mice. Restoration of gut homeostasis via FMT attenuated these alterations. Higher plasma levels of acetylcholine (ACh) were observed in COPD mice, while the highest ACh levels were found in ABX treated COPD mice compared to controls. Notably, ACh levels correlated positively with genus Parasutterella, which was more abundant in COPD mice, and inversely with genera Candidatus Saccharimonas and Lactobacillus, which were predominant in control mice. Metabolomic pathways analysis revealed enrichment in unsaturated fatty acids biosynthesis and purine metabolism in COPD mice relative to controls.<br><br>CONCLUSION: These findings highlight the involvement of the gut microbiome in COPD development and suggest that maintaining gut homeostasis may represent a novel therapeutic strategy for COPD.}, }
@article {pmid42110624, year = {2026}, author = {Liu, Z and Liu, Z and Sun, W and Zhu, L and Lyu, T}, title = {Causal association between oral microbiome and chronic kidney disease: two-sample Mendelian randomization.}, journal = {Archives of medical science : AMS}, volume = {22}, number = {1}, pages = {377-386}, pmid = {42110624}, issn = {1734-1922}, abstract = {INTRODUCTION: Chronic kidney disease (CKD) contributes to 1.2 million deaths annually. Oral dysbiosis may influence CKD, highlighting the need for further research on its role as a risk factor and preventive target.<br><br>MATERIAL AND METHODS: We obtained summary statistics for genome-wide association studies (GWAS) of the oral microbiome from the GWAS Catalog and CKD from the CKDGen Consortium. Inverse variance weighting (IVW) was used as the principal analysis method, supplemented by MR-Egger, weighted median, and weighted mode to assess causal relationships. Sensitivity analyses, including MR-PRESSO and Cochran's Q, validated the robustness of the results.<br><br>RESULTS: The IVW results showed that Veillonella species was causally associated with CKD (OR = 0.96, 95% CI (0.93-0.99)), Order Fusobacteriales (OR = 1.01, 95% CI (1-1.01)) and Rothia species (OR = 0.99, 95% CI (0.99-1)) were causally associated with urinary albumin-to-creatinine ratio (UACR); Order Bacteroidales (OR = 0.97, 95% CI (0.94-1)) and Species micronuciformis (OR = 0.95, 95% CI (0.91-0.99)) were causally associated with CKDi25; and Streptococcus species was causally associated with dialysis (OR = 0.82, 95% CI (0.69-0.97)). There was no significant causal association between other oral microbiome features and CKD at the genetic level. Sensitivity analysis indicated that the results were robust.<br><br>CONCLUSIONS: Our study suggests that there are associations between the oral microbiome and CKD. To better understand its mechanism of action and to develop broader strategies for preventing chronic kidney disease, further research is required.}, }
@article {pmid42110715, year = {2026}, author = {Rumão, MS and Andrade, MT and Costa, RJ and Santana, GJ and Cerqueira, JPC and Lima, GSO and Garcia, NC and Heller, D and Espinosa, CN and Arantes, RME and Moraes, MM and Mendes, TT}, title = {Human Microbiome Alterations in Antarctic Isolated, Confined, and Extreme (ICE) Environments: A Systematic Review and Meta-Regression.}, journal = {International journal of microbiology}, volume = {2026}, number = {}, pages = {3405549}, pmid = {42110715}, issn = {1687-918X}, abstract = {Antarctica is one of the most extreme and isolated environments on Earth, serving as a natural laboratory for studying human physiological and microbial adaptation under stress. This systematic review and meta-regression evaluated how exposure to Antarctica's isolated, confined, and extreme (ICE) environments impacts the human microbiome, considering environmental and behavioral factors that may modulate these alterations. Following PRISMA guidelines and being registered with PROSPERO (CRD42024558423), comprehensive searches were conducted in PubMed, Scopus, Embase, Cochrane, and LILACS without language or date restrictions. Seven studies conducted between 2014 and 2024, enrolling 77 healthy participants in total, investigated oral, gut, or skin microbiota changes under Antarctica's ICE conditions at field camps, research stations, or shipboard environments. The findings suggest that ICE environments could induce measurable changes in microbial composition, relative abundance, and diversity across gut, oral, and skin sites, with age, type of accommodation, and sampling site emerging as significant predictors. Specifically, older individuals and those stationed at research bases exhibited greater odds of microbial alterations, while the gut microbiota showed greater stability compared to skin and oral sites. Although some studies explored the effects of probiotic supplementation and physical activity as modulators, evidence remains limited. The review highlights that environmental stressors such as confinement, duration of stay, extreme climate, diet, and physical exertion may collectively influence microbiome dynamics. These findings highlight the influence of age, accommodation type, and sampling site on microbial shifts in ICE environments, while underscoring the need for standardized longitudinal studies to clarify the biological and operational relevance of these changes.}, }
@article {pmid42110826, year = {2026}, author = {Garcia, BA and Dornelas-Figueira, LM and Katrak, C and Roesch, LFW and Tomar, SL and Adams, G and Oliveira, D and Nascimento, MM and Abranches, J}, title = {Co-infection with Cbp[+] Streptococcus mutans and Candida albicans is associated with root caries in older adults.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2667029}, pmid = {42110826}, issn = {2000-2297}, abstract = {BACKGROUND: Gingival recession increases with age, exposing root surfaces and raising susceptibility to root caries. As the global population ages, root caries prevalence is expected to rise, underscoring the need to better understand its risk factors.<br><br>OBJECTIVE: To investigate the association between co-infection with Cbp[+] Streptococcus mutans and Candida albicans and root caries in older adults with gingival recession, while characterizing the root plaque microbiome and evaluating multifactorial risk factors.<br><br>DESIGN: This cross-sectional study included 117 adults &#x2265;65 years; 56 with root caries and 61 without. Saliva and site-specific supragingival plaque samples were collected to assess Mutans streptococci and Candida spp., along with microbiome composition. Demographic, behavioral, biological, dental, and medical factors were also evaluated.<br><br>RESULTS: Participants with root caries had higher salivary levels of Mutans streptococci and Candida spp. (p&#x2009;=&#x2009;0.0122 and p&#x2009;=&#x2009;0.0013). Co-infection with Cbp[+] S. mutans and C. albicans was significantly associated with root caries (p&#x2009;=&#x2009;0.0003). Microbiome analysis showed enrichment of Capnocytophaga leadbetteri in diseased root surfaces. Individuals with root caries were more likely to report xerostomia and less likely to use an electric toothbrush or floss daily.<br><br>CONCLUSIONS: These findings highlight microbial and behavioral factors associated with root caries, offering insights into potential prevention and management strategies.}, }
@article {pmid42110914, year = {2026}, author = {Zhao, YQ and Kuang, BF and Dusenge, MA and Liu, Q and Zhang, FY and Zhou, YH}, title = {Sex-specific variations in subgingival microbiome of elderly patients with moderate periodontitis: an exploratory study.}, journal = {Frontiers in genetics}, volume = {17}, number = {}, pages = {1791446}, pmid = {42110914}, issn = {1664-8021}, abstract = {INTRODUCTION: Periodontitis, a leading cause of alveolar bone destruction and tooth loss, is associated with oral microbiota dysbiosis and shows higher susceptibility in males than in females. This study investigated sex-specific variations in the subgingival microbiome of elderly patients with moderate periodontitis.<br><br>METHODS: Subgingival plaque samples were collected from 25 patients with moderate periodontitis (8 males, 17 females; aged 50-73 years). The microbial composition was analyzed using 16S rRNA gene sequencing (V3-V4 region). Functional prediction was conducted utilizing the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.<br><br>RESULTS: Males exhibited higher Chao1 diversity, and beta diversity analysis revealed sex-based clustering. Wilcoxon rank-sum tests and LEfSe analysis identified Lactobacillus was enriched in females. KEGG analysis predicted a trend of enrichment of Immune system and Metabolic pathways in females.<br><br>CONCLUSION: This exploratory study observed sex-specific subgingival microbiome variations of elderly patients with moderate periodontitis. Females exhibited specific enrichment of Lactobacillus, which may be associated with predicted Immune system and Metabolic pathways. These findings suggest that sex-specific microbiome differences may be a relevant biological variable in future periodontitis research, and their potential link to alveolar bone loss deserves further exploration.}, }
@article {pmid42110957, year = {2026}, author = {Skidmore, AM and Goodfellow, SM and Nofchissey, RA and Jiang, L and Dunnum, J and Cook, JA and Guo, Y and Mali, I and Bradfute, SB}, title = {Characterization of the gut microbiome of wild Peromyscus sonoriensis in New Mexico, USA.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1672092}, pmid = {42110957}, issn = {2813-4338}, abstract = {The microbiome is highly important to the physiologies of all multicellular organisms, particularly metazoans. However, the microbiomes of many wild animals remain understudied and poorly understood. Peromyscus mice are commonly used as models of adaptation, mental health, and human disease in biomedical research, and are also common in the environment across North America, frequently coming into close contact with humans. Additionally, Peromyscus sonoriensis are implicated as the primary reservoir for Sin Nombre hantavirus, a rare but severe disease of high morbidity and mortality in humans. Here we characterize the fecal microbiomes of 311 Peromyscus sonoriensis, the western deer mouse, collected from across New Mexico, USA, which will further their usefulness as models of disease and behavior as well as increase our understanding of their ecology. The animals used in this study are geographically diverse, collected from multiple ecoregions, and encompass mice of all ages and sexes. We sequenced the entire 16S rRNA gene in a PCR independent approach and characterized the microbiomes with Shannon entropy, Faith phylodiversity, and weighted UNIFRAC. We found that these mice have diverse microbiomes, with individuals varying in the presence and proportions of various identified bacteria. We analyzed the total population of mice according to age, sex, and trapping location, and found that trapping location was the only condition to significantly impact the microbiome. When the mice were subdivided by the location of collection, there were mild effects of age and sex. When comparing mice from archival museum storage, storage of samples in 95% ethanol resulted in significant alterations to the microbiome when compared to cryopreservation. Differential bacterial family presence was determined using ANCOMBC at the 0.05 significance threshold, and there were many differentially abundant families across all groups of mice. This data set can now be used as a reference for further research into the microbiomes of related Peromyscus species, enhance the use of P. sonoriensis as model laboratory animals, and as a source of novel research questions regarding the physiology of these rodents.}, }
@article {pmid42111177, year = {2026}, author = {Liu, X and Wen, C and Gu, S and Hao, Y and Xiong, Y and Chen, C and Zeng, S and Zhang, P}, title = {Gut microbial-host isozymes: A novel perspective on gut microbiota-host interactions.}, journal = {iScience}, volume = {29}, number = {5}, pages = {115226}, pmid = {42111177}, issn = {2589-0042}, abstract = {The interaction between gut microbiota and host health has garnered significant attention since its initial discovery. Dysbiosis of the gut microbiota is implicated in various diseases, particularly metabolic disorders such as diabetes, as well as neuro-, cardiovascular-, and hepatic-metabolic diseases. In recent years, the concept of microbial-host isozymes (MHIs) has emerged as a novel research area within the microbiome field. These enzymes, encoded by intestinal microbiota, can replicate the functions of host enzymes and contribute to disease development, presenting potential new therapeutic targets. In this review, we examine the current understanding of the discovery, function, and potential applications of MHIs. We summarize the distribution and functional enrichment of identified MHIs, provide examples of MHI-targeted interventions aimed at optimizing diabetes treatment, and discuss existing challenges and future research directions in this area.}, }
@article {pmid42111183, year = {2026}, author = {Rastelli, E and Tangherlini, M and Corinaldesi, C and Dell'Anno, A and Lo Martire, M and Giorgetti, A and De Luca, P and Bakran-Petricioli, T and Kipson, S and Pajusalu, L and Rinde, E and Tunka Bengil, EG and Tüney, &#x130; and Danovaro, R}, title = {Seagrasses host unique and vulnerable microbiomes, structured by inter-domain microbial interactions.}, journal = {iScience}, volume = {29}, number = {5}, pages = {115757}, pmid = {42111183}, issn = {2589-0042}, abstract = {Seagrass meadows are vital for coastal ecosystems but are declining worldwide due to human impacts. Microbes play key roles in seagrass health, yet their diversity and functions remain poorly understood. We investigated prokaryotes and microbial eukaryotes associated with different seagrass species across multiple regions by analyzing leaves, roots, and surrounding sediments. Microbiome similarity was minimal among seagrass and sediments (<5% shared small subunit (SSU|)-rRNA amplicon sequence variants -ASVs), among species (<2%), and between leaves and roots within species (<12%). Seagrass species, rather than environmental factors, primarily shaped microbiome composition. Network analysis revealed all seagrass microbiomes as highly vulnerable to the loss of keystone microbes, including bacterial taxa potentially supporting seagrass health through nutrient supply and detoxification processes. Although microbial eukaryotes have been traditionally linked to seagrass diseases, we found mostly positive interactions with keystone bacteria, suggesting overlooked roles in holobiont stability. These findings provide a benchmark for integrating microbiomes into seagrass conservation.}, }
@article {pmid42111202, year = {2026}, author = {Abrahamsson, T and Wejryd, E and Pujolassos, M and Calle, ML and Sverremark-Ekström, E and Jenmalm, MC and Martí, M}, title = {Dynamics of early gut microbiota maturation in extremely preterm infants and neurodevelopment at 2 years of age in a probiotic intervention trial.}, journal = {iScience}, volume = {29}, number = {5}, pages = {115802}, pmid = {42111202}, issn = {2589-0042}, abstract = {Preterm birth is associated with a high risk of long-term neurological deficits. Although research underscores the role of the gut microbiome in the gut-brain axis, the mechanisms of neurodevelopmental impairment remain elusive. In this prospective observational study (PROPEL), we evaluated whether early gut microbiota development and Limosilactobacillus reuteri supplementation to extremely preterm infants with extremely low birth weight (EPT-ELBW) are associated with neurodevelopment at 2 years. Gut microbiota was characterized by 16S sequencing, and neurodevelopment was assessed by Bayley-III score. Microbiota composition constellations and lower microbial diversity, but not single bacteria, are associated with impaired neurodevelopment. Microbial maturation over the first month was discriminative for motor development, with higher abundance of E. coli and Enterococcus relative to Cutibacterium associated with impairment. L. reuteri supplementation did not seem to affect neurodevelopment via the gut microbiome. In conclusion, dynamics of gut microbiota maturation during early life may impact neurodevelopment in EPT-ELBW infants.}, }
@article {pmid42111290, year = {2026}, author = {Serrana, JM and Tian, R and Nascimento, FJA and Broman, E and Dessirier, B and Posselt, M}, title = {Pollutant biodegradation profile mediated by multi-trophic microbial dynamics in rivers.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag089}, pmid = {42111290}, issn = {2730-6151}, abstract = {Microbial communities and environmental conditions are closely linked to ecosystem functions and directly govern the biodegradation of pollutants in aquatic environments. However, the role of multi-trophic interactions and their spatiotemporal dynamics in these processes remains poorly understood. Here, we examined how seasonal and spatial variations, mediated by trophic interactions within benthic microbial communities, influence their composition, functional capacity, and collective potential to degrade a diverse array of organic pollutants in rivers. By characterizing both prokaryotic (i.e. archaea and bacteria) and eukaryotic taxa (i.e. algae, fungi, protists, and metazoans), and inferring metabolic pathways, we explored the connections between community composition and pollutant degradation in wastewater-receiving rivers across four seasons. Mediation analysis revealed that variation in multi-trophic community structure statistically mediates the total effect of environmental factors on the biodegradation profiles of 96 organic pollutants, with prokaryotic communities explaining 60% of the total environmental influence. Eukaryotic groups also showed significant indirect mediation effects, with fungal, protistan, algal, and metazoan communities accounting for 56%, 53%, 26%, and 38% of the mediated effect, respectively. Across the two rivers studied, spatial variation explained more of the variance in community composition than seasonality did over the sampled year. Together, these results provide ecosystem-level insights into how multi-trophic microbial community organization is associated with pollutant biodegradation potential in dynamic river environments and support the development of predictive frameworks for sustainable water management.}, }
@article {pmid42111291, year = {2026}, author = {Marcos, S and Odriozola, I and Aizpurua, O and Eisenhofer, R and Mak, SST and Martin-Bideguren, G and Kale, V and Baldi, G and Richardson, LJ and Finn, RD and Tarradas, J and Estonba, A and Gilbert, MTP and Alberdi, A}, title = {Functional gut microbiota dynamics of generalist and specialist bacteria in association with chicken growth.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag091}, pmid = {42111291}, issn = {2730-6151}, abstract = {The early-life development of the gut microbiome in broiler chickens is a dynamic ecological process with significant implications for host physiology and productivity. Using 388 genome-resolved metagenomic and 61 metatranscriptomic samples across two replicated trials, we analysed the compositional and functional succession of the caecal microbiome in chickens from hatching to slaughter age. We reconstructed 822 bacterial genomes and distilled gene annotations into comprehensive metabolic traits that captured the functional capacities of each genome. We observed that the increase in microbial diversity with chicken age was accompanied by a decline in community-level average metabolic capacity, driven by a shift from metabolically versatile generalists (Lachnospiraceae) to hitherto uncultured, genome-reduced specialists (RF39, RF32, and UBA1242). However, the specific identity of the dominant genome-reduced specialists varied among individuals, resulting in contrasting associations with host body weight. At slaughter age, only 10 UBA660 (RF39) bacteria were positively associated with body weight, while other genome-reduced lineages, such as UBA1242 (Christensenellales), were among 190 negatively associated bacteria. Gene expression analyses revealed that despite their reduced functional repertoire, UBA660 exhibited greater metabolic activity than UBA1242, particularly in the production of two key metabolites for host nutrition and intestinal homeostasis: the essential amino acid lysine and the signaling molecule indole-3-acetate. These findings provide new insights into the functional ecology of the chicken gut microbiome and highlight the relevance of cultivation approaches to retrieve underexplored and uncultured bacterial taxa, which could open new avenues for microbiome-based strategies aimed at improving poultry growth and health in intensive production systems.}, }
@article {pmid42111293, year = {2026}, author = {Stewart, JD and Klein, M and Jaupitre, S and Oyarte-Galvez, L and Dong, L and Bouwmeester, HJ and Kiers, ET and Kokkoris, V and Weedon, JT}, title = {Root traits correlate with crop rhizosphere microbiome diversity independent of legume relatedness.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag087}, pmid = {42111293}, issn = {2730-6151}, abstract = {Predicting the composition of rhizosphere microbiomes has become increasingly important for sustainable agriculture. A key open question is whether a plant's rhizosphere community is shaped more by the specific traits or host phylogeny, under different soil conditions. We conducted a greenhouse experiment on 15 legume species, including three pairs of crop-wild relative pairs, under different phosphorus conditions. We then sequenced the bacterial and fungal rhizosphere communities. Using Bayesian models, we found rhizosphere composition was shaped by individual species identity, independent of host phylogeny (intraclass correlation = 0.40-0.79). This suggests that closely related plants do not necessarily share similar rhizosphere microbiomes. These patterns remained consistent across host intraspecific variation and nutrient treatments. Using a custom-built root imaging platform, we quantified root architectural traits and applied machine learning to correlate with rhizosphere community composition (R[2] = 0.46-0.80). Root diameter and carbon content were the strongest drivers. Notably, these key root traits were largely uncorrelated with phylogeny, yet strongly explained variation in rhizosphere community composition. Our results indicate that even closely related legume species may host divergent rhizosphere communities.}, }
@article {pmid42111294, year = {2026}, author = {Yergaliyev, T and Enokela, SO and Eberhardt, G and Flisikowski, K and Hornburg, SC and Reyer, H and Tetens, J and Wimmers, K and Zentek, J and Camarinha-Silva, A}, title = {Toward reproducible pig gut microbiome profiling through standardized methodologies.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag097}, pmid = {42111294}, issn = {2730-6151}, abstract = {Reproducible microbiome profiling is essential for linking microbial communities to host health, yet methodological variation continues to undermine reproducibility across studies. This problem is acute in pig microbiome research, where no standardized DNA extraction protocols exist despite the species' importance in agriculture and biomedicine. Here, we benchmark how 12 widely used extraction kits influence microbiome outcomes in 16S rRNA gene amplicon sequencing and shotgun metagenomics of pig fecal samples. We demonstrate that extraction choice biases 16S rRNA gene datasets, affecting DNA yield, diversity, community composition, and spike-in recovery, whereas metagenomic taxonomy and functional profiles are comparatively robust. Kit-dependent recovery of Gram-positive versus Gram-negative taxa revealed systematic biases with direct consequences for biological interpretation. By integrating spike-in controls, taxonomic resolution, and metagenome-assembled genomes, we establish a framework for evaluating DNA extraction methods in animal microbiome research. Our findings demonstrate that 16S rRNA gene amplicon sequencing is more susceptible to extraction-driven artifacts than metagenomics, highlighting the need for standardized protocols to ensure reproducibility and comparability across pig microbiome studies. Moreover, while shotgun metagenomics was comparatively robust to DNA extraction choice, the number of assembled good-quality metagenome-assembled genomes recovered was strongly dependent on the extraction kit selection.}, }
@article {pmid42111446, year = {2026}, author = {Zulaika, G and Nordgren, R and Agingu, W and Chaudhary, A and Dibondo, E and Wambua, P and van Eijk, AM and Rusie, L and Naqib, A and Otieno, F and Phillips-Howard, PA and Mehta, SD}, title = {Characterizing the bacterial surface profiles of menstrual cups and their association with user characteristics and vaginal microbiomes in an adolescent cohort from western Kenya.}, journal = {Gates open research}, volume = {10}, number = {}, pages = {25}, pmid = {42111446}, issn = {2572-4754}, mesh = {Humans ; Female ; Kenya ; *Vagina/microbiology ; *Microbiota/genetics ; Adolescent ; *Menstrual Hygiene Products/microbiology ; *Bacteria/genetics/isolation &amp; purification/classification ; RNA, Ribosomal, 16S/genetics ; Cohort Studies ; Menstruation ; Escherichia coli/isolation &amp; purification ; }, abstract = {BACKGROUND: Menstrual cups are increasingly promoted in low-resource settings as long-lasting and cost-effective menstrual hygiene solutions. However, no studies have been done among cup users to characterize the bacterial communities found on cups with long-term use when stored. This study sought to comprehensively characterize the bacterial surface profile of the menstrual cup, identify factors associated with putative pathogens, and quantify the vaginal microbiome as potential source for menstrual cup bacterial communities.<br><br>METHODS: Over 30 months of follow-up, 369 menstrual cup samples were collected from 172 secondary schoolgirls participating in a randomized controlled trial in western Kenya. Samples were obtained from cups brought to school by girls during study visits. Menstrual cup and vaginal microbiomes were assessed using 16S rRNA gene amplicon sequencing. Mixed effects models were applied to identify factors associated with putative pathogens (Escherichia coli, Staphylococcus aureus, coliform bacteria), and factors associated with vaginal microbiome as potential source environment to bacterial surface profile of the menstrual cup, estimated via fast expectation-maximization for microbial source tracking (FEAST).<br><br>RESULTS: Menstrual cup bacterial surface profile composition was primarily comprised of soil and water bacteria. However, taxa specific to the vaginal microbiome (e.g., Lactobacillus crispatus, L. iners, and Gardnerella vaginalis) were also recovered from cups. The mean relative abundance (presence) of E. coli and S. aureus was 0.09% (36%) and 0.36% (24%), respectively, with higher relative abundance among participants with HSV-2 or non-optimal vaginal community state type 4. Damaged cups were also associated with higher relative abundance of putative pathogens, while antibiotic use was inversely associated with E. coli. On average, 25.1% of cup microbiota originated from the vagina, with lower contributions among older participants and those with damaged cups. No serious adverse events related to the menstrual cup were observed in the cohort.<br><br>CONCLUSIONS: Interventions focused on improved cleaning and storage tools and methods, and access to clean water and sanitation infrastructure are required to maximize safety of menstrual cup use in low-resource settings.}, }
@article {pmid42111471, year = {2026}, author = {Balagoni, S and Evelyne, DG and Mathews, A and Dugyala, RR and Biradar, M and Deekshith, V and Goel, A and Verma, A}, title = {Unveiling the Bidirectional Relationship on the Effect of Gut Microbiota and Female Infertility: A Narrative Review.}, journal = {Health science reports}, volume = {9}, number = {5}, pages = {e72399}, pmid = {42111471}, issn = {2398-8835}, abstract = {BACKGROUND AND AIMS: Dysbiosis is the substitution of the normal gut flora with a dysfunctional array of organisms that influences the outcome of multiple inflammatory pathways, contributing to systemic inflammation and various disease states. It has historically been understudied, with outcomes that may directly or indirectly cause pathologies. This review aims to emphasize the understanding of the effects of dysbiosis on female fertility and various approaches to addressing it.<br><br>METHODS: A comprehensive review was conducted using databases such as PubMed, Scopus, Cochrane Library, and Google Scholar, applying search terms like "Dysbiosis", "Female Infertility", "Gut-Brain Axis", "Reproductive Health", "Estrobolome", "Polycystic Ovary Syndrome (PCOS)", and "Endometriosis". Articles published in the English language from January 2007 to April 2025, encompassing original research, systematic reviews, randomized controlled studies, and meta-analyses, were included. Studies not pertinent to therapeutic applications, lacking outcome, or restricted to editorials were excluded.<br><br>RESULTS: Gut dysbiosis may be associated with female reproductive disorders (PCOS, endometriosis, ovulatory dysfunction), complications during pregnancy, thyroid dysfunction, and infertility. Altered microbial diversity affects estrogen metabolism, which in turn impacts GnRH, LH regulation, and systemic inflammation. An imbalance in Prevotella and other organisms is correlated with hormonal and metabolic dysregulation, poor oocyte quality, and thus infertility.<br><br>CONCLUSION: Gut dysbiosis plays a pivotal role in female reproductive health. The current evidence suggests potential benefits of microbiome modulation therapy, including the use of probiotics or dietary modifications. Many of these studies are observational, small-scale, and use different methodologies, which restrict our scope. So, larger and standardized interventional studies are required to establish the gut microbiome as a viable therapeutic target for female infertility.}, }
@article {pmid42111712, year = {2026}, author = {Sha, Q and He, Q and Zeng, L and Liu, Y and Luo, L and Zhu, H and Hu, M and Huang, Y and Wu, Y and Wang, Q and Deng, X and Tao, L and Zhang, W and Guan, Y and Yuan, W and Shi, N and Li, Y and Qin, Y and Wang, B and Wang, X}, title = {The soil microbiome and metabolome in concert shape the flavor profile of ancient tea plants from Laowu mountain region.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1797648}, pmid = {42111712}, issn = {1664-462X}, abstract = {INTRODUCTION: Ancient tea plants from small tea-producing areas in Yunnan possess irreplicable flavor characteristics, yet the mechanisms underlying flavor formation remain unclear.<br><br>METHODS: This study focused on the core production region of ancient tea plants in the Laowu Mountain Region, including Shahe Village, Hetou Village, and Luojia Village. Differences in tea quality among production regions were analyzed, together with soil physicochemical properties and soil microbial communities, using correlation analysis and amplicon sequencing.<br><br>RESULTS: Significant differences in tea quality were observed among different production regions, with catechins, amino acids, and caffeine collectively contributing to these variations. Soil organic carbon, organic matter, and nitrate nitrogen showed significant differences between production regions. Correlation analysis revealed that soil organic carbon was significantly positively correlated with epigallocatechin (EGC) (r > 0.8, P < 0.05), while soil nitrate nitrogen and organic matter were significantly negatively correlated with epicatechin (r < -0.8, P < 0.05). Amplicon sequencing indicated that the dominant bacterial phyla in the soil included Chloroflexi, Acidobacteriota, Proteobacteria, and Actinobacteriota, while the dominant fungal phyla were Ascomycota, Basidiomycota, and Mortierellomycota. Spearman correlation analysis showed that g:Streptomyces was negatively correlated with amino acid metabolites but positively correlated with total amino acids (AA) in tea, whereas amino acid metabolites were negatively correlated with AA. Meanwhile, g:Bacillus was negatively correlated with gibberellin A7 and GA, but positively correlated with EGC, while gibberellin A7 was positively correlated with GA and negatively correlated with EGC.<br><br>DISCUSSION: These results shed new light on the mechanisms by which soil microorganisms and metabolites collaboratively shape the flavor compounds of ancient tea plants, while also providing a basis for the soil ecological management of Yunnan ancient tea plants.}, }
@article {pmid42111744, year = {2026}, author = {Tang, S and Chen, X and Ma, J and Tu, P and Shi, X and Chen, G}, title = {Integrating multi-omics and epiphytic microbial communities to decipher the spatiotemporal dynamics of flower color dynamic regulation in Hibiscus mutabilis.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1803034}, pmid = {42111744}, issn = {1664-462X}, abstract = {The dynamic change of flower color is a key trait for plant environmental adaptation and pollinator attraction, yet its spatiotemporal regulatory mechanisms remain poorly understood. Hibiscus mutabilis L., known for its remarkable diurnal color-changing phenomenon, provides an ideal model for deciphering the dynamic regulation of flower color. This study integrated metabolomics, transcriptomics, and epiphytic microbial community analyzes to systematically compare the spatiotemporal differences between petals and the flower base of H. mutabilis. Metabolomic analysis revealed that differential metabolites between petals and the flower base were primarily enriched in pathways such as glycolysis and glutathione metabolism. Differences between morning and afternoon in the flower base were concentrated in flavonoid biosynthesis and amino acid metabolism pathways. Transcriptomic analysis identified MYB114-like was significantly upregulated in the afternoon, with its expression co-enriched with genes from the plant hormone signaling and MAPK pathways, suggesting it participates in the regulatory mechanism of environmental signal responses. Microbial community analysis showed a significant increase in the relative abundance of Actinomycetota in the flower base from morning to afternoon. Functional prediction suggested that these microbes might be involved in processes such as redox metabolism and nucleotide degradation. This study reveals a multidimensional regulatory network involving metabolism, transcription, and microbes governing the dynamic color change in H. mutabilis, from the perspective of spatial heterogeneity and plant-microbe interactions, providing novel insights into the mechanisms of flower color formation and the adaptability of ornamental plants.}, }
@article {pmid42111748, year = {2026}, author = {Chowdhary, R and Goyal, MK and Arora, K and Sehgal, T and Dawer, P and Anirudh, FNU and Berinstein, J and Bishu, S and Matt-Amaral, L}, title = {Gut Microbiota and Extraintestinal Cancers: Mechanistic Insights and Microbiome-Targeted Interventions.}, journal = {JGH open : an open access journal of gastroenterology and hepatology}, volume = {10}, number = {}, pages = {e70409}, pmid = {42111748}, issn = {2397-9070}, abstract = {The gut microbiota is a dynamic community of bacteria, viruses, fungi, and archaea that plays a pivotal role in regulating host immunity, metabolism, and systemic homeostasis. Dysbiosis, characterized by an imbalance in the microbial composition, is being increasingly recognized as a contributor not only to gastrointestinal cancers but also to extraintestinal malignancies. Mechanistic studies highlight the gut-microbiota-cancer axis, where microbial metabolites such as bile acids, short-chain fatty acids (SCFAs), and tryptophan derivatives influence genetic, epigenetic, and immune pathways, influencing carcinogenesis. Germ-free models demonstrate that commensal signals are essential for CD4[+] and CD8[+] T-cell differentiation, IgA production, and anti-tumor immunity. Dysbiosis-induced immune dysregulation is believed to impair immune checkpoint inhibitor (ICI) efficacy, while specific taxa such as Bifidobacterium and Akkermansia have been shown to enhance therapeutic responses. Emerging evidence links gut microbiota to breast cancer via estrogen metabolism "estrobolome" to lung cancer through the gut-lung axis and modulation of ICI responses, to melanoma by shaping systemic T-cell function and immunotherapy outcomes, and to prostate cancer through androgen receptor signaling and microbial metabolite interactions. These findings underscore the systemic oncogenic and tumor-suppressive potential of microbial communities. Microbiome-targeted interventions, including fecal microbiota transplantation (FMT), defined live biotherapeutics, probiotics, prebiotics, dietary modulation, and postbiotic delivery, are being actively investigated to optimize cancer treatment. While early trials have demonstrated feasibility, variability between individuals and methodological challenges remain significant hurdles. Hence, understanding how gut microbes influence extraintestinal cancers could revolutionize diagnostics, risk prediction, and treatment strategies.}, }
@article {pmid42112079, year = {2026}, author = {Kurniawan,  and Milanda, T and Kusuma, SAF}, title = {Comparative Profiling of Yeast Communities in Kefir Grains and Liquid Kefir Using ITS Amplicon Next-Generation Sequencing.}, journal = {International journal of food science}, volume = {2026}, number = {}, pages = {2572378}, pmid = {42112079}, issn = {2314-5765}, abstract = {Kefir is a fermented dairy beverage produced by a complex microbial consortium of bacteria and yeasts coexisting within a polysaccharide-protein matrix known as kefir grains. Although the bacterial communities are well-characterized, the distribution of yeast taxa, specifically those transitioning into the fermented liquid phase, remains insufficiently described. This study is aimed at characterizing and comparing the fungal community composition in both the kefir grains and the resulting fermented liquid. Using internal transcribed spacer (ITS) amplicon sequencing on samples from a traditionally propagated culture, we identified 122 yeast taxa in the grains and 221 taxa in the liquid fraction, with 182 taxa shared between both habitats. Crucially, taxonomic profiling of the liquid phase revealed a high diversity of yeasts, with Saccharomyces cerevisiae, Kluyveromyces marxianus, and Pichia kudriavzevii being significantly more abundant compared with the grain matrix. In contrast, grain samples were relatively enriched in Pichia fermentans. Several taxa maintained moderate abundance across both fractions, suggesting ecological persistence during fermentation. These patterns reflect the spatial distribution of yeast taxa within the system rather than functional specialization. Although based on a single culture without biological replication, these findings provide a detailed descriptive map of the kefir mycobiome, distinguishing dominant fermentation-associated yeasts in the liquid phase from low-abundance environmental fungi.}, }
@article {pmid42112126, year = {2026}, author = {Seo, Y and Jung, JE and Oh, S and Kwon, IG and Park, JS}, title = {Effects of red ginseng on gut microbiome in patients after gastrointestinal cancer surgery: A pilot, randomized controlled trial.}, journal = {Journal of ginseng research}, volume = {50}, number = {3}, pages = {100932}, pmid = {42112126}, issn = {1226-8453}, abstract = {BACKGROUND: The gut microbiome plays diverse roles in human health. Although Korean red ginseng (KRG) has shown therapeutic potential in animal models, its effects on the human gut microbiome after gastrointestinal (GI) cancer surgery remain underexplored. This prospective randomized controlled study aimed to evaluate postoperative safety of KRG and its impact on the gut microbiome and postoperative outcomes after GI cancer surgery.<br><br>METHODS: Patients were randomly assigned 1:1 to the red ginseng or control groups. Microbiome analysis of preoperative and postoperative fecal samples was performed using 16S rRNA sequencing. The alpha and beta diversities, taxonomic composition changes of microbiome, nutritional index, clinical symptoms, GI symptoms, and quality of life (QOL) were assessed.<br><br>RESULTS: A total of 60 patients were enrolled and 16 patients in the red ginseng group and 25 in the control group were included in the final analysis. Postoperative alpha diversity decreased significantly in the control group, but remained relatively stable in the red ginseng group. Postoperative Lactobacillus levels increased significantly in the red ginseng group compared to the control group (18.34&#xa0;% vs. 0.23&#xa0;%; p&#xa0;<&#xa0;0.001), whereas Bifidobacterium levels decreased (p&#xa0;=&#xa0;0.002). Serum albumin levels were significantly higher in the red ginseng group at 3 months postoperatively (p&#xa0;=&#xa0;0.003), and global health status/QOL scores were improved in the red ginseng group (p&#xa0;=&#xa0;0.047).<br><br>CONCLUSION: Red ginseng supplementation may play a protective role in gut microbiome, improving clinical outcomes in patients undergoing GI cancer surgery, as a safe and supportive therapy for enhancing postoperative recovery.}, }
@article {pmid42112348, year = {2026}, author = {Hua, M and Luo, J and Li, P and Zhang, Y and Zhang, X and Wu, Y and Dong, H}, title = {The microbiota-systemic lupus erythematosus axis: mechanisms, diagnostics, and therapeutic frontiers.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1782828}, pmid = {42112348}, issn = {1664-3224}, mesh = {Humans ; *Lupus Erythematosus, Systemic/therapy/diagnosis/immunology/microbiology ; Dysbiosis/immunology ; Animals ; *Microbiota/immunology ; *Gastrointestinal Microbiome/immunology ; Autoimmunity ; }, abstract = {Systemic lupus erythematosus (SLE) is a prototypical autoimmune disease in which host-microbiota crosstalk plays a pivotal role in immune dysregulation. Recent metagenomic studies have revealed that disease-specific dysbiosis--characterized by the expansion of pathobionts and depletion of immunoregulatory commensals--occurs across the gut, oral cavity, skin, and genital tract. Integrative multi-omics analyses have identified three mechanistic pathways linking microbial imbalance to autoimmunity: (1) microbial peptides trigger molecular mimicry and epitope spreading, activating autoreactive lymphocytes: (2) microbial metabolites disrupt redox homeostasis, impair epithelial barriers, and skew the AhR-mediated Th17/Treg balance; and (3) dysbiosis alters epigenetic regulation by inhibiting DNA methyltransferases, leading to hypomethylation of SLE-risk genes. Translational studies have shown that microbiome-targeted interventions, including probiotics, prebiotics, fecal microbiota transplantation, and even B cell-depleting chimeric antigen receptor T-cell (CAR-T) therapy, can restore microbial balance, reduce autoantibody levels, and modulate the gut-immune axis. Furthermore, microbial signatures are emerging as potential biomarkers for disease activity and treatment response. Despite this promise, challenges remain, such as the impact of immunosuppressants on the microbiota, spatial heterogeneity in host-microbe interactions, and limitations in causal inference. Looking forward, integrating single-cell metagenomics, microbiota-directed diets, and engineered microbial consortia may pave the way for personalized microbiome-based therapies. Reframing SLE as a "meta-organismal imbalance" positions microbial ecology at the forefront of precision medicine.}, }
@article {pmid42112377, year = {2026}, author = {Tschang, MA and Deo-Campo Vuong, R and Eilers, B and Chac, D and Waalkes, A and Penewit, K and Easton, A and Schuessler, B and Daniels, R and Weil, AA and Salipante, SJ and Gibbons, SM and Schindler, AG}, title = {If you give a mouse a poopsicle: a novel fecal microbiota transplant method for exploring the role of the gut microbiome in stress-related outcomes in mice.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1816919}, pmid = {42112377}, issn = {1664-3224}, mesh = {Animals ; *Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome ; Mice ; Corticosterone/blood ; *Stress, Psychological/therapy/microbiology ; Male ; Feces/microbiology ; Disease Models, Animal ; Mice, Inbred C57BL ; Anxiety ; Behavior, Animal ; Stress, Physiological ; }, abstract = {BACKGROUND: The microbiome-gut-brain axis is a mediator of stress-related disorders. The number of preclinical studies exploring the potential causal mechanism of this connection using fecal microbiota transplantation (FMT) is growing. However, the most common method for delivering fecal transplants in rodent models is still oral gavage, which creates an adverse experience that may confound stress-related outcomes. Here, we establish an alternative methodology for FMT that decreases stress induced by traditional experimental procedures.<br><br>METHODS: We first used preference and anxiety behavior assays to identify antibiotic therapies having maximal tolerability and minimal anxiolytic properties. We then collected feces from donor mice and homogenized them with a microbe-stabilizing buffer to create a slurry, which was frozen into aliquots ("poopsicles") for subsequent FMT. Recipient mice voluntarily consumed the frozen aliquots, and blood was collected to compare corticosterone relative to that after delivery via traditional gavage.<br><br>RESULTS: Plasma corticosterone levels were found to be significantly lower in mice receiving frozen aliquots compared to oral gavage. Furthermore, relative to controls, microbial signatures of mice receiving FMT via frozen aliquots were more similar to those of the donors at one week following final FMT and were sustained for up to six weeks, as assessed by comparing Bray-Curtis beta diversity distances.<br><br>CONCLUSION: Together, these results establish antibiotic and FMT methods that minimize treatment-induced stress, while effectively transplanting fecal microbes between murine conspecifics.}, }
@article {pmid42112384, year = {2026}, author = {Oyedokun, PA and Oyeleke, BT and Akanji, OO and Oyelaran, AO and O, KP and Akanbi, GB and Oyedokun, PO and Oyedokun, MD and Naomi, CC and Imoleayo, OO and Akhigbe, RE}, title = {The role of the microbiome in gynecological cancers: implications for diagnosis and treatment.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1718883}, pmid = {42112384}, issn = {1664-3224}, mesh = {Humans ; Female ; *Genital Neoplasms, Female/therapy/diagnosis/microbiology/etiology ; *Microbiota ; Dysbiosis ; Animals ; Tumor Microenvironment ; Fecal Microbiota Transplantation ; }, abstract = {Gynecological malignancies such as cancer of the cervix, ovary, endometrium, vulva, and vagina pose a severe global health burden. Although conventionally attributed to genetic mutation, hormonal imbalance, and chronic viral infection, including high-risk human papillomavirus, recent evidence suggests that the human microbiome plays a central role in their pathogenesis and development. This review summarizes existing evidence that microbial dysbiosis, specifically the depletion of beneficial Lactobacillus species and overrepresentation of anaerobic organisms such as Fusobacterium, Atopobium, and Sneathia, is implicated in carcinogenesis pathways. These include chronic inflammation, immune modulation, loss of epithelial barrier integrity, microbial metabolite toxicity, and estrogen metabolism by the estrobolome. Dysbiosis in the gut and reproductive tract has been associated with HPV persistence, tumor microenvironment remodeling, and immune surveillance/therapy resistance. Consequently, microbial signatures are being investigated as a potentially successful non-invasive biomarker for early diagnosis, prognosis, and monitoring of therapy in gynecological oncology. In addition, emergent microbiome-based therapies are being considered as potential adjunct therapies, including probiotics, prebiotics, dietary manipulation, vaginal microbiota transplantation, and fecal microbiota transplantation. This review connects the basic research microbiome research to translational and clinical practice, identifies associated limitations, and highlights how it may transform gynecological cancer prevention, detection, and treatment.}, }
@article {pmid42112428, year = {2026}, author = {Du, S and Jia, H and Lu, H and Li, X and Yang, M and Zhang, H and Wu, H and Wang, L and Zhu, B}, title = {Characterization and genomic analysis of DSF2: a novel lytic phage infecting multidrug-resistant Shigella.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1740847}, pmid = {42112428}, issn = {1664-302X}, abstract = {BACKGROUND: Multidrug-resistant Shigella flexneri (MDR S. flexneri) serotype 2a is the predominant cause of shigellosis in China, presenting a major public health challenge amid escalating antibiotic resistance and limited treatment options. Bacteriophages are gradually emerging as a highly promising alternative to antibiotics because of its highly specific bactericidal ability. However, only 113 Shigella phage genomes are available in NCBI as of August 2025, highlighting the need for novel lytic phages targeting prevalent MDR strains.<br><br>METHODS: A novel lytic phage, vB_SflP_DSF2 (DSF2), was isolated from untreated sewage at the 305 Hospital of PLA using MDR S. flexneri 2a strain 301 as host. Morphology was examined by transmission electron microscopy. Host range and efficiency of plating were determined against 41 bacterial strains (33 Shigella, 6 Escherichia coli, and others) using double-layer agar spot assays. One-step growth curves, pH and thermal stability, and biological properties were assessed using standard plaque assays. The complete genome was sequenced via Illumina NovaSeq, with comparative genomic and phylogenetic analyses performed using VIRIDIC, TerL phylogeny, AlphaFold structural predictions, and Swiss-Model for protein structure comparisons.<br><br>RESULTS: The DSF2 is a Schitoviridae phage with an elongated prolate head, short non-contractile tail. It produces haloed 1-2 mm plaques indicating depolymerase activity, with a 60-min latent period and 115 PFU/cell burst size. The DSF2 remains stable from 4 &#xb0;C to 50 &#xb0;C and active at pH 4-10, selectively lysing all S. flexneri serotype 2/X strains. Genomic analysis revealed that DSF2 possesses a 72,532 bp dsDNA genome with a G+C content of 44.89%, containing 89 predicted open reading frames. The DSF2 harbors no virulence or antibiotic resistance genes. Closest relative Shigella virus Moo19 shares 94.1% identity, defining the DSF2 as a new species. The prolate head of DSF2 closely resembles that of Escherichia coli phage PH444, driven by divergent Hoc-like head decoration, despite the conservation of capsid and portal proteins when compared to Shigella virus Moo19.<br><br>CONCLUSION: The DSF2 represents a novel Schitoviridae species that expands the limited Shigella phage repertoire, offering precision biocontrol against MDR S. flexneri serotype 2/X with minimal microbiome disruption. Hoc-like head decoration likely drives DSF2's unique prolate morpholog through intercapsomer angular constraints.}, }
@article {pmid42112429, year = {2026}, author = {Mbaraka, A and Meena, RR and Menghani, E and Verma, N}, title = {Targeting biofilm-driven antibiotic resistance: emerging mechanisms and next-generation therapeutic interventions.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1823476}, pmid = {42112429}, issn = {1664-302X}, abstract = {Biofilm mediated antimicrobial resistance (AMR) has become a critical global health and economic challenge, affecting both community and healthcare settings. Microbial Biofilms significantly enhance the antibiotic tolerance and cause the persistent and device-associated infections via limited drug penetration, degradation of antibiotics, and assist horizontal gene transfer. Biofilm-mediated antimicrobial resistance remains a major obstacle to treating infectious diseases today. Biofilms can boost antibiotic tolerance by up to 1,000 times and lead to chronic, persistent, and device-associated infections. The lack of FDA-approved anti-biofilm drugs highlights the urgent need for new therapeutic strategies and mechanistic insights. Redefining the treatment landscape and improving outcomes for resistant infections could be achieved through a multi-platform therapeutic approach. This review summarizes recent developments in our knowledge of how biofilms contribute to antibiotic resistance and highlights new therapeutic strategies, such as nanotechnology, antimicrobial peptides, bacteriophage-derived enzymes, quorum-sensing inhibitors, CRISPR-based tools, microbiome engineering, and AI-driven drug discovery.}, }
@article {pmid42100955, year = {2026}, author = {Alsheikh, ZSA and Qingsong, T and Qinjie, L and Youkun, C}, title = {Re-arming checkpoint blockade in MSS colorectal cancer: A precision-microbiome playbook from mechanisms to clinic.}, journal = {Turkish journal of surgery}, volume = {}, number = {}, pages = {}, doi = {10.47717/turkjsurg.2026.2025-8-3}, pmid = {42100955}, issn = {2564-6850}, abstract = {Immune checkpoint blockade transforms outcomes for the 15% of colorectal cancers (CRCs) with mismatch-repair deficiency; yet most tumours remain refractory. Beneficial gut microbes can change this. Akkermansia muciniphila, Bacteroides fragilis, and short-chain fatty acid producers prime dendritic cells to produce interleukin (IL)-12, polarise Th1 cells, and reinvigorate CD8[+] T-cells. Antibiotics, Western-style diets, and Fusobacterium nucleatum foster myeloid suppression and β-catenin- or IL-17-mediated signalling, which blunt checkpoint activity. Multi-omics analyses link biosynthetic genes for inosine, riboflavin, and folate to durable clinical benefit. Faecal microbiota transplantation from responders has produced objective regressions in otherwise refractory microsatellite-stable disease. This narrative review maps CRC-microbiota-immune crosstalk, evaluates biomarkers and interventions, and proposes a CRC-specific, three-tiered clinical algorithm. We outline standards for trial design and manufacturing processes to facilitate the translation of microbiota-guided therapy into routine practice.}, }
@article {pmid42101034, year = {2026}, author = {Walker, JR and Bachand, PT and Turner, JW and Labonté, JM}, title = {Viral Assemblages of a Hypersaline Estuary Show Divergent Responses to Freshwater and Temperature Disturbances.}, journal = {Environmental microbiology reports}, volume = {18}, number = {3}, pages = {e70354}, pmid = {42101034}, issn = {1758-2229}, support = {NA19NOS4190106//Texas General Land Office/ ; }, mesh = {*Estuaries ; *Fresh Water/chemistry/microbiology/virology ; Salinity ; *Viruses/genetics/classification/isolation &amp; purification ; Bacteria/genetics/classification/isolation &amp; purification ; Temperature ; Metagenomics ; Ecosystem ; }, abstract = {Hypersaline environments harbor extremely dense bacterial and viral populations unique from other aquatic ecosystems. Changes to the hydrologic cycle and anthropogenic disturbances have the potential to alter these poorly described communities. Here, we aimed to assess the variation within the viral and bacterial communities of one of the world's largest hypersaline estuaries over 13 months. Using metagenomics, we identified viruses associated with two different salinity regimes, and we showed how viruses responded to pulse disturbances including freshwater inundation and freeze events. We identified 17, 324 viral species, of which 12,132 were found in only one of the salinity regimes. Our results demonstrate a potential association between freshwater pulses throughout June 2021 and shifts in viral community composition. Freeze events showed a greater propensity to alter the auxiliary metabolic genes (AMGs), or genes carried by viruses to alter host metabolism during infection. Viruses associated with low temperatures led to higher incidences of AMGs associated with sulfur cycling and oxidative phosphorylation as opposed to photosynthesis with freshwater inundation and no extreme weather. The contrasting responses to different pulse disturbances make evident the need to better understand how different types of disturbances alter viral communities and their potential to modulate important biogeochemical cycles.}, }
@article {pmid42101085, year = {2026}, author = {El Sehrawy, AAMA and Aljumaili, OI and Axmedov, U and Khasawneh, MAS and Alanazi, MA and Smerat, A and Basunduwah, TS}, title = {Personalized Medicine in Autism Spectrum Disorder: Integrating Epigenomics, Microbiome Research and Early Diagnostics.}, journal = {International journal of developmental neuroscience : the official journal of the International Society for Developmental Neuroscience}, volume = {86}, number = {3}, pages = {e70128}, doi = {10.1002/jdn.70128}, pmid = {42101085}, issn = {1873-474X}, mesh = {Humans ; *Autism Spectrum Disorder/diagnosis/genetics/therapy/microbiology ; *Precision Medicine/methods ; *Epigenomics/methods ; *Microbiota/physiology ; Early Diagnosis ; Biomarkers ; *Gastrointestinal Microbiome ; }, abstract = {Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental condition characterized by persistent difficulties in social communication together with restricted, repetitive patterns of behaviour and sensory-processing differences. Growing evidence suggests that ASD is shaped by complex interactions among genetic susceptibility, epigenetic regulation, immune signalling, maternal and early-life exposures and gut microbiome-related pathways. However, many of these associations remain biologically plausible rather than definitively causal, particularly when findings from experimental models are considered alongside human clinical data. This narrative review examines recent advances across these interconnected domains, with particular emphasis on maternal immune activation, prenatal nutrition, gut microbial imbalance, epigenetic and molecular mechanisms, emerging therapeutic directions and developing biomarker platforms. We also discuss current diagnostic limitations and evaluate the potential of salivary microRNAs, perinatal metabolic and epigenetic markers, oxidative stress-related measures and microbiome-based profiles as early and biologically informative indicators of ASD risk. Special attention is given to the need for biologically informed stratification, although current subgrouping frameworks remain preliminary and not yet sufficiently validated for routine clinical use. Likewise, candidate biomarkers remain investigational and require stronger evidence for reproducibility, external validation, longitudinal performance and clinically meaningful sensitivity and specificity before they can be considered for screening or precision-guided care. Emerging therapeutic strategies targeting immune, epigenetic and microbiome-related pathways are also reviewed, but most remain preclinical or early-stage and face substantial translational barriers. The convergence of epigenomics, microbiome research and early diagnostic science may help advance a more personalized medicine framework for ASD, provided that future studies improve cross-cohort reproducibility, clarify brain relevance of peripheral signals and develop practical multiomics models that can support clinically meaningful integration.}, }
@article {pmid42101126, year = {2026}, author = {Azarkan, SY and Ünal, HSA and Akçay, S}, title = {Pharmacomicrobiomics in Precision Pharmacotherapy: Bidirectional Microbial-Drug Interactions as a Key Determinant of Therapeutic Response.}, journal = {Drug metabolism reviews}, volume = {}, number = {}, pages = {1-31}, doi = {10.1080/03602532.2026.2671428}, pmid = {42101126}, issn = {1097-9883}, abstract = {Interindividual variability in drug efficacy and toxicity remains a major challenge in clinical pharmacotherapy. Although pharmacogenomics has substantially advanced personalized medicine, host genetic variation alone cannot fully explain differences in drug disposition, response, and adverse effects. Increasing evidence identifies the human gut microbiotaas an additional, functionally relevant metabolic layer that complements host drug-metabolizing enzymes, giving rise to the field of pharmacomicrobiomics. This discipline examines bidirectional interactions between drugs and microbial communities that influence absorption, metabolism, enterohepatic circulation, and pharmacodynamic outcomes. The gut microbiota can directly biotransform or sequester drugs through diverse enzymatic reactions, including deconjugation, reduction, and decarboxylation, thereby modifying systemic drug exposure and toxicity. In parallel, microbially derived metabolites and bile acid-mediated signaling pathways regulate host drug-metabolizing enzymes and transporters, including cytochrome P450 enzymes and ATP-binding cassette transporters. Conversely, many commonly used medications-such as antibiotics, chemotherapeutic agents, targeted therapies, immunotherapies, psychotropic drugs, and proton pump inhibitors-can substantially reshape microbial composition and function, resulting in dysbiosis that feeds back onto drug metabolism and therapeutic outcomes. This review summarizes the mechanistic basis and clinical relevance of microbiota-drug interactions across key therapeutic areas, including oncology (chemotherapy and immunotherapy), neuropsychiatric disorders, and metabolic diseases. Well-established examples, including microbial β-glucuronidase-mediated reactivation of irinotecan, microbiota-dependent modulation of levodopa and antidepressant pharmacokinetics, and microbiota-driven variability in immune checkpoint inhibitor efficacy, are discussed to illustrate causality. Emerging microbiome-informed strategies-such as selective inhibition of microbial enzymes, microbiota modulation, and microbial biomarker-based patient stratification-are highlighted. Finally, we examine integration of pharmacomicrobiomics with pharmacogenomics within multi-omic and systems pharmacology frameworks, emphasizing implications for predictive modeling and precision drug metabolism.}, }
@article {pmid42101202, year = {2026}, author = {Yashar, M and Thigale, UY and Karakus, S}, title = {Role of microbiome in ocular surface disease: interpreting biology in a low-biomass environment.}, journal = {Current opinion in ophthalmology}, volume = {}, number = {}, pages = {}, doi = {10.1097/ICU.0000000000001228}, pmid = {42101202}, issn = {1531-7021}, abstract = {PURPOSE OF REVIEW: Growing use of sequencing technologies has accelerated investigation of the ocular surface microbiome, yet this environment is characterized by extremely low microbial biomass, complicating data interpretation. This review assesses current evidence linking microbial communities to ocular surface disease, discusses methodological and biological factors influencing interpretation of microbiome-disease associations, and proposes a framework in which microbial roles may be considered as drivers, modifiers, or markers.<br><br>RECENT FINDINGS: Studies across multiple ocular surface diseases report alterations in microbial composition, including reduced &#x3b1;-diversity and shifts in dominant taxa. Genera such as Staphylococcus, Corynebacterium, and Cutibacterium are frequently reported as resident members of the ocular surface microbiome, although their abundance varies across individuals and sampling sites. Across diseases, microbial patterns often overlap and remain inconsistent between studies. Emerging mechanistic evidence has identified specific microbial products, such as lipoteichoic acid, that promote ocular surface inflammation through defined signaling pathways, providing initial support for a potential driver or modifier role. In low-biomass environments such as the ocular surface, contamination, host DNA predominance, and methodological variability can strongly influence detected microbial signals.<br><br>SUMMARY: Interpretation of ocular surface microbiome data remains inherently challenging in this low-biomass context. However, the emergence of mechanistic studies suggests a transition from purely associative observations toward functional and translational investigation. Future studies should be designed to better define microbial roles by integrating standardized methodologies with multiomics approaches and detailed clinical phenotyping. Until such evidence emerges, microbiome research is best viewed as advancing biological insight rather than informing clinical decision-making.}, }
@article {pmid42101281, year = {2026}, author = {Wang, Z and Mao, J and Ma, L}, title = {A Tree-Based Model for Addressing Sparsity and Taxa Covariance in Microbiome Compositional Count Data.}, journal = {Statistics in medicine}, volume = {45}, number = {10-12}, pages = {e70584}, pmid = {42101281}, issn = {1097-0258}, support = {R01-GM135440/GM/NIGMS NIH HHS/United States ; DMS-2013930//National Science Foundation/ ; DMS-1749789//National Science Foundation/ ; }, mesh = {Humans ; Bayes Theorem ; *Microbiota ; *Models, Statistical ; Computer Simulation ; Logistic Models ; Infant ; Normal Distribution ; Multivariate Analysis ; }, abstract = {Microbiome compositional data are often high-dimensional, sparse, and exhibit pervasive cross-sample heterogeneity. We introduce the "logistic-tree normal" (LTN) model, a generative model that allows flexible covariance among the microbiome taxa, enables scalable computation, and effectively captures other key characteristics of microbiome compositional data such as the abundance of zeros. LTN incorporates a tree-based decomposition for effective aggregation over sparse taxa counts and models the relative abundance at the tree splits jointly using a (multivariate) logistic-normal distribution. The latent Gaussian structure allows a wide range of multivariate analysis and modeling tools for high-dimensional data-such as those enforcing sparsity or low-rank assumptions on the covariance structure-to be readily incorporated. As a general-purpose, fully generative model, LTN can be applied in a wide range of contexts, while at the same time, efficient computational recipes for Bayesian inference under LTN are available through conjugate blocked Gibbs sampling enabled by pólya-gamma augmentation. We demonstrate the use of LTN in a compositional mixed-effects model for differential abundance analysis through both numerical experiments and a reanalysis of the infant cohort in the DIABIMMUNE study. We explain and showcase through numerical experiments and the case study how LTN, through adequately accounting for the cross-sample heterogeneity, is capable of generating the appropriate proportion of zeros without incurring an explicit zero-inflation component. This confirms a recent viewpoint that "zero-inflation" in count-based sequencing data are often results of unaccounted cross-sample variation.}, }
@article {pmid42101372, year = {2026}, author = {Zhang, H and Zhang, S and Zhu, J}, title = {Molecular-level host-microbe interactions: mechanisms, molecules, and modeling toward precision probiotics.}, journal = {Expert opinion on therapeutic targets}, volume = {}, number = {}, pages = {}, doi = {10.1080/14728222.2026.2671689}, pmid = {42101372}, issn = {1744-7631}, abstract = {INTRODUCTION: Advancing next-generation probiotics (NGPs) as precision therapeutics depends on a detailed understanding of host - microbe molecular interactions, as these organisms exert targeted effects through defined bioactive molecules rather than broad, nonspecific mechanisms. This review addresses the need to systematically organize emerging knowledge on microbe-derived molecules (MDMs) that underpin NGP efficacy.<br><br>AREAS COVERED: This narrative review summarizes recent discoveries of MDMs isolated from NGPs and classifies them based on three principal molecular interaction interfaces: protein - protein/peptide, protein - lipid or glycopeptide, and protein - metabolite interactions. We discuss how these molecules - encompassing proteins/peptides, lipids, glycoconjugates, and small metabolites - modulate host immune and metabolic pathways to maintain homeostasis. The literature was identified through targeted searches of recent peer-reviewed studies focusing on host - microbe molecular mechanisms and probiotic-derived bioactives. We also review the application of molecular docking, molecular dynamics simulations, and artificial intelligence - based tools in predicting host - microbe interactions and accelerating therapeutic discovery.<br><br>EXPERT OPINION: By integrating experimental insights with computational strategies, we propose a framework to guide the development of precision microbiome-based interventions tailored to specific diseases and individual microbiome profiles. These advances lay the foundation for rational design of targeted NGP therapies for metabolic, inflammatory, infectious, and neurodegenerative disorders.}, }
@article {pmid42101618, year = {2026}, author = {Nguyen, PN and Rehan, SM}, title = {Microbial Communities Across Social Roles in Small Carpenter Bee Nests.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02787-2}, pmid = {42101618}, issn = {1432-184X}, abstract = {Bee microbiota form important symbiotic relationships with their hosts, but microbial communities vary across bee species, sociality, and environment. Comparing the microbiome of bees with different social roles and foraging behaviours may uncover the ways in which microbiota are environmentally acquired and subsequently introduced and spread into the nest environment. Here, we performed metabarcoding of the 16S rRNA, ITS, and ribulose biphosphate carboxylase large (rbcL) regions on mothers, dwarf eldest daughters, and regular daughters in nests of the facultatively social, small carpenter bee, Ceratina calcarata, contrasting bacteria, fungi, and plant associates. We also performed two different sampling types by characterizing the microbiome using whole-guts and whole-bodies. Social role in nest impacted the microbial community composition and mothers were found to demonstrate increased plant diversity compared to their daughters, more specifically in whole-bodies, highlighting the ability to determine plants that bees are visiting during foraging through DNA metabarcoding. We also found that metabarcoding of the whole-body recovered increased fungal and plant diversity compared to whole-guts, suggesting that including microbiota from beyond the gut offers an opportunity to characterize uncommon associates that bees encounter, particularly through plant-pollinator relationships. As the transmission of beneficial symbionts and pathogens between individuals are studied for its impact on bee health, microbial analyses of bees across different environments and levels of sociality provides unique biomonitoring that can indicate the health of the larger bee community.}, }
@article {pmid42101639, year = {2026}, author = {Makkar, P and Singh, CK and V, N and Narang, PK and Sodhi, KK}, title = {Insect immunity unveiled: exploring the molecular and cellular defenses against microbial threats.}, journal = {Archives of microbiology}, volume = {208}, number = {8}, pages = {}, pmid = {42101639}, issn = {1432-072X}, mesh = {Animals ; *Immunity, Innate ; *Insecta/immunology/microbiology ; Receptors, Pattern Recognition/immunology ; Microbiota/immunology ; Hemocytes/immunology ; Symbiosis ; Drosophila melanogaster/immunology/microbiology ; Bombyx/immunology/microbiology ; }, abstract = {Insects, as diverse and ecologically dominant organisms, rely exclusively on innate immunity to defend against a wide array of microbial threats. This paper presents an integrative review of insect immune mechanisms, highlighting the molecular, cellular, and systemic components that underpin host defense. The immune response is orchestrated through physical barriers, cellular processes and humoral factors. Evolutionarily conserved pattern recognition receptors (PRRs) are essential to these processes. Emphasis is laid on pivotal functions of hemocytes, the significance of microbiome interactions in immune regulation, and the emerging influence of non-coding RNAs. Furthermore, the paper explores defensive symbiosis, environmental and evolutionary influences on immune dynamics, and applications in biotechnology and pest management. Model organisms, such as Drosophila melanogaster and Bombyx mori, serve as critical systems for unravelling innate immunity, with translational relevance to vertebrate immunology and vector control strategies. Understanding these mechanisms offers valuable insights into conserved immune pathways and holds promise for advancing strategies in human disease prevention, therapeutic innovation, and global health.}, }
@article {pmid42101655, year = {2026}, author = {Miwa, T and Hsu, CL and Shimizu, M and Bloom, PP and Schnabl, B}, title = {Covert hepatic encephalopathy as a multi-organ syndrome: the gut-liver-muscle-brain axis, diagnosis, treatment, and multidisciplinary care.}, journal = {Journal of gastroenterology}, volume = {}, number = {}, pages = {}, pmid = {42101655}, issn = {1435-5922}, support = {JP24K18908//Japan Society for the Promotion of Science/ ; }, abstract = {Covert hepatic encephalopathy (CHE) is a highly prevalent complication of liver cirrhosis. Despite the absence of overt symptoms, CHE is strongly associated with impaired quality-of-life, overt hepatic encephalopathy, and mortality. Over the past two decades, evidence regarding the pathophysiology, diagnosis, and treatment of CHE has accumulated considerably, and clinical guidelines recommend screening in patients with cirrhosis. Nevertheless, diagnostic and therapeutic algorithms have not been fully implemented in real-world practice, and many patients remain undiagnosed and untreated. Understanding the natural history of CHE is essential to improve cirrhosis care, as it provides a framework for appropriate screening, treatment decision-making, and patient counseling. CHE is a multi-organ syndrome with complex interactions between the liver, gut, skeletal muscle, kidneys, and brain, with impaired ammonia handling and systemic inflammation acting as central drivers of this organ crosstalk. Hyperammonemia induces astrocytic dysfunction, brain edema, and neuroinflammation, while systemic inflammation, oxidative stress, sarcopenia, gut dysbiosis, and altered microbial metabolites, including bile acids and short-chain fatty acids, further modulate disease expression. In this review, we summarize current understanding of CHE pathophysiology, diagnostic testing, including psychometric batteries and point-of-care tools, such as the Stroop test and animal naming test, and therapeutic options, ranging from lactulose and rifaximin to microbiome-targeted approaches, including fecal microbiota transplantation. We also highlight major challenges in CHE management, including limited implementation of testing, inadequate biomarkers, diagnostic difficulties in geriatric cirrhosis, and unmet needs in fall and driving risk management, and emphasize the importance of multidisciplinary team-based approaches to improve patient outcomes.}, }
@article {pmid42101775, year = {2026}, author = {Szpytma, M and Dobrzyński, J}, title = {Interactions of PGPR from the phylum bacillota with native rhizosphere microbiota: current insights and future perspectives.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {6}, pages = {}, pmid = {42101775}, issn = {1573-0972}, mesh = {*Rhizosphere ; *Soil Microbiology ; *Microbiota ; *Bacteria/classification/genetics ; Crops, Agricultural/microbiology/growth &amp; development ; Plant Development ; Soil/chemistry ; Plant Roots/microbiology ; Agriculture ; }, abstract = {The intensive use of synthetic fertilizers and pesticides has increased crop productivity but also contributed to soil degradation and biodiversity loss, highlighting the need for more sustainable agricultural strategies. Among emerging solutions, plant growth-promoting rhizobacteria (PGPR), particularly members of the Bacillota phylum, are gaining attention as effective bioinoculants that enhance plant growth and tolerance to biotic and abiotic stresses. However, introduced strains do not function in isolation. They enter complex microbial communities, shaped by plant type and developmental stage, influenced by soil properties and environmental conditions. While the positive effects of PGPR on plant performance are well documented, their impact on indigenous rhizosphere microbiota remains less studied. This review synthesizes current knowledge on how Bacillota-based inoculants influence native microbial communities in cereals, vegetables, orchard crops, and fiber plants. Most studies report shifts toward plant-beneficial taxa and reduced abundance of potential pathogens following Bacillota application. Frequently enriched genera include Bacillus, Pseudomonas, Lysobacter, Sphingomonas, Streptomyces, Azotobacter, Arthrobacter, Pseudarthrobacter, Bradyrhizobium, Devosia, Flavobacterium, Klebsiella, Herbaspirillum, and Rhodanobacter. These changes are often associated with improved plant growth and yield, and stress resilience. However, responses strongly depend on strain, plant and methodological approach. We summarize commonly applied approaches used to assess these interactions. Despite technological advances, limitations remain, such as single time-point sampling, simplified experimental systems, and insufficient integration of inoculant persistence with community analyses. Standardized, multi-site experimental frameworks, with multiple sampling terms are needed to improve predictability and ensure the safe implementation of PGPR-based solutions in sustainable agriculture.}, }
@article {pmid42101879, year = {2026}, author = {Theys, C and Decaestecker, E and Stoks, R}, title = {Extending space-for-time substitutions: the missing role of the gut microbiome.}, journal = {Journal of evolutionary biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jeb/voag032}, pmid = {42101879}, issn = {1420-9101}, abstract = {The space-for-time substitution (SFTS) approach is widely used to predict evolutionary trait responses to global warming. The current approach ignores the explicit role of the gut microbiome in shaping the future host phenotype, despite its strong influence on thermal adaptation and its ability to show more rapid adaptation than the host. We propose integrating reciprocal gut microbiome transplants into SFTS and identify a set of contrasts between treatment combinations to disentangle host and gut microbiome contributions to thermal adaptation under future warming. To illustrate our approach, we apply the proposed contrasts between treatment groups to re-interpret data on immune functioning of Ischnura elegans damselfly nymphs of which the gut microbiome was reciprocally transplanted between nymphs from warm-adapted low-latitude and cold-adapted high-latitude populations reared at both the cold (high-latitude) and warm (low-latitude) thermal regime. By disentangling the contributions of the host and its gut microbiome, our conceptual approach shows that gut microbiome adaptation can buffer against immune suppression in the high-latitude populations under future warming, while adaptation of the host will not. Incorporating the gut microbiome into SFTS may enhance realism in predicting species resilience to climate change and better inform conservation strategies under future climates.}, }
@article {pmid42102024, year = {2026}, author = {Abu, BAZ and Zhang, L and Beblavy, R and Wu, Y and Lu, X and Fiscella, K and Sohn, MB and Xiao, J}, title = {Effects of pica practice on oral bacteriome and mycobiome profiles among pregnant women: A comparative study.}, journal = {PloS one}, volume = {21}, number = {5}, pages = {e0328198}, pmid = {42102024}, issn = {1932-6203}, mesh = {Humans ; Female ; Pregnancy ; Adult ; *Pica/microbiology ; Cross-Sectional Studies ; *Mycobiome ; *Microbiota ; *Mouth/microbiology ; Saliva/microbiology ; Young Adult ; Bacteria/genetics/classification ; }, abstract = {INTRODUCTION: Pica, the excessive craving and consumption of non-food substances such as clay, and ice, is common among pregnant women but may pose risks for oral and systemic infections.<br><br>OBJECTIVE: Assessed the comparative effect of pica practice on the oral microbiome (bacteriome and mycobiome) profiles of pregnant women.<br><br>METHODS: A cross-sectional study was conducted in Upstate New York among pregnant women. Demographic, socioeconomic, pica practices (current and past), and oral hygiene practices were collected via questionnaires. The medical history of anemia was self-reported and verified using electronic records. A calibrated dentist assessed dental caries, periodontal status, and a comprehensive oral examination (plaque index, bleeding on probing). Oral samples (saliva and supragingival plaque) and pica samples were collected for the microbiome for Genomic DNA using I6S rRNA and ITS DNA sequencing and analyzed using linear regression with and without anemia as a covariate.<br><br>RESULTS: Of the 20 pregnant women in the study, 17 were minority women (75% non-white). The mean age of participants was 29 years, and 29 weeks of gestational age. Eight participants (40.0%) reported practicing pica, and six provided samples, namely ice (and popsicles), and chalk. Streptococcus, Actinomyces, and Prevotella dominated in both saliva and plaque samples, but the microbial compositions differed. Between the pica and the non-pica groups, two differentially abundant (DA) bacterial taxa were identified in saliva samples with and without anemia namelyOribacterium sinus (p&#x2009;<&#x2009;0.05). In plaqueseven identical DA bacterial taxa including Prevotella nigrescens were seen except for Leptotrichia goodfellowii, which was unique to when anemia was controlled for (p&#x2009;<&#x2009;0.05). Network analysis showed the co-occurrence of Candida albicans and Lactobacillus in the pica group.<br><br>CONCLUSION: Pica practice was associated with specific oral taxa abundance change in saliva and supragingival plaque, reflecting distinct microbiome distributions. In the regression model, including anemia as a covariate had almost no impact on the overall DA results. These findings are preliminary, indicating that future large prospective cohort studies are warranted to thoroughly assess the impact of pica practice on oral flora.}, }
@article {pmid42102421, year = {2026}, author = {Li, X and Liu, J and Yue, W and Yang, W and Zhang, L and Guo, C and Qing, W}, title = {Chronic endometritis and reproductive failure: The paradigm shift from microbial eradication to ecological restoration.}, journal = {Journal of reproductive immunology}, volume = {175}, number = {}, pages = {104906}, doi = {10.1016/j.jri.2026.104906}, pmid = {42102421}, issn = {1872-7603}, abstract = {Despite advancements in assisted reproductive technologies, such as preimplantation genetic testing, clinical success rates have plateaued, thereby increasing the clinical focus on the endometrial factor. Chronic endometritis (CE), a persistent and often asymptomatic mucosal inflammation, is an underdiagnosed condition associated with reproductive failure, particularly in cohorts with repeated implantation failure (RIF) and recurrent pregnancy loss (RPL). This review examines the evolving understanding of CE pathophysiology, transitioning from a traditional infection model toward a framework involving endometrial dysbiosis and potential bacterial biofilm formation. These microbial alterations are hypothesized to trigger maladaptive immune activation and may induce persistent epigenetic modifications that desynchronize endometrial receptivity. We critically evaluate current diagnostic modalities, addressing controversies regarding CD138 immunohistochemistry thresholds and the interpretive limitations of molecular microbiome screening associated with relic DNA. Therapeutically, while antibiotic regimens remain the standard of care, there is conflicting evidence regarding their universal clinical efficacy. Consequently, we review the rationale for transitioning from generalized broad-spectrum microbial eradication toward antibiotic stewardship and targeted ecological restoration using biotherapeutics. Synthesis of current evidence, including data from euploid embryo transfers, suggests that resolving histopathological inflammation improves live birth rates in specific high-risk cohorts. The future management of CE necessitates the implementation of risk-stratified algorithms and therapeutic strategies that focus on functional endometrial recovery rather than isolated histological clearance.}, }
@article {pmid42102504, year = {2026}, author = {IJdema, F and Broeckx, L and Deruytter, D and Frooninckx, L and van Miert, S and De Smet, J}, title = {Short communication: The persistent influence of host lineage on the gut microbiomes of black soldier fly and yellow mealworm.}, journal = {Animal : an international journal of animal bioscience}, volume = {20}, number = {5}, pages = {101828}, doi = {10.1016/j.animal.2026.101828}, pmid = {42102504}, issn = {1751-732X}, abstract = {Production insects such as the black soldier fly (BSF) and yellow mealworm (YM) are increasingly recognised as sustainable protein sources, and selective breeding of genetically distinct lines offers opportunities to improve production efficiency. However, insect performance is also influenced by the gut microbiome, which provides essential metabolic and protective functions. Despite this, current breeding programmes typically focus on host genetics and phenotypes, assuming that microbiome composition remains stable under consistent rearing conditions. However, this hypothesis remains largely untested. We examined gut bacterial communities in ten distinct BSF and YM populations reared for multiple generations under identical conditions. Each species shared a distinct set of ten zero-radius operational taxonomic units (zOTUs) across all populations, but their relative abundances varied, indicating host-specific effects on microbiome composition. Strain-specific zOTUs also persisted despite uniform environments. These findings suggest that host genetic background exerts a more persistent influence on gut microbiome composition than previously assumed.}, }
@article {pmid42102652, year = {2026}, author = {Al-Salihy, AAS}, title = {Toward an immunological classification of autism spectrum disorder: A PRISMA-ScR-compliant scoping review.}, journal = {Journal of neuroimmunology}, volume = {417}, number = {}, pages = {578962}, doi = {10.1016/j.jneuroim.2026.578962}, pmid = {42102652}, issn = {1872-8421}, abstract = {Autism Spectrum Disorder (ASD) is a heterogeneous neurodevelopmental condition increasingly linked to disturbances in immune signaling and neuroimmune cross-talk. This PRISMA-ScR-guided scoping review synthesizes contemporary evidence to propose a structured immunological classification of ASD comprising six immune-related subtypes: immune overactivation, immune deficiency, autoimmunity-linked ASD, gut-immune axis dysregulation, post-infectious or immune-triggered onset patterns, and maternal immune activation. Each subtype is defined by characteristic neuroimmune features - including cytokine imbalances, aberrant microglial activation, altered microbiome-immune communication, and prenatal immune priming - reflecting distinct biological pathways through which immune dysfunction may influence neurodevelopment. Based on 42 mapped sources identified through a search strategy that primarily emphasized literature published between 2020 and 2025, while incorporating selected foundational earlier studies through citation chaining when necessary for conceptual and mechanistic context, and spanning human clinical and epidemiological studies, animal models, and integrative neuroimmune reviews, this synthesis identifies candidate biomarkers and immune signatures relevant to each subtype, including systemic and CNS-localized inflammation, autoantibodies, disrupted gut-immune-brain pathways, and maternal cytokine profiles. The framework also clarifies ongoing debates by distinguishing immune-mediated vulnerability and timing-dependent unmasking of susceptibility from assumptions of direct causation regarding environmental or infectious exposures. Conceptualizing ASD along immune-related subtypes provides a foundation for precision-based diagnostic and therapeutic approaches, highlighting opportunities for targeted immunomodulation, microbiome-informed interventions, and biomarker-driven stratification, thereby advancing translational efforts at the interface of immunology, neuroscience, and developmental psychopathology.}, }
@article {pmid42102900, year = {2026}, author = {Hamerlinck, H and Boelens, J and De Looze, D and Messiaen, AS and Vandendriessche, S and Holvoet, T and Verhasselt, B}, title = {Seven years of stool banking: clinical and microbiological insights from the Ghent Stool Bank.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108744}, doi = {10.1016/j.ijid.2026.108744}, pmid = {42102900}, issn = {1878-3511}, abstract = {OBJECTIVES: The Ghent Stool Bank (GSB) was founded in 2018 at Ghent University Hospital to provide safe, ready-to-use faecal suspensions for faecal microbiota transplantation (FMT), primarily targeting recurrent Clostridioides difficile infection (rCDI) and supporting clinical trials.<br><br>METHODS: This retrospective cohort study explores the relationship between donor characteristics and rCDI treatment outcomes following FMT.<br><br>RESULTS: Between 2018 and 2024, 12.0% of screened candidates qualified as donors after rigorous evaluation, resulting in 159 approved donations. Forty-four FMT procedures were carried out in forty rCDI patients, achieving a primary cure rate of 77.1%, which increased to 85.7% following a second treatment. Donor microbiome diversity did not show association with treatment outcomes, and no statistically significant differences in taxa abundance were observed. Notably, faecal suspensions stored for up to five years were as effective as those stored for shorter periods. Additionally higher donor age did not appear to negatively impact treatment success in rCDI patients.<br><br>CONCLUSION: These findings support the role of stool banks like the GSB in ensuring safe FMT procedures. Allowing higher donor age and longer storage periods may help sustain sufficient high&#x2011;quality donor availability. Future efforts should focus on improving safety, enhancing donor-recipient compatibility through microbiome profiling and increasing public awareness.}, }
@article {pmid42103091, year = {2026}, author = {Todua, I}, title = {Management of salt-sensitive hypertension in clinical settings: how should we approach it?.}, journal = {The American journal of medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.amjmed.2026.05.003}, pmid = {42103091}, issn = {1555-7162}, abstract = {Salt sensitivity is a major component of highly prevalent uncontrolled hypertensive disease. Multiple disease determinants, such as age, sex, genetic predisposition, pro-inflammatory factors, renal and vascular dysfunction, disrupted blood-brain barrier integrity, as well as gut microbiome health, effectively regulate sodium turnover and associated adverse outcomes. Salt sensitive blood pressure can be commonly observed in patients with both primary and secondary hypertension. Furthermore, patients suffering from obesity and insulin-resistant states, heart failure, chronic kidney disease, as well post-menopausal females and senior citizens, may be particularly sensitive to excessive salt exposure. Despite paramount importance, diagnosis or treatment of salt sensitive blood pressure remain challenging, often pushing clinicians into complicated management labyrinths. Significant discordance between objective findings, such as degree of thirst and edema on presentation, and results of laboratory testing, such as serum sodium, potassium, NT-proBNP, or RAAS essay, is often observed delaying the provision of appropriate care. This review offers detailed description of underlying pathophysiology, diagnosis and treatment of salt sensitive blood pressure in clinical settings, intending to ameliorate the burden of uncontrolled hypertension.}, }
@article {pmid42103112, year = {2026}, author = {Kumwan, B and Meachasompop, P and Adisornprasert, Y and Rajitdumrong, C and Chaemlek, P and Srisapoome, P and Phaksopa, J and Buncharoen, W and Thangsunan, P and Thangsunan, P and Rodkhum, C and Paankhao, N and Kingwascharapong, P and Uchuwittayakul, A}, title = {Sequential nanoimmersion and hydrogel-based multivalent vaccination induce durable multilayered immunity against four bacterial pathogens in Nile tilapia (Oreochromis niloticus).}, journal = {Fish &amp; shellfish immunology}, volume = {175}, number = {}, pages = {111398}, doi = {10.1016/j.fsi.2026.111398}, pmid = {42103112}, issn = {1095-9947}, abstract = {Bacterial infections caused by Flavobacterium oreochromis, Aeromonas veronii, Streptococcus agalactiae, and Edwardsiella tarda represent major threats to Nile tilapia aquaculture. This study evaluated a multistage mucosal vaccination strategy combining sequential nanoemulsion immersion priming with oral hydrogel-based boosters against these four pathogens in Oreochromis niloticus. Vaccination was associated with significant enhancement of both mucosal and systemic humoral immunity, as evidenced by elevated pathogen-specific IgM levels in gills, skin mucus, intestine, and serum across three successive challenge rounds. Immune-related gene expression analysis revealed significant upregulation of ighm, ighd, and ight in key immune tissues, consistent with broad activation of B cell-mediated responses. Label-free quantitative proteomic profiling demonstrated extensive immune remodeling in vaccinated fish, characterized by increased abundance of antigen-presentation molecules, complement factors, lysozyme, serpins, and mucosal defense-associated enzymes. Intestinal microbiome analysis revealed that vaccination reshaped microbial community composition toward a more stable and pathogen-resistant structure, with markedly reduced colonization by all four target pathogens. These immunological and microbial changes were associated with significantly higher survival rates under both immersion and intraperitoneal challenge conditions. Taken together, these findings suggest that multistage sequential vaccination may induce broad-spectrum, durable, multilayered protection in Nile tilapia through synergistic enhancement of humoral immunity, immunoglobulin gene expression, proteomic remodeling, and microbiome stabilization, providing a promising framework for sustainable disease management in intensive aquaculture.}, }
@article {pmid42103122, year = {2026}, author = {Dhayalan, A and Manoharan, S and Waheeb, MQ and Rabbee, MF and Govindasamy, B and Selvan, ST and Pachiappan, P}, title = {An examination of the microbiome of Bacillus cereus (PS5) isolated from Puntius sarana (Olive barb) for α-amylase production, optimization, macromolecule extraction, and structural characterization with industrial and agricultural applications.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {152420}, doi = {10.1016/j.ijbiomac.2026.152420}, pmid = {42103122}, issn = {1879-0003}, abstract = {The α-amylase enzyme plays a vital role in enzyme therapy and the intestinal digestive system, and is widely utilized in the food and pharmaceutical industries. Thus, this study aimed to isolate intestinal bacterial strains that produce α-amylase, optimize enzyme production, and characterize the molecular properties of the produced proteins. A total of 11 strains were isolated from the fish gut; 9 strains were positive for α-amylase production. The PS5 strain exhibited the highest enzymatic activity and was confirmed as Bacillus cereus. Optimization of B. cereus culture conditions revealed parameters of pH 7.0, temperature 35 °C, incubation time 40 h, and starch and yeast extracts of 1.5% and 2.53%, respectively. The bacterial protein was extracted, purified, and shown to have a molecular weight of 55 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. FTIR spectroscopy confirmed the presence of functional groups, such as phenols, alkanes, amides, and aromatic and aliphatic amines. Matrix-assisted laser desorption/ionization (MALDI)-time-of-flight (TOF)-tandem mass spectrometry (MS/MS) analysis identified 12 peptides, with the major peptide sequence being SVGLLLVLLLPMLGAAAPLTTQMLDSGWQFR (m/z 2383.97; S/N 69.3). The α-amylase protein sequence (513 amino acids) was used for structural prediction, while protein-protein interaction analysis revealed a significant interaction with pullulanase (interaction score 0.945). Molecular docking analysis showed strong binding energy of propoxur (-7.2 kcal/mol) and the hormone indole-3-acetic acid (-6.9 kcal/mol) with α-amylase protein. These findings indicate that Bacillus cereus (PS5) is a promising source of α-amylase for diverse industrial and agricultural applications. Further investigation into the activity and stability of these enzymes in natural environments could enhance the associated potential biotechnological applications.}, }
@article {pmid42103208, year = {2026}, author = {Abdelhalim, KA and Wang, Y and Amirkhani Namagerdi, A and Alfuraiji, N and Mburu, D and Hassan, HA}, title = {Gut Oxalate Transport and Gut Microbiome as Potential Therapeutic Targets for Hyperoxaluria and Hyperoxalemia: Implications for Related Human Disease.}, journal = {Mayo Clinic proceedings}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.mayocp.2026.04.020}, pmid = {42103208}, issn = {1942-5546}, abstract = {Besides kidney stones (KS), oxalate potentially contributes to chronic kidney disease (CKD) and its progression, CKD- and end stage kidney disease (ESKD)-associated cardiovascular diseases, and poor kidney transplant survival. KS affect about 1 in 5 men and 1 in 11 women and the recurrence rate remains high (50% in 5 years and up to 80% in 10-20 years), reflecting that current interventions are inadequate, and novel therapies are needed. 70-80% of KS are composed of calcium oxalate and small increases in urine oxalate enhance the KS risk. The gastrointestinal tract (gut) plays a major role in oxalate homeostasis by acting as a site for oxalate absorption and secretion. Therefore, the gut potentially represents a novel therapeutic pathway for body oxalate elimination. Strategies aiming at reducing the gut's ability to absorb oxalate and/or enhancing its ability to secrete oxalate can lead to decreased plasma and urinary oxalate levels and therefore can serve as novel approaches for the prevention and/or treatment of hyperoxalemia and hyperoxaluria. Humans lack oxalate metabolizing enzymes, and they rely on gut bacteria referred to as oxalate-degrading bacteria (oxalobiome) for gut oxalate degradation. This limits net gut oxalate absorption, thereby helping with maintaining normal oxalate homeostasis. This review focuses on the role of gut oxalate transport and gut microbiome in overall oxalate homeostasis and how they can be therapeutically targeted. Importantly, the majority of evidence for gut oxalate transport is derived from animal studies, but the relevance of these findings to human gut oxalate transport remains to be established.}, }
@article {pmid42103277, year = {2026}, author = {Yan, J and Jin, N and Xu, C and Wu, H and Jiang, Q and Liu, H and Yuan, J and Yin, D and Lin, F and Wang, R and Liang, Y and Feng, Y and Lan, Y and Lin, X and Wang, Y and Zhang, N and Dai, L and Li, T and Dong, S and Cheng, L and Sun, X}, title = {Multi-omics landscape and machine learning predictors of acute and chronic coronary syndrome diagnosis in young patients.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2026.05.015}, pmid = {42103277}, issn = {2090-1224}, abstract = {BACKGROUND: Acute coronary syndrome (ACS) is a leading global cause of death, and its incidence is increasingly rising in young adults, who exhibit distinct clinical characteristics from elderly patients. However, multi-omics studies focusing specifically on young coronary heart disease (CHD) patients remain scarce, hindering precise diagnosis and mechanism exploration.<br><br>METHODS: Here, we enrolled 206 young chest pain patients (18-45&#xa0;years old), including 122 ACS patients, 38 chronic coronary syndrome (CCS) patients, and 46 individuals with healthy coronary arteries (NC). We performed integrated analyses of peripheral blood mononuclear cell transcriptomics, serum metabolomics, stool metabolomics, and gut microbiome metagenomics to characterize CHD subtypes and develop targeted diagnostic tools.<br><br>RESULTS: Our results showed that single omics layers had limited ability to distinguish CHD subtypes, while multi-omics integration significantly improved diagnostic efficacy. We identified unique molecular signatures for different subtypes: STEMI was associated with abnormal amino acid and carbohydrate metabolism, CCS was dominated by amino acid metabolism disturbances, and both STEMI and ACS showed enriched inflammation-related pathways. Novel biomarkers including p-chlorobenzene sulfonamide, cotinine, and the gut bacterium Streptococcus parasanguinis were identified, with Streptococcus parasanguinis validated as an atherogenic pathogen in a murine model. We constructed three multi-omics fusion diagnostic models (ACS vs. NACS, CCS vs. NC, STEMI vs. NSTE-ACS) with AUC values of 0.99, 0.95, and 0.96, respectively, and integrated them into a comprehensive diagnostic pipeline. Furthermore, multi-omics functional analysis unraveled a synergistic "microbiota-metabolism-immunity" regulatory network underlying CHD subtypes, linked to disordered amino acid and carbohydrate metabolism and aberrant inflammatory activation.<br><br>CONCLUSION: This study provides a systematic molecular landscape of young CHD, a high-precision diagnostic strategy, and novel targets for mechanism research and targeted intervention, addressing the unmet clinical need for precise management of young CHD patients.}, }
@article {pmid42103586, year = {2026}, author = {Liu, WC and Chang, TT}, title = {From intratumoral microbiome association to spatial microbiome biology in primary liver cancer: a response and perspective.}, journal = {Journal of the Formosan Medical Association = Taiwan yi zhi}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jfma.2026.05.021}, pmid = {42103586}, issn = {0929-6646}, }
@article {pmid42103590, year = {2026}, author = {Fukuda, K and Hozaka, Y and Ohtsuka, T}, title = {Reply to the Letter to the Editor regarding microbiome-genetic interplay in intraductal papillary mucinous neoplasms of the pancreas.}, journal = {Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.]}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pan.2026.04.016}, pmid = {42103590}, issn = {1424-3911}, }
@article {pmid42103597, year = {2026}, author = {Fan, Z and Shahgaleh, H and Ding, S}, title = {Nitrous oxide mitigation in hybrid maize mediated by Massilia.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2026.04.015}, pmid = {42103597}, issn = {1878-4372}, abstract = {Massilia presents a functional paradox in maize heterosis: its enrichment correlates with lower nitrous oxide (N2O) emissions, yet it lacks reduction genes. We propose that Massilia functions as an ecological hub, coordinating the rhizosphere microbiome and engineering the microenvironment to suppress N2O emissions. This paradigm guides new strategies for breeding climate-smart crops.}, }
@article {pmid42103701, year = {2026}, author = {Wu, H and Wang, M and Ouyang, Q and Zhang, X and Liao, L and Wang, Y and Tang, N and Wang, Z}, title = {Comprehensive analysis of microbiome and transcriptome revealed the mechanisms of Flammulina velutipes stem-base enhance intestinal health in Gymnocypris eckloni.}, journal = {Journal of fish biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jfb.70490}, pmid = {42103701}, issn = {1095-8649}, support = {23ZR102//Chengdu Agricultural College/ ; 23BS03//Chengdu Agricultural College/ ; }, abstract = {Although Flammulina velutipes residues are increasingly used in fish feeds, their mode of action in the gut is poorly defined. Here, we show that feeding Gymnocypris eckloni diets supplemented with F. velutipes stem-base (FVS) or its polysaccharides (FVP) selectively enhance foregut morphology-increasing both villus height and muscle layer thickness-without affecting mid- or hindgut regions. Transcriptome profiling revealed that 1831 differentially expressed genes (DEGs) were generated by FVS diet in the foregut mainly enriched in the signalling pathways related to DNA replication, fat digestion and absorption and HIF-1 signalling pathway. In addition, the differential genes between the FVP group and the control group were enriched in cell adhesion molecules, MAPK signalling pathway and cytokine-cytokine receptor interaction. Consistent with this, KEGG enrichment highlighted HIF-1α and MAPK as key pathways activated by FVS and FVP, respectively. Importantly, FVP also shifted the gut microbiota composition, boosting Weissella and other putative beneficial bacteria. These findings imply that F. velutipes has the potential to strengthen the intestinal barrier and improve intestinal health, offering valuable insights for the aquaculture of G. eckloni.}, }
@article {pmid42103708, year = {2026}, author = {Basler, N and De Smet, L and Bouras, G and Swinnen, J and Pranga, K and Brussaard, CPD and Vandamme, P and de Graaf, DC and Matthijnssens, J}, title = {The honey bee triad: a comprehensive catalogue of phages in the Apis mellifera gut microbiome.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-72757-2}, pmid = {42103708}, issn = {2041-1723}, support = {955974//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 817622//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; H2020//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; }, abstract = {Honey bees (Apis mellifera) contribute to crop production and floral biodiversity via pollination, but their health is increasingly challenged by stressors including pathogens, parasites and agricultural practices. Although the honey bee gut microbiome is relatively simple, its phages are not well studied. Here, we conducted a metagenomic study, providing a comprehensive catalogue of honey bee gut phages from 450 virus-enriched samples from 63 hives, across eight European countries, three seasons and three gut sections. We describe a diverse phageome including many phages that appear to belong to novel taxa, as well as a core set of 97 highly prevalent phages. In addition, we identify potential auxiliary metabolic genes, such as a sulfur metabolism gene carried by phages that are predominantly temperate and likely infect mutualistic honey bee core bacteria. This gene is associated with land use around the sampled hives, indicating complex ecological interactions in the tripartite system of the honey bee, its microbiota and the phages therein.}, }
@article {pmid42103720, year = {2026}, author = {Easter, QT and Huynh, KLA and Stolf, CS and Xie, J and Matuck, BF and Hasuike, A and Alvarado-Martinez, Z and Kim, WS and Chen, Z and Ribeiro, AA and Pareek, N and Azcarate-Peril, AM and Wu, D and Casarin, R and Ko, KI and Liu, J and Byrd, KM}, title = {CD38[+] endothelial remodeling marks spatially patterned vasculopathy in rapidly advancing periodontitis and peri-implantitis.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-72452-2}, pmid = {42103720}, issn = {2041-1723}, support = {Volpe Research Scholar Award//ADA Foundation (American Dental Association Foundation)/ ; Large Research Grant//American Academy of Implant Dentistry (AAID)/ ; #1RM1DE035338-01//U.S. Department of Health &amp; Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; #1R03DE034507-01//U.S. Department of Health &amp; Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; #5R01DE030415-05//U.S. Department of Health &amp; Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; startup funds//Virginia Commonwealth University (VCU)/ ; #2021/11082-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (S&#xe3;o Paulo Research Foundation)/ ; Overseas Researcher Grant//Nihon University/ ; Schoenleber Grant//University of Pennsylvania (Penn)/ ; #P30CA016059//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; #UM1TR004360//U.S. Department of Health &amp; Human Services | NIH | National Center for Advancing Translational Sciences (NCATS)/ ; }, abstract = {Oral inflammatory diseases affect nearly half of all humans, yet mechanisms underlying rapidly-destructive inflammation remain poorly understood. We compared peri-implantitis with moderate- and high-grade periodontitis using integrated microbial and single-cell sequencing (>967,169-cells; single-cell RNA-seq, spatial proteotranscriptomics). Laser capture microdissection with compartmental microbiome analysis revealed reduced bacterial load and diversity in peri-implantitis. Expansion of the Human Periodontal Atlas with peri-implantitis single-cell RNA-seq data (36-samples; 121,395 cells) identified CD34[+] vascular endothelial cell (VEC) rarefaction and oxidative stress, hypoxia, and NAD[+] metabolism-associated transcriptional programs enriched in a TNFRSF6B[+]/ICAM1[+] post-capillary venule (PC-VEC) subpopulation. NAD[+]-consuming ectoenzyme CD38 was selectively enriched and orthogonally confirmed by spatial transcriptomics (6-samples; 283,377-cells) and proteomics (23-samples; 562,397-cells). Spatial neighborhood analyses demonstrated CD38[+]-high PC-VEC expansion, closer proximity, and higher IL16-CD4 T cell signaling in peri-implantitis. Matched high-grade periodontitis biopsies confirmed spatially restricted CD38[+]-VECs despite similar microbial burden, identifying endothelial vasculopathy underlying rapidly advancing oral inflammation and a potential therapeutic axis.}, }
@article {pmid42103800, year = {2026}, author = {Bahuguna, M and Diwan, P and Wahlang, J and Gupta, RK}, title = {Comparative microbiome profiling of betel quid chewers and non-chewers to identify dysbiotic microbial signatures.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-46533-7}, pmid = {42103800}, issn = {2045-2322}, support = {2019-3072//Indian Council of Medical Research/ ; 2019-3072//Indian Council of Medical Research/ ; 2019-3072//Indian Council of Medical Research/ ; }, abstract = {Recent studies are showing an association between oral microbiome community changes and oral diseases, including oral cancer. The prevalence of betel quid chewing has been linked to the incidence of oral cancer, particularly in the Northeast region of India. Hence, the study to understand the bacterial community shifts induced by betel quid to identify dysbiotic microbial signatures will not only aid in early diagnosis of oral cancers but also facilitate the development of strategies to restore microbial balance and potentially prevent disease progression. The present cross-sectional study evaluated the oral microbiome of 92 adults in Meghalaya, India, using a 16 S rRNA sequencing approach. Significant differences were observed in the bacterial community in betel quid chewers and non-chewers. Alpha diversity, assessed using Chao1 and observed genera metrics, was significantly higher in betel quid chewers as compared to non-chewers, especially among long-term users and male individuals. Beta diversity analysis revealed significant community compositional differences between Betel quid chewers and non-chewers, more notably in males and individuals aged 40-60 years. Betel quid chewers demonstrated a higher number of unique taxa (63 Overall; 102 Male; 123 in 40-60 years old) compared to non-chewer samples. Linear discriminant analysis identified Haemophilus, Fusobacterium, and Lautropia enriched in non-chewers, while Lachnoclostridium, Ottowia, and Prevotella were enriched in chewers. Additionally, Pediococcus pentosaceus and Leuconostoc citrenum were found exclusively in older, long-term chewers; Lactobacillus reuteri and Lactobacillus salivarius in non-chewers. These findings highlight profound BQ-associated oral microbiome dysbiosis.}, }
@article {pmid42103814, year = {2026}, author = {Petrás, S and Szabó, BV and Kiss, T and Bahar, MA and Csupor, D and Tóth, B}, title = {Prenatal maternal antibiotic use increases the risk of childhood eczema: a systematic review and meta-analysis.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-51441-x}, pmid = {42103814}, issn = {2045-2322}, abstract = {Early-life disruption of microbiome development is known to impair health; however, the long-term effects of pregnancy-related pharmacological alterations to the maternal gut microbiota on offspring health remain unclear. This meta-analysis aimed to evaluate the impact of maternal antibiotic use (either prenatal or intrapartum) on the risk of childhood atopic dermatitis, based on cohort and case-control studies. Literature searches were conducted in EMBASE, PubMed, Cochrane, and Web of Science databases using predefined PICO (patients, intervention, comparison, outcome) criteria. Overall, our meta-analysis included 30 studies with a total of 4,125,143 mothers and 4,346,050 children. Using the random effects model, our study found that prenatal antibiotic use was associated with higher odds of atopic dermatitis in childhood (aOR: 1.32; 95% CI: 1.12; 1.56). This result remained significant after adjusting publication bias by the trim-and-fill method (aOR: 1.22; 95% CI: 1.03; 1.44), highlighting the potential relevance of antibiotic prescribing practices during pregnancy in relation to childhood atopic disease risk. Intrapartum antibiotic use was not associated with elevated risk for atopic dermatitis in the children (OR: 1.64; 95% CI: 0.84; 3.17). Prenatal antibiotic use appears to have a modest effect on atopic dermatitis in offspring.}, }
@article {pmid42103910, year = {2026}, author = {Lyu, WN and Shen, CY and Tsai, YJ and Chen, LH and Lee, YH and Chen, SK and Lee, JM and Lou, PJ and Chuang, EY and Tsai, MH}, title = {Intratumoral microbial networks as biomarkers for second primary oral cancer risk in esophageal squamous cell carcinoma.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-52247-7}, pmid = {42103910}, issn = {2045-2322}, support = {PL-202208034-V//Fu Jen Catholic University Hospital/ ; 115KKZA3T1//Development Center for Medical Devices, National Taiwan University/ ; }, abstract = {Esophageal squamous cell carcinoma (ESCC) survivors remain at elevated risk of developing second primary oral cancer (SPOC), yet the role of intratumoral microbiomes in SPOC emergence is not fully understood. We performed 16 S rRNA V3-V4 sequencing on tumor brushings from 28 ESCC patients (20 SPOC-negative, 8 SPOC-positive) to profile microbial diversity, taxonomic composition, functional potential, and interaction networks. Alpha diversity metrics (Chao1, Shannon) did not differ significantly between groups (p > 0.05), whereas sparse partial least squares-discriminant analysis of beta diversity robustly separated SPOC-positive from SPOC-negative tumors (p < 0.001), identifying 32 discriminant amplicon sequence variants (ASVs) linked to 41 differential KEGG pathways. Intratumoral Spearman correlation networks (|r| > 0.3, p < 0.05) between the ten most abundant genera and these pathways revealed two distinct modules: a SPOC-associated network centered on Prevotella pallens and P. scopos, enriched in carbohydrate metabolism, PI3K-Akt signaling, and glycosaminoglycan degradation; and a non-SPOC network anchored by Alcaligenaceae, Cyanobiaceae, Rhodobacteraceae, and Prevotella oris, associated with macrolide biosynthesis and aminobenzoate degradation. These findings demonstrate that specific intratumoral microbial interaction networks distinguish ESCC patients who develop SPOC, and highlight network-based microbial signatures as promising biomarkers for SPOC risk stratification.}, }
@article {pmid42103925, year = {2026}, author = {Anil,  and Ramesh, KB and Gouda, MNR and Subramanian, S}, title = {Microbial zonation and functional roles in the gut of white grub (Maladera insanabilis) larvae.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-52250-y}, pmid = {42103925}, issn = {2045-2322}, abstract = {Maladera insanabilis, a widespread and destructive agricultural pest in India, thrives in nitrogen-deficient subsoil environments due to its dependency on gut bacteria. In particular, the hindgut is an anaerobic fermentation chamber, supporting microbial-driven nitrogen transformations essential for larval development. Despite its ecological significance, detailed studies exploring gut bacterial diversity and functional role in M. insanabilis are lacking. This study integrates metagenomics, culture-based techniques, enzymatic assays, and gene expression analyses to characterize the nitrogen-cycling potential of gut microbiota along the different gut compartments. The culture-based analysis isolated 16 aerobic and 8 anaerobic bacterial strains, predominantly from Bacillota and Pseudomonadota. High-throughput 16 S rRNA Illumina sequencing revealed 134 shared amplicon sequence variants (ASVs), with distinct bacterial assemblages, Burkholderia and Pseudomonas in the foregut, Paenibacillus in the midgut, and anaerobic genera such as Bacteroides and Desulfovibrio dominating the hindgut. Functional annotation using the KEGG database indicated that anaerobic gut bacteria are actively involved in nitrification, denitrification, and nitrogen fixation. The Enzyme assays confirmed high nitrate and nitrite reductase activity, with Burkholderia contaminans and Bacillus cepacia showing the highest activities. Michaelis-Menten kinetics and Lineweaver-Burk analysis (R[2] = 0.9871) showed a higher capacity (Vmax) for nitrate and nitrite reduction; a small Km indicates a high affinity for nitrate and nitrite. Gene expression studies viz., hzo, nifH, amx, nirS, and nirK revealed a significantly high expression level in the hindgut, especially under vermicompost treatment. This study provides the first comprehensive insight into nitrogen-cycling gut bacteria in M. insanabilis, highlighting their role in host nutrition and nitrogen transformation. These findings lay a foundation for future microbiome-targeted pest control strategies aimed at disrupting nutrient acquisition in soil-dwelling grubs.}, }
@article {pmid42104127, year = {2026}, author = {Byrne, D}, title = {How a passion for baking fermented a fresh career move.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/d41586-026-01390-2}, pmid = {42104127}, issn = {1476-4687}, }
@article {pmid42104135, year = {2026}, author = {Cheong, KL and Pan, T and Wang, M and Wang, D and Zhong, S}, title = {Impact of prebiotics, probiotics, and postbiotics on maternal and fetal health: mechanisms, efficacy, and safety across pregnancy.}, journal = {Pediatric research}, volume = {}, number = {}, pages = {}, pmid = {42104135}, issn = {1530-0447}, abstract = {Microbiome-directed biotics are gaining attention in obstetrics. This review clarifies terminology, mechanisms, clinical effects, and safety for prebiotics, probiotics, and postbiotics. Prebiotics are nondigestible substrates that are selectively used by host microbes to confer health benefits. Probiotics are defined as live microorganisms that improve health when given in adequate amounts. Postbiotics are preparations of nonviable microbes or their components that trigger beneficial responses. We summarize how these agents may influence maternal and fetal physiology across gut, immune, metabolic, vaginal, placental, and human milk contexts. In the gut, they reshape short-chain fatty acid and bile acid pools, modulate enteroendocrine hormones, and recalibrate basal immunity. They also tighten epithelial junctions and stimulate goblet cell mucin, which reduces microbial translocation, endotoxemia, and vascular strain. In the vaginal and urogenital niches, lactobacilli maintain acidity, suppress pathobionts, and may lower colonization risk. At the placenta and in milk, microbial metabolites and immune mediators, including human milk oligosaccharides and secretory IgA, carry maternal cues that shape fetal and neonatal development. Safety profiles differ by class. Prebiotics are generally well tolerated, with dose-dependent gastrointestinal symptoms most common. Probiotics require strain-level validation, viability control, and contaminant-free production. Postbiotics need to be verified inactivation and structural characterization. IMPACT: Provides a comprehensive, mechanism-based overview of how prebiotics, probiotics, and postbiotics influence maternal and fetal health across multiple physiological systems. Clarifies definitions, safety profiles, and quality standards for biotics in pregnancy, addressing current inconsistencies in research and commercial products. Integrates emerging evidence on postbiotics and vertical microbial transmission, offering a timely framework for future clinical applications and regulatory guidance.}, }
@article {pmid42104237, year = {2026}, author = {An, L and Liu, X and Li, X and Chu, Y and Sun, X and Chu, J and Nie, Y}, title = {Contact-mediated bacterial transmission and infection risk dynamics in a newly opened hospital ward.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05030-7}, pmid = {42104237}, issn = {1471-2180}, support = {32500094//National Natural Science Foundation of China/ ; }, abstract = {The hospital microbiome significantly influences patient recovery and clinical outcomes. However, the dynamics of microbial colonization and transmission following initial patient occupancy remain poorly understood. Here, we employed 16 S rRNA gene amplicon sequencing of the V3-V4 region (Illumina platform) to investigate bacterial community dynamics on surfaces within neurosurgery ward and patients as a new hospital became operational. Our results showed that bacterial colonization in hospital wards follows distinct site-specific patterns, after hospital opening, alpha diversity was significantly increased on floors and drawer handles but decreased on bedrails and faucet handles compared to preopening. Beta diversity analysis showed that surfaces frequently contacted by patients exhibited the greatest compositional turnover, such as bedrails, drawer handles, and faucet handles, bacterial communities in after-opening were more homogeneous across sites than preopening, indicating potential bacterial transmission. Moreover, we found that following patient admission, patient hand-derived microbiomes exert a significant influence on the bacterial communities in hospital wards, with a particularly pronounced impact on bedrails. Additionally, the potential pathogenic potential of the microbial community at the taxonomic level of bedrails in post-opening was significantly higher than preopening, which does not reflect direct clinical infection risk. Taken together, these findings underscore the critical role of human contact in shaping hospital microbiomes and highlight the importance of targeted infection control strategies to mitigate potential pathogen transfer.}, }
@article {pmid42104530, year = {2026}, author = {Bibinger, S and Nosenko, T and Sivaprakasam Padmanaban, PB and Schulz, S and Schroeder, H and Kersten, B and Zimmer, I and Buegger, F and Schloter, M and Schnitzler, JP}, title = {Provenance legacies override species effects in shaping oak rhizosphere microbiomes and metabolomes.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71213}, pmid = {42104530}, issn = {1469-8137}, support = {457330647//Deutsche Forschungsgemeinschaft/ ; 2220WK09A4//German Federal Ministry of Food and Agriculture (BMEL), Federal Ministry for the Environment, Nature Conservation and Nuclear Safety (BMU)/ ; 2220WK09B4//German Federal Ministry of Food and Agriculture (BMEL), Federal Ministry for the Environment, Nature Conservation and Nuclear Safety (BMU)/ ; }, abstract = {As climate change drives more frequent drought-heat extremes, selecting drought-tolerant trees is crucial for future forest resilience. However, the role of tree-microbial associations remains largely unclear. We investigated how geographic origin, species identity, and intrinsic water use efficiency (iWUE) shape the rhizosphere microbiome and root-rhizosphere metabolome of Quercus robur L. and Q. petraea (Matt.) Liebl. In a 6-yr common garden experiment, we analyzed trees from two distinct geographic origins (upper Rhine basin and north German lowland) using 16S/ITS metabarcoding and untargeted metabolomics. We found a consistent legacy effect of seed origin on the prokaryotic rhizosphere microbiome and metabolome, whereas tree species had no significant impact. The bacterial family Pseudonocardiaceae was enriched for trees from the drier origin (NGL), while Blastocatellaceae and Micromonosporaceae were associated with iWUE. Higher iWUE also correlated with lower prokaryotic diversity. Ellagic acid, a polyphenol associated with drought tolerance, was enriched in the drier origin. The rhizosphere fungal community, however, was largely unaffected by origin or species. Our findings suggest that ecotypic adaptation linked to origin can outweigh species-level traits in shaping the oak rhizosphere. These findings emphasize that provenance-driven adaptation influences plant-microbe interactions and underscore the need for provenance-aware selection to strengthen forest drought resilience.}, }
@article {pmid42104576, year = {2026}, author = {Ii C, JF and Vidal, MJS and Dela Cruz, FSE and Tantengco, OAG and Menon, R}, title = {The Microbiome Signature of the Placenta and its Role in Spontaneous Preterm Birth: A Systematic Review and 16S rRNA Re-Analysis.}, journal = {American journal of reproductive immunology (New York, N.Y. : 1989)}, volume = {95}, number = {5}, pages = {e70246}, doi = {10.1111/aji.70246}, pmid = {42104576}, issn = {1600-0897}, mesh = {Humans ; Female ; Pregnancy ; *Placenta/microbiology ; *Premature Birth/microbiology/immunology ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; }, abstract = {PROBLEM: The advent of high-throughput 16S rRNA sequencing has enabled deeper insights into microbial communities associated with adverse pregnancy outcomes, including spontaneous preterm birth (sPTB). While microbial dysbiosis in the cervicovaginal and oral-gut microbiomes has been implicated in sPTB, the existence of a placental microbiome remains contentious. Traditional paradigms of a "sterile womb" have been challenged by studies suggesting a low-biomass microbial community in the placenta, though recent evidence disputes this claim, attributing findings to contamination or transient microbial DNA signals.<br><br>METHOD: This study systematically reviewed placental microbiome studies employing 16S rRNA sequencing and re-analyzed publicly available datasets to determine microbial signatures in term and preterm placentas. Following a comprehensive search of three databases and stringent inclusion criteria, seven studies were included. The risk of bias was assessed using a modified Joanna-Briggs tool, revealing moderate-to-low risk across studies. Methodological heterogeneity, including differences in contamination controls, sequencing regions, and analytical platforms, was a significant limitation.<br><br>RESULTS: A re-analysis of sequencing data showed no consistent microbiome signature distinguishing the term from preterm placentas. Beta diversity analysis revealed no group clustering, while alpha diversity indices showed comparable species richness. Bacterial DNA in placental tissues was primarily attributed to contamination from the urogenital tract or laboratory processes.<br><br>CONCLUSION: Findings underscore the importance of robust contamination control and standardized protocols in low-biomass microbiome research. Future studies should employ advanced techniques, such as metagenomics and fluorescence in situ hybridization, to evaluate the functional relevance of microbial communities in the placenta, as well as rule out microbial DNA deposited in the placenta through circulating bacterial extracellular vesicles (EVs).}, }
@article {pmid42104937, year = {2026}, author = {Kang, X and Hu, L and Song, J and Zhang, Z and Li, Y and Zhang, Q and Luo, C and Pang, Y and Guo, P and Yue, B and Li, P and Fan, Z}, title = {Snake Gut Microbiota as a Source of Anti-Inflammatory Probiotics: Isolation and Functional Characterization of Two Novel Strains.}, journal = {Integrative zoology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1749-4877.70118}, pmid = {42104937}, issn = {1749-4877}, support = {2023NSFSC1935//Sichuan Science and Technology Program/ ; }, abstract = {The intestinal microbiome is fundamental to host physiological homeostasis, while deviations from its balanced state have been linked to inflammatory bowel diseases (IBD). To address the limitations of conventional antibiotic therapies, this study explored snake gut microbiota as a novel source of anti-inflammatory probiotics. We explored the gut microbiota of five snake species (Deinagkistrodon acutus, Trimerodytes annularis, Trimerodytes percarinatus, Lycodon rufozonatus, and Trimeresurus stejnegeri) through metagenomic sequencing. Community composition analysis revealed that the phylum-level composition was mainly Proteobacteria, Bacteroidetes, Actinomycetota, and Firmicutes. We further detected some potential probiotic species, such as Enterococcus, Lactobacillus, and Limosilactobacillus. From 196 isolated strains, Lactobacillus johnsonii DA0116 and Limosilactobacillus reuteri DA0218 were selected through rigorous safety and functional assessments, including acid/bile tolerance, pathogen inhibition, and adhesion capacity. In a DSS-induced murine colitis model, both strains significantly reduced disease activity index (DAI), pro-inflammatory cytokines (TNF-α, IL-6, and IL-8), and restored gut microbiota diversity. Additionally, whole-genome analysis identified bacteriocin synthesis clusters (gassericin-S/T) and carbohydrate metabolism genes, explaining their antimicrobial and immunomodulatory properties. This study not only emphasizes the untapped latent value of reptilian gut microbiota for probiotic discovery but also provides two candidate strains with therapeutic promise for IBD and functional food applications.}, }
@article {pmid42105032, year = {2026}, author = {Saeed, T and Grover, M and Singh, AK and Prasanna, R and Kaushik, R and Meena, MC and Mandal, PK and Kumar, P}, title = {Hydrophyte root microbiome: a novel reservoir of plant growth-promoting bacteria for enhancing lettuce (Lactuca sativa L.) growth and nutritional quality under soilless cultivation.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {6}, pages = {}, pmid = {42105032}, issn = {1573-0972}, mesh = {*Lactuca/growth &amp; development/microbiology ; *Plant Roots/microbiology/growth &amp; development ; *Microbiota ; Soil Microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Biomass ; Plant Growth Regulators/metabolism ; Nutritive Value ; Soil/chemistry ; Germination ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Soilless cultivation is a major component of modern protected agriculture; however, often lack the beneficial microbial communities that support plant health in natural soils. This study explored hydrophyte root microbiomes as an eco-friendly and novel source of plant growth-promoting bacteria (PGPB) for engineering beneficial microbial communities in soilless systems. Bacteria associated with the roots of Eichhornia crassipes, Pistia stratiotes, and Alternanthera philoxeroides, expressing PGP traits were assessed for their growth-promoting potential on lettuce (Lactuca sativa L. cv. 'Lolo Red') using cocopeat-based soilless media and soil under polyhouse conditions. Hydrophyte associated rhizobacteria exhibited diverse PGP functions, including nutrient solubilization and phytohormone production, similar to those exhibited by rhizobacteria associated with terrestrial plants. Under soil and soilless conditions, lettuce crop inoculated with hydrophyte associated rhizobacteria significantly enhanced germination, plant biomass, root architecture, photosynthetic pigments and leaf quality traits, including TSS (total soluble solids), total phenolics, vitamin C, anthocyanins, antioxidant enzyme activities, DPPH (2,2-Diphenyl-1-picrylhydrazyl) radical scavenging and FRAP (Ferric Reducing Antioxidant Power) responses in both the cultivation systems. Two strains viz. Bacillus aerius Aq35 and Pseudomonas protegens Aq45 were particularly very promising. Under soilless cultivation, Aq35 enhanced root fresh weight and surface area by 90.0% and 83.5%, respectively, while Aq35 and Aq45 increased lettuce yield by 39.62% and 28.70%, respectively. Bacterial inoculation significantly enhanced the availability of soil and plant macro (N, P, and K) and micronutrients (Fe, Mn, Zn, and Cu) along with a marked increase in enzymatic activities and microbial biomass carbon (MBC). Under soilless substrate, dehydrogenase activity increased from 43.40 to 64.65 µg TPF g[-1] day[-1], while alkaline phosphatase activity increased from 261.53 to 380.87 µg PNP g[-1]h[-1] inoculated (Aq35) treatment over uninoculated treatment indicating enhanced substrate biological quality. These results demonstrate that hydrophytes as rich, pre-adapted reservoirs of potent PGPB, and strains such as B. aerius Aq35 and P. protegens Aq45 hold strong potential as biostimulants for sustainable soilless agriculture.}, }
@article {pmid42105271, year = {2026}, author = {Meijer, GW and Fogliano, V and Lähteenmäki, L and Ahrné, LM and Labbe, D and Forde, CG}, title = {From fiction to facts: on the safety, rules, perception, and role of food additives.}, journal = {Critical reviews in food science and nutrition}, volume = {}, number = {}, pages = {1-26}, doi = {10.1080/10408398.2026.2669055}, pmid = {42105271}, issn = {1549-7852}, abstract = {Consumer perceptions of food additives are often negative, driven by unfamiliar terminology, associations with "ultra‑processed food," and concerns about reduced naturalness. Despite this, additives play essential roles in food preservation, sensory quality, and safety, and undergo rigorous safety evaluation in jurisdictions worldwide by authoritative bodies such as JECFA, EFSA, and the (US-)FDA. While some studies suggest possible effects of specific emulsifiers or sweeteners on the microbiome or metabolism, evidence is limited and often not reflective of real dietary exposure. Broader claims-such as additives causing "hyper‑palatability" or "food addiction"-lack scientific support, with research showing that overeating is more closely linked to energy density and food availability than additives themselves. Reducing additives use, without sound scientific justification, may inadvertently worsen nutrient profiles of foods, and increase food waste and health risks. Improving public understanding of additives safety and function is essential to counter misconceptions and avoid counterproductive reformulation decisions.}, }
@article {pmid42105460, year = {2026}, author = {Ma, C and Chang, M and Zang, S and Shi, K and Sha, Z}, title = {Dual-omics links host genomic variation to gut microbiome restructuring under Mycobacterium marinum challenge in Cynoglossus semilaevis.}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {59}, number = {}, pages = {101838}, doi = {10.1016/j.cbd.2026.101838}, pmid = {42105460}, issn = {1878-0407}, abstract = {Disease outbreaks caused by Mycobacterium marinum pose a major challenge to marine aquaculture and threaten the sustainable production of Cynoglossus semilaevis. Increasing evidence suggests that host genetic variation and gut microbial communities may jointly influence disease-related phenotypes, yet their interaction under mycobacterial challenge remains poorly understood. In this study, we combined host whole-genome resequencing and gut 16S rRNA sequencing to explore host-microbiome associations in C. semilaevis following M. marinum challenge. Gut microbiota analysis revealed significant differences in community structure and composition between the experimental and control groups, with marked shifts in dominant taxa and differential enrichment of several bacterial genera. Genome-wide association analysis identified nine significant SNPs (λ = 1.02) associated with infection status, distributed across chromosomes 5, 10, 13, 18, and 19. Functional annotation showed that most of these loci were located in non-coding or regulatory regions, including six intronic SNPs, one ncRNA_exonic SNP, one ncRNA_intronic SNP, and one intergenic SNP. Correlation network analysis further linked host genetic variants with changes in gut microbial taxa, suggesting a potential association between host genomic variation and microbiome restructuring under challenge conditions. Overall, these results provide preliminary evidence that host genomic variation may be associated with gut microbiome dynamics during M. marinum infection in C. semilaevis. Although limited by sample size, this dual-omics framework offers a useful basis for future validation of host-microbiome markers relevant to disease-resilience breeding in aquaculture. CONCLUSION: Host genomic variation in C. semilaevis may be associated with gut microbiome restructuring under M. marinum challenge, particularly involving Acinetobacter dynamics. Although limited by sample size, this dual-omics framework provides a preliminary basis for future disease-resilience breeding in aquaculture.}, }
@article {pmid42105533, year = {2026}, author = {Nizam, A and Shireen, N and Hasan, MR and Singh, S and Farooqui, M and Naithani, D and Farooqi, H}, title = {Artificial intelligence, omics, and biomarkers: Redefining lung cancer early detection.}, journal = {Current problems in cancer}, volume = {63}, number = {}, pages = {101312}, doi = {10.1016/j.currproblcancer.2026.101312}, pmid = {42105533}, issn = {1535-6345}, abstract = {Lung cancer, the leading cause of death worldwide, claims millions of lives yearly, largely due to limited early interventions. Currently used lung cancer screening methods are still limited in their reach and accuracy due to invasiveness, radiation exposure, and low sensitivity, especially in early stages, necessitating the need for innovative technologies. This review examines emerging tools for the early detection of lung cancer, utilizing biomarkers in conjunction with omics approaches and AI technology, which could significantly impact its clinical landscape. Tumor cells release specific biological indicators called biomarkers, which can be cellular components, nucleic acid fragments, protein fragments, or metabolites, detected from bodily fluids through non-invasive methods. The integration of biomarkers with omics technologies (such as proteomics and genomics) or multi-omics provides a comprehensive insight into the molecular profiles of various cancer subtypes and stages. Artificial intelligence, including machine learning and deep learning tools, further increases the accuracy and precision of these techniques. However, challenges still persist in its clinical translation, including technical limitations, regulatory hurdles and ethical concerns. Overcoming these limitations requires standardised protocols, interdisciplinary collaborations, and strategies for equitable access to innovative technologies. Novel, cutting-edge technological interventions, such as advanced imaging techniques, sensor technology, nanotechnology, breathomics, and microbiome analysis, have the potential to enhance early lung cancer diagnosis, ultimately improving patient outcomes and reducing the global burden of this disease.}, }
@article {pmid42105545, year = {2026}, author = {Shan, X and Wang, H and Liu, X and Li, P and Zhang, F and Wang, R and Xue, M and Li, F}, title = {Remodeling distinct rhizosphere interactions of plant-microbiome by legacy and alternative PFASs: A multi-omics insight and biphasic role of iron plaque.}, journal = {Journal of hazardous materials}, volume = {512}, number = {}, pages = {142313}, doi = {10.1016/j.jhazmat.2026.142313}, pmid = {42105545}, issn = {1873-3336}, abstract = {Rhizosphere microhabitat as a dominant sink for per(poly)fluoroalkyl substances (PFASs) and hotspot for redox reactions and root iron plaque (IP) forming is largely affected by the interactions between plants and bacteria. However, whether PFOA and its substitute (HFPO-DA) modulated distinct rhizosphere symbiotic patterns and what roles IP played remain unclear. This study integrated plant physiology, metabolism and rhizosphere microbiome to systematically elucidate their differences in remodulating plant-microbiome interactions and IP roles. Results showed that PFOA preferred to accumulate in roots and induced serious oxidative stress, while HFPO-DA was more easily transported to shoots directly affecting photosynthesis. Molecular docking suggested higher proteinic affinity of HFPO-DA, inhibiting superoxide dismutase activity. PFOA and HFPO-DA increased organic acids and sugars in root exudates recruiting differential beneficial bacteria. However, HFPO-DA downregulated the glycerophospholipid metabolism, shaped a more vulnerable and simpler bacterial network. Remarkably, PFASs concentration determined the double-edged roles of IP. At environmental levels, IP promoted glycerophospholipids and small peptides release facilitating azotobacter recruitment and photosynthesis. But under high-dose stress, it induced accelerated pollutant migration especially HFPO-DA, thereby exacerbating phytotoxicity. Partial least squares path modeling revealed that PFOA indirectly influenced plant phenotypes via shaping bacterial community, while HFPO-DA not only modified that but also altered root exudates. This work unveils distinct rhizosphere symbiotic patterns and IP biphasic role remodulated by legacy and alternative PFASs, and provides a reference for their risk assessment and control through nature-based solutions.}, }
@article {pmid42105760, year = {2026}, author = {Fitzpatrick, CR and Allen Smith, R and Hige, J and Law, TF and Russ, D and Ajayi, OE and Eida, AA and Jacob, P and Jowers, M and Kumar, N and Lai, CTU and Anguita-Maeso, M and Peterson, SB and Saha, C and Skelly, T and Zhao, Q and Zhou, W and Grant, SR and Mougous, JD and Jones, CD and Dangl, JL}, title = {Streptomyces enrichment in roots during drought is uncoupled from plant benefit and is driven by host suppression of iron uptake and immunity.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2026.04.027}, pmid = {42105760}, issn = {1097-4172}, abstract = {Drought reshapes the plant root microbiota, yet the mechanistic drivers and consequences of this observation remain unclear. We discovered that suppression of host immunity and iron homeostasis is required for Streptomyces enrichment in roots during drought across diverse soils. Genetic and physiological manipulation of these host pathways confirmed their requirement in modulating Streptomyces root enrichment. Drought-induced suppression of iron uptake was conserved across the ∼160 mya monocot-eudicot divergence. Some Streptomyces strains enhanced plant growth and rescued iron uptake under drought. These benefits were uncoupled from Streptomyces root enrichment. They were instead shaped by intra-Streptomyces antagonism. We propose a two-step model: drought-driven downregulation of host iron and immune pathways enriches Streptomyces, while intra-genus dynamics fine-tune strain-level assembly and functional outcomes. Our data refine the idea that Streptomyces are enriched in roots during drought in response to a plant "cry for help" and consequently contribute to the alleviation of this abiotic stress.}, }
@article {pmid42105814, year = {2026}, author = {Khan, YA and Anas, M and Khan, F and Ali, M and Al-Zharani, M and Nasr, FA and Qamar, W and Rahman, S}, title = {Cannabinoids in autoimmune diseases: mechanistic insights and translational challenges.}, journal = {Biochemical pharmacology}, volume = {}, number = {}, pages = {118032}, doi = {10.1016/j.bcp.2026.118032}, pmid = {42105814}, issn = {1873-2968}, abstract = {Cannabinoids are traditionally recognized for their effect on the nervous system. Emerging evidence suggests that cannabinoids mitigate inflammation driven by Th1/Th17 responses, which are linked to autoimmune diseases. In addition to their symptomatic, and analgesic effects, cannabinoids suppress the immune response by modulating regulatory T-cell activity, reducing microglial activation, and help in maintaining the integrity of the epithelial barrier. These findings suggest that cannabinoids may be involved in immune, and metabolic regulatory pathways. Despite the promising preclinical data, translating these findings into effective treatments for autoimmune disorders has proven challenging. Current human studies have primarily focused on symptomatic relief such as reducing spasticity, managing pain, improving sleep quality, and boosting appetite. However, few trials have included immune profiling, i.e., assessed cytokine panels, performed immune cell phenotyping, tracked relapses, or utilized inflammation-focused imaging endpoints. Consequently, documented benefits are primarily symptomatic, while potential disease-modifying effects are not yet adequately studied. Cannabinoids interact with CB1, CB2, TRP, and PPAR-γ receptor proteins, suggesting that they may offer targeted immune modulation rather than broad immunosuppression, potentially overcoming limitations of conventional therapies. Moreover, new compounds like cannabigerol (CBG), cannabidivarin (CBV), and CB2-selective agonists with minimal psychoactivity offer expanded therapeutic options. However, challenges persist due to variability in formulations, bioavailability issues, regulatory hurdles, and a lack of long-term safety data. Future clinical development will require standardised GMP-grade preparations, robust pharmacokinetic evaluation, and trials that include immune-related endpoints such as T-cell polarisation, inflammasome markers, oxidative stress profiles, microbiome signatures, and longitudinal imaging, to clarify their therapeutic potential in autoimmune diseases.}, }
@article {pmid42105827, year = {2026}, author = {Bottaro, F and Enrico, P and Ratti, G and Brambilla, P and Delvecchio, G}, title = {Gut Microbiome Variability and Brain Alterations in Schizophrenia: A Scoping Review of Structural and Functional MRI Studies.}, journal = {Neuroscience and biobehavioral reviews}, volume = {}, number = {}, pages = {106739}, doi = {10.1016/j.neubiorev.2026.106739}, pmid = {42105827}, issn = {1873-7528}, abstract = {INTRODUCTION: Schizophrenia (SCZ) is increasingly considered a multifactorial disorder involving gut-brain interactions. Current evidence supports gut microbiome alterations in SCZ, along with well-established structural and functional brain abnormalities. However, findings linking gut microbiome variability to neuroimaging alterations in SCZ have not yet been comprehensively integrated.<br><br>METHODS: Following the Joanna Briggs Institute methodology for scoping reviews and the PRISMA-ScR checklist, a literature search was performed in PubMed, Scopus, and Web of Science, selecting structural magnetic resonance imaging (sMRI) and resting-state functional MRI (fMRI) studies examining the associations between gut microbiome variability and brain alterations in first-episode and chronic SCZ.<br><br>RESULTS: Eight studies (one sMRI-only, one fMRI-only, and six combining sMRI and fMRI) met the inclusion criteria. The sMRI studies primarily showed associations between gut microbiome composition and gray matter volume in frontal, temporal, and limbic regions, while the fMRI studies found microbial variations associated with resting-state activity and functional connectivity across cortico-subcortical and large-scale brain networks. Notably, gut microbiome-neuroimaging associations differed between early and chronic stages of the disorder, suggesting stage-dependent gut-brain relationships.<br><br>CONCLUSIONS: Available evidence supports an association between gut microbiome variability and neuroimaging alterations in SCZ, with emerging differences between first-episode and chronic patients. Despite methodological heterogeneity and predominantly cross-sectional designs, these findings highlight the relevance of a multimodal gut-brain framework. Future longitudinal, multimodal studies integrating gut microbiome, neuroimaging, and clinical features may help disentangle biological heterogeneity and improve patient stratification in SCZ.}, }
@article {pmid42105950, year = {2026}, author = {Kuna, A and Killi, K and Mettu, TR}, title = {Quantum-Enabled Approaches to Precision Nutrition: Linking Molecular Interactions with Metabolic Prediction.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {101584}, doi = {10.1016/j.tjnut.2026.101584}, pmid = {42105950}, issn = {1541-6100}, abstract = {Precision nutrition aims to tailor dietary guidance to individual biology, yet current methods struggle to integrate complex molecular and multi-omic data into clinical care. Emerging quantum-driven technologies encompassing quantum computing, quantum chemistry and quantum-enhanced sensors link detailed molecular modelling with real-time metabolic forecasting. Quantum chemical simulations and machine learning model nutrient protein interactions at the atomic level, while quantum algorithms and echo state networks have been applied to create digital metabolic avatars that predict weight and metabolic trajectories from daily diet and activity data. Quantum computing enables rapid integration of genomic, metabolomic and microbiome datasets and supports optimization of personalised diet plans. Advances in computational molecular modelling now allow prediction of molecular structures and properties relevant to food components, and prototype quantum metabolic twins have demonstrated the capacity to forecast weight trends from incomplete real-world data. The clinical implications include proactive dietary interventions, noninvasive nutrient deficiency screening and improved prediction of disease risk from metabolic profiles, all of which can enhance patient outcomes and clinical decision making. This perspective synthesizes recent advances and delineates research directions at the intersection of quantum science, medical diagnostics, metabolism and clinical nutrition, with implications for clinicians, physicians, dietitians and clinical decision support in patient care.}, }
@article {pmid42105976, year = {2026}, author = {Gomes, J and Rodrigues, ES and Carvalhinho-Lopes, PS and Comis-Neto, AA and Pujol Arena, RV and Birmann, PT and Fidelis, EM and Meus, SS and Rodrigues, BG and Alves de Jesus, GF and Ávila, DS and Pesarico, AP and Ribeiro, AM and Rosa, SG and Pinton, S}, title = {Paraprobiotics attenuate oxidative stress, dopaminergic neuron loss, and gut microbiome imbalance in an intranasal MPTP rat model of Parkinson's disease.}, journal = {Neuropharmacology}, volume = {}, number = {}, pages = {111011}, doi = {10.1016/j.neuropharm.2026.111011}, pmid = {42105976}, issn = {1873-7064}, abstract = {Intestinal dysbiosis may contribute to the progression of Parkinson's disease (PD) by promoting inflammation and oxidative stress. Paraprobiotics, defined as non-viable microbial cells, have emerged as a promising therapeutic strategy. This study evaluated the neuroprotective, gastroprotective, and microbiota-modulating effects of a paraprobiotic blend comprising Lactobacillus casei CCT 7859, Bifidobacterium lactis CCT 7858, and Streptococcus thermophilus ATCC 19258 in a murine PD model induced via intranasal administration of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). Seventy female Wistar rats received either intranasal MPTP or saline, followed 24 hours later by 14 days of paraprobiotic treatment (100 mg/kg/day, intragastrically). Fecal and tissue samples were collected for microbiota, oxidative stress, dopaminergic neurodegeneration, and physiological parameter analyses. Antioxidant enzymes (superoxide dismutase and catalase), oxidative damage markers (malondialdehyde, reactive oxygen and nitrogen species), gut microbiota composition, immunohistochemistry for tyrosine hydroxylase, and physiological variables such as body weight, intestinal length, fecal water content, and ash levels were assessed. Paraprobiotic administration enhanced antioxidant defenses, reduced oxidative damage in brain and intestinal tissues, preserved dopaminergic neurons within the nigrostriatal pathway, improved fecal hydration (indicating constipation relief), and decreased fecal mineral content, suggesting improved nutrient absorption. Notably, modulation of gut microbiota, including an increased abundance of beneficial families (Lactobacillaceae and Sutterellaceae) and a reduced abundance of potentially harmful families (Clostridiaceae and Peptostreptococcaceae), may have contributed to oxidative stress attenuation, preservation of gut health, and prevention of dopaminergic neuron loss. Collectively, these findings suggest that paraprobiotics may modulate microbiota composition and oxidative stress in both intestinal and brain tissues, and may attenuate dopaminergic neurodegeneration in an experimental model of PD.}, }
@article {pmid42106160, year = {2026}, author = {Wang, Y and Liu, J and Verbeke, K and Retamal, NG and Akkerman, R and de Vos, P}, title = {Dietary fiber and GLP-1 receptor agonists in obesity management: converging mechanisms, interactions, and strategies for durable weight control.}, journal = {Advances in nutrition (Bethesda, Md.)}, volume = {}, number = {}, pages = {100647}, doi = {10.1016/j.advnut.2026.100647}, pmid = {42106160}, issn = {2156-5376}, abstract = {Glucagon-like peptide-1 receptor agonists (GLP-1RAs) have transformed the management of obesity by producing substantial and durable weight loss. However, gastrointestinal adverse effects, including nausea, vomiting, and constipation, are a common, dose-dependent, and frequent cause of discontinuation. Furthermore, weight regain is typical after drug withdrawal, reflecting the chronic and relapsing nature of obesity. Long-term adherence is essential but often constrained by high cost, injection burden, and patient preference. Moreover, the consequences of chronic GLP-1 receptor activation on gut physiology, microbiota composition, and immune tolerance remain incompletely defined. In parallel, dietary fibers offer a physiological means of engaging the same gut-brain axis through microbial fermentation and the stimulation of endogenous GLP-1. Fibers deliver broad benefits as they strengthen gut barrier function, enrich short chain fatty acid, and recalibrate immunity toward an anti-inflammatory state. Nevertheless, weight loss with fiber alone is typically more modest than with GLP-1RAs and depends on the type, dose, and duration of use. Tolerability can be limited by bloating or gas, particularly if intake is increased too rapidly. This review critically examines the convergence and divergence between GLP-1RAs and dietary fibers. We discuss their mechanistic overlaps in appetite control, metabolism and immune modulation, and highlight potential interactions, such as altered fermentation dynamics during pharmacological slowing of gastric emptying and the potential for GLP-1R desensitization. We explore opportunities for fibers to mitigate GLP-1RA-related adverse effects, support bowel regularity, and stabilize the microbiota during treatment or after discontinuation. A pragmatic framework is raised to place dietary fiber and lifestyle measures as the foundation of care, reserves GLP-1RA therapy for highest-risk individuals, and plans for fiber supplements once pharmacotherapy is reduced. Well-designed trials that combine GLP-1RAs with well-characterized fibers, include microbiome end points, and assess long-term outcomes are needed to optimize efficacy and reduce dependence on costly pharmacotherapy.}, }
@article {pmid42106331, year = {2026}, author = {Davin, ME and Ortís Sunyer, J and Delgado, LF and Tavis, SL and Lowndes, T and Zafar, Z and Caussin, J and Halder, R and Hickl, O and Laczny, CC and Hanslian, E and Koppold, DA and Rajput-Khokhar, A and Steckhan, N and Schade, S and Schneider, J and Mollenhauer, B and Michalsen, A and May, P and Hettich, RL and Wilmes, P}, title = {High-resolution multi-omics enhances prediction and detection of smORF-encoded proteins in the human gut microbiome.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-72762-5}, pmid = {42106331}, issn = {2041-1723}, support = {863664//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; Graduate Research Fellowship Program//National Science Foundation (NSF)/ ; }, abstract = {Small open reading frames (smORFs), which encode proteins under 100 amino acids, represent an underexplored dimension of the human gut microbiome, despite growing evidence of their essential biological roles. Due to small size and poor annotation, smORFs are typically excluded from metagenomic/metaproteomic analyses. Here, we present a high-resolution multi-omic workflow that integrates smORF prediction into metaproteome searches and enables ultra-deep detection of smORF-encoded proteins (SEPs), without experimental size-based enrichment, utilizing state-of-the-art mass spectrometry instrumentation. Applied to human gut microbiomes, this approach resulted in the largest number of detected SEPs to date, allowing identification of over 25,000 SEPs in the metaproteome, alongside the measurements of the larger proteins. Our multi-omics integrative strategy is critical for advancing human metaproteome research. It also provides a generalizable strategy for comprehensive SEP discovery across diverse microbial ecosystems greatly expanding the previously hidden proteomic landscape.}, }
@article {pmid42106335, year = {2026}, author = {Xue, H and Godneva, A and Tang, F and Li, H and Li, Y and Hu, M and Li, R and Su, J and Segal, E and Razzak, I}, title = {Population-scale characterization of the oral microbiome and associations with metabolic health.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-72748-3}, pmid = {42106335}, issn = {2041-1723}, abstract = {The oral microbiome may capture system-specific information about host metabolic health, yet large-scale, multi-system evidence remains scarce. We analyzed 9,431 participants in the Human Phenotype Project (HPP), integrating buccal-swab oral whole metagenome profiles with 44 metabolic measures spanning liver ultrasound, continuous glucose monitoring (CGM), and dual energy X ray absorptiometry (DXA). Here we show that using a microbiome-wide association study (MWAS) framework, we constructed a multilayer map across strains, gene families and pathways, revealing widespread associations: 213 strains, 124,603 gene families and 299 pathways were significantly associated with metabolic measures. Prioritizing the strongest and cross-phenotype signals, we identified multiple oral features with most significant associations to metabolic health. For example, acyl carrier protein (ACP) was associated with lower liver inflammation and reduced adiposity, whereas polyamine biosynthesis and ceramide α oxidation tracked higher glucose variability and adverse liver and adiposity phenotypes. Leveraging these MWAS-derived signals, we trained disease classification models using phenotype-selected oral features, which outperformed full-feature oral models across six metabolic diseases. These association signals were also robust in oral-health sensitivity analyses in HPP, and key BMI and waist-circumference associations directionally replicated at the genus level in an independent cohort (n = 20, 293). Together, these findings provide a population-scale oral-metabolic association map and highlight the potential of oral microbial markers as non-invasive tools for metabolic risk stratification.}, }
@article {pmid42106361, year = {2026}, author = {Sun, Y and Wu, S and Wu, Z and Zhu, W and Gao, H and Xing, J and Zhao, J and Fan, X and Su, X}, title = {Instance-based transfer learning enables cross-cohort early detection of colorectal cancer.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01001-y}, pmid = {42106361}, issn = {2055-5008}, support = {2021YFF0704500//National Key Research and Development Program of China/ ; 20251ZDYF020482//Innovation Yongjiang 2035 Key R&amp;D Programme/ ; }, abstract = {Colorectal cancer (CRC) continues to be a major global public health challenge. Extensive research has underscored the critical role of the gut microbiome for diagnostics of CRC. However, early-stage prediction of CRC, particularly at the precancerous adenomas (ADA) stage, remains challenging due to the instability of microbial features across cohorts. In this study, we conducted a systematic analysis of 2053 gut metagenomes from 14 globally-sampled public cohorts and a newly recruited cohort. Despite substantial regional and cohort-level heterogeneity in microbiome composition, we elucidated that the consistent differences between groups in microbial signatures provide the fundamental basis for CRC detection. These patterns enabled robust performance in both inter-cohort and independent validations using an optimized bioinformatics framework. In contrast, such basis was lacking in ADA-associated microbial markers, limiting the generalizability of early detection models. To address this, we developed an instance-based transfer learning approach, Meta-iTL, which effectively leveraged knowledge from existing datasets to detect CRC risk at the ADA stage in the newly recruited cohort. Thus, Meta-iTL overcomes challenges posed by cohort-specific variability and limited data availability and advances the application of non-invasive approaches for the early screening and prevention of CRC.}, }
@article {pmid42106371, year = {2026}, author = {Shi, X and Hu, Y and Wang, C and Hua, G and Liu, S}, title = {Gut microbiota and their role in male reproductive health.}, journal = {NPJ science of food}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41538-026-00845-0}, pmid = {42106371}, issn = {2396-8370}, support = {No. 2023YFD1300604)//the National Key R&amp;D Program of China/ ; }, abstract = {The gut microbiota, as the "second genome" of the human body, plays a central regulatory role in maintaining host physiological homeostasis; conversely, its dysbiosis can impair male reproductive function via the "gut-testis axis", leading to a series of pathological manifestations such as abnormal semen quality, sexual dysfunction, and reproductive organ damage. Gut microbiota exerts multidirectional effects on host metabolism, immunity, endocrinology, and the neural system, collectively forming a complex regulatory network for male reproduction. Among these, microbiota-derived metabolites such as short-chain fatty acids (SCFAs), serotonin (5-HT), and secondary bile acids, function as systemic signaling molecules that exert direct and indirect effects on the testis through blood circulation and modulation of gut barrier integrity, regulation of systemic inflammation, epigenetic reprogramming, respectively. The potential and limitations of microbiota-targeted intervention strategies, including probiotics, prebiotics, synbiotics, traditional natural herbal extracts, and fecal microbiota transplantation (FMT), are also discussed. Finally, we propose that future interventions should be tailored to individual gut microbiota profiles to achieve precise regulation of male reproductive function. This review aims to provide a new systems biology perspective for understanding the complex etiology of male infertility and to lay a theoretical foundation for the development of innovative microbiome-based diagnostic tools and therapeutic strategies.}, }
@article {pmid42106412, year = {2026}, author = {Guo, L and Holyoak, GR and DeSilva, U}, title = {Insights from healthy mares reveal that mammalian uteri harbor a diverse virome.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-49532-w}, pmid = {42106412}, issn = {2045-2322}, abstract = {The Earth's estimated 10[31] virions, primarily phages, significantly impact microbial ecosystems. Despite their abundance, viromes remain relatively understudied-particularly in domestic animals. While recent studies have described a dynamic commensal microbiome in mammalian uteri, no research has yet characterized the commensal virome in a mammalian uterus. In this study, we report for the first time the presence of a sparse, but diverse native virome in the equine uterus. The resulting virome database consists of 513 non-redundant viral genomes (> 2 kb). Taxonomic annotations revealed the prevalence of taxadominated by the genera Gammaretrovirus, Mamastrovirus, Sapovirus and Rosenblumvirus. Notably, 75% of the assembled genomes represented novel species. Phylogenetic analysis revealed distinct clades suggesting unexplored viral diversity within the uterine environment. Furthermore, bacterial hosts for equine uterine phages were predicted, aligning with previous studies' findings. Most notably, the study identified antibiotic resistance genes within the virome, hinting at potential gene transfer mechanisms between bacteria and viruses. This study establishes the first uterine virome of any mammal, shedding light on a previously unexplored domain. The findings highlight the potential for phage therapy in reproductive infectious diseases and the importance of understanding the maternal gestational environment. Moreover, the study emphasizes the need for further research to expand the uterine virome databases and deepen our understanding of uterine microbiome and its implications for animal and human health.}, }
@article {pmid42106741, year = {2026}, author = {Chopra, S and Madokoro, N and Bal, M and McNagny, KM}, title = {Prenatal training grounds: the developmental origins of chronic immune disease.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-08213-y}, pmid = {42106741}, issn = {1479-5876}, support = {PJT-518208//Institute of Infection and Immunity/ ; PJT-4488212//Institute of Infection and Immunity/ ; MRT-168048/CAPMC/CIHR/Canada ; MRT168044/CAPMC/CIHR/Canada ; Vanier Canada Graduate Scholarships/CAPMC/CIHR/Canada ; }, abstract = {BACKGROUND: Immune cells seed tissues in orchestrated waves beginning in utero. While the impact of prenatal environmental exposures is well-documented in neuroimmunology, the influence of maternal-fetal interactions on systemic immune development and its contribution to lifelong chronic inflammatory disease remains underappreciated.<br><br>MAIN BODY: This narrative review synthesizes recent ontogeny data to demonstrate how diverse prenatal cues, ranging from maternal infection to microbial-derived metabolites, function as a "prenatal training ground" for the developing fetal immune system. These maternal signals interact with specific waves of hematopoiesis to shape long-lived tissue-resident immune cells. In many tissues, these prenatally programmed populations persist into adulthood, acting as lifelong immunological rheostats that dictate the type and intensity of local inflammatory responses. Furthermore, we critically evaluate the translational gaps in the field, highlighting fundamental species-specific differences in developmental timelines that necessitate careful alignment between preclinical animal models and human biology.<br><br>CONCLUSIONS: We propose that many chronic immune conditions are not strictly adult-onset in their etiology, but rather adult-manifesting, making prenatal immune seeding a critical, yet overlooked, determinant of long-term health. Current interventions largely focus postnatally, but reorienting research and clinical focus toward prenatal factors provides new insights into the developmental origins of chronic inflammation and offers a novel therapeutic window to optimize the health trajectory of the next generation.}, }
@article {pmid42106848, year = {2026}, author = {Knapp, DG and Nagy, A and Badalzadehe, E and Molnár, A and Kroon, J and Romeralo, C and Diez, JJ and Witzell, J}, title = {Microbiome legacy influences necrosis formation in Diplodia sapinea-infected Scots pine shoots.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00904-9}, pmid = {42106848}, issn = {2524-6372}, abstract = {BACKGROUND: Fungal endophytes are important members of the holobiont of all plants, including that of Scots pine (Pinus sylvestris), potentially affecting host performance. One of the most important pathogens of Scots pine in Europe is Diplodia sapinea, which causes necrotic lesions and is becoming increasingly prevalent in northern regions. Although endophytes are known to affect plant performance, it remains unclear whether naturally established fungal communities in Scots pine shoots can modulate D. sapinea-induced necrosis. Using a field experiment, we tested the hypothesis that exclusion of airborne fungal inoculum shapes the endophytic community in shoots of pine seedlings, and that such alterations in this community influence the necrosis-inducing capacity of D. sapinea.<br><br>RESULTS: In the field site, airborne fungal inoculum was reduced in half of the saplings by covering shoots with mesh bags. Covered (bagged) and free (unbagged) shoots were transported to the laboratory and inoculated with D. sapinea. The morphology and physiological status of the shoots were monitored using a multispectral 3D scanner, and the necrotic lesion development was assessed. The propagule exclusion resulted in endophytic communities with slightly lower richness, while shoots showed no detectable morphological or physiological differences prior to inoculation. Shoots inoculated with D. sapinea developed clear necrotic lesions, which were significantly larger in covered shoots than in the free ones. Long-read Oxford Nanopore metabarcoding revealed that community shifts following inoculation were more pronounced in covered shoots. Community composition clearly separated necrotic and healthy tissues.<br><br>CONCLUSIONS: Our findings suggest that the structure of the resident fungal endophytic community may influence the extent of necrotic lesions caused by D. sapinea in Scots pine shoots. A more established, diverse fungal community was associated with smaller lesion sizes, whereas shoots exposed to lower propagule pressure developed larger lesions following inoculation. These results highlight the functional role of fungal community assembly in shaping disease outcomes and suggest that endophyte-based approaches may provide new opportunities for improving disease resistance in forest tree species. The results also suggest that endophytic status may need to be considered when lesion size is used to evaluate resistance to pathogens in tree breeding programs.}, }
@article {pmid42106858, year = {2026}, author = {Turnlund, AC and O'Brien, PA and Rix, L and Ferguson, S and Webster, NS and Diaz-Pulido, G and Wahab, MA and Lurgi, M and Vanwonterghem, I}, title = {Insights into the role of crustose coralline algae microbiomes on coral larval settlement in the Great Barrier Reef.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00907-6}, pmid = {42106858}, issn = {2524-6372}, abstract = {BACKGROUND: Crustose coralline algae (CCA) enhance coral recruitment, but the response of coral larval settlement to CCA varies between CCA species. Furthermore, it is unclear whether coral larvae respond to settlement cues from the algal host itself or its associated microorganisms. To determine whether CCA-derived settlement cues have a microbial origin, we interrogated the microbiome of 14 coralline algal species and a calcareous non-coralline alga eliciting varying levels of settlement across 14 coral species from a wide diversity of families found in the Great Barrier Reef.<br><br>RESULTS: Linear regression, differential abundance, indicator species, and random forest analyses were used to identify microbial taxa associated with high or low coral settlement. We found that the relative abundance of specific microbial amplicon sequence variants (ASVs) correlated with settlement and that these responses were largely coral species-specific. A select few microbial taxa associated with high or low settlement were shared across the corals Dipsastrea favus, Echinophyllia aspera, Lobophyllia corymbosa, Mycedium elephantotus, and Platygrya sinensis, suggesting potential shared settlement or inhibition cues. While shared ASVs associated with high coral settlement were found across multiple CCA species, low settlement ASVs were confined to few low settlement CCA species. Candidatus Nitrosopumilus and Filomicrobium microbes were found as potential shared microbial inducers, and members of Pirellulaceae and Flavobacteriaceae were identified as potential settlement inhibitors.<br><br>CONCLUSIONS: These findings contribute to our growing knowledge of potential coral larval settlement cues and provide deeper insights into the link between the CCA microbiomes and coral recruitment.}, }
@article {pmid42107197, year = {2026}, author = {Soleimani, RA and Abdoli, A and Milani, PG and Khani, N and Homayouni-Rad, A}, title = {Antiviral activity of postbiotics from Bifidobacterium animalis subsp. lactis BB-12 and Lacticaseibacillus rhamnosus GG against SARS-CoV-2: In-vitro and food model evaluation.}, journal = {Enzyme and microbial technology}, volume = {199}, number = {}, pages = {110899}, doi = {10.1016/j.enzmictec.2026.110899}, pmid = {42107197}, issn = {1879-0909}, abstract = {The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has presented ongoing global health, economic, and societal challenges. In addition to respiratory complications, increasing evidence suggests that disruptions to the gut microbiota may influence disease susceptibility and severity, highlighting the importance of microbiome-based interventions in supporting host immunity. While probiotics have been widely explored for their immunomodulatory and antiviral effects, limitations regarding their stability and safety under certain conditions remain a concern. Postbiotics, defined as non-viable microbial metabolites, secreted factors, and ultrasonicated bacterial lysate components, represent a promising alternative due to their enhanced safety profile, stability, and emerging antiviral properties. This study investigated the antiviral efficacy of postbiotics derived from Lacticaseibacillus rhamnosus GG and Bifidobacterium animalis subsp. lactis BB-12 against SARS-CoV-2 using Vero E6 cells cultures. Furthermore, a novel food-based antiviral model was developed by incorporating postbiotic supernatants and ultrasonicated bacterial lysate at a concentration of 1500 μg/mL into a yogurt matrix. The postbiotic-enriched yogurt achieved a 1.87-2.48 log10 reduction in viral titer against the Wuhan strain of SARS-CoV-2 in vitro. These findings support the potential of postbiotics as functional food ingredients for viral risk reduction and contribute to the advancement of microbiome-derived antiviral strategies.}, }
@article {pmid42107297, year = {2026}, author = {Petrović, M and Bez, C and Janakiev, T and Kruščić, K and Bertani, I and Ćurčić, &#x17d; and Duduk, N and Duduk, B and Venturi, V and Dimkić, I}, title = {Development of bioformulations for sugar beet growth promotion and resilience using tailored microbial consortia.}, journal = {Microbiological research}, volume = {310}, number = {}, pages = {128540}, doi = {10.1016/j.micres.2026.128540}, pmid = {42107297}, issn = {1618-0623}, abstract = {Sugar beet production in Serbia is increasingly threatened by the combined effects of 'Candidatus Phytoplasma solani' and Macrophomina phaseolina, a pathogen pair known to interact synergistically and cause severe root rot. To evaluate whether tailored microbial consortia can improve plant performance and stabilize the microbiome under these pressures, we tested three multi-strain inoculants (Mix1, Mix2, and Mix3) in pot and semi-field conditions. In pot experiments, Mix2 enhanced above-ground biomass, while Mix3 maintained or increased microbial diversity over time. Colonization assays and metabarcoding revealed clear differences in strain persistence, with P. polymyxa C3-36, C. pusillum ED2-6 and several Bacillus spp. establishing most consistently. Phytoplasma infection markedly reduced the native root microbiota of sugar beet, indicating a strong disruption of the natural root-associated microbial community. In response, Skermanella and Blastococcus were enriched in root tissues, while Mix3 treatment notably altered the root microbial profile by enriching oligotrophic and soil-stable taxa such as 'Candidatus Udaeobacter', 'Candidatus Solibacter', Gemmatimonas, and Acidobacteria-associated lineages (e.g., RB41, Vicinamibacterales). In the rhizosphere, sugar beet actively recruited Arthrobacter and Blastococcus, whereas bacterial inoculation with Mix3 led to the enrichment of Pseudarthrobacter, Kozakia, and Streptomyces in response to phytoplasma infection. Collectively, these results highlight a stress-responsive and compartment-specific modulation of microbiome assembly driven by both phytoplasma infection and bacterial treatment, although further optimization is required to counteract phytoplasma-M. phaseolina-driven decline.}, }
@article {pmid42107405, year = {2026}, author = {Guo, Y and Zhou, W and Dong, M and Qiu, W and Gao, X and Ahmad, T and Farid, B and Lyu, W and Sun, L}, title = {Root-secreted aminosalicylic acid and 4,6-dioxoheptanoic acid: Dual roles in enhancing 4-nonylphenol bioavailability and regulating rhizospheric microbiota community.}, journal = {Journal of hazardous materials}, volume = {512}, number = {}, pages = {142282}, doi = {10.1016/j.jhazmat.2026.142282}, pmid = {42107405}, issn = {1873-3336}, abstract = {Root exudates and rhizospheric microorganisms are key drivers of organic pollutant degradation in soil. However, the mechanisms underlying their coordinated effects are not yet fully understood. This paper analyzes the changes in the composition of Astragalus sinicus root exudates induced by 4-nonylphenol (4-NP) exposure and investigates the effects of key exudate components on 4-NP sorption-desorption, rhizospheric degradation, and soil microbial community. Metabolomic analysis indicated significant alterations in profile composition induced by 4-NP exposure, with organic acids representing the major responsive category. Specifically, aminosalicylic acid and 4,6-dioxoheptanoic acid-two pivotal organic acids-markedly enhanced 4-NP desorption from soil at a concentration of 50 μmol/L. Their addition reduced the desorption coefficient by 6.4-fold and 3.2-fold, respectively, compared to the control. A pot experiment further validated that application of the two organic acids significantly increased rhizospheric dissipation of 4-NP by 20.0-23.0% compared to soils planted with A. sinicus alone. Metagenomic analysis demonstrated that the key root exudates selectively enriched pollutant-degrading microorganisms (Pseudoxanthomonas sp. A, Cupriavidus, Rhodococcus, and Penicillium), and increased the abundance of functional genes (Cox1, ligB, ligI, and pcaF) and pathways associated with xenobiotic biodegradation. These findings indicate that specific root exudates enhance microbial degradation capacity by improving 4-NP bioavailability, providing a mechanistic basis for the targeted optimization of phytoremediation strategies for 4-NP-contaminated soils.}, }
@article {pmid42107605, year = {2026}, author = {Pinzerato, M and Dieni, C and Giacomini, I and Cocetta, V and Bertin, W and Ghirardello, L and Amadio, E and Perin, S and Frison, C and Brun, P and Agostino, E and Trombetta, D and Smeriglio, A and Montopoli, M}, title = {From phytochemical complexity to biological function: A comparative study of Capparis spinosa fruit extracts.}, journal = {Fitoterapia}, volume = {}, number = {}, pages = {107270}, doi = {10.1016/j.fitote.2026.107270}, pmid = {42107605}, issn = {1873-6971}, abstract = {Capparis spinosa L. is a Mediterranean species traditionally used for the treatment of inflammatory and skin-related disorders and increasingly explored as a source of multifunctional ingredients for dermocosmetic applications. In this study, three commercially available C. spinosa fruit extracts obtained through different extraction strategies (two aqueous extracts, CAP1 and CAP2, and one hydroalcoholic extract, CAP3) were comparatively investigated using an integrated phytochemical and biological approach. Phytochemical profiling by LC-DAD-ESI-MS/MS. revealed a complex composition dominated by flavonol glycosides (mainly quercetin- and kaempferol-based derivatives), phenylpropanoid esters, and glucosinolates, which define the core chemical signature of caper fruits. While the extracts shared a largely overlapping qualitative profile, marked differences in relative metabolite abundance were related to the extraction solvent, the drug-to-extract ratio, and formulation parameters. The biological relevance of the extracts was evaluated using skin-related cellular models and antimicrobial assays. All extracts showed good cytocompatibility in human keratinocytes and preserved epithelial barrier integrity. Distinct, concentration-dependent effects were observed on intracellular ROS modulation, UVB-induced cellular senescence, collagen type I production in dermal fibroblasts, and antimicrobial activity. CAP1 exhibited the most pronounced antioxidant and antimicrobial effects, CAP2 showed intermediate and balanced activity, whereas CAP3 displayed a more complex redox behaviour combined with marked anti-senescent activity. Overall, these findings demonstrate that extraction strategy critically influences the biological performance of C. spinosa fruit extracts and support their potential as multifunctional dermocosmetic ingredients targeting skin homeostasis, photoaging, and the balance of the skin microbiome (including bacterial and fungal components).}, }
@article {pmid42107800, year = {2026}, author = {Wu, R and Ma, Y and Wang, Y and Liang, Q and Gao, L and Hou, L}, title = {Polymer-environment interplay drives microplastic degradation in a surface-flow wetland: New insights into bacterial assembly, network structure, and function across aquatic and sedimentary habitats.}, journal = {Bioresource technology}, volume = {455}, number = {}, pages = {134839}, doi = {10.1016/j.biortech.2026.134839}, pmid = {42107800}, issn = {1873-2976}, abstract = {It remains unclear how polymer types (petroleum- vs. bio-based) and environmental media interact to affect microplastic (MP) biodegradation in wetlands. We conducted a 120-day in situ experiment, incubating five MPs (polylactic acid [PLA], polyurethane [PU], polyethylene terephthalate [PET], polyethylene [PE], and polypropylene [PP]) in a surface-flow wetland. A distinct degradation order was observed: PU (15.2 ± 3.2% in sediment; 12.0% ± 3.9% in water) > PE (11.9% ± 2.9%; 8.2% ± 4.0%) > PLA (4.4% ± 2.2%; 5.0% ± 3.1%) ≈ PET (2.4% ± 1.5%; 7.1% ± 3.5%) ≫ PP (0.0-0.3%), showing faster degradation of most petroleum-based MPs than bio-based PLA. Integrating 16S rRNA sequencing, co-occurrence network analysis, neutral and null model analyses, we demonstrated plastisphere community assembly was governed by deterministic habitat filtering (>85% contribution) over polymer type. Functional specialization diverged between habitats, with aquatic plastispheres being enriched in nitrate reducers and aromatic hydrocarbon degraders (Nitrospira, Methyloversatilis, and Hydrogenophaga), whereas sedimentary ones were dominated by plastic/polysaccharide degraders (Psychrobacter and Microbulbifer). Co-occurrence networks contrasted sharply, being high-modularity/low-connectivity structures in water but low-modularity/high-connectivity ones in sediment. Structural equation modeling identified the plastisphere microbiome as the direct degradation driver. This degradation is enhanced by light irradiation (loadings: 0.888) in water and but is inhibited by the contents of organic matter (-0.738), DGT-labile Fe (-0.876) and S (-0.876) in sediment. These findings underscore the critical interplay between habitat and polymer type in controlling MP fate in wetlands.}, }
@article {pmid42107801, year = {2026}, author = {Walt, HK and Smith, MB and Harris, E and McPeek, S and Meyer, F and Behmer, ST and Hoffmann, FG and Tomberlin, JK and Picard, CJ and Jordan, HR}, title = {Dietary shifts illuminate host-microbiome-diet interplay in black soldier fly larvae.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134821}, doi = {10.1016/j.biortech.2026.134821}, pmid = {42107801}, issn = {1873-2976}, abstract = {Understanding the tripartite interaction between diet, the microbiome, and host physiology is essential for optimizing the bioconversion efficiency of black soldier fly larvae (Hermetia illucens). These interactions were investigated by analyzing life-history traits and metatranscriptomes of larvae fed carbohydrate-rich (1P:5C), protein-rich (5P:1C), and balanced ratio macronutrient (1P:1C) diets. The results showed that dietary macronutrients correlated with shifts in the microbial community and gene expression. In particular, optimal larval performance, characterized by the highest weight and survivorship, was achieved on the balanced ratio diet. While the carbohydrate-rich diet increased microbial alpha diversity and enriched microbial transcripts for carbohydrate metabolism and transport, it significantly delayed pupation, reduced larval weight, and induced host immune genes related to pathogen recognition. Larval guts were predominantly composed of the fungal genus Magnusiomyces, no matter the diet, whereas the frass microbiome was primarily bacterial. In the frass, Klebsiella dominated the carbohydrate-rich diet, while Streptococcus, Lactobacillus, and Klebsiella were the most prevalent taxa in the balanced and protein-rich treatments. Significant correlations were identified between host gene expression and microbial alpha diversity and transcript expression, suggesting host-microbe crosstalk in response to nutritional stress. Ultimately, these findings demonstrate that balanced macronutrient ratios are required to synchronize host-microbiota metabolic synergy and mitigate physiological stress, providing a definitive mechanistic framework for optimizing industrial black soldier fly rearing outcomes.}, }
@article {pmid42107897, year = {2026}, author = {Lu, W and Liu, Y and Hao, H and Li, X and Hou, G and Zhang, J and Li, W and Wang, Q and Huang, Q}, title = {Lacticaseibacillus paracasei 18 effectively ameliorates dextran sodium sulfate-induced colitis in mice through regulating gut microbiota metabolite-mediated PI3K/AKT/NF-κB signaling pathway.}, journal = {International immunopharmacology}, volume = {182}, number = {}, pages = {116807}, doi = {10.1016/j.intimp.2026.116807}, pmid = {42107897}, issn = {1878-1705}, abstract = {Ulcerative colitis (UC) is a persistent inflammatory bowel disorder marked by mucosal inflammation and dysbiosis of the gut microbiome. Lacticaseibacillus paracasei 18 (LP18) is a versatile carbohydrate-degrading bacteria that may work as a probiotic to improve gut health by modulating gut microbiota. However, its exact function and mechanisms in UC remain ambiguous. This research employed integrated microbiome, metabolome, and transcriptome analysis to investigate the therapeutic benefits and underlying mechanisms of Lacticaseibacillus paracasei on dextran sulfate sodium (DSS)-induced colitis in murine models. After the intervention of LP18, colitis mice demonstrated an improvement in body weight loss and a mitigation of colonic shortening, accompanied by a moderate increase of expressions in colonic tight junction-related genes (Claudin-1, Claudin-2, Claudin-5, ZO-1, and Occludin). Additionally, LP18 improved the structure and diversity of the gut microbiota in these DSS-induced mice. Metabolomic study suggested that LP18 substantially influenced the intestinal metabolic profile, particularly compounds associated with tryptophan metabolism. The metabolic alterations were closely linked to the enhancement of the microbial community makeup. The analysis of colon RNA sequencing indicated that, in comparison to the DSS group, LP18 significantly downregulated various immune-related signaling pathways, especially the PI3K/AKT/NF-κB pathways. Correlation analysis of microbiota, metabolism, and genes uncovered a substantial association between the taxa enhanced by LP18 and the critical genes in the NF-κB signaling pathways. Overall, the integrated analysis of multiple omics approaches revealed that LP18 may function as a probiotic therapeutic agent for UC. It represents novel dietary and therapeutic strategies for controlling UC through the regulation of gut microbiota, modification of metabolic profiles, reinforcement of the intestinal barrier, and downregulation of the PI3K/AKT/NF-κB signaling pathway.}, }
@article {pmid42108103, year = {2026}, author = {Funatsu, O and Ishii, H and Shimatsu, R and Shimokawa, Y and Asahina, A and Dekio, I}, title = {Polyamines induce prolonged maintenance of stationary phase turbidity in coagulase-negative Staphylococcus.}, journal = {The Journal of general and applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.2323/jgam.2026.04.002}, pmid = {42108103}, issn = {1349-8037}, abstract = {Microorganisms on the human skin and host form a close and complex community. Abnormal proliferation of certain commensal microorganisms can disrupt this balanced interaction, resulting in the development of skin diseases. Cosmetics is a significant factor affecting the balance of the skin microbiome. We focused a major commensal coagulase-negative Staphylococcus and evaluated the growth effect by five cosmetic ingredients including polyamines. Two polyamines showed notable effects, although others showed no impact effects. They significantly reduced the turbidity during the active growth phase and recovered in the stationary phase. During the death phase, they prolonged the stationary phase turbidity in a concentration-dependent manner, continued by the end of experiments. Our findings could be a previously uncharacterized effect under these experimental conditions.}, }
@article {pmid42108149, year = {2026}, author = {Wang, WT and Lee, CY and Hsieh, YC and Huang, PH and Hsu, PF and Leu, HB and Lu, TM and Wang, YP and Wang, CT and Chiou, SH and Huang, SS and Luo, JC and Hou, MC and Wu, TC}, title = {Distinct gut microbiota signatures and predicted lipid metabolism pathways in Taiwanese patients with acute versus chronic coronary syndromes.}, journal = {Journal of the Formosan Medical Association = Taiwan yi zhi}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jfma.2026.04.127}, pmid = {42108149}, issn = {0929-6646}, abstract = {BACKGROUND: The gut microbiota plays a pivotal role in host lipid metabolism and cardiovascular health. However, comparative profiling of microbial composition and predicted metabolic functions between acute coronary syndrome (ACS) and chronic coronary artery disease (CAD) remains limited, especially in Asian populations.<br><br>METHODS: This study employed a cross-sectional microbiome analysis of prospectively enrolled patients, including 20 ACS and 22 CAD patients whose paired stool and serum samples were collected. Fecal bacterial DNA was analyzed using 16S rRNA gene sequencing. Microbial diversity and taxonomic composition were assessed using QIIME2-based pipelines. Functional predictions were performed via PICRUSt2, Tax4Fun, and BugBase, with KEGG and Clusters of Orthologous Groups (COG) annotations. Correlations with serum lipid parameters were also evaluated.<br><br>RESULTS: Distinct microbial signatures were observed between the ACS and CAD groups. In ACS, Bacteroides plebeius, Tyzzerella, and Sutterella were enriched, whereas Parasutterella and Actinobacteriota were more abundant in CAD. Several taxa were correlated with serum triglyceride, LDL, and HDL levels. Although most lipid metabolism-related pathways were comparable between the groups, nominal differences were noted in linoleic acid metabolism and the biosynthesis of unsaturated fatty acids (p&#xa0;<&#xa0;0.05; all q&#xa0;>&#xa0;0.05). BugBase analysis revealed a significantly greater abundance of potentially pathogenic bacteria in ACS patients (q&#xa0;=&#xa0;0.027). The NSTI scores (mean&#xa0;&#xb1;&#xa0;SD&#xa0;=&#xa0;0.073&#xa0;&#xb1;&#xa0;0.03) supported the reliability of the functional predictions.<br><br>CONCLUSIONS: Patients with ACS and CAD demonstrated distinct gut microbiota profiles, with ACS showing enrichment of pro-inflammatory and potentially pathogenic taxa. Although the predicted lipid metabolic functions are largely similar, subtle pathway differences and phenotypic traits suggest that a potential microbiota-lipid axis is associated with cardiovascular disease severity. These findings warrant further investigation in larger cohorts.}, }
@article {pmid42108153, year = {2026}, author = {Marsh, R and Tricker, JM and Delhaes, L and Bomberger, JM and van der Gast, C}, title = {The gut microbiome: Recent findings and future opportunities in cystic fibrosis.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jcf.2026.05.003}, pmid = {42108153}, issn = {1873-5010}, abstract = {The gut microbiome is a key modulator of human health throughout life, from infancy to old age. Within this relatively young field, microbiome characteristics are being utilized as useful clinical endpoints and indicators of health. Moreover, microbiome-based interventions have been developed to modulate the gut microbiome to ameliorate a range of disorders, including inflammatory bowel disease, obesity, and diabetes. Conversely, there is a paucity of knowledge on the cystic fibrosis (CF) gut microbiome, despite its obvious importance in gastrointestinal (GI) symptoms in this disorder. In this short review we focus on recent findings in CF gut microbiome research and draw upon advances and knowledge from the wider field of gut microbiome research. We recommend increased efforts to improve our understanding of the CF gut microbiome, with knowledge transfer from the field of gut microbiome research being a pragmatic approach to both guiding and providing novel interventions to manage and improve CF GI pathophysiology and associated comorbidities.}, }
@article {pmid42098757, year = {2026}, author = {Jiang, X and Zhang, C and Zhang, Y and Li, J and Ren, J and Wang, J and Hou, X and Zhang, Z and Wu, S and Yao, J}, title = {Multi-omics analysis of soy isoflavone-induced responses in rumen fermentation, endocrine status and milk production in cows with varying milk yields.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42098757}, issn = {1674-9782}, support = {2024-KFKT-011//the National Center of Technology Innovation for Dairy/ ; 32272829//National Natural Science Foundation of China/ ; 2022GD-TSLD-46-0501//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; }, abstract = {BACKGROUND: Improving milk yield and feed efficiency is pivotal for climate-smart dairy systems, as rumen mediated fermentation governs energy and nitrogen utilization and thereby greenhouse-gas emission intensity. Soybean isoflavones (SIF) may modulate rumen fermentation, yet their effects on rumen function, microbiome features, host endocrine/metabolic responses, and lactation performance-particularly across cows with divergent milk-yield phenotypes-remain unclear.<br><br>RESULTS: Fifty&#x2011;six lactating Holstein cows (28 high&#x2011;yield cows, HY; 28 low&#x2011;yield cows, LY) were divided into two categories by milk yield. Within each yield category, cows were randomly assigned to one of two dietary treatments: a basal diet (Control) or the basal diet supplemented with SIF at 0.01% of dry matter. This yielded a 2&#x2009;&#xd7;&#x2009;2 factorial design with four experimental groups (n&#x2009;=&#x2009;14 per group): high&#x2011;yield control (HCON), high&#x2011;yield SIF (HSIF), low&#x2011;yield control (LCON), and low&#x2011;yield SIF (LSIF). SIF increased milk yield by 8.75% and improved fat-corrected milk (+&#x2009;7.20%), dry matter intake (+&#x2009;3.20%), and feed efficiency (+&#x2009;3.26%), with larger gains in HY cows (milk yield&#x2009;+&#x2009;8.89%; feed efficiency&#x2009;+&#x2009;4.55%). Rumen fermentation shifted toward a more energetically favorable profile, with lower acetate (-&#xa0;2.70%), higher propionate (+&#x2009;4.55%), and a reduced acetate-to-propionate ratio (-&#xa0;7.02%), accompanied by increased microbial crude protein (+&#x2009;21.53%) without changes in pH or NH3-N. SIF altered endocrine status irrespective of phenotype, increasing estradiol and progesterone while decreasing prolactin and growth hormone, and reduced blood ALP, lactate, and triglycerides. Metagenomics indicated phenotype-dependent microbial and functional responses to SIF: HY cows showed enrichment of taxa (e.g., Caudoviricetes sp., Eubacterium sp., and Butyrivibrio sp.) associated with amino-acid, cofactor metabolism and propionate pathways, whereas LY cows exhibited enrichment of Prevotella sp. and Bacteroides sp. with functions favoring carbohydrate degradation. The HCON group exhibited greater abundances of Prevotella sp. and Hallella spp. with enhanced carbohydrate degradation functions, whereas the LCON group was enriched in Ruminococcus sp. and Methanobrevibacter sp., associated with methane metabolism.<br><br>CONCLUSIONS: In conclusion, this study highlights the potential of SIF supplementation to improve lactation efficiency, modulate rumen microecology and endocrine function in dairy cows. These findings establish a theoretical framework for achieving efficient and precise feeding management on large-scale dairy farms.}, }
@article {pmid42098796, year = {2026}, author = {Monteleone, E and Cianci, MA and Albano, A and Loperfido, F and Griffante, G and Brasi, L and Borella, F and Gallio, N and Preti, M and Marchi, A and Gardella, B and Molineris, I and Donati, G and Proserpio, V}, title = {Unleashing the potential of mRNA-seq to uncover the microbiome structure and their crosstalk with host cells: the vulvar ecosystem.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42098796}, issn = {2049-2618}, support = {IG 2023 - Id. 28831//Fondazione AIRC per la ricerca sul cancro ETS/ ; MFAG 2023 - ID. 29203//Fondazione AIRC per la ricerca sul cancro ETS/ ; CRT 2023 RF = 106089 / 2023.1841//Fondazione CRT/ ; COD. 2022CLTAYH//Ministero dell'Universit&#xe0; e della Ricerca/ ; 2025.0983//Compagnia di San Paolo/ ; }, mesh = {Humans ; Female ; *Microbiota/genetics ; *Vulva/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; Metagenomics/methods ; *RNA, Messenger/genetics ; Vagina/microbiology ; *Host Microbial Interactions/genetics ; *RNA-Seq/methods ; Transcriptome ; }, abstract = {BACKGROUND: To describe both host gene expression and microbiome composition in a single sample, parallel experimental and computational workflows (mRNA-sequencing and either 16S rRNA gene or metagenomics) have been traditionally applied. The vulvar milieu represents an area of emerging research for its role in health and disease. Located at the interface between the vagina and the perineum, the vulvar microbiome displays an intermediate signature, with influx from both ecosystems.<br><br>RESULTS: Following validation of the reliability of poly(A)-enriched mRNA-sequencing in reconstructing the microbiota composition using both a quantitative microbial standard (mock) and metagenomic analysis, we analyze a full cohort of 30 healthy vulvar samples. Crucially, the analysis of the entire cohort relies solely on mRNA-sequencing without the use of parallel DNA metagenomics. This unified approach allows us to analyze not only the vulvar cell transcriptome, but also the composition and dynamics of microbial communities, including the microbial gene expression signatures. This three-level analysis (host-mRNA, individual bacterial species, bacterial gene pathways) on the very same specimens further enables a gene-level exploration of host-microbe molecular crosstalk. Using this unified framework, we reveal marked heterogeneity and high inter-individual variability in the vulvar microbiota, identifying community state types that mirror those described in the vagina. Importantly, we show that distinct microbial configurations are associated with specific host transcriptional programs: Lactobacillus crispatus correlates with epithelial differentiation and barrier integrity, whereas communities enriched in Gardnerella vaginalis, or other taxa associated with dysbiosis, exhibit transcriptional signatures linked to inflammation. Interestingly, Lactobacillus gasseri, which has been associated with lower protection, shows an intermediate effect on vulvar cells.<br><br>CONCLUSIONS: Beyond providing new biological insights into an understudied anatomical niche, our study introduces a broadly applicable strategy with substantial impact for the field. With tens of thousands of human RNA-seq datasets already available in public repositories, our approach enables retrospective extraction of microbiome information and host-microbe interaction signals from existing transcriptomic data, without the need for additional sequencing or specialized microbiome protocols. This unlocks a powerful and cost-effective opportunity to revisit archived RNA-seq studies across tissues, diseases, and low-biomass environments, revealing previously inaccessible layers of host-microbiome crosstalk and maximizing the scientific value of published data. Video Abstract.}, }
@article {pmid42098798, year = {2026}, author = {Evens, KC and Bakke, I and Bohannan, BJM}, title = {Aquaculture facility-specific microbiota shape the zebrafish gut microbiome.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00573-6}, pmid = {42098798}, issn = {2524-4671}, abstract = {BACKGROUND: Environmental microbiomes, such as those in recirculating aquaculture systems (RAS), can play a key role in shaping host-associated microbial communities. In zebrafish (Danio rerio) research, these interactions can introduce uncontrolled sources of variation, potentially confounding experimental outcomes across multiple facilities. Despite widespread zebrafish use in microbiome studies, few have characterized the microbial composition of both tank water and fish across multiple independent facilities to evaluate the consequences of environmental microbiome variation on the host microbiome.<br><br>RESULTS: We compared water and zebrafish gut microbiomes across five aquaculture facilities two in the United States and three in Norway- using a nested sampling design and 16S rRNA gene sequencing. Alpha diversity was consistently higher in tank water than in fish guts, and beta diversity analyses revealed significant clustering by sample type, facility, and geographic location, with facility identity explaining the largest proportion of compositional variance. Multivariate dispersion also differed significantly across facilities, indicating that observed compositional differences reflect both shifts in community composition and differences in within-facility variability. Each facility harbored a distinct microbial community in both water and fish gut samples, with geographic location further structuring community composition between Oregon and Norwegian facilities. Similarity Percentage analysis identified key taxa driving facility differences, including Cetobacterium, Vibrio, and Aeromonas in fish gut microbiomes and Pseudomonas and Rheinheimera in tank water. Microbial source tracking using FEAST revealed that facility-level tank water contributed measurably to fish gut microbiome composition in most facilities, though unknown sources dominated estimates across all facilities (71-99%) and the strength of fish-water microbiome association varied substantially across facilities.<br><br>CONCLUSIONS: This study demonstrates that zebrafish aquaculture facilities harbor unique microbial communities shaped by both environmental and geographic factors. While tank water microbiomes show associations with zebrafish gut microbiome composition, the dominant contribution of unknown sources to gut microbiome composition suggests that factors beyond the immediate tank water environment- including diet, host physiology, and other facility-specific conditions- are primary drivers of gut microbiome variation. The strength of this association varied considerably across facilities and appeared related to fish domestication history, a pattern that warrants direct experimental investigation. These findings underscore the importance of incorporating environmental microbiome assessments into zebrafish experimental design, particularly for studies focused on host-microbe interactions. Without such consideration, unaccounted variation in environmental microbiota may affect microbiome composition and reduce cross-study reproducibility. Moving forward, standardized reporting of environmental conditions and microbial composition across facilities will be critical for strengthening reproducibility and interpretation in zebrafish microbiome research.}, }
@article {pmid42098855, year = {2026}, author = {Sattayawat, P and Promubon, K and Sripinta, K and Chunguaongsuk, W and Juntama, C and Noirungsee, N and Panya, A and Disayathanoowat, T}, title = {Proof-of-concept engineering of Escherichia coli expressing a bee-derived cytochrome P450 monooxygenase for thiamethoxam detoxification.}, journal = {Journal of biological engineering}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13036-026-00686-1}, pmid = {42098855}, issn = {1754-1611}, abstract = {Bees are unintentionally exposed to pesticides applied to control other insect pests. Although bees possess endogenous detoxification mechanisms, their efficiency may not always be sufficient. To this end, the use of probiotics that can assist in pesticide detoxification may offer an additional layer of protection. In this study, we engineered Escherichia coli BL21(DE3) to heterologously express the bee-derived cytochrome P450 monooxygenase (CYP450), CYP9Q1, from Apis mellifera as a proof-of-concept microbial platform for thiamethoxam biotransformation and future microbiome-assisted pesticide detoxification strategies. We first assessed the toxicity of thiamethoxam, a systemic insecticide, on E. coli, which showed obvious impaired growth at relatively high concentrations (5 and 10 g/L). Subsequently, we computationally modeled the 3D structure and modified the CYP450 to improve its solubility when expressed in E. coli. Molecular docking of the CYP450 and thiamethoxam was also performed to confirm their potential interaction. pRSFDuet-1 plasmid was used to carry the modified CYP450 gene for expression in E. coli and the induction condition was optimized, with 0.5 mM isopropyl 𝛽-D-1-thiogalactopyranoside (IPTG) yielding the most favorable expression level. A whole-cell detoxification assay subsequently showed reduced concentrations of thiamethoxam after 46 h of biocatalytic activity, as monitored by High-Performance Liquid Chromatography (HPLC). Liquid Chromatography-Mass Spectrometry (LC-MS) analysis further revealed the presence of desnitro thiamethoxam corresponding to m/z 247.04105 confirming enzymatic transformation of thiamethoxam. To our knowledge, this study provides the first demonstration of bee CYP9Q1 heterologous expression in E. coli for whole-cell thiamethoxam biotransformation, highlighting its potential as a platform for developing probiotic or gut microbiome-based detoxification strategies to support bee pesticide tolerance.}, }
@article {pmid42098876, year = {2026}, author = {Liu, Z and Guo, Y and Xiao, L and Guo, J and Chen, Y and Wang, H and Nan, X and Zhou, M and Zhang, F and He, Y and Yu, Z and Wang, R and Ren, Z and Wu, J and Wang, M and Tang, X and Xiong, B}, title = {Proanthocyanidins inhibit methane emissions by interacting with methyl-coenzyme M reductase and reshaping rumen microbiome function.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02406-9}, pmid = {42098876}, issn = {2049-2618}, support = {2023YFD2000703//National Key R&amp;D Program of China/ ; 2023YFD2000701//National Key R&amp;D Program of China/ ; 32525054//National Natural Science Foundation of China/ ; CAAS-CSSAE-202402//Innovation Program of Chinese Academy of Agricultural Sciences/ ; 2022YFD1301100//Integrated Demonstration of Scalable and Efficient Healthy Breeding for Cattle and Sheep/ ; }, abstract = {BACKGROUND: Enteric methane (CH4) emissions from ruminants are a major source of agricultural greenhouse gases and represent an energy loss to the host. Methyl-coenzyme M reductase (MCR) is the terminal enzyme in methanogenesis and represents a key target for CH4 mitigation. This study integrated computational screening, in vitro fermentation, and in vivo experiments to identify plant-derived compounds capable of reducing enteric CH4.<br><br>RESULTS: Molecular docking of 3,900 phytochemicals identified proanthocyanidins (PAC) as top candidate, exhibiting strong predicted affinity to the MCR active site (-8.150&#xa0;kcal/mol). In vitro rumen fermentation assays showed that PAC supplementation reduced CH4 production by 22% while increasing dry matter degradability. In lactating dairy cows, dietary PAC supplementation (10 or 20&#xa0;g/kg dry matter) decreased daily CH4 emissions by&#x2009;~&#x2009;8%, and improved ruminal nitrogen utilization without affecting milk yield or ruminal volatile fatty acid production. Amplicon sequencing and metagenomic analyses revealed PAC supplementation shifts in rumen microbial community, characterized by increased relative abundance of Bacteroidota taxa and a decreased relative abundance of methanogenesis-related genes. Functional genes associated with carbohydrate, lipid, and nitrogen turnover were more abundant, indicating potential improvements in nutrient utilization. Consistent with these changes, untargeted metabolomics likewise identified shifts in metabolite profiles that may associated with alternative routes for utilizing reducing equivalents.<br><br>CONCLUSIONS: This study provides integrated computational, microbial, and physiological evidence that PAC supplementation can reduce enteric CH4 emissions in lactating dairy cows, inducing rumen microbial and functional shifts and improving nitrogen utilization. These findings support the potential of PAC as a natural approach to lowering CH4 emissions and advancing sustainable dairy production. Video Abstract.}, }
@article {pmid42098920, year = {2026}, author = {Zhang, H and Ni, T and Zha, X and Elsabagh, M and Wang, M}, title = {The Involvement of Gut Microbiota and Their Key Metabolites in Regulating Fetal Development via the Gut-Placental Axis.}, journal = {Cellular reprogramming}, volume = {}, number = {}, pages = {21524971261450000}, doi = {10.1177/21524971261450000}, pmid = {42098920}, issn = {2152-4998}, abstract = {The gut is the organ with the largest number of microorganisms in the organism, and host-microbe interactions allow the host to shape the composition of the microbiome and thus its numbers and diversity. The gut microbiome is integral to the facilitation of vital host functions that have a direct impact on the overall health of the host. This paper aims to present a thorough overview of the composition and function of the gut microbiome and its main metabolites (such as lipopolysaccharides, short-chain fatty acids, and bile acids), as well as their key roles and mechanisms in fetal development. The theme highlights the significance of the gut microbiome in fetal development, and the paper aims to establish their relationship and importance in a systematic manner. In the latter portion of the article, an analysis is presented regarding the proposed mechanism of the gut-placental axis, with an effort to outline strategies for regulating maternal gut microbiology in order to enhance fetal growth and development. By delving into this subject matter extensively, we aim to enhance comprehension of the correlation between maternal gut microbes and fetal development. This can contribute to safeguarding the mother's health, enhancing the survival and well-being of the fetus, and carrying significance for both human and animal reproduction. Furthermore, it can provide valuable insights for future research and clinical practices.}, }
@article {pmid42099162, year = {2026}, author = {Kurmi, S and Shirodkar, S and Parab, SB and Doshi, G}, title = {A Multimodal Framework for Alzheimer's Prevention: Diet, Exercise, Fasting, Sleep, and Gut Microbiota.}, journal = {Current Alzheimer research}, volume = {}, number = {}, pages = {}, doi = {10.2174/0115672050467997260323164241}, pmid = {42099162}, issn = {1875-5828}, abstract = {Alzheimer's Disease (AD) and related dementias arise from a multifactorial interplay of genetic susceptibility, metabolic dysfunction, neuroinflammation, and lifestyle determinants. With limited disease-modifying pharmacotherapies, lifestyle interventions have emerged as compelling, evidence-based avenues for prevention and early management. This review integrates mechanistic, translational, and clinical insights on major modifiable behaviours, physical activity, diet, intermittent fasting, sleep regulation, and gut-microbiome-based approaches that collectively shape cognitive ageing. Aerobic, anaerobic, and resistance exercises exert neuroprotective effects by activating BDNF-TrkB signalling, enhancing hippocampal neurogenesis, improving synaptic plasticity, and stimulating peripheral myokines (CTSB, IGF-1, GPLD1) that cross the blood-brain barrier to support neuronal resilience. Dietary interventions such as the Mediterranean, Mediterranean- DASH Intervention for Neurodegenerative Delay (MIND), and ketogenic diets mitigate AD pathology by reducing oxidative stress, inhibiting Aβ deposition, improving mitochondrial efficiency, and modulating APOE4-linked metabolic vulnerability. Intermittent fasting induces a metabolic shift toward ketone utilisation, activates autophagy pathways (AMPK, SIRT3, Nrf2), remodels the gut microbiome, and promotes angiogenesis through GDF11 signalling. The gut-brain axis contributes to cognitive health through microbial metabolites, such as Short-Chain Fatty Acids (SCFAs), tryptophan derivatives, modulation of neuroinflammation, and enhanced neuronal survival. Meanwhile, sleep quality, particularly slow-wave sleep, optimises glymphatic clearance and prevents the pathological accumulation of Aβ and tau. Collectively, the evidence suggests that multidomain lifestyle approaches offer synergistic benefits that exceed those of individual interventions, representing promising strategies for delaying cognitive decline. However, gaps remain regarding dose-response relationships, personalised protocols for APOE4 carriers, and long-term validation in diverse populations. Strengthening these research directions is crucial for integrating lifestyle medicine into preventive neurology and public health frameworks.}, }
@article {pmid42099164, year = {2026}, author = {Nayak, RK and Mohapatra, SR and Sahoo, SK and Sahu, SK and Chowdhury, B and Banu, Z and Das, NR}, title = {Gut Microbiota Dysbiosis in Alzheimer's Disease and Possible Therapeutic Options.}, journal = {Current Alzheimer research}, volume = {}, number = {}, pages = {}, doi = {10.2174/0115672050448298260303052535}, pmid = {42099164}, issn = {1875-5828}, abstract = {Human microbiota consists of trillions of microbial cells dominated by bacteria, which live in the human body, while the term microbiome refers to the collective genetic material of microorganisms. Among them, the gut microbiota has emerged as pivotal, producing its own metabolites, neurotransmitter precursors, and immune mediators that affect brain development and function. These signals function via the complex, bidirectional Gut-Brain Axis (GBA). This is a communication network that connects the gastrointestinal tract to the central nervous system. This axis plays an important role in the regulation of gastrointestinal homeostasis, neurodevelopment, emotional regulation, and cognitive processes. Increasing evidence suggests that microbial dysbiosis within the gastrointestinal tract is involved in the pathogenesis and progression of several neurological and neurodegenerative disorders, including mood disorders, schizophrenia, autism spectrum disorder, Alzheimer's Disease (AD), Parkinson's Disease (PD), and Huntington's Disease. These insights have opened new therapeutic possibilities, and multiple microbiota-targeted interventions, such as dietary modification, prebiotics, probiotics, postbiotics, psychobiotics, antibiotics, and Fecal Microbiota Transplantation (FMT), are now being explored for their therapeutic value, especially in Alzheimer's disease.}, }
@article {pmid42099232, year = {2026}, author = {Song, J and Cui, H and Yang, P and Xu, Y and Liu, Y and Zhang, G and Liu, Y and Tian, A and Che, J and Sun, H and Zhang, Z}, title = {Gut microbiota and its metabolites: Key factors of drug resistance in the treatment of advanced prostate cancer (Review).}, journal = {Molecular medicine reports}, volume = {34}, number = {1}, pages = {}, doi = {10.3892/mmr.2026.13900}, pmid = {42099232}, issn = {1791-3004}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; *Prostatic Neoplasms/metabolism/drug therapy/microbiology/pathology/therapy ; *Drug Resistance, Neoplasm ; Antineoplastic Agents/therapeutic use/pharmacology ; Animals ; }, abstract = {Prostate cancer (PCa) is a leading cause of cancer‑related deaths among men, and its incidence is increasing worldwide. Current treatments include androgen deprivation therapy, surgery, radiotherapy, chemotherapy and immunotherapy, among others. Surgical treatment has a less effective therapeutic effect in patients with advanced PCa. However, drug‑based treatments often lead to the development of drug resistance, highlighting the need to adopt new treatment strategies. The present review summarizes the role of gut microbiota and its metabolites in the treatment resistance of advanced PCa, potential microbiome‑targeted therapies and future research directions, for developing novel therapeutic approaches to overcome drug resistance and improve prognosis.}, }
@article {pmid42099457, year = {2026}, author = {Liu, Y and Zhang, Z and Wu, G and Li, B and Wang, L and Wang, J and Wei, Z and Wang, Z and Yang, J and Zhang, K and Zhang, T and Tao, X and Chen, T and Fan, J and Zhou, J and Yang, X and Zhao, L and Wei, Y}, title = {Two stable gut microbiome guilds predict liver tumor class and treatment responses.}, journal = {iMeta}, volume = {5}, number = {2}, pages = {e70123}, pmid = {42099457}, issn = {2770-596X}, abstract = {Gut microbiome alterations are increasingly associated with hepatocellular carcinoma (HCC), highlighting the gut-liver axis as a key contributor to tumor progression and prognosis. Taxon-based HCC microbiome studies have shown limited reproducibility because they are affected by database dependency, taxonomic ambiguity, and overlooked ecological interactions. The Two Competing Guilds (TCG) model, based on stable gut microbiome interactions, provides a structurally grounded framework for robust, generalizable biomarkers. Using shotgun metagenomic data from a newly recruited cohort of 120 surgically resectable HCC cases and 76 benign liver tumor controls, we constructed co-abundance networks to identify stably correlated genome pairs and assembled a hepatic cancer-TCG (HCC-TCG) model composed of 142 genomes. Functionally, one Guild had more genes for butyrate production from carbohydrate fermentation while the other Guild was enriched in genes for virulence factors and antibiotic resistance, highlighting its potential proinflammatory roles. Classifiers trained on the abundance profiles of HCC-TCG genomes successfully distinguished HCC from benign liver tumors (area under the receiver operating characteristic, AUROC = 0.70) and from colorectal liver metastases (CRLM) (AUROC = 0.78). In an external validation cohort, the model further discriminated against HCC from intrahepatic cholangiocarcinoma (iCCA) (AUROC = 0.72), and from healthy controls (AUROC = 0.79-0.85), demonstrating its broad applicability for tumor stratification across clinical contexts. Moreover, HCC-TCG profiles predicted post-resection recurrence risk and response to adjuvant therapies (AUROC up to 0.83). Importantly, external validation in two independent cohorts of advanced HCC patients treated with PD-1/PD-L1 inhibitors demonstrated consistent predictive performance (AUROC = 0.64-0.73), confirming the model's generalizability in nonsurgical and immunotherapy contexts. This genome-specific, ecologically structured, and database-independent framework identifies a conserved Guild-based microbiome signature for HCC. Our findings demonstrate that a fixed genome-resolved ecological structure retains transferable discriminatory signal across clinical contexts. The HCC-TCG framework provides a genome-specific, interaction-based foundation for future development of non-invasive microbiome stratification strategies requiring prospective validation.}, }
@article {pmid42099459, year = {2026}, author = {Bai, D and Fang, O and Li, C and Cai, B and Tan, X and Jiang, M and Gan, B and Fu, J and Gao, Y and Wang, Y and Liu, YX}, title = {Accu16S/AccuITS: Accurate and broadly applicable amplicon sequencing for absolute microbiome quantification.}, journal = {iMeta}, volume = {5}, number = {2}, pages = {e70116}, pmid = {42099459}, issn = {2770-596X}, abstract = {Traditional 16S rRNA gene and Internal Transcribed Spacer region amplicon sequencing provides only relative abundance, often leading to biased ecological interpretations. To overcome this limitation, we developed Accu16S/AccuITS, an absolute quantification method for bacterial and fungal amplicons based on synthetic internal spike-in DNA with known copy numbers. By adding internal standards prior to Polymerase Chain Reaction and sequencing, absolute microbial abundances can be calculated using standard curve regression. Accu16S/AccuITS exhibits sensitivity and consistency comparable to quantitative Polymerase Chain Reaction and is applicable to diverse sample types. A single sequencing run simultaneously yields relative abundance, total absolute abundance, and taxon-specific absolute abundance. Case studies across diverse ecosystems demonstrate that absolute quantification provides ecologically and functionally meaningful insights beyond those obtained from relative abundance analyses.}, }
@article {pmid42099462, year = {2026}, author = {Zhang, C and Du, Y and Wu, M and Li, C and Jiang, R and Qi, E and Li, S and Yi, X and Chu, B and Feng, S and Zhou, H}, title = {Spinal cord injury induces acute microbiome shock and system-wide transcriptomic reprogramming.}, journal = {iMeta}, volume = {5}, number = {2}, pages = {e70128}, pmid = {42099462}, issn = {2770-596X}, abstract = {This study investigates the systemic consequences of spinal cord injury (SCI), with a particular focus on alterations in the gut microbiome and multi-organ transcriptomic responses. We identify a rapid and severe disruption of the gut microbiota-termed "microbiome shock"-that emerges within 12 h post-SCI and persists before gradually resolving by 5 days post-injury. To support further research in this field, we established an open-access resource, the Spinal Cord Injury Gut Microbiome and Multi-Organ Gene Expression Atlas (SCIGAMA).}, }
@article {pmid42099557, year = {2026}, author = {Cui, G and Wang, X and Hong, W and Chen, Z and Kang, Y}, title = {Beyond antibiotics: Multidimensional interventions and coordinated governance against ESKAPE resistance.}, journal = {Biosafety and health}, volume = {8}, number = {2}, pages = {81-85}, pmid = {42099557}, issn = {2590-0536}, abstract = {ESKAPE, including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. pose a significant global health threat due to their extensive drug resistance and rapid evolutionary capacity. This article advocates a paradigm shift from conventional antibiotic warfare to "ecological co-management", integrating four innovative strategies plus an overarching framework: (1) microbiome-based interventions using probiotics, phages, and niche modulation; (2) a One Health 2.0 framework that incorporates wastewater surveillance and artificial intelligence (AI)-driven stewardship; (3) evolutionary constraint methods including anti-virulence agents and clustered regularly interspaced short palindromic repeats (CRISPR)-based targeting; (4) metabolic pathway intervention and antimetabolite therapy such as biotin biosynthesis inhibition; and (5) the establishment of a clinical translation and risk management system for innovative antimicrobial strategies. These multidimensional efforts aim to disrupt resistance transmission, restore antibiotic susceptibility, and promote sustainable pathogen control through ecological and systems-level integration.}, }
@article {pmid42099577, year = {2026}, author = {Penton, CR and Vadakattu, G}, title = {The root rhizosphere as a functional analog to the gut microbiome: Cases for microbial symbiosis and dysbiosis in parallel contexts.}, journal = {PNAS nexus}, volume = {5}, number = {5}, pages = {pgag132}, pmid = {42099577}, issn = {2752-6542}, abstract = {Microbiomes associated with both the human gut and plant root rhizosphere are essential for the maintenance of host health and function as holobionts where both the host and microbiome operate as an integrated unit. Though substantial differences exist in both host biology and environment, these systems share functional parallels: both are enriched by host-derived nutrients, undergo successional shifts during development, and maintain core microbiomes that are taxonomically variable yet functionally redundant. Central to both systems is the balance that is maintained where beneficial microbes regulate nutrient cycling, modulate host immune response, and suppress pathogens in the presence of biotic and abiotic influences that may serve to disrupt this equilibrium. When dysbiosis occurs, there is a disruption in the composition and/or function of the associated microbiome and a loss of beneficial functional guilds, which results in a reduction in host fitness. These shared dynamics underscore dysbiosis as a cross-kingdom pathology that may be treated with similar interventions. Probiotics and prebiotics mirror microbial inoculants and organic amendments; synbiotics incorporate both biotic and abiotic factors, while fecal and soil microbiome transplants represent parallel strategies to restore a beneficial microbiome. By framing dysbiosis within a "One Health" perspective and illustrating the connectedness between human and plant health, this review advocates for microbial stewardship as a unifying strategy to mitigate disease, enhance resilience, and ensure sustainable health across both systems.}, }
@article {pmid42099587, year = {2026}, author = {Xie, X and Chen, X and Wang, Z and Chen, Y and Li, J}, title = {The role of gut microbiota-immune-endocrine crosstalk in the pathogenesis of osteoporosis.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1813653}, pmid = {42099587}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Osteoporosis/immunology/metabolism/microbiology/etiology ; Animals ; Dysbiosis/immunology ; *Endocrine System/immunology/metabolism ; Female ; Bone and Bones/metabolism/immunology ; }, abstract = {Osteoporosis (OP) is a common metabolic bone disorder characterized by decreased bone mass and deterioration of bone microarchitecture that result in increased bone fragility and fracture risk, especially in postmenopausal women and older adults. The gut microbiota-immune-endocrine axis has recently emerged as an important regulator of bone homeostasis, but its mechanistic role in OP pathogenesis remains incompletely understood. This review synthesizes current evidence on how gut dysbiosis, immune dysregulation, and endocrine changes interact to promote bone loss. Clinical and preclinical studies indicate that gut dysbiosis in OP is characterized by reduced microbial diversity and an increased Firmicutes/Bacteroidetes ratio, leading to altered levels of key microbial metabolites-such as decreased short-chain fatty acids (SCFAs) that normally promote bone formation, and increased lipopolysaccharide (LPS) that drives inflammation. Immune changes include chronic low-grade inflammation with elevated pro-inflammatory cytokines [e.g., tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6)] and an imbalanced T-cell profile skewed toward osteoclastogenic T helper 17 (Th17) over anti-osteoclastogenic regulatory T (Treg) cells, which together favor bone resorption. Endocrine factors further modulate this gut-bone crosstalk: estrogen deficiency (in postmenopausal OP) promotes gut dysbiosis and Th17 expansion; excess glucocorticoids compromise the gut barrier and induce dysbiosis; gut-derived incretin hormones [e.g., glucagon-like peptide-1 (GLP-1) and peptide YY (PYY)] are influenced by microbial metabolites like butyrate; and parathyroid hormone (PTH) effects on bone are both regulated by and dependent on the gut microbiota. Overall, OP can be viewed as a multi-system disorder involving an interplay among the gut microbiome, the immune system, and the endocrine system. This integrated perspective on the "gut-bone axis" suggests that interventions targeting the gut microbiota (probiotics, prebiotics, etc.) could complement traditional therapies for OP. Enhancing skeletal health may require a multidisciplinary approach that considers gut microbial status, immune function, and hormonal milieu in tandem.}, }
@article {pmid42099620, year = {2026}, author = {Mo, M and Chen, L and Wang, Y and Lin, X and Li, H and Chen, B and Yuan, J and Tao, E}, title = {The gut-lung axis in childhood asthma: from early-life programming to microbiome-informed precision medicine-a narrative review.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1814901}, pmid = {42099620}, issn = {1664-3224}, mesh = {Humans ; *Asthma/microbiology/immunology/etiology/therapy ; *Gastrointestinal Microbiome/immunology ; Precision Medicine ; *Lung/immunology/microbiology ; Child ; Dysbiosis ; }, abstract = {The gut-lung axis links early-life microbial programming to long-term respiratory health, offering a pivotal framework for understanding childhood asthma pathogenesis. This review synthesizes current evidence on how disruptions in microbial-immune crosstalk during critical developmental windows shape asthma susceptibility. Perinatal determinants-including maternal diet, delivery mode, antibiotic exposure, and breastfeeding-establish gut microbial communities that educate the developing immune system. Distinguishing itself from recent reviews, this review offers three novel contributions: (i) an integrated multi-omics framework linking early-life microbial maturation trajectories to specific asthma endotypes; (ii) a systematic synthesis of the molecular mechanisms by which microbial metabolites-including short-chain fatty acids, tryptophan derivatives, and bile acids-orchestrate gut-lung immune crosstalk; and (iii) a clinically actionable precision medicine algorithm that translates multi-omics profiling into personalized risk prediction, endotype-driven therapy selection, and targeted preventive strategies. Dysbiosis, characterized by delayed microbial maturation and depletion of short-chain fatty acid-producing taxa, compromises epithelial barrier integrity and skews immune homeostasis toward pro-allergic type-2 responses. Microbial metabolites, particularly short-chain fatty acids (acetate, propionate, butyrate) and tryptophan derivatives (indole-3-lactic acid, indole-3-propionic acid), serve as key molecular mediators that regulate regulatory T cells differentiation, reinforce mucosal barriers, and modulate distal airway inflammation. Microbial signatures correlate with specific asthma endotypes, offering opportunities for patient stratification. We critically evaluate emerging microbiome-targeted interventions-including strain-specific probiotics, prebiotics, postbiotics, and fecal microbiota transplantation-highlighting both therapeutic promise and the need for rigorous, well-powered clinical trials. Integrating multi-omics microbial profiling with host genetics and clinical phenotyping holds potential for microbiome-informed precision medicine, enabling personalized risk prediction, endotype-driven therapy selection, and novel preventive strategies targeting the gut-lung axis from the earliest stages of life.}, }
@article {pmid42099642, year = {2026}, author = {Li, J and Chen, H and Zhou, Y and Sun, L and Xing, Y and Sun, Y and Yang, Y and Shi, Y}, title = {Angel or demon? The dual role of branched-chain amino acids in chronic inflammatory and injury-related diseases.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1778455}, pmid = {42099642}, issn = {1664-3224}, mesh = {Humans ; *Amino Acids, Branched-Chain/metabolism ; Animals ; *Inflammation/metabolism ; Mechanistic Target of Rapamycin Complex 1/metabolism ; Signal Transduction ; Diabetes Mellitus, Type 2/metabolism ; Chronic Disease ; }, abstract = {Branched-chain amino acids (BCAAs)-leucine, isoleucine, and valine-are essential nutrients that exhibit context-dependent, paradoxical effects on human health, with mTORC1 (mechanistic target of rapamycin complex 1) signaling serving as a central mechanistic node through which physiological BCAA concentrations support anabolism and repair while chronic pathological elevation drives metabolic and inflammatory injury. While their anabolic properties in promoting muscle protein synthesis, modulating immune responses, and conferring hepatoprotection are well-documented, accumulating evidence demonstrates that chronically elevated circulating BCAA concentrations are strongly associated with the pathogenesis and progression of metabolic, inflammatory, and injury-related diseases, including insulin resistance, type 2 diabetes mellitus (T2DM), cardiovascular disease (CVD), metabolic dysfunction-associated steatotic liver disease (MASLD, formerly NAFLD), and certain malignancies. This biological duality is mechanistically rooted in a network of interconnected pathological processes, in which BCAA-mediated modulation of mTORC1 signaling-already introduced above-represents one central hub operating alongside impaired catabolic flux, accumulation of branched-chain α-keto acids (BCKAs) and branched-chain acylcarnitines, mitochondrial redox imbalance, and cellular stress pathway activation. Physiological BCAA concentrations support anabolic processes and cellular repair, whereas chronic pathological elevation is associated with mTORC1 hyperactivation alongside impaired BCKDH-mediated catabolic flux, accumulation of branched-chain α-keto acids (BCKAs) and branched-chain acylcarnitines, mitochondrial redox imbalance, and activation of cellular stress pathways-collectively contributing to disrupted metabolic homeostasis, amplified inflammatory cascades, and mitochondrial dysfunction. The ultimate biological impact of BCAAs is not intrinsic to these amino acids but rather is determined by a complex interplay of factors including: dosage and duration of exposure, individual metabolic status (particularly insulin sensitivity and mitochondrial oxidative capacity), specific disease context, and genetic polymorphisms affecting BCAA metabolism alongside gut microbiome composition. This review comprehensively synthesizes current understanding of BCAA biology and advocates for a paradigm shift toward precision nutrition approaches. Evidence supports therapeutic BCAA supplementation in hypercatabolic conditions such as sarcopenia and hepatic cirrhosis, while suggesting potential adverse metabolic consequences in insulin-resistant or obese individuals. Future nutritional and therapeutic strategies should transition from universal dietary recommendations to personalized interventions based on comprehensive metabolic phenotyping and genetic profiling, thereby optimizing BCAA intake for individual health trajectories and providing novel preventive and therapeutic opportunities for chronic disease management.}, }
@article {pmid42099660, year = {2026}, author = {Leal, F and Filho, RM and Inoue, LT and Heidrich, V and Dos Santos, EX and Bastos, DA and Camargo, AA and Jardim, DLF}, title = {Urinary microbiota diversity and composition in patients with advanced renal cell cancer.}, journal = {BJUI compass}, volume = {7}, number = {5}, pages = {e70186}, pmid = {42099660}, issn = {2688-4526}, abstract = {OBJECTIVES: This study aims to investigate the role of urinary microbiota in renal cell carcinoma; we analysed urinary microbiota in kidney cancer patients and explored its potential role as biomarker.<br><br>SUBJECTS AND METHODS: Samples were collected from 49 males (28 patients planned to undergo systemic therapy and 21 healthy volunteers). Two samples were collected from each patient, one prior to treatment and one after 8 to 12&#x2009;weeks of systemic therapy. Microbiota was analysed by 16S rRNA sequencing. Microbiota diversity, taxonomic composition and relative abundance were compared between groups and longitudinal samples.<br><br>RESULTS: Amplicon sequence variant (ASV) richness was higher in renal cancer patients (p&#x2009;=&#x2009;0.042) than controls. Beta diversity also differed between patients and controls by means of Jaccard (p&#x2009;=&#x2009;0.001), Bray-Curtis (p&#x2009;=&#x2009;0.008), and nonweighted UniFrac metrics (p&#x2009;=&#x2009;0.001). Acetobacter, Lacticaseibacillus, Alloscardovia, Brevibacterium and the family Propicionibactericeae had higher relative abundance in cancer patients, while Prevotella, Microbacterium and Sphingomonas were more abundant in controls. Beta diversity differed between pretreatment and posttreatment samples (p&#x2009;=&#x2009;0.008). After systemic treatment, we found an increased relative abundance for Prevotella, Rothia, Bradyrhizobium, Methylobacterium/Methylobrum, Porphiromonas and Fusobacterium and a decreased one for the Burkeholderia-Caballeronia-Paraburkholderia group. Higher ASV richness was predictive of poor prognosis for RCC patients (p&#x2009;=&#x2009;0.043) but not of treatment response.<br><br>CONCLUSIONS: Urinary microbiota in patients with renal cell carcinoma differed from controls. Changes in microbiota composition were observed after systemic treatment. Urinary microbiota should be further investigated as a potential biomarker in renal cell carcinoma.}, }
@article {pmid42099859, year = {2026}, author = {Hwang, I and Seo, M}, title = {Complex food matrices reveal microbiota-nutrient balance interactions that modulate gut microbiome diversity in vitro.}, journal = {Current research in food science}, volume = {12}, number = {}, pages = {101423}, pmid = {42099859}, issn = {2665-9271}, abstract = {Diet-microbiome relationships are often evaluated using isolated nutrients, yet microbes encounter complex food matrices in which nutrient accessibility and baseline microbial community context jointly shape gut fermentation outcomes. This study integrated an in vitro digestion and gut fermentation to examine the nutrient-baseline microbiota interaction to modulate community diversity. Nutrient-defined matrix classes were grouped using free saccharides, free amino acids, and free fatty acids content in food digesta. Two machine learning models-a classification model that predicted nutrient-defined matrix class from genus-level relative abundance changes (0-12 h) and regression models that predicted α-diversity change using nutrient and baseline (0 h) community features-were developed. SHAP-based feature attribution revealed that three nutrient-defined matrix classes exhibited distinct microbial response signatures (Turicibacter/Alistipes/Staphylococcus-centered), suggesting post-digestion nutrient associations with gut microbial restructuring patterns. However, α-diversity shifts within the same nutrient class were bidirectional, and inclusion of baseline microbiota features improved model performance for predicting diversity change from R[2] = 0.34 to R[2] = 0.72, consistent with a role for baseline-nutrient interactions. Fermented food matrices further illustrated that food-associated microbial contexts can modify restructuring trajectories beyond nutrient profiles. Overall, these findings propose that diversity outcomes during fermentation may depend on baseline-conditioned responses to bioaccessible nutrients, highlighting a matrix-specific but context-dependent diet-microbiome effects.}, }
@article {pmid42099956, year = {2026}, author = {Vigneron, M and Halary, S and Crochemore, S and Plaisance, L and Parthuisot, N and Bettarel, Y}, title = {Uncovering leaf and root microbiomes of mangrove trees in French Guiana.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1782119}, pmid = {42099956}, issn = {2813-4338}, abstract = {Microorganisms are now widely acknowledged as essential contributors to the health and resilience of coastal environments. Yet, mangrove ecosystems, despite offering numerous ecological and economic services, remain relatively overlooked in microbial research. In this study, we examined the bacteriome of the rhizosphere and the phyllosphere of two mangrove tree species: Avicennia germinans and Rhizophora mangle. Both species were sampled along the banks of the Sinnamary estuary in French Guiana. Our results revealed notable differences in microbiome composition between the two organs and between the two tree species. On average, only 0.3% of ASVs were shared between the leaves and roots and 2.2% between A. germinans and R. mangle. The taxonomic differences were characterized mainly by the significant presence of Rhodothermia and Bacteroidia in the leaves and Cyanobacteria and Planctomycetia in the roots. Furthermore, our results showed that the root microbiome of both species was only weakly influenced by the surrounding water and sediment, with an average of less than 0.7% of ASVs shared. Finally, our study indicates a strong specificity in the bacterial communities of both the phyllosphere and rhizosphere and also raises questions regarding the near absence of Gammaproteobacteria in both the leaves and roots, which remain to be elucidated.}, }
@article {pmid42099957, year = {2026}, author = {Alali, MA and Shori, AB}, title = {Understanding the human gut microbiome: from composition to disease association.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1717288}, pmid = {42099957}, issn = {2813-4338}, abstract = {The human gut microbiota is critical for regulating host metabolism, immune responses, epithelial integrity, and systemic homeostasis, and disturbance has been linked to metabolic, inflammatory, and immune-mediated illnesses. Despite significant advances in microbiome research, the interpretation of gut microbiota-disease relationships is still limited by an overreliance on taxonomic profiling and observational study designs, which frequently overlook functional, strain-level, and mechanistic aspects of host-microbiota interactions. Growing research suggests that microbial functional capacity, metabolic activity, and ecological features such as resilience and functional redundancy are better markers of gut health than compositional measurements alone. Nonetheless, significant inter-individual variability, methodological heterogeneity, and dependence on fecal-based analysis continue to limit reproducibility and causal inference across studies. This review integrates current evidence on gut microbiota composition, functional features, and important influencing variables, while emphasizing mechanistic linkages between microbial dysbiosis and major human illnesses, filling significant conceptual gaps in modern microbiome research.}, }
@article {pmid42099988, year = {2026}, author = {Minhajuddin, F and Colgan, SP and Cartwright, IM}, title = {Impact of Neutrophils on the Tissue Microenvironment During Intestinal Inflammation.}, journal = {Journal of inflammation research}, volume = {19}, number = {}, pages = {540855}, pmid = {42099988}, issn = {1178-7031}, abstract = {Neutrophils (polymorphonuclear leukocytes, PMN) are abundant innate immune cells that rapidly accumulate at mucosal surfaces during inflammation. While their antimicrobial functions are essential for host defense, sustained PMN activation profoundly alters the tissue microenvironment, driving epithelial barrier disruption, ECM remodeling, metabolic imbalance, and microbiome dysbiosis. In chronic inflammatory diseases such as inflammatory bowel disease (IBD), these processes contribute to persistent tissue injury and therapeutic resistance. In this review, we synthesize evidence from human mucosal biopsies, experimental models of intestinal inflammation, and emerging single-cell, spatial, and metabolic approaches to define how PMN shape the inflamed mucosal microenvironment. We highlight mechanisms governing PMN recruitment, retention, and survival; effector programs including reactive oxygen species production, protease release, and PMN extracellular trap formation; and bidirectional crosstalk with epithelial, stromal, and immune cell compartments. We further discuss how PMN-driven metabolic and microbiome alterations reinforce chronic inflammation and influence responses to biologic therapy. Collectively, these insights reframe PMN as context-dependent regulators of mucosal pathology and repair and identify PMN-centered pathways as promising targets for precision therapies aimed at restoring barrier function and promoting durable inflammatory resolution.}, }
@article {pmid42100045, year = {2026}, author = {Panwar, N and Stewart, JE and Ibarra Caballero, JR and Szczepaniec, A}, title = {Characterizing fungal community shifts associated with Amauromyza karli Hendel (Diptera: Agromyzidae) infestation in quinoa.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1741091}, pmid = {42100045}, issn = {1664-462X}, abstract = {INTRODUCTION: Fungal communities are central elements of phytobiomes, yet their roles in mediating plant-insect interactions remain poorly understood. Here, we addressed this knowledge gap in quinoa, which has recently suffered significant losses due to a stem-boring pest.<br><br>METHODS: We used culture-based isolation from stems and amplicon-based profiling of rhizosphere soils to characterize quinoa-associated fungi across six site-year combinations in Colorado and to relate community patterns to abundance of stem-boring fly Amauromyza karli Hendel (Diptera: Agromyzidae).<br><br>RESULTS: Eighteen stem endophytes dominated by Ascomycota were isolated. Soil sequencing resolved 23 core amplicon sequence variants detected across all site-years; the core was primarily Ascomycota, with Fusarium spp., Alternaria spp., and Plectosphaerella spp. comprising over half of relative abundance of the entire community. Alpha diversity (richness, Shannon, inverse Simpson) differed significantly among site-years, and beta-diversity analyses revealed clustering by site and year. Abundance of adult A. karli was correlated positively with soil fungal richness and Shannon diversity and was also significantly associated with differences in community composition. Indicator and differential-abundance analyses identified taxa linked to low fly abundance (e.g., Cladosporium herbarum, Alternaria spp.) versus high abundance (e.g., Fusarium solani, Microdochium spp.). Fusarium spp., and Alternaria spp. were more prevalent in fields with high larval abundance, whereas antagonistic endophytes such as Gibellulopsis piscis and Heydenia spp. dominated in low-abundance fields.<br><br>DISCUSSION: These results indicated that community composition impacted pest pressure, with pathogenic fungi coinciding with higher fly abundance and entomopathogenic fungi enriched where larval pressure was lower. These findings identify candidate taxa for microbiome-informed integrated pest management and underscore the potential of site-specific practices (e.g., intercrops, organic amendments) to foster fungal communities that enhance quinoa resilience.}, }
@article {pmid42100046, year = {2026}, author = {Li, X and Zhao, D and Zhao, J and Li, C and Deng, W and Gao, S and Chen, G and Hu, H}, title = {Response of Morus alba L. to cadmium stress with potential for restoration: physiological and microbiological perspectives.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1795556}, pmid = {42100046}, issn = {1664-462X}, abstract = {Cadmium (Cd) contamination threatens plant productivity and the stability of soil ecosystems. However, the mechanisms by which woody plants tolerate Cd stress remain incompletely understood. In this study, one-year-old Morus alba L. saplings were exposed to a gradient of Cd concentrations to investigate plant physiological responses, metal allocation patterns, cellular ultrastructure, and rhizosphere microbial communities. Increasing Cd concentrations progressively reduced plant growth, nutrient status, pigment content, and photosynthetic performance, while oxidative stress and membrane damage increased. In contrast, low Cd exposure induced a mild hormetic response, characterized by enhanced antioxidant activity, osmotic regulation, and a temporary increase in photosynthetic capacity. Bioaccumulation indices together with ultrastructural observations revealed a dose-dependent change in Cd handling. Under lower Cd exposure, Cd was more readily translocated to shoots, whereas higher Cd levels promoted root sequestration and intracellular compartmentalization. Despite Cd treatment, rhizosphere bacterial α-diversity remained relatively stable, although several Cd-tolerant taxa increased in relative abundance. Overall, these results demonstrate the tolerance capacity of M. alba to Cd stress and highlight its potential for the phytoremediation of mildly to moderately Cd-contaminated soils.}, }
@article {pmid42100057, year = {2026}, author = {Gimignani, G and Borello, A and Panetta, C and Lucchetti, L and Caorsi, R and Gattorno, M and Conforti, A}, title = {Age-Related Microbiota Signatures in Inflammatory Diseases: Comparative Insights into Paediatric and Adult Crohn's Disease, Ulcerative Colitis, and Spondyloarthritis.}, journal = {Mediterranean journal of rheumatology}, volume = {37}, number = {1}, pages = {146-155}, pmid = {42100057}, issn = {2529-198X}, abstract = {OBJECTIVES: The study investigated the relationship among the human microbiota in the development and progression of inflammatory bowel diseases (IBD), specifically Crohn's Disease (CD) and Ulcerative Colitis (UC), as well as Spondyloarthritis (SpA), comparing paediatric and adult populations.<br><br>METHODS: The research elaborated the distinct characteristics and impacts of CD, UC, and SpA across age groups. It further explored the developmental stages of the paediatric microbiota, identifying factors like delivery method, feeding, and antibiotics as critical influencers. It examined specific dysbiosis patterns in paediatric IBD and SpA associated to disease activity. Subsequently, it addressed the adult microbiota's stability and variations due to diet, lifestyle, and medications, detailing microbial alterations in adult CD, UC, and SpA.<br><br>RESULTS: A comparative analysis underscores age-related differences in microbiota composition, clinical manifestations, and treatment responses, indicating greater yet weaker microbial populations in adults. In paediatric patients, there was a marked decrease in Faecalibacterium prausnitzii and other bacteria responsible for producing short-chain fatty acids. In contrast, adults tended to show a more persistent form of dysbiosis and lower microbiome resilience. These disparities in microbial and metabolic phenotypes were strongly associated with the activity of the disease and the response to the treatment, which suggests the potential of microbiota-based biomarkers to create age-specific diagnostic and therapeutic approaches.<br><br>CONCLUSION: This research found that microbiota play a great role in the inflammatory diseases and they can be of great use in the current treatments as well as serve as a biomarker. The new targeted therapies underscored the necessity of patient specific microbiome studies to enhance diagnostics and therapies of these disorders throughout the lifespan.}, }
@article {pmid42100141, year = {2026}, author = {Doyle, WJ and Schumacher, SM and Gates, MR and Sofaly, N and Angelo, E and Hedelius, H and Johnson, DR and Wells, J and Perlmutter, M and Caradonna, K and Ochoa-Repáraz, J}, title = {Sexual dimorphism in the colonic microbiome and host's transcriptomics profiles of a murine model of multiple sclerosis.}, journal = {Clinical immunology communications}, volume = {9}, number = {}, pages = {102-114}, pmid = {42100141}, issn = {2772-6134}, support = {P20 GM148321/GM/NIGMS NIH HHS/United States ; R15 NS107743/NS/NINDS NIH HHS/United States ; }, abstract = {BACKGROUND: Multiple Sclerosis is a chronic autoimmune disease that attacks the myelin sheath in the central nervous system, with a higher prevalence among female patients. We and others have documented significant changes in microbial taxa in response to the induction of active experimental autoimmune encephalomyelitis (EAE), an MS model.<br><br>OBJECTIVE: To evaluate sex as a biological variable in both the host and colonic microenvironment during active EAE.<br><br>METHODS: We conducted colonic transcriptomics and microbiota analysis of colonic fecal content in male and female EAE C57BL/6 J mice and controls at the time of disease induction, pre-onset, and peak disease.<br><br>RESULTS: Analysis showed significant sex-specific differences in colonic gene expression during EAE. As disease severity increased, the profiles of colon microbiome and transcriptomics became less distinct.<br><br>CONCLUSIONS: Our results suggest early changes in colonic inflammatory pathways, with notable differences between males and females associated with microbiota alterations triggered by disease induction.}, }
@article {pmid42100225, year = {2026}, author = {Tang, Q and Qiu, D and Wen, C and Bu, Z and Huang, Y and Zou, C and Wu, H and Chen, F and Liu, L and Li, Z and Xie, X and Huang, H and Gan, K and Liu, Y}, title = {Effects of dietary rumen-degradable protein on growth performance, nitrogen metabolism, and rumen microbiome in dairy buffalo heifers.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1806578}, pmid = {42100225}, issn = {2297-1769}, abstract = {INTRODUCTION: Buffaloes are globally important dairy animals, but their low feed nitrogen utilization efficiency and excessive dietary rumen-degradable protein (RDP) results in aggravated nitrogen pollution and high breeding costs. Studies on the optimal RDP levels for 7-10-month-old dairy buffalo heifers remain scarce, limiting precise nutritional management.<br><br>MATERIALS AND METHODS: Dairy buffalo heifers (n&#x202f;=&#x202f;36, 7-10-month-old, 193.39&#x202f;&#xb1;&#x202f;4.10&#x202f;kg) were selected, and randomly assigned to six groups (n&#x202f;=&#x202f;6 heifers/group, with one heifer in each replicate; Dietary RDP: 60.85-88.90&#x202f;g/kg). The 73-day trial (15-day adaptation) included measurements of growth performance, nitrogen metabolism, serum indices, rumen parameters, and microbiome (16S rRNA/ITS sequencing).<br><br>RESULTS: (1) No differences in initial/final body weight or dry matter intake were found among the groups (p&#x202f;>&#x202f;0.05). The low-RDP group (LP-1, 67.31&#x202f;g/kg) had the highest average daily gain (0.79&#x202f;kg/d) and lowest feed-to-gain ratio (7.88) (p&#x202f;<&#x202f;0.05). (2) With a decrease in dietary RDP levels, intake nitrogen (IN), urinary nitrogen (UN), digested nitrogen, and UN /IN efficiency decreased (p&#x202f;<&#x202f;0.05). The low-RDP group (LP-1) had the highest retention nitrogen/IN efficiency (32.31%) (p&#x202f;<&#x202f;0.05). (3) The serum total protein and urea levels decreased with decreasing dietary RDP levels (lowest in LP-2: 64.52&#x202f;g/L and 5.15&#x202f;mmol/L, p&#x202f;<&#x202f;0.05), with no differences in liver or kidney function or glucose-lipid metabolism (p&#x202f;>&#x202f;0.05). (4) LP-1 had the highest rumen total volatile fatty acids, acetate, and butyrate levels (p&#x202f;<&#x202f;0.05), while rumen pH and NH3-N decreased with RDP (p&#x202f;<&#x202f;0.05). (5) Dietary RDP levels significantly altered the rumen microbial structure. Pichia in LP-1 was 28.81-fold and 39.68-fold higher than in HP-1 and MP-1 groups, respectively (p&#x202f;<&#x202f;0.05), along with the presence of group-specific taxa.<br><br>DISCUSSION: An optimal dietary RDP level for 7-10-month-old dairy buffalo heifers was 67.31&#x202f;g/kg, which improved the ADG and nitrogen utilization efficiency without compromising health, while also altering the rumen microbial structure. Therefore, when formulating diets for buffaloes, it is advisable to consider to note only meet the DCP requirements but also appropriately regulate the dietary RDP levels.}, }
@article {pmid42100351, year = {2026}, author = {Hu, Y and Yan, X and Gao, F and Xu, D and Yang, Y and Cheng, J and Chen, S and Cui, Z}, title = {Probiotic-driven microbiome remodeling is associated with coordinated immune and metabolic responses, improving growth and disease resistance in farmed tongue sole (Cynoglossus semilaevis).}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100600}, pmid = {42100351}, issn = {2666-5174}, abstract = {In flatfish aquaculture, labour-intensive tank cleaning represents a major operational challenge, limiting sustainability due to its high labour requirements and associated costs. We tested a new semi-closed recirculating aquaculture system (RAS) protocol for Cynoglossus semilaevis (tongue sole), replacing manual cleaning with post-feeding water exchange (80% drained) and probiotic application. Compared with control groups, the probiotic-water exchange protocol significantly improved growth (+0.18%/day) and survival (+7.9%), while shifting the gut microbiota from a Vibrio-dominated configuration to a Photobacterium-dominated one. Metagenomics revealed that Photobacterium damselae became the predominant taxon (86%) in the probiotic group, accompanied by the enrichment of quorum sensing pathways, CAZymes (CEs, AAs), and nutrient metabolism functions. Histological examination showed improvements in the intestinal muscular layer and villi structure. Multi-tissue transcriptomics identified systemic changes in immune and metabolic pathways, including activation of intestinal immune networks (IgA production, NF-κB signaling) and antimicrobial peptide genes. Liver, gill, and skin transcriptomes revealed enhanced DNA repair, cytokine signaling, and barrier pathways. JAK-STAT pathway was also activated, linking microbial metabolite sensing to growth promotion (stat5b, igf2bp3). The probiotic-integrated protocol modifies the gut microbiome by shifting microbial composition through changes in competitive interactions and microbial signaling pathways. It also improves the intestinal wall, overall immunity, and nutrient absorption. These findings provide insights into the microbiome-host interaction under probiotic treatment and suggest that this strategy may offer potential benefits under farm conditions, but further studies are needed to validate its safety and ecological implications.}, }
@article {pmid42100398, year = {2026}, author = {Akintola, A and Dareng, EO and Adebamowo, SN and ,  and Adebamowo, CA}, title = {Impact of educational intervention on the uptake of self-sampling for HPV test-based cervical cancer screening.}, journal = {Frontiers in oncology}, volume = {16}, number = {}, pages = {1810950}, pmid = {42100398}, issn = {2234-943X}, abstract = {BACKGROUND: Self-sampling for HPV testing is increasingly adopted for cervical cancer screening globally, including in Sub-Saharan Africa. However, concerns remain regarding women's willingness and ability to collect samples and the effectiveness of educational interventions. Although prior studies in Africa and Nigeria have examined acceptability and barriers, there is limited evidence on whether structured educational interventions can modify women's attitudes toward HPV self-sampling in routine screening contexts. We evaluated the effect of a structured educational intervention on women's attitudes toward self-sampling and, secondarily, explored baseline correlates of willingness to self-sample among Nigerian women.<br><br>METHODS: We conducted a single-group pre-post quasi-experimental study nested within the African Collaborative Center for Microbiome and Genomics (ACCME) prospective cohort study in central Nigeria. A total of 220 eligible women undergoing cervical cancer screening were enrolled. Baseline measurements were obtained prior to the intervention. The standardized educational intervention, delivered by trained research staff, included brochures, leaflets, an instructional video, verbal instructions, and hands-on familiarization with the Evalyn[&#xae;] self-sampling brush. Participants subsequently performed self-sampling privately at participating screening facilities. Post-intervention measurements were collected immediately after the educational session and procedure. Samples were analyzed using DEIA/LIPA HPV assays.<br><br>RESULTS: Most participants were married (63.2%), belonged to the middle socioeconomic group (69.5%), had prior knowledge of cervical cancer (61.8%), and had never undergone screening (89.5%). At baseline, 91.8% were willing to self-sample. The intervention significantly improved mean attitude scores from 42.6 (SD 8.3) to 50.8 (SD 9.8) (p<0.001). Among women unwilling to self-sample, 50.0% (9/18) were in the lower SES group compared with 12.9% (26/202) among willing participants (p<0.001). In exploratory analyses, younger age (OR 0.95, 95% CI 0.90-1.00), cervical cancer knowledge (OR 1.42, 95% CI 1.00-1.99), middle SES (OR 3.69, 95% CI 1.07-12.66), and pre-intervention attitude (OR 0.89, 95% CI 0.81-0.99) were associated with willingness.<br><br>CONCLUSIONS: A structured educational intervention significantly improved attitudes toward HPV self-sampling. Baseline willingness was high, and exploratory analysis indicate that younger age, better knowledge, and middle SES are associated with willingness. These findings support context-specific educational strategies to optimize HPV self-sampling uptake in Nigeria and similar low-resource settings.}, }
@article {pmid42100420, year = {2026}, author = {Zhang, J and Zhi, J and Li, J and Li, L and Zhang, S and Niu, J and Wang, W}, title = {Gut microbiome restructuring in laryngeal squamous cell carcinoma identifies stable microbial biomarkers with diagnostic potential.}, journal = {Frontiers in oncology}, volume = {16}, number = {}, pages = {1788705}, pmid = {42100420}, issn = {2234-943X}, abstract = {BACKGROUND: Alterations in the gut microbiota have been reported in various malignancies, but its role in laryngeal squamous cell carcinoma (LSCC) remains unclear.<br><br>METHODS: This retrospective study included 101 patients undergoing laryngeal surgery (46 benign, 55 malignant). Preoperative fecal samples were collected and subjected to 5R 16S rRNA sequencing. Sequencing data were processed using DADA2 and QIIME2, followed by &#x3b1;/&#x3b2; diversity analysis, differential abundance detection (Wilcoxon test, LEfSe, random forest), and LASSO regression. Functional pathway differences were inferred using PICRUSt2.<br><br>RESULTS: There were no significant differences in &#x3b1; diversity metrics between groups, whereas &#x3b2; diversity analysis revealed significant separation between Benign and LSCC (PERMANOVA, P<0.01). Distinct community composition differences were observed: Malignant cases showed enrichment of genera such as Streptococcus and Lactobacillus, while Benign cases exhibited enrichment of genera including Bacteroides and Lachnospira. Multimethod integration identified 17 core bacterial genera, which were further refined via LASSO regression to select a stable set of genera (e.g., Streptococcus, Eubacterium, Lachnospira) capable of reliably distinguishing benign from malignant cases. The logistic regression model based on stable genera demonstrated excellent diagnostic performance (AUC > 0.8), particularly in distinguishing benign from LateLSCC. Functional prediction revealed pathway imbalances: malignant cases showed enrichment in cell wall and amino acid synthesis pathways, while benign cases favored vitamin and steroid metabolism pathways.<br><br>CONCLUSION: LSCC patients exhibit structural remodeling of their gut microbiota, characterized by distinct taxonomic and functional alterations. Stable microbial signatures holding potential as a foundation for the future development of non-invasive diagnostic and staging biomarkers, though their clinical translation necessitates further large-scale validation.}, }
@article {pmid42100577, year = {2026}, author = {Chen, H and Chen, Y and Liu, Y and Chen, C}, title = {Oral microbiota and urinary system diseases: from mechanistic insights to clinical implications-a comprehensive review.}, journal = {Frontiers in dental medicine}, volume = {7}, number = {}, pages = {1803961}, pmid = {42100577}, issn = {2673-4915}, abstract = {The human oral microbiome has attracted considerable attention due to its role in oral health and potential implications for systemic diseases. Oral microbes provide real-time insights into health and disease status, making them valuable for early disease risk stratification and treatment outcome prediction. Accumulating evidence indicates that oral microbiota contribute to the pathogenesis of urinary system diseases. Notably, in pediatric populations, the oral microbiome-shaped by age, feeding patterns, and immune maturation-may modulate susceptibility to renal-related systemic conditions; clinical observations specifically link untreated early childhood caries to an increased risk of Henoch-Schönlein purpura nephritis (HSPN). This review critically appraises the existing literature to clarify the nature and magnitude of the association between the oral microbiome and urinary system diseases, including chronic kidney disease, urolithiasis, benign prostatic hyperplasia, and urologic cancers, as well as pediatric HSPN. We also analyze the potential mechanisms through which the oral microbiota are involved in the pathogenesis and progression of these relevant diseases, and explore its potential implications for the prevention, diagnosis, and management of urinary system disorders.}, }
@article {pmid42100652, year = {2026}, author = {Luo, J and Feng, Y and Chen, J and Xu, N and Zhang, G and Ni, J and Li, C}, title = {Functional metagenomic reconstruction of microbial pathways altered by probiotic supplementation in liver failure.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1799729}, pmid = {42100652}, issn = {2235-2988}, mesh = {Animals ; *Probiotics/administration &amp; dosage ; Rats, Wistar ; Male ; Metagenomics ; Rats ; Feces/microbiology/chemistry ; Disease Models, Animal ; *Gastrointestinal Microbiome ; *Liver Failure ; Cytokines ; Ammonia/blood ; Dysbiosis ; Galactosamine ; }, abstract = {INTRODUCTION: Liver failure is a severe condition marked by circulatory failure, systemic inflammation, and gut microbial dysbiosis. This dysbiosis worsens liver damage by reducing beneficial metabolites and increasing harmful products. This study investigates the effects of probiotics on gut microbial functional pathways in liver failure. The aim is to link microbial metabolic reprogramming with host biochemical, inflammatory, and gut barrier responses through functional metagenomic reconstruction.<br><br>METHODS: Acute liver failure was induced in male Wistar rats using D-galactosamine (700 mg/kg) and lipopolysaccharide (10 &#x3bc;g/kg). Probiotic treatment began 24 hours after induction and was administered daily for 14 consecutive days before euthanasia. Two doses were used: low (1&#xd7;10&#x2078; CFU/day) and high (1&#xd7;10&#x2079; CFU/day). Fecal samples underwent shotgun metagenomic sequencing, followed by functional pathway reconstruction. These predictions were validated using metabolite profiling, quantitative PCR of microbial genes, intestinal barrier assays, and immune cell cytokine analysis. Host phenotypic markers were correlated with microbial pathways.<br><br>RESULTS AND DISCUSSION: Liver failure significantly elevated serum ALT (42.6&#xb1;6.8 to 512.4&#xb1;48.9 U/L), AST (78.3&#xb1;9.5 to 684.7&#xb1;62.1 U/L), and plasma ammonia (38.9&#xb1;5.2 to 128.6&#xb1;14.3 &#x3bc;mol/L). Probiotic supplementation showed a dose-dependent improvement. ALT dropped to 382.7&#xb1;41.6 U/L (low dose) and 248.9&#xb1;32.4 U/L (high dose). Ammonia levels decreased to 86.4&#xb1;9.7 &#x3bc;mol/L and 59.8&#xb1;7.6 &#x3bc;mol/L, respectively. Metagenomic analysis revealed a 1.7- and 2.6-fold increase in short-chain fatty acid (SCFA) biosynthesis pathways and a 38% and 61% decrease in urease-associated nitrogen metabolism. These changes were confirmed by higher fecal SCFAs (31.8&#xb1;4.2 to 63.9&#xb1;6.4 mM), lower ammonia (8.9&#xb1;1.1 to 3.7&#xb1;0.5 mM), improved intestinal barrier integrity (TEER: 462&#xb1;38 to 721&#xb1;44 &#x3a9;&#xb7;cm&#xb2;), and reduced TNF-&#x3b1; (214.6&#xb1;22.8 to 74.9&#xb1;12.3 pg/mL). Probiotic supplementation significantly reprogrammed the gut microbiome in liver failure. This highlights its potential as a therapeutic modulator of the gut-liver axis.}, }
@article {pmid42100658, year = {2026}, author = {Wu, J and Lu, Y and Zheng, Z and Zheng, J and Fu, Q}, title = {A primary study: high-throughput sequencing analysis of amniotic fluid microbiota in 50 high-risk pregnant women during the second trimester.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1748232}, pmid = {42100658}, issn = {2235-2988}, mesh = {Humans ; Female ; Pregnancy ; *Amniotic Fluid/microbiology ; *Pregnancy Trimester, Second ; High-Throughput Nucleotide Sequencing ; Adult ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Amniocentesis ; *Pregnancy, High-Risk ; Gestational Age ; DNA, Bacterial/genetics ; Maternal Age ; }, abstract = {OBJECTIVE: Whether bacteria exist in the pregnancy uterus without pathological infection has long been a controversial topic. Through this study, we aim to determine whether characteristic amniotic fluid microbiota exists in the uterus of high-risk pregnant women during the second trimester.<br><br>METHODS: This study recruited high-risk pregnant women in the second trimester from September 1, 2024, to August 30, 2025, and recorded their age and gestational age. Amniotic fluid samples were obtained through amniocentesis under strictly sterile conditions, and 16S rRNA high-throughput sequencing was performed on the samples. The inclusion criteria mainly consisted of: advanced maternal age, non-invasive prenatal test results indicating chromosomal abnormalities, abnormal fetal ultrasound findings, history of adverse pregnancy outcomes, and high-risk Down syndrome screening results.<br><br>RESULTS: This study included a total of 50 high-risk pregnant women who underwent amniocentesis. The results showed that bacteria were present in all amniotic fluid samples, primarily composed of Actinobacteriota and Proteobacteria. There was no difference in amniotic fluid microbiota diversity between pregnant women under 35 years old and those 35 years or older; however, the abundances of Cutibacterium and Leifsonia differed between the two groups. A slight difference in microbiota diversity was observed between women with gestational ages below 20 weeks and those at 20 weeks or above, but no significant difference was found in microbial composition between the two groups.<br><br>CONCLUSION: There was bacterial DNA in amniotic fluid of high-risk pregnant women in the second trimester, with Actinobacteriota and Proteobacteria being the predominant phyla, showing limited correlation with maternal age or gestational age. This study provided evidence for the presence of microorganisms in amniotic fluid during pregnancy and might offer some preliminary data for future research related to eugenics and reproductive health.}, }
@article {pmid42100662, year = {2026}, author = {Ding, X and Fan, L and Ma, X and Li, J and Qian, P and Qiu, N and Xu, L and Yue, J}, title = {Alterations of the skin microbiome in HIV infection with pruritus.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1749838}, pmid = {42100662}, issn = {2235-2988}, mesh = {Humans ; *Pruritus/microbiology/etiology ; *HIV Infections/complications/microbiology ; *Skin/microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Adult ; Male ; Female ; Middle Aged ; Interleukin-10/blood ; Bacteria/classification/genetics/isolation &amp; purification ; Cytokines/blood ; Interleukin-6/blood ; DNA, Bacterial/genetics ; Skin Microbiome ; }, abstract = {INTRODUCTION: Pruritus is one of the main common symptoms of human immunodeficiency virus (HIV) infection. Skin changes caused by scratching, or the absence of skin findings despite ongoing pruritus, impact patients' quality of life. With cutaneous HIV infection, pruritus is continuous, though it is unknown whether HIV infection affects the skin microbiota to cause pruritus.<br><br>METHODS: The skin microbiomes and plasma of HIV infection with pruritus, HIV and healthy were investigated in this study. Swabs were taken from four body sites and the composition of the microbiome at those sites was assessed using 16S rRNA amplification. Cytokines(interleukins 10 and 6) in plasma were detected by enzyme-linked immunosorbent assay.<br><br>RESULTS: The skin microbiome in the pruritus group was characterized by a significant depletion of protective commensals, specifically Cutibacterium and the Burkholderia-Caballeronia-Paraburkholderia. Conversely, opportunistic microbiome, including Prevotella and Leptotrichia, were markedly enriched and identified as key microbial signatures by Random Forest analysis. Correlation analysis revealed that the loss of protective commensals was positively associated with anti-inflammatory IL-10 levels, while the expansion of opportunistic pathogens was linked to elevated pro-inflammatory IL-6, indicating a microbial-driven immune imbalance.<br><br>CONCLUSIONS: The results reveal that skin microbiota collapse and the loss of inherent anti-inflammatory defenses are pivotal features of HIV infection with pruritus.}, }
@article {pmid42100688, year = {2026}, author = {Yadav, J and Gehlot, P and Soni, P and Jain, T}, title = {Plant microbiome engineering: from inoculation to genome editing.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1781381}, pmid = {42100688}, issn = {1664-302X}, abstract = {Plant-associated microbiomes are central to crop productivity, nutrient efficiency, and stress resilience, yet conventional microbiome manipulation strategies, largely based on microbial inoculation and agronomic management, often suffer from inconsistent field performance and limited persistence. Although several recent reviews have discussed CRISPR-mediated plant-microbe engineering and synthetic microbial community (SynCom) design separately, few reviews integrate genome editing, ecological stability of microbiomes, and climate-resilient agricultural applications within a unified conceptual framework. Recent advances in molecular biotechnology are transforming this landscape by enabling precision engineering of plant-microbe interactions at genetic, metabolic, and community levels. In particular, synthetic biology tools including CRISPR/Cas genome editing, RNA interference, and synthetic microbial communities (SynComs), now allow targeted modification of plant traits governing microbial recruitment, microbial pathways underpinning nutrient cycling and stress tolerance, and community-level functional complementarity. This review integrates molecular genetics, microbial ecology, and systems-level microbiome design to frame the plant and its microbiome as an engineerable holobiont. We integrate insights from genome editing in plants and microbes, omics-guided SynCom design, climate-resilience mechanisms, and emerging AI-assisted decision frameworks, including machine learning and ecological modeling approaches used to analyze multi-omics datasets, and predict plant-microbiome interactions across experimental and field-based studies. Importantly, we critically assess limitations related to ecological stability, trait trade-offs, biosafety, and regulatory challenges that constrain large-scale deployment. By bridging genome-enabled microbiome manipulation with ecological design principles, this review proposes an integrative framework for climate-smart microbiome engineering and identifies key research priorities required to transition from empirical inoculation toward predictive, sustainable, and socially responsible agricultural biotechnology.}, }
@article {pmid42100690, year = {2026}, author = {Gao, Q and Xiong, M and Zhou, S and Lu, J and Ren, B and Peng, Q and Zeng, M and Song, H}, title = {Gut microbiota and uveitis: exploring novel mechanisms of inflammatory ocular diseases via the gut-eye axis.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1749111}, pmid = {42100690}, issn = {1664-302X}, abstract = {Uveitis is an inflammatory ocular condition that primarily affects young adults and is often associated with systemic and autoimmune disorders. This disease primarily affects intraocular structures such as the iris, ciliary body, and choroid. Clinically, it manifests through a series of symptoms, including eye redness, pain, and blurred vision, which significantly impact the quality of life for patients worldwide. Recently, the role of gut microbiota (GM) in the immune regulation and pathogenesis of inflammatory diseases has garnered significant scientific interest. This study aimed to investigate the potential association between GM and uveitis, with the objective of demonstrating novel mechanisms underlying inflammatory ocular diseases through the emerging concept of the "gut-eye axis." Current research suggests that gut dysbiosis may influence the immune status of distal organs via various pathways, including molecular mimicry, modulation by microbial metabolites, disruption of intestinal immune homeostasis, and compromise of the intestinal mucosal barrier. Building on these mechanisms, we further explored innovative therapeutic strategies targeting GM and its metabolites, including probiotics, prebiotics, antibiotics, immunomodulators, phage therapy, fecal microbiota transplantation, and dietary interventions. This review systematically examined the association between GM dysbiosis and uveitis pathogenesis, offering new insights and directions for future research in this emerging field and establishing a theoretical foundation for developing targeted therapies based on the modulation of the microbiome.}, }
@article {pmid42100694, year = {2026}, author = {Yu, C and Wang, M and Zhao, M and Zhang, S and Cao, M and Liu, Z and Jiang, J and Zhang, Y and Pan, Y and Zhao, X}, title = {Root-associated bacterial community dynamics and assembly mechanisms in healthy and root rot-infected soybeans.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1789440}, pmid = {42100694}, issn = {1664-302X}, abstract = {INTRODUCTION: Soybean root rot, a devastating soil-borne disease, severely limits global soybean yield and quality. Traditional control measures cause environmental pollution and have regional limitations. Root-associated microbiomes are vital for plant health, but most studies use relative abundance sequencing that distorts actual microbial quantities. This study used absolute quantitative high-throughput sequencing to clarify soil chemical properties and bacterial community assembly in healthy and diseased soybeans, laying a theoretical foundation for microbiome-based root rot management.<br><br>METHODS: Samples were collected from bulk soil, and the endosphere, rhizoplane, rhizosphere of healthy and diseased soybeans in black soil fields of Heilongjiang. Soil chemical properties, including pH, soil organic carbon (SOC), total nitrogen (TN), available nitrogen (AN), available phosphorus (AP), and available potassium (AK), were determined. Absolute quantitative sequencing of bacterial 16S rRNA V4-V5 region was performed, combined with qPCR for absolute abundance calibration. Bioinformatics analyses included &#x3b1;/&#x3b2; diversity, co-occurrence network, community assembly (&#x3b2;NTI &amp; RCbray), random forest and correlation analysis to identify key taxa and their relationships with environmental factors.<br><br>RESULTS: Root rot significantly reduced rhizosphere SOC (by 29.13%), TN (8.57%), AN (24.18%), AP (18.86%), while increased AK (12.82%) and pH. However, the contents of certain bacterial taxa at the genus levels showed significant differences in both absolute and relative abundances. The bacterial co-occurrence network indicate that the interaction in the healthy soybean (H) group was more complex than that in the diseased soybean (S) group. Specifically, 1 module hub and 21 connectors were identified in the H group, whereas 55 connectors were detected in the S group. Community assembly in both the H and S groups was governed by deterministic processes, with homogeneous selection primarily observed in the S group. Random forest and correlation heatmap analyses revealed ASV115 (Candidatus Koribacter) in H group was positively correlated with SOC, pH and AN; ASV16 (Streptomyces), ASV42 (Agrobacterium) and ASV46 (Mesorhizobium) were keystones in S group.<br><br>DISCUSSION: Root rot destroyed rhizosphere nutrient balance and reshaped bacterial community structure, reducing network complexity. Absolute quantification effectively compensated for the defects of relative abundance, accurately reflecting community changes. These findings clarify the microecological mechanism of soybean root rot, supporting the development of biocontrol strategies targeting rhizosphere microbiome for sustainable soybean production.}, }
@article {pmid42100703, year = {2026}, author = {Liu, L and Liang, G and Gao, H and Xing, S and Wang, K and Zhou, X and Huang, X and Li, C}, title = {Integrated transcriptome-microbiome analysis reveals a host-microbe interplay associated with insecticide resistance in Aedes albopictus.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1788609}, pmid = {42100703}, issn = {1664-302X}, abstract = {INTRODUCTION: Aedes albopictus is the primary vector of major arboviral diseases such as dengue fever, chikungunya fever, and Zika virus disease, and its control is highly dependent on chemical insecticides. However, the long-term use of pyrethroid insecticides has led to the development of insecticide resistance in Ae. albopictus, which severely undermines the efficacy of vector control programs.<br><br>METHODS: Ae. albopictus populations were collected from five sites in Guangdong and Hainan provinces, China. Beta-cypermethrin resistance levels were determined via bioassays, with resistance ratios at the median lethal concentration (RR50) calculated. Target-site resistance was evaluated via kdr mutation detection in the voltage-gated sodium channel (VGSC) gene. Transcriptome sequencing identified differentially expressed genes (DEGs), and 16S rRNA sequencing characterized gut microbiome alterations. Correlation analysis and Cedecea neteri dietary supplementation assays verified the role of gut microbiota in resistance.<br><br>RESULTS: The results showed that all four populations (except the CP population) exhibited varying degrees of resistance to beta-cypermethrin, with resistance ratios at the median lethal concentration (RR50) ranging from 2.84 to 29.18. Detection of kdr mutations revealed three mutations (F1534C, F1534L, F1534S) at codon 1534 of the voltage-gated sodium channel (VGSC) gene in all field populations, with mutation frequencies ranging from 49.4% to 100.0%, and a low-frequency V1016G mutation at codon 1016. Transcriptome analysis identified a total of 2,566 commonly upregulated genes and 994 commonly downregulated genes across the resistant populations. Gut microbiome analysis revealed a significant alteration in the intestinal microbial community structure of resistant populations; specifically, the relative abundance of the genus Cedecea differed significantly between resistant and susceptible populations and correlated strongly with the expression of most differentially expressed genes. Furthermore, dietary supplementation with Cedecea neteri significantly increased the survival rate of Ae. albopictus exposed to &#x3b2;-cypermethrin (73.86% vs 40.00%; P < 0.0001).<br><br>DISCUSSION: From the perspectives of target-site mutations, gene expression regulation, and gut microbe interactions, this study providing a foundation for further studies on resistance mechanisms in Ae. albopictus, thereby providing a theoretical foundation for further dissection of resistance mechanisms and optimization of vector control strategies.}, }
@article {pmid42098513, year = {2026}, author = {Wang, L and Zhou, J and Wei, W and George, TS and Feng, G}, title = {Deciphering bacterial community composition and function at critical interfaces of plant-arbuscular mycorrhizal fungi-bacterial holobiont.}, journal = {Mycorrhiza}, volume = {36}, number = {3}, pages = {}, pmid = {42098513}, issn = {1432-1890}, support = {32401431//National Natural Science Foundation of China/ ; 32272807//National Natural Science Foundation of China/ ; GZB20230852//Postdoctoral Fellowship Program of CPSF/ ; 2023M743792//China Postdoctoral Science Foundation/ ; 31711530217//National Nature Fund and Royal Society Joint Project/ ; }, mesh = {*Mycorrhizae/physiology ; *Soil Microbiology ; *Bacteria/classification/genetics ; *Microbiota ; Plant Roots/microbiology ; *Zea mays/microbiology ; Phylogeny ; Rhizosphere ; Symbiosis ; }, abstract = {Arbuscular mycorrhizal (AM) fungi connect plant roots and soil bacteria, forming a cross-kingdom holobiont driven by plant-derived carbon flux and soil-derived nutrient flux. This holobiont encompasses not only roots and rhizosphere but also interfaces expanded by slender AM fungal hyphae. Our understanding of the microbiomes across these interconnected interfaces remains limited and fragmented. We used a split-root microcosm to inoculate the same maize root system with three AM fungal species, establishing a simplified holobiont. Amplicon sequencing, Biolog-ECO plates, and [13]CO2 labelling revealed the bacterial diversity and community-level physiological profiles (CLPPs). Bacterial communities colonizing non-mycorrhizal roots, mycorrhizal roots, and hyphae exhibited distinct structures and CLPPs. AM fungal species significantly influenced these bacterial communities, particularly in the mycorrhizosphere and hyphosphere, where notable changes occurred in key nutrient-cycling groups, such as phosphate solubilizers and nitrogen fixers. The diversity of the hyphosphere microbiome was closely aligned with fungal phylogeny. Additionally, a stable core microbiome persisted across all interfaces within the plant-AM fungi-bacterial holobiont, with key taxa such as Pseudomonas and Bacillus harboring the P-mobilizing genes encoding quinoprotein glucose dehydrogenase (gcd) and β-propeller phytase (bpp), highlighting their functional importance in nutrient cycling. Our study provides a comprehensive and precise hyphal-scale characterization of microbial communities across key interfaces, offering detailed insights into plant-microbial dynamics driving nutrient cycling and ecosystem functioning.}, }
@article {pmid42090762, year = {2026}, author = {Barnabei, G and Destri, D and Franco-Benito, M and Cebrian-Aldana, M and Mishra, A and Gil-Guerrero, S and Castilla-Alcantara, JC and Velasco-Arroyo, B and Barros-Garcia, R and Di Mambro, R and Bertelloni, N and Di Gregorio, S}, title = {Region-specific patterns of soil bacterial communities' adaptation to hexachlorocyclohexane contamination.}, journal = {Journal of hazardous materials}, volume = {511}, number = {}, pages = {142224}, doi = {10.1016/j.jhazmat.2026.142224}, pmid = {42090762}, issn = {1873-3336}, abstract = {Hexachlorocyclohexane (HCH) is a persistent organochlorine pollutant whose attenuation at former production sites relies on microbial degradation. The canonical lin pathway, predominantly associated with Sphingomonadaceae, is considered the main aerobic route for HCH transformation, yet its environmental distribution remains limited. We investigated soil bacterial communities and enrichment-derived bacterial consortia from three historically contaminated sites in Germany, Italy, and Spain using HCH depletion assays, 16S rDNA metabarcoding, and functional inference, based on a curated BIOSYSMOdb dataset developed by the BIOSYSMO project. Based on the ASL-level functional inference, the Spanish samples uniquely encoded a complete lin pathway restricted to Sphingobium sp., whereas German and Italian communities harboured respectively partial (LinB-C) or single-step (LinB) modules. Despite these differences, efficient depletion of all HCH isomers occurred across all enrichment cultures. Core-microbiome and differential-abundance analyses identified several non-Sphingomonadaceae taxa, including Stenotrophomonas, Pseudomonas, Achromobacter, Pseudolabrys, and Cupriavidus, which consistently increased during selective enrichment and likely contribute to HCH depletion. Overall, our findings suggest that effective HCH degradation is not restricted to the canonical lin pathway nor to Sphingomonadaceae but it might be mediated also by diverse soil bacteria via alternative lin-independent mechanisms. These results broaden the known ecological and functional landscape of HCH biodegradation and support the exploration of non-Sphingomonadaceae taxa for bioremediation of legacy lindane-contaminated sites.}, }
@article {pmid42090907, year = {2026}, author = {Su, X and Li, A and Liu, J and Guo, Y and Yu, H and Yu, J and Wang, R and Garza, DR and Qu, J and Wen, B and Liu, B}, title = {From microbes to molecules: Gut microbiota as a prerequisite threshold determinant for cancer immunotherapy efficacy.}, journal = {Microbiological research}, volume = {309}, number = {}, pages = {128539}, doi = {10.1016/j.micres.2026.128539}, pmid = {42090907}, issn = {1618-0623}, abstract = {Cancer immunotherapy, represented by immune checkpoint inhibitors, adoptive cell therapy, and cancer vaccines, has revolutionized the clinical management of multiple malignant tumors, yet profound interindividual heterogeneity in treatment response and widespread primary/acquired resistance remain the most critical bottlenecks restricting its long-term clinical benefits. Accumulating preclinical and clinical evidence has unequivocally established the gut microbiota as a pivotal regulator of host anti-tumor immune responses. However, the vast majority of existing studies and reviews frame the gut microbiota as a mere adjuvant enhancer of immunotherapy efficacy, focusing solely on its role in boosting the upper limit of treatment effects, while neglecting its more fundamental role as a prerequisite for establishing a responsive immune baseline. In this review, we propose a unifying, evidence-based original core hypothesis: the gut microbiota is not merely an enhancer of cancer immunotherapy efficacy, but an indispensable prerequisite condition that sets the minimal baseline threshold for therapeutic responsiveness-a central thesis that distinguishes this review from previous descriptive work. Guided by this hypothesis, we systematically dissect the taxonomic and functional characteristics of threshold-determining gut microbiota, and clarify that microbial metabolites (e.g., short-chain fatty acids, bile acids, tryptophan derivatives) act as core molecular mediators translating microbial signals into host immune activation, which is critical for establishing the baseline efficacy threshold required for effective immunotherapy. We further perform a critical synthesis of clinical data from prospective cohorts, randomized controlled trials, and microbiota intervention studies, validating that threshold-based microbial signatures serve as non-invasive predictive biomarkers for immunotherapy outcomes, and propose mechanism-driven translational strategies targeting the gut microbiota (e.g., fecal microbiota transplantation, probiotic supplementation, dietary modulation) to reset the impaired immunotherapy efficacy threshold. This review provides a novel theoretical framework for understanding the microbiota-immunotherapy axis, which not only deepens the mechanistic insight into microbial metabolite-mediated immune regulation, but also facilitates the development of microbiota-guided personalized cancer immunotherapy and the overcoming of primary treatment resistance.}, }
@article {pmid42090982, year = {2026}, author = {Ghanam, AR and Gatermann, S and Juckel, G}, title = {Reduced gut microbiome alpha diversity associates with depressive symptom severity and somatic symptom burden in major depression.}, journal = {Journal of psychiatric research}, volume = {199}, number = {}, pages = {237-242}, doi = {10.1016/j.jpsychires.2026.04.022}, pmid = {42090982}, issn = {1879-1379}, abstract = {OBJECTIVE: Alteration in gut microbiome have been increasingly linked to many psychiatric disorders inclusive depression. However, findings regarding microbiome diversity in depression remain inconsistent. Differences in depression subtypes, particularly the somatic versus affective symptoms profiles may partly explain this heterogeneity in previous results.<br><br>METHODS: This cross-sectional study included 31 Participants diagnosed with major depressive disorder. The participants divided into two groups by severity of depression (BDI-II >34 vs. <34) and severity of somatic symptoms of depression (somatic dimension vs. cognitive-affective dimension of BDI-II). Fecal samples were collected, and 16S rRNA gene sequencing of the V3/V4 region was performed on an Illumina platform to profile the gut microbiome. Amplicon Sequence Variants (ASVs) were used to analyze microbial alpha diversity, including ACE, Chao1 and Shannon.<br><br>RESULTS: Participants with higher depressive severity showed significantly reduced gut microbiome alpha diversity compared to lower depressive state (ACE; p&#xa0;=&#xa0;0.019, Chao1; p&#xa0;=&#xa0;0.019, and Shannon; p&#xa0;=&#xa0;0.053). Across the total sample, BDI-II total score correlated negatively with alpha diversity significantly for ACE (r&#xa0;=&#xa0;-0.435, p&#xa0;=&#xa0;0.015), Chao1 (r&#xa0;=&#xa0;-0.435, p&#xa0;=&#xa0;0.015) and Shannon (r&#xa0;=&#xa0;-0.376, p&#xa0;=&#xa0;0.037). While the somatic dimension of the BDI-II showed significant negative correlation with all tested alpha diversity indices, no significant correlations were detected between gut microbiome alpha diversity and the cognitive-affective dimension. Shannon diversity further correlated negatively with HDRS-17 scores (p&#xa0;=&#xa0;0.033).<br><br>CONCLUSION: In conclusion, the results show that a lower diversity of gut microbiota alpha is linked to more severe depressive symptoms, specifically the somatic aspect of depression. These results emphasize the importance of considering somatic symptom profiles in microbiome research and point to the gut-brain axis as a potential target for future therapeutic interventions.}, }
@article {pmid42091112, year = {2026}, author = {Gao, S and Zhao, W and Jiang, J and Guan, X and Pan, Y and Zhao, Z and Wang, B and Xiao, Y and Zhang, G and Zhao, D and Mi, R and Zhou, Z}, title = {Bottom Grinding Increases the Phototrophic Bacteria While Reduces Bacterial Community Stability in Sea Cucumber Cultural Ponds.}, journal = {Environmental microbiology reports}, volume = {18}, number = {3}, pages = {e70357}, pmid = {42091112}, issn = {1758-2229}, support = {U24A200104//National Natural Science Foundation of China/ ; XLYC2203191//Liaoning Revitalization Talents Program/ ; 2023JH1/10200007//Science and Technology Project of Liaoning Province/ ; 2023RJ007//Dalian Science and Technology Talent Innovation Support Program/ ; 2025HQ1304//undamental Research Funds of Liaoning Academy of Agricultural Sciences/ ; 2025JCX1008//undamental Research Funds of Liaoning Academy of Agricultural Sciences/ ; }, mesh = {*Ponds/microbiology ; Animals ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Microbiota ; *Sea Cucumbers/microbiology/growth &amp; development ; *Aquaculture/methods ; Phototrophic Processes ; Geologic Sediments/microbiology ; Water Microbiology ; }, abstract = {Bottom grinding (BG), which suspends the anaerobic microorganisms deposited at the bottom of the pond through aeration, is a common practice in sea cucumber aquaculture for maintaining water quality. However, little is known about the effects of BG on the environmental microbiome. This study investigated differences in bacterial communities from three niches (surface water, bottom water and sediments) of culture ponds with and without BG operations. Only minor changes in sediment bacterial communities were observed between BG-treated and control ponds. In contrast, the composition of the bacterial communities in the water was also significantly altered by the BG operation, with an increase in Cyanobacteria and a decrease in Proteobacteria. Additionally, functional prediction revealed increased phototrophy and decreased chemoheterotrophy in aquatic bacterial communities following BG treatment. Co-occurrence network analysis revealed that bacterial communities in all three niches were more complex but unstable with BG treatment compared to without, indicating some remedial operations for farming practice. Analysis of community assembly mechanisms showed increased stochastic assembly of bacterial communities in all three niches induced by BG treatment. Overall, this study revealed the effects of BG operation on the bacterial communities in culture ponds, providing insights into the ongoing evolution of farming techniques.}, }
@article {pmid42091350, year = {2026}, author = {Monday, L and Krishna, A and Chopra, T}, title = {Prevention and Control of Clostridioides difficile Infection for the Infectious Diseases Clinician.}, journal = {Infectious disease clinics of North America}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.idc.2026.02.009}, pmid = {42091350}, issn = {1557-9824}, abstract = {This article highlights the challenges of preventing Clostridioides difficile infection (CDI) in health care settings. It emphasizes a multifaceted approach including hand hygiene, contact precautions, environmental cleaning, and antimicrobial stewardship. Diagnostic stewardship, using combined testing algorithms and electronic alerts, helps reduce unnecessary testing and misdiagnosis. Emerging strategies like microbiome restoration, vaccines, and monoclonal antibodies are under active investigation. When CDI rates remain high despite standard measures, additional interventions such as sporicidal disinfectants and no-touch technologies may be necessary. Overall, a comprehensive, adaptive approach is essential to effectively reduce CDI incidence and improve patient outcomes.}, }
@article {pmid42091967, year = {2026}, author = {Vinayagam, S and Bhowmick, IP and Rajendran, D and Arumugam, DK and Sekar, K and Renu, K and Kaur, H and Sattu, K}, title = {Genetic diversity and gut microbiome of Anopheles mosquitoes in Tamil Nadu by using COI DNA barcoding and 16S rRNA metagenomics.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-48529-9}, pmid = {42091967}, issn = {2045-2322}, support = {NER/85/2022-ECD-I//ICMR- Adhoc/ ; }, abstract = {Anopheles mosquitoes transmit infections to humans. Identifying the right mosquito species is crucial for vector control evaluation. This study uses COI gene DNA barcoding and 16S rRNA metagenomics to show the genetic diversity and gut microbial profile of undiscovered mosquito species. Three genera were found, including eight morphologically different Anopheles mosquitoes, and six mosquito species were molecularly validated, including An. moghulensis. The analysis of genetic diversity indicated that there is a state of balanced natural selection present. The species An. maculatus s.s. and An. stephensi exhibited nearly identical mutations, while An. moghulensis demonstrated evidence of purifying selection within the studied population. The gut microbiomes of An. moghulensis (149,377 reads), An. maculatus (51,016 reads), and An. dravidicus (33,126 reads) mosquitoes were also revealed. Afipia felis and Prevotella copri were the leading bacterial species, followed by other phyla including Proteobacteriota, Spirochaetes, and Firmicuteota. In An. moghulensis, alpha diversity assessments of Chao I incidence were dominating, whereas Shannon index was plentiful in An. maculatus s.s. mosquitoes. The mosquito's distinct bacterial species and shared microbial community are shown in the Venn diagram. These results suggest that the discovered bacterial taxa might be exploited to create vector control techniques for vector-borne illnesses.}, }
@article {pmid42092044, year = {2026}, author = {Loukas, A and Kalaentzis, K and Venetsianou, NK and Damianou, C and Paragkamian, S and Lagani, V and Jensen, LJ and Pafilis, E}, title = {CCMRI: a classification and curated database of climate change-related microbiome studies.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-51914-z}, pmid = {42092044}, issn = {2045-2322}, support = {2772//Hellenic Foundation for Research and Innovation/ ; }, abstract = {Climate Change (CC) is reshaping all ecosystem processes and structures. Microbial data provide valuable insights into how microbial processes contribute to CC and how CC, in turn, alters microbial communities. However, the growing volume of environmental genomics data makes identifying CC-related records challenging. The Climate Change Metagenomic Record Index (CCMRI) has been developed to harvest metagenomic/microbiome records pertaining to CC and to provide researchers with a curated database of CC-related microbiome studies (https://ccmri.hcmr.gr). To guide interpretation, the database's 169 metagenomic studies have been labelled according to their relation to CC as CC-caused, CC-causing, and CC-mitigating. They have also been annotated with the CC phenomena they explore, like methane production, temperature rise, permafrost thawing, greenhouse gas emission, methanotrophy, and ocean acidification. To ease navigation, they have also been classified according to their biome as aquatic, terrestrial, host-associated, and engineered. The CCMRI database was initially constructed through manual curation of all aquatic and terrestrial studies in the MGnify resource. It was then expanded with the help of the CCMRI curation-assistant system. This leveraged Large Language Models to scan the remaining MGnify studies, filtered them for relevance, and proposed candidates for inclusion. With a recall greater than 90%, the system achieved high accuracy in identifying CC-related studies. The final decisions on CC-relatedness and categorization were performed by a human curator. This approach combines the efficiency of automation with human oversight and greatly reduces the curation effort, ensuring sustainability and scalability.}, }
@article {pmid42092115, year = {2026}, author = {Xu, W and Yuan, X and Cao, J and Cui, X and Fu, K and Wang, G and Ling, N and Yin, Y and Shi, Q and Shi, Z}, title = {Trichoderma-based fertilizer enhances quality of Elymus breviaristatus silage via microbial and metabolic modulation.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-10028-y}, pmid = {42092115}, issn = {2399-3642}, abstract = {Elymus breviaristatus is an important alpine forage, there is limited information regarding its potential use as silage and how fertilizer treatments affect the ensiling process in this forage crop. Here, we investigated how organic fertilizer (M), nitrogen-phosphorus-potassium fertilizer (NPK), and Trichoderma harzianum fertilizer (B) affect Elymus breviaristatus silage quality (30 days and 60 days ensiling) via microbiome and metabolome analyses. Before ensiling, plant height and chlorophyll content increased by 29.93% and 39.72%, respectively, in the B group. After 60 days of ensiling, the M group had reduced crude protein and elevated butyric acid, the NPK group had higher ammonia nitrogen and butyric acid, and the B group had increased crude protein and lactic acid. These quality shifts correlated with microbial and metabolic changes. In the M group, alpha-linolenic acid metabolism was downregulated and Alternaria enriched, while the NPK group had enhanced flavone biosynthesis and a reduced level of Lactiplantibacillus. The B group had enhanced glycine, serine, and threonine metabolism, and displayed the most complex microbial networks along with increased levels of Lactiplantibacillus and Aspergillus. Overall, these results demonstrate that Trichoderma-based fertilization enhances silage quality by promoting accumulation of beneficial microbes and increasing flux through specific metabolic pathways, potentially offering a sustainable strategy for alpine forage improvement.}, }
@article {pmid42092154, year = {2026}, author = {Yu, XA and Strachan, CR and Herbold, CW and Lang, M and Gasche, C and Makristathis, A and Segata, N and Pollak, S and Tett, A and Polz, MF}, title = {Genome-wide sweeps create ecological units in the human gut microbiome.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {42092154}, issn = {1476-4687}, abstract = {The human gut microbiome is shaped by diverse selective forces that originate from host and environmental factors and it substantially influences health and disease. Whereas the association of microbial lineages with various health conditions has been shown at different taxonomic levels[1-5], the extent to which unifying adaptive mechanisms sort microbial lineages into ecologically differentiated populations remains poorly understood. Here we show that genome-wide selective sweeps are a pervasive mechanism that differentiates bacteria in the microbiome. This mechanism leads to population structures akin to global epidemics across geographically and ethnically diverse human populations. Such sweeps arise when an adaptation allows a clone to outcompete others in its niche followed by rediversification, and they manifest as clusters of closely related genomes on long branches in phylogenetic trees. This structure is revealed by excluding recombination events that mask the clonal descent of the genomes. Indeed, we show that genome-wide sweeps originate under a wide range of recombination rates in at least 66 taxa from 25 bacterial families. Estimated ages of divergence suggest that sweep clusters can spread globally within decades and that this process has occurred throughout human history. Sweep clusters are associated with different host conditions-such as age, colorectal cancer, inflammatory bowel diseases and type 2 diabetes-as an indication of their ecological differentiation. Our results reveal an evolutionary mechanism for the observation of stably inherited strains with differential associations and provide a theoretical foundation for analysing adaptation among microbial populations.}, }
@article {pmid42092264, year = {2026}, author = {Vargas-Robles, D and Santos Agrait, JL and Suárez-Pérez, J and Vázquez, F and Dominicci-Maura, A and Sariol, CA and Zorrilla, C and Romaguera, J and Godoy-Vitorino, F}, title = {Oral Microbiome Resilience During SARS-CoV-2 Infection and Diversity Shifts After COVID-19 Vaccination in a Hispanic Population.}, journal = {MicrobiologyOpen}, volume = {15}, number = {3}, pages = {e70310}, pmid = {42092264}, issn = {2045-8827}, support = {U54 MD007600/MD/NIMHD NIH HHS/United States ; U54GM133807/GM/NIGMS NIH HHS/United States ; 1P20GM156713-01/GM/NIGMS NIH HHS/United States ; 2U54MD007600/MD/NIMHD NIH HHS/United States ; U54 GM133807/GM/NIGMS NIH HHS/United States ; U01CA260541/CA/NCI NIH HHS/United States ; COVID-19 RAPID GRANT #2020-00269//Puerto Rico Science, Technology and Research Trust/ ; P20 GM103475/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *COVID-19/prevention &amp; control/microbiology/immunology/virology ; *Microbiota ; Hispanic or Latino ; Female ; Male ; SARS-CoV-2 ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Adult ; *Mouth/microbiology ; *COVID-19 Vaccines/administration &amp; dosage/immunology ; Longitudinal Studies ; Vaccination ; Bacteria/classification/genetics/isolation &amp; purification ; Aged ; White ; }, abstract = {The relationship between SARS-CoV-2 infection and the oral microbiome remains poorly understood, particularly in the Hispanic population. Oral samples from 62 individuals (38 SARS-CoV-2 positive, 24 negative) were analyzed using 16S rRNA sequencing, comparing diversity and taxa by infection and symptoms. Longitudinal data from 11 participants assessed microbiome changes as the infection resolved over time. To assess the impact of vaccination, we further examined 68 consistently SARS-CoV-2-negative individuals with paired samples collected before and after vaccination. SARS-CoV-2 infection was not significantly associated with alpha diversity, while beta diversity showed a non-significant but marginal trend (p = 0.051). Prevotella nanceiensis was consistently depleted in infected individuals, even after excluding recent antibiotic users, suggesting a reproducible association with infection status rather than a diagnostic marker. Among infected participants, mucosa-related symptoms were associated with lower Veillonella parvula abundance. Longitudinal data revealed stable microbiome profiles with slightly reduced variance in alpha diversity following viral clearance. In contrast, COVID-19 vaccination in consistently negative individuals was associated with significant increases in Shannon (p = 0.050) and Simpson diversity (p = 0.017), indicating greater evenness without expansion of richness. Beta diversity analyses showed vaccination-related shifts in community composition (PERMANOVA p = 0.026), with increases in Treponema, Campylobacter, Oribacterium, and Selenomonas, and a decrease in Haemophilus. The oral microbiome of Hispanics with mild SARS-CoV-2 infection appeared resilient, with only subtle taxonomic alterations. In contrast, COVID-19 vaccination was associated with short-term increases in diversity and compositional shifts, highlighting its influence on oral microbial ecology.}, }
@article {pmid42092273, year = {2026}, author = {Wang, N and Li, X and Wang, L and Zhu, Z and Gu, M and Zou, K and Zhang, J}, title = {Global Trends in Postoperative Sepsis After Pancreatoduodenectomy: A Bibliometric Analysis.}, journal = {The Journal of surgical research}, volume = {323}, number = {}, pages = {48-57}, doi = {10.1016/j.jss.2026.04.010}, pmid = {42092273}, issn = {1095-8673}, abstract = {INTRODUCTION: Postoperative sepsis after pancreatoduodenectomy (PSPD) remains a major determinant of morbidity and mortality. Although extensive clinical studies have explored its risk factors and management, the global research landscape and evolving priorities of PSPD have not been systematically characterized.<br><br>METHODS: Publications related to PSPD from 1980 to July 2025 were retrieved from the Web of Science Core Collection. CiteSpace, VOSviewer, and R-based bibliometrix were used to analyze publication trends, collaborative networks, influential journals and references, research hotspots, and emerging trends.<br><br>RESULTS: A total of 297 studies were included. Global PSPD research has grown steadily over the past 45 years, with rapid acceleration since 2020. The United States, Japan, Germany, Italy, and China were the leading contributors, supported by high-output institutions such as the University of Verona, Vita-Salute San Raffaele University, and Mayo Clinic. Research hotspots centered on risk stratification, surgical technique optimization, prevention of postoperative pancreatic fistula, and perioperative infection control. Emerging frontiers include surgical site infection prevention, microbiome-gut barrier and bacterial translocation mechanisms, precision risk prediction using machine learning models, and individualized perioperative strategies.<br><br>CONCLUSIONS: Global PSPD research has evolved from descriptive clinical studies toward mechanistic, predictive, and precision-oriented investigations. Future progress will likely depend on integrating surgical innovation with microbiological, immunological, and data-driven approaches to enable earlier identification and targeted prevention of PSPD.}, }
@article {pmid42092351, year = {2026}, author = {Dohlman, AB and Mjelle, R and Wood, HM and Jiang, K and Shumate, A and Lee, I and Piccinno, G and Serna, G and Yakubu, AR and Nuciforo, P and Quirke, P and Huttenhower, C and Segata, N and Meyerson, M}, title = {Biodiversity and biogeography of the multi-kingdom cancer microbiome.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2026.04.015}, pmid = {42092351}, issn = {1097-4172}, abstract = {Microorganisms represent an important component of the tumor microenvironment, but conflicting reports have left the extent of microbial prevalence across cancer types unclear, necessitating more robust methods for characterizing tumor-associated microbiomes. We built and benchmarked a host-subtraction and classification pipeline to identify microbiota in whole-genome sequencing data and applied it to 16,369 high-depth tumor whole genomes from the UK 100,000 Genomes Project. After decontamination, microbial signatures were indistinguishable from the background in most cancer types. However, in orodigestive tumors, we detected multi-kingdom polymicrobial communities, including bacteria, fungi, viruses, archaea, and, in some cases, Trichomonas, a protozoan parasite. These communities varied by tumor site and subtype, with increased microbial colonization of microsatellite-instable and polymerase ε (POLE)/polymerase δ (POLD1)-mutated tumors, supported by a correlation between microbial load and tumor mutation burden observed across orodigestive cancers. This analysis helps to resolve pan-cancer microbial structure and links the tumor microbiome to host phenotype and tumor genomic context.}, }
@article {pmid42092466, year = {2026}, author = {Gavini, CK and Raux, L and Labouèbe, G and Gornick, E and Mc Hugh, S and Elshareif, N and Calcutt, NA and Di Summa, PG and Gorostidi, F and Vonaesch, P and Mansuy-Aubert, V}, title = {A gut-adipose-nerve axis mediates inulin protection against Western diet-induced somatosensory dysfunction.}, journal = {Brain, behavior, and immunity}, volume = {137}, number = {}, pages = {106795}, doi = {10.1016/j.bbi.2026.106795}, pmid = {42092466}, issn = {1090-2139}, abstract = {Westernized diets (WDs)-high in fat and sugar and low in fiber-produce somatosensory deficits, chronic pain, and neuropathy, yet the mechanisms linking diet to peripheral nervous system (PNS) pathology remain incompletely defined. Emerging evidence implicates gut-derived metabolites in sensory homeostasis; for example, fecal microbiota transplantation (FMT) from lean donors to WD fed mice reduces hypersensitivity and attenuates PNS inflammation potentially via modifying short chain fatty acid (SCFA) levels, although FMT outcomes are variable. We therefore tested whether targeted modulation of the gut microbiota with fermentable complex carbohydrates (inulin) producing SCFA could reproducibly improve somatosensory function in WD-fed mice. Using an integrated pipeline-behavioral and physiological assays, peripheral nerve electrophysiology, and molecular and immune profiling-we show that inulin improved thermal and mechanical sensory function indirectly by improving metabolic health and remodeling immune cells in adipose tissue depots. Interestingly, in separate genetic experiments we found that deletion of the SCFA receptor FFAR2 (GPR43) in myeloid cells altered thermal sensitivity and adipose inflammatory gene expression, indicating that immune SCFA sensing can modulate pain-related behavior. These findings identify mechanisms by which dietary fiber indirectly preserves PNS function through effects on adiposity and systemic inflammation and provide a tractable alternative to FMT for mitigating WD-associated sensory neuropathy.}, }
@article {pmid42092549, year = {2026}, author = {Wester, RJ and Samera, GJ and Walcott, JR and Williams, R and Atkins, G and McCarthy, GC and Baillie, LL and Adams, PJ}, title = {Molecular surveillance of Mycoplasmopsis bovis across dairy farms in Western Canada and 16s microbiome assessment in pneumonic calves.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2026-28245}, pmid = {42092549}, issn = {1525-3198}, abstract = {Mycoplasmopsis bovis (M. bovis) is an important bacterial pathogen that severely impacts the Canadian dairy industry and has been linked to bovine respiratory disease (BRD), a complex that includes pneumonia, as well as mastitis, otitis media, and arthritis. Despite its clinical relevance, limited data exists on its prevalence in Western Canadian dairy herds, and its role within the microbiome in the context of pneumonia remains unclear. This study aimed to determine the prevalence of M. bovis in British Columbia and Alberta and to assess microbial shifts in pneumonic calves to investigate its potential role in BRD. A total of 60 farms were screened for M. bovis using qPCR on bulk tank milk (BTM) and swab samples. M. bovis DNA was detected in 20% of screened farms. However, there were notable differences in detection between swab and BTM samples, highlighting the importance of considering both sample types in surveillance initiatives. Additionally, 82 swab samples from calves in a single herd were analyzed using 16S rRNA sequencing to compare microbial communities across clinical groups. Microbial diversity, differential abundance (ANCOM-BC2), and taxa correlations (SECOM) were assessed. M. bovis presence was not significantly associated with clinical status, although calves with pneumonia exhibited significantly altered microbial diversity compared with healthy calves. M. bovis abundance was significantly enriched, and several commensal taxa were significantly depleted in the pneumonic microbiome. M. bovis abundance was also inversely correlated with some of these taxa, supporting a role in dysbiosis. Overall, these findings suggest that M. bovis is associated with dysbiosis within the respiratory microbiota and may contribute to BRD pathogenesis under conditions of microbial disruption.}, }
@article {pmid42092559, year = {2026}, author = {Niu, Y and Wang, C and Nie, C and Wu, Y and Huang, R and Zhang, W}, title = {Integrated multi-omics reveals that replacing corn silage with triticale silage improves milk quality via rumen microbiome-metabolome crosstalk in dairy cows.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2025-28155}, pmid = {42092559}, issn = {1525-3198}, abstract = {The objective of this study was to evaluate the effects of replacing corn silage with triticale (× Triticosecale Wittmack) silage on lactation performance, milk fatty acid profile, and rumen microbiome-metabolome interactions in dairy cows. In this study, 27 mid-lactation dairy cows were used in replicated 3 × 3 Latin squares with 3 28-d periods and 3 treatments, in which 0, 25, or 50% of the corn silage (DM basis) was replaced with triticale silage. Replacing 25% of corn silage maintained DMI and milk yield, whereas 50% replacement reduced both variables. Diets containing triticale silage lowered SCC and increased the proportion of oleic acid in milk fat. The 50% replacement further increased the proportions of linoleic acid (LA), α-linolenic acid (ALA), and milk protein concentration. In the rumen, the 50% replacement increased pH and NH3-N concentration, and triticale diets increased the proportions of ALA and several C18:1 and C18:2 biohydrogenation intermediates, resulting in a greater UFA proportion and a lower SFA: UFA ratio in rumen fluid. Metataxonomic analysis revealed higher relative abundances of Butyrivibrio_A, Ruminococcus_E, and Prevotella in triticale diets, whereas metabolomic profiling indicated enrichment of pathways related to LA, ALA, and amino acid metabolism. Correlation analysis associated Butyrivibrio_A and Ruminococcus_E with LA oxidation products and amino acid derivatives, indicating the involvement of rumen microbiome-metabolome interactions in shaping the milk UFA responses. Overall, partial replacement of corn silage with triticale silage improved the milk fatty acid profile and udder health indicators without compromising performance at 25% inclusion, indicating that winter triticale is a promising component of forage systems.}, }
@article {pmid42092564, year = {2026}, author = {Freund, L and Ramirez Leal, B and Hsu, CL}, title = {Impact of alcohol on gut microbial metabolism and the gut-liver-brain axis.}, journal = {Alcohol (Fayetteville, N.Y.)}, volume = {134}, number = {}, pages = {44-53}, doi = {10.1016/j.alcohol.2026.04.009}, pmid = {42092564}, issn = {1873-6823}, abstract = {The gut microbiome includes a large and diverse microbial community that plays a central role in host health, supported by an extensive genomic repertoire that is distinct from and complementary to mammalian enzymatic pathways. Alcohol consumption disrupts this ecosystem, inducing microbial dysbiosis and altering functional interactions between the host and its gut bacteria that can lead to systemic effects. In this review, we examine how alcohol affects gut bacteria, and how these changes impair essential bacterial functions, including short-chain fatty acid production, mucin metabolism, biofilm formation, and bile acid metabolism, that support intestinal, liver, and brain health. We further describe how certain gut bacteria tolerate or produce ethanol, and how these traits contribute to the systemic harms associated with alcohol-induced dysbiosis. Finally, we highlight therapeutic strategies aimed at targeting ethanol-tolerant or ethanol-producing bacteria as potential avenues for preventing or mitigating intestinal inflammation, liver injury, and other metabolic disorders.}, }
@article {pmid42092736, year = {2026}, author = {Prasad, B}, title = {Predicting Pharmacokinetic Variability and Drug Interaction Risk Using Omics-Based Biomarkers.}, journal = {Clinical and translational science}, volume = {19}, number = {5}, pages = {e70591}, pmid = {42092736}, issn = {1752-8062}, support = {R01 HD081299/HD/NICHD NIH HHS/United States ; //National Institutes of Health (NIH)/ ; }, mesh = {Humans ; Drug Interactions/genetics ; *Biomarkers/analysis ; Pharmacogenetics/methods ; *Pharmacokinetics ; Precision Medicine/methods ; Risk Assessment/methods ; }, abstract = {Interindividual variability in drug pharmacokinetics and susceptibility to drug-drug interactions remain major barriers in precision dosing, particularly for narrow therapeutic index drugs. While genetic factors contribute, much variability arises from dynamic influences such as physiology, disease, age, diet, microbiome, and concomitant medications. Conventional approaches provide limited retrospective insight. Emerging phenotypic biomarkers offer a proactive, mechanism-based strategy to quantify variability, improve exposure prediction, assess drug interaction risk, and individualize dosing beyond pharmacogenomics.}, }
@article {pmid42092753, year = {2026}, author = {Palanisamy, M and Babalola, OO and Ramalingam, S}, title = {Shotgun metagenomic dataset of leaf endophytic microbiome of the garden sage (Salvia officinalis L.).}, journal = {BMC genomic data}, volume = {27}, number = {1}, pages = {}, pmid = {42092753}, issn = {2730-6844}, support = {CMRG2400927//Chief Minister`s Research Grant (CMRG), Government of Tamil Nadu, India/ ; }, mesh = {*Salvia officinalis/microbiology ; *Plant Leaves/microbiology ; *Metagenomics ; *Endophytes/genetics/classification ; *Microbiota ; *Metagenome ; Bacteria/genetics/classification ; Fungi/genetics ; }, abstract = {OBJECTIVES: Garden sage (Salvia officinalis L.) is a traditional medicinal plant known for its rich bioactive secondary metabolites. However, there is limited information about the diversity of endophytic microbial communities, including bacteria, fungi, archaea, and viruses. Therefore, the study employs shotgun metagenomics to generate and make publicly available a dataset representing the leaf endophytic microbiome of Salvia officinalis.<br><br>DATA DESCRIPTION: Metagenomic DNA was extracted from leaves of S. officinalis collected as three biological replicates and sequenced using the Illumina NovaSeq X platform. Host-derived and contaminant sequences were removed by mapping reads to the S. officinalis reference genome using BWA-MEM. The resulting high-quality FASTQ files were analyzed to characterize the taxonomic composition of the endophytic microbiome using Kraken2-based classification.}, }
@article {pmid42092798, year = {2026}, author = {Liu, J and He, S and Zhang, H and Mai, H and Li, X and Liang, H and Cui, P and Lan, L and Liao, W and Huang, Q and Ning, H and Li, Z and Liang, Y and Yang, X and Huang, J}, title = {Machine learning-driven clinical decision support for liver cirrhosis: a gut microbiome-based web prediction model with explainable AI integration.}, journal = {BMC gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12876-026-04890-7}, pmid = {42092798}, issn = {1471-230X}, support = {82160385//National Natural Science Foundation of China/ ; 82273694//National Natural Science Foundation of China/ ; 2024GXNSFBA010104//Natural Science Foundation of Guangxi Zhuang AutonomousRegion/ ; 2023GXNSFDA026036//Natural Science Foundation of Guangxi Zhuang AutonomousRegion/ ; GXJKKJ2025ZC004//Science and Technology Project for Disease Control and Prevention of Guangxi Zhuang Autonomous Region/ ; }, abstract = {BACKGROUND: Liver cirrhosis (LC) is a chronic liver disease with global prevalence. Current diagnostic methods for LC still face limitations in safety and accessibility. We aimed to develop an interpretable machine learning (ML) prediction model for LC using gut microbes and deploy it as a web-based clinical decision support tool.<br><br>METHODS: Data were retrieved from PubMed and BioProject databases. Bioinformatics re-analysis and discriminant analysis effect size (LEfSe) analysis was conducted to preliminarily identify key genera associated with LC. Further feature selection was performed using Least Absolute Shrinkage and Selection Operator (LASSO) regression. The independent datasets were combined to form an integrated dataset, which was then subjected to five-fold cross-validation and leave-one-dataset-out (LODO) analysis. Model performance was evaluated using metrics such as the area under the receiver operating characteristic curve (AUC), and the optimal model was selected. The decision mechanism of the optimal model was interpreted using SHapley Additive exPlanations (SHAP), and the model was deployed as a web application using the Streamlit framework.<br><br>RESULTS: We ultimately included 11 datasets related to LC. The genera Veillonella, Lachnospira, Romboutsia, Akkermansia, Erysipelatoclostridium, Prevotella, UCG.005, and Streptococcus were identified as key predictors distinguishing LC patients from healthy controls. The Random Forest (RF) model demonstrated the best predictive performance (AUC in five-fold cross-validation: 0.875, 95% CI: 0.823-0.905; AUC in LODO analysis: 0.793, 95% CI: 0.702-0.940) and was deployed as an online LC prediction tool.<br><br>CONCLUSION: The interpretable RF model, along with its web-based implementation, has the potential to provide decision support for healthcare professionals and shows promise as a valuable auxiliary tool for LC screening and early clinical intervention.}, }
@article {pmid42093056, year = {2026}, author = {Itoh, H and Shimoji, H and Nakane, D and Jang, S and Kikuchi, Y}, title = {Soil pH as an external filter shaping stink bug-Burkholderia gut symbiosis.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42093056}, issn = {2049-2618}, support = {19K15724//Japan Society for the Promotion of Science/ ; 22H05065//Japan Society for the Promotion of Science/ ; }, mesh = {Animals ; *Symbiosis ; *Burkholderia/physiology/isolation &amp; purification/genetics/classification ; *Soil/chemistry ; Hydrogen-Ion Concentration ; *Soil Microbiology ; *Gastrointestinal Microbiome ; *Heteroptera/microbiology ; }, abstract = {BACKGROUND: Many animals and plants establish intimate symbiotic relationships with specific microorganisms acquired from the environment. Given the immense diversity of environmental microbiomes, selecting appropriate partners from such a vast microbial pool poses a critical challenge for host organisms. To meet this challenge, hosts have evolved sophisticated internal partner-choice mechanisms that ensure stable associations with beneficial microbes. However, because these symbionts primarily inhabit external environments, environmental conditions themselves are also expected to influence the establishment of symbiosis. Despite this expectation, the mechanistic role of external environmental filters in shaping the intended symbiosis remains largely unexplored. Focusing on stink bugs, which acquire their symbiotic bacteria from soil each generation, we investigated how soil properties influence the establishment of gut symbiosis in terrestrial insects.<br><br>RESULTS: Microbiome analyses confirmed that Burkholderia sensu lato overwhelmingly dominates a specific gut organ in six stink bug species from the superfamilies Coreoidea and Lygaeoidea, including serious agricultural pests (relative abundance ranging from 74.5 to 100%). Rearing experiments with isolated Burkholderia revealed that insects were strictly dependent on this symbiont; failure to acquire it from soil severely reduced host growth and reproduction, indicating that the availability of symbionts from soil can represent an ecological constraint. Field surveys identified patches of exceptionally high stink bug density in weedy fields with soil pH&#x2009;<&#x2009;7.0, whereas such aggregations were absent in fields with pH&#x2009;&#x2265;&#x2009;7.0. Laboratory experiments with collected field soils showed that the abundance of Burkholderia in soils was negatively correlated with soil pH, and stink bugs readily acquired their symbionts from soils with pH&#x2009;<&#x2009;7.0 but rarely from soils with pH&#x2009;&#x2265;&#x2009;7.0. Experimental manipulations of soil pH followed by rearing experiments confirmed that increasing soil pH to 7-8 markedly suppressed symbiont acquisition by the host, likely by impairing symbiont growth and motility.<br><br>CONCLUSIONS: We demonstrate that, beyond host-intrinsic mechanisms, a soil chemical property can act as an externally filter that constrains symbiont acquisition prior to colonization inside the host in a stink bug-Burkholderia symbiosis. This finding highlights how local environmental conditions can shape the assembly of environmentally acquired insect-microbe symbioses. Video Abstract.}, }
@article {pmid42093248, year = {2026}, author = {Durkin, ES and La Luz Maldonado, A and Keiser, CN}, title = {Exploring microbiome diversity between behavioural strategies in a facultatively parasitic mite.}, journal = {Parasitology}, volume = {}, number = {}, pages = {1-21}, doi = {10.1017/S0031182026102121}, pmid = {42093248}, issn = {1469-8161}, }
@article {pmid42093578, year = {2026}, author = {Alcamán-Arias, ME and Ramos-Tapia, I and Fuentes, F and Bastías, R and Manzano, CA and Plaza, N and Higuera, G and Araneda, D and Troncoso, M and Ugalde, JA and Vergara, K}, title = {Atmospheric Dispersal and Local Drivers Shape Snow and Air Microbial Communities in the Western Antarctic Peninsula.}, journal = {Environmental microbiology}, volume = {28}, number = {5}, pages = {e70316}, doi = {10.1111/1462-2920.70316}, pmid = {42093578}, issn = {1462-2920}, support = {11200413//ANID/FONDECYT/INACH/ ; 1523A0002//ANID/FONDAP/ ; ATE220061//ANID ANILLO/ ; 1221209//ANID/FONDECYT/ ; }, mesh = {Antarctic Regions ; *Microbiota ; *Snow/microbiology ; RNA, Ribosomal, 16S/genetics ; *Air Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; }, abstract = {Microbial communities in Antarctica's snow and atmosphere are critical for nutrient cycling and are highly sensitive to environmental change. We characterised the bacterial composition, diversity, and co-occurrence network structure of surface snow and airborne microbiomes from two contrasting bays along the Western Antarctic Peninsula (WAP): Arturo Prat Base (APB; Chile Bay, Greenwich Island) and Yelcho Base (YB; South Bay, Doumer Island), sampled during consecutive austral summers (2022-2023). Surface snow and air samples were analysed using 16S rRNA gene sequencing, diversity indices, and network analyses to evaluate spatial and interannual dynamics. Proteobacteria and Bacteroidota dominated both environments, but community structures differed between sites: APB showed stronger local and anthropogenic signals near logistic stations, whereas YB reflected more stable deposition regimes and distant atmospheric inputs. Airborne communities displayed limited interannual variation and high compositional similarity between sites, consistent with atmospheric seeding by polar air masses. Co-occurrence networks revealed denser, more structured interactions within snow communities, with keystone taxa linking snow and air, sustaining deposition-resuspension dynamics. These findings highlight that long-range atmospheric transport and local conditions shape Antarctic microbial dynamics, providing insights for forecasting microbiome responses and assessing airborne health risks amid human activity and climate change in polar regions.}, }
@article {pmid42093609, year = {2026}, author = {Harberts, A and Fondevila, MF and Kreimeyer, H and Miwa, T and Lang, S and Demir, M and Schnabl, B}, title = {Faecal Cathepsin B and S Are Associated With Liver Disease Severity and Adiposity in MASLD.}, journal = {Liver international : official journal of the International Association for the Study of the Liver}, volume = {46}, number = {6}, pages = {e70663}, doi = {10.1111/liv.70663}, pmid = {42093609}, issn = {1478-3231}, support = {R01 AA24726/NH/NIH HHS/United States ; R01 AA031710/NH/NIH HHS/United States ; R37 AA020703/NH/NIH HHS/United States ; P30 DK120515/NH/NIH HHS/United States ; }, mesh = {Humans ; *Cathepsin B/analysis/metabolism ; Female ; Male ; Middle Aged ; *Feces/chemistry ; Gastrointestinal Microbiome ; Severity of Illness Index ; *Adiposity ; Case-Control Studies ; *Cathepsins/analysis/metabolism ; Adult ; *Fatty Liver/metabolism ; Aged ; }, abstract = {BACKGROUND &amp; AIMS: Dysregulation of hepatic cathepsins contributes to metabolic dysfunction-associated steatotic liver disease (MASLD) by promoting inflammation, apoptosis, and fibrosis. However, the role of intestinal cathepsins in MASLD has not been investigated. Given the central role of the gut-liver axis in disease progression, this represents an important knowledge gap.<br><br>METHODS: Faecal cathepsin B and S activity was measured in 95 patients with MASLD and 18 healthy controls. Cathepsin activity was correlated with liver disease severity, metabolic parameters, and gut microbiome composition.<br><br>RESULTS: Faecal cathepsin B and S activity was higher in patients with MASLD than in healthy controls. Cathepsin B activity was further increased in patients with metabolic dysfunction-associated steatohepatitis. Cathepsin B and S activity correlated with serum transaminases and hepatic steatosis, while cathepsin B activity was additionally associated with liver stiffness. Cathepsin B and S activity correlated with adiposity but showed no associations with other metabolic dysfunction-related parameters. Moreover, gut microbiome composition differed between patients with low vs. high faecal cathepsin B or S activity, respectively.<br><br>CONCLUSION: Increased faecal cathepsin B and S activity is associated with liver disease severity and adiposity in MASLD and is linked to alterations of the gut microbiome, suggesting a potential role of intestinal cathepsins in gut-liver axis dysfunction.}, }
@article {pmid42093690, year = {2026}, author = {Liao, J and Cui, Y and Wang, Y and Zeng, X and Chen, T and Xiang, Y and Wang, D}, title = {Comparative analysis of the rhizosphere microbiome and transcriptome in clubroot-susceptible and resistant rapeseed (Brassica napus).}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1729220}, pmid = {42093690}, issn = {1664-462X}, abstract = {Clubroot disease, caused by Plasmodiophora brassica, severely threatens the rapeseed industry in China, with an annual affected area exceeding 667000 hectares. To elucidate the mechanisms in clubroot resistance, we compared the differences in soil physicochemical properties, rhizosphere microbiome, and transcriptomic responses between a susceptible variety, HYZ62 (disease index 54.86), and a resistant variety, HYZ5R (disease index 17.05), following P. brassicae infection. The results showed that the electrical conductivity of HYZ5R (R) was 1.73 and 1.57 times that of HYZ62 (S) in the inoculated and uninoculated treatments, respectively. Compared to the 17.18% decrease in alkali-hydrolysable nitrogen content in HYZ62 (S) after inoculation, its content in HYZ5R (R) showed no significant difference. The rhizosphere microbial community significantly differed between HYZ5R (R) and HYZ62 (S), with HYZ5R (R) exhibiting higher relative abundances of several microbial genera, such as Burkholderia-Caballeronia-Paraburkholderia, Humibacter, Dyella, and Trichoderma. Although Bacillus had a significantly higher relative abundance in the rhizosphere of uninoculated HYZ62 (S), its relative abundance decreased by 30.36% after infection. Transcriptome analysis revealed that, compared to HYZ62 (S), the expression of pattern-triggered immunity-related genes, such as CML, WRKY, and PR1, was higher in HYZ5R (R) and was more strongly induced upon inoculation. Effector-triggered immunity-related genes, such as RIN4, RPS5, and HSP90, were consistently expressed at higher levels. In contrast, HYZ62 (S) showed a broad suppression of defense-related gene expression after inoculation. Furthermore, although P. brassicae infection generally suppressed defense-related secondary metabolic pathways, including phenylpropanoid biosynthesis, the expression levels of multiple genes in this pathway remained higher in HYZ5R (R). Together, these results suggest that the higher relative abundances of specific microbial taxa in the rhizosphere and the high expression of defense-related genes are associated with the clubroot resistance in HYZ5R (R).}, }
@article {pmid42093732, year = {2026}, author = {Shen, Z and Xing, X and Rong, K and Geng, Z and Yang, N and Xu, L and Ge, H and Sang, W}, title = {Short-Term Longitudinal Analysis of Gut Microbiota Dynamics During Anti-CD19 CAR-T Cell Therapy in Diffuse Large B-Cell Lymphoma Patients.}, journal = {Blood and lymphatic cancer : targets and therapy}, volume = {16}, number = {}, pages = {598958}, pmid = {42093732}, issn = {1179-9889}, abstract = {PURPOSE: Alterations in gut microbiota may influence immune response and treatment outcomes in patients with diffuse large B-cell lymphoma (DLBCL). However, the dynamics during anti-CD19 CAR-T cell therapy remain unclear.<br><br>METHODS: We conducted a short-term longitudinal microbiome analysis in DLBCL patients (n=12) undergoing CAR-T cell therapy targeting CD19. Stool samples were collected at baseline, 1&#xa0;week, and 2&#xa0;weeks post-infusion. 16S rRNA gene sequencing was used to assess microbial diversity, taxonomic composition, and functional pathways. Correlation analyses were then conducted between microbial taxa and inflammatory biomarkers.<br><br>RESULTS: Alpha diversity indices showed no statistically significant differences across time points. Beta diversity analysis revealed distinct clustering between baseline and week 1 samples in sPLS-DA, although PERMANOVA did not reach statistical significance. At the phylum level, Bacteroidota abundance significantly increased at week 2 compared with baseline (P = 0.008), accompanied by a marked reduction in the Firmicutes/Bacteroidota ratio. Genus-level heatmap and LEfSe analysis identified enrichment of Parabacteroides, and Prevotella at week 2, whereas baseline samples were enriched in Clostridium sensu stricto 13 and Fusobacterium. Functional prediction indicated that lipoic acid metabolism pathways were significantly upregulated at weeks 1 and 2 compared with baseline (both P < 0.05). Correlation analysis demonstrated that specific bacterial taxa, including Parabacteroides and Prevotella, were positively associated with lymphocyte counts and inversely correlated with C-reactive protein levels.<br><br>CONCLUSION: Gut microbiota alterations following CAR-T infusion, characterized by increased Bacteroidota abundance, specific taxonomic shifts, and enhanced lipoic acid metabolism, may provide early microbial signatures for monitoring immune modulation in DLBCL patients.}, }
@article {pmid42093801, year = {2026}, author = {Busmail, H and Weerakoon, S and Mandefro, BT and Sundara, SV and Lu, X and Avula, S and Mohammed, L}, title = {Fecal Microbiota Transplantation in Inflammatory Bowel Disease: A Systematic Review of Efficacy and Safety.}, journal = {Cureus}, volume = {18}, number = {4}, pages = {e106453}, pmid = {42093801}, issn = {2168-8184}, abstract = {Inflammatory bowel disease (IBD), comprising ulcerative colitis (UC) and Crohn's disease (CD), is a chronic inflammatory condition of the gastrointestinal tract associated with immune dysregulation and alterations in the gut microbiota. Growing evidence suggests that intestinal microbial dysbiosis plays an important role in disease pathogenesis, prompting interest in microbiome-targeted therapies, such as fecal microbiota transplantation (FMT). This systematic review aimed to evaluate the efficacy and safety of FMT in adult patients with IBD. A comprehensive literature search was conducted in PubMed, Embase, Scopus, and the Cochrane Library for studies published between 2020 and 2025 using keywords related to "fecal microbiota transplantation" and "inflammatory bowel disease." Eligible studies included randomized controlled trials (RCTs), cohort studies, systematic reviews, and meta-analyses involving adult patients with UC or CD. Due to clinical and methodological heterogeneity, a structured narrative synthesis was performed in accordance with Synthesis Without Meta-analysis (SWiM) guidelines. Nine studies comprising 1,847 participants met the inclusion criteria, including five RCTs, two systematic reviews, and two meta-analyses. In patients with UC, clinical remission rates ranged from 32% to 40%, with response rates between 44% and 52%. In CD, remission rates ranged from 24% to 31%, although evidence remained limited and heterogeneous. Multi-donor stool preparations and repeated FMT administrations were associated with improved clinical outcomes compared with single-donor protocols or single-dose protocols. Adverse events occurred in approximately 12-15% of patients and were predominantly mild gastrointestinal symptoms, while serious adverse events were rare (<2%). Current evidence suggests that FMT may induce clinical remission in a subset of patients with UC, while evidence in CD remains less consistent. Larger randomized trials with standardized protocols and long-term follow-up are needed to determine optimal donor selection, dosing strategies, and long-term safety.}, }
@article {pmid42093897, year = {2026}, author = {Zhang, H and Du, Z and Lu, P and Jiang, A and Guo, Y and Liu, Y and Song, Z and Dai, B and Zhang, W}, title = {Intratumoral Microorganisms in Tumors: Current Understanding and Emerging Therapeutic Strategies.}, journal = {MedComm}, volume = {7}, number = {}, pages = {e70754}, pmid = {42093897}, issn = {2688-2663}, abstract = {Recent advances in high-throughput sequencing, spatial omics, and integrative multiomics analyses have established reproducibly detectable microbial communities within tumor tissues, leading to the conceptualization of tumors as complex ecosystems encompassing an "intratumoral microbiota." These microorganisms have increasingly been recognized as contributing to tumorigenesis, progression, and therapeutic response through interactions with the immune system, immunometabolic reprogramming of tissues, chronic inflammation, and genomic instability. Nevertheless, current evidence remains piecemeal and descriptive, with limited systematic consolidation of microbial composition, functional mechanisms, and translation to clinical application, particularly across tumor types and microenvironmental contexts. This review summarizes microbial diversity, tumor-type-specific associations, and multilayered mechanisms including immune modulation, metabolic reprogramming, and signaling rewiring, and discusses emerging applications such as biomarker discovery, prognostic stratification, and microbiome-targeted therapeutics. Special focus is placed on tumor microenvironment, microbiota-derived metabolites, and determinants of immunotherapy responsiveness. Overall, this review underscores the intratumoral microbiota as a dynamic and context-dependent regulatory layer in cancer biology and offers an integrated framework to realize microbiome-informed precision oncology, along with avenues for enhanced patient stratification and personalized therapeutic approaches.}, }
@article {pmid42093997, year = {2026}, author = {Kuang, J and Zhang, M and Bian, X and Wang, X and Li, X and Wu, Q and Li, J}, title = {Diagnostic and metabolic insights into secondary lactose intolerance in infants via fecal lactose quantification and gut microbiome profiling.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1711945}, pmid = {42093997}, issn = {1664-3224}, mesh = {Humans ; *Lactose Intolerance/diagnosis/metabolism/microbiology ; *Feces/chemistry/microbiology ; *Gastrointestinal Microbiome ; *Lactose/analysis/metabolism ; Infant ; Male ; Female ; Fatty Acids, Volatile/metabolism ; Dysbiosis ; }, abstract = {BACKGROUND: Secondary Lactose intolerance (SLI) is common among infants in China, primarily resulting from secondary lactase deficiency due to mucosal damage. Current diagnostic methods are limited by poor sensitivity and specificity.<br><br>OBJECTIVE: To investigate gut microbial composition and metabolic dysfunction in infants with SLI and to explore the potential utility of residual fecal lactose as a non-invasive indicator related to SLI.<br><br>RESULTS: SLI infants exhibited significantly higher residual fecal lactose and lactate levels accompanied by reduced fecal short-chain fatty acid (SCFA) availability, consistent with incomplete lactose digestion and altered microbial fermentation. Microbiota profiling revealed marked depletion of Bacteroidetes and certain Firmicutes (e.g. Ruminococcaceae, Erysipelotrichaceae, Peptostreptococcaceae, Megasphaera), along with reduced glycolysis pathways. In vitro fermentation assays demonstrated a consistent reduction in total acid, acetate, and propionate production across multiple media, while lactate and gas production were significantly elevated in SLI samples under lactose, FOS, GOS, and starch-enriched conditions. Butyrate synthesis was partially preserved under protein-rich or minimal carbon media, indicating selective resilience of butyrogenic pathways. Microbial &#x3b2;-diversity analysis confirmed structural dysbiosis, with increased abundance of gas-associated taxa, including Clostridium.<br><br>CONCLUSION: Residual fecal lactose, when interpreted alongside microbial and metabolic profiles, may serve as a non-invasive indicator associated with secondary lactose intolerance in infants. These findings delineate microbiota-metabolism features consistent with SLI pathophysiology and provide a conceptual framework for future validation studies and the development of nutritional or probiotic interventions.}, }
@article {pmid42094015, year = {2026}, author = {Öz, M and Üstüner, E and Çifci, S}, title = {Medicinal and Aromatic Plant Oils in Aquafeeds: Mechanistic Perspectives on Growth Promotion, Immunomodulation, and Stress Resilience.}, journal = {Aquaculture nutrition}, volume = {2026}, number = {}, pages = {8992384}, pmid = {42094015}, issn = {1365-2095}, abstract = {The aquaculture industry is increasingly transitioning toward sustainable aquafeeds, driven by the economic and environmental necessity to replace marine-derived fishmeal and fish oil with plant- and insect-based alternatives. This nutritional shift introduces physiological challenges, accelerating the search for natural, sustainable functional additives. The primary goal of this review is to comprehensively evaluate the application of medicinal and aromatic plant oils (MAPOs) in aquafeeds, providing mechanistic perspectives on their roles in growth promotion, immunomodulation, and stress resilience. We synthesize current literature to link MAPO chemical composition, particularly phenolic monoterpenes and phenylpropenes, with biological responses, advanced delivery systems, and metabolic pathways. Key findings demonstrate that MAPOs can effectively stimulate appetite, modulate the gut microbiome, and enhance antioxidant defenses via the Nrf2-Keap1 pathway, thereby improving disease resistance. However, a critical limitation in the current literature is the high variability and inconsistent outcomes reported across different aquatic species and developmental stages. These discrepancies are largely attributed to strong chemotypic variability of essential oils, unstandardized extraction protocols, and dose-dependent responses that can sometimes yield neutral or suppressive effects. To successfully transition MAPOs from experimental trials to reliable commercial applications, future research must prioritize standardized dose-response evaluations, address species-specific variability, and utilize advanced formulation technologies such as nanoemulsions.}, }
@article {pmid42094080, year = {2026}, author = {Park, EM and Makowski, L and Cook, KL}, title = {Editorial: The microbiome in cancer therapy response.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1815455}, pmid = {42094080}, issn = {2813-4338}, }
@article {pmid42094244, year = {2026}, author = {Hasib, A and Ogada, S and Maina, S and Kuria, S and Peng, MS and Yu, J and Ommeh, SC}, title = {Fecal Microbiota Profiling in Indigenous Backyard and Commercial Chickens Reveals Distinct Taxonomic Signatures.}, journal = {Veterinary medicine international}, volume = {2026}, number = {}, pages = {3146713}, pmid = {42094244}, issn = {2090-8113}, abstract = {Farm management conditions and feeding practices in free-range (backyard), semi-intensive, or intensive production systems significantly influence the poultry gut microbiome, thereby impacting their productive performance and overall health. Here, fecal samples from asymptomatic indigenous backyard chickens raised in a free-range production system, characterized by little to no biosecurity measures in place, and from commercial chickens raised in an intensive production system with enhanced biosecurity measures were subjected to 16S rRNA sequencing analysis. Taxonomic assignment identified 19 bacterial phyla, 137 families, and 238 genera. The most prevalent phyla in indigenous backyard and commercial chickens were Firmicutes, Proteobacteria, Bacteroidetes, Fusobacteria, and Spirochaetes. Similarities were detected between bacterial families and genera in both indigenous backyard and commercial chickens; however, the bacterial family Bacillaceae and genus Anoxybacillus were only observed in commercial chickens. Statistical tests performed to evaluate the alpha-diversity and beta-diversity metrics showed no significant difference in the fecal bacterial microbiota of indigenous backyard and commercial chickens, as indicated by the Wilcoxon rank-sum (p = 0.94) and PERMANOVA tests (p = 0.26). This study highlights bacteria that may affect the growth, development, and health of indigenous and commercial poultry raised under various production systems, thereby providing vital insights for the development of effective poultry farm management practices.}, }
@article {pmid42094309, year = {2026}, author = {Amevor, FK and Uyanga, VA and Velleman, SG and Scanes, CG}, title = {Editorial: Integrated approaches to understanding and improving poultry health, immunity, and productivity: unraveling the role of metabolism.}, journal = {Frontiers in physiology}, volume = {17}, number = {}, pages = {1844387}, pmid = {42094309}, issn = {1664-042X}, }
@article {pmid42094360, year = {2026}, author = {Yang, R and Severn, M and Aiken, E and Zhou, W and Voigt, A and Walker, G and Koh, A and Gong, M and Thapa, M and Li, S and Milstone, L and Oh, J}, title = {Species and strain diversity in Staphylococcus drive divergent host responses in human skin.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.30.720712}, pmid = {42094360}, issn = {2692-8205}, abstract = {The skin microbiome regulates key skin processes, yet the functional diversity of a dominant genus, Staphylococcus, remains poorly resolved at the strain level for multiple species across its pathogenic and commensal continuum. It is likely that Staphylococcus' effects on skin are diverse at these finest taxonomic resolutions, but current skin models lack the physiological relevance and scalability needed to profile this diversity. Using an organotypic 3D human skin model (reconstructed human epidermis, RHE), we profiled skin responses to 187 Staphylococcus strains across seven dominant species. Canonically 'pathogenic' species (e.g., S. aureus) induced broad inflammatory responses, whereas prototypical 'commensal' species (e.g., S. hominis) elicited more nuanced effects on innate immune and skin barrier responses. Strikingly, S. epidermidis displayed pronounced strain-level heterogeneity, with subsets inducing either 'commensal' or 'pathogen'-like responses despite lacking canonical virulence factors, suggesting pleiotropic effects. Comparative genomics, dual-transcriptomics, untargeted metabolomics, and growth phenotyping revealed species- and strain-specific traits underlying these differential effects on RHE, including the presence of select cell surface proteins and differential arginine metabolism. Together, our study provides the first high-throughput, species- and strain-resolved analysis of skin-Staphylococcus interactions, offering mechanistic insights and a platform for microbiome-based strategies to modulate skin inflammation and diseases.}, }
@article {pmid42094415, year = {2026}, author = {Wills, LJ and Wang-Heaton, H and Polichnowski, AJ and Thomas, KL and Jewett, BE and Jewett, S and Aldridge, G and Ordway, GA and Brown, RW and Chandley, MJ}, title = {PARP inhibition with 3-aminobenzimide attenuates behavioral, cardiovascular, and neuroinflammatory effects of chronic stress.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.28.721400}, pmid = {42094415}, issn = {2692-8205}, abstract = {BACKGROUND: Major depressive disorder (MDD) affects approximately 20% of the population, with over 30% of cases demonstrating treatment resistance. Postmortem analyses have revealed increased poly (ADP-ribose) polymerase 1 (PARP-1) expression in prefrontal cortical white matter of individuals with MDD, suggesting PARP-1 as a potential therapeutic target. Chronic stress, a major risk factor for depression, affects multiple physiological domains including behavior, cardiovascular function, neuroinflammation, and gut-brain axis signaling.<br><br>METHODS: We conducted a comprehensive multi-system investigation of PARP inhibition effects on stress-induced pathophysiology using the social defeat stress/chronic unpredictable stress (SDS+CUS) rodent model. In the primary study, male Sprague-Dawley rats (N=32) underwent 10 days of SDS+CUS while receiving daily treatment with the PARP inhibitor 3-aminobenzamide (3-AB; 40mg/kg), selective serotonin reuptake inhibitor fluoxetine (FLX; 10mg/kg), or saline (0.9% NaCl), with non-stressed controls included. Behavioral outcomes were assessed via sucrose preference and social interaction tests. Neurobiological analyses examined PARP-1 expression, microglial morphology, and proinflammatory cytokine levels (IL-1&#x3b2;, TNF-&#x3b1;, IL-6) in relevant brain regions. In a parallel cardiovascular study, a separate cohort of stressed rats (N=8) received either saline or 3-AB treatment while hemodynamic parameters were monitored via telemetry before, during, and after stress exposure. Exploratory gut microbiome analyses were also conducted (see Supplemental Materials).<br><br>RESULTS: Saline-treated stressed rats demonstrated significantly elevated anhedonia and social avoidance compared to all other groups, while 3-AB treatment prevented these behavioral deficits. Cardiovascular monitoring revealed that stressed saline-treated rats developed significant elevations in systolic and mean blood pressure with decreased heart rate compared to baseline, whereas 3-AB treatment prevented these hemodynamic changes. Neurobiological analyses showed that FLX-treated stressed rats unexpectedly exhibited elevated PARP-1 expression in prefrontal cortical gray matter. Microglial morphological analysis revealed significantly more prolate (activated) microglia in the saline-treated stressed rats compared to all other treatment groups. Saline-treated stressed rats exhibited significantly increased hippocampal proinflammatory cytokines, with 3-AB treatment specifically normalizing TNF-&#x3b1; levels.<br><br>CONCLUSION: PARP inhibition with 3-AB provides multi-system protection against chronic stress effects, preventing behavioral deficits, cardiovascular dysfunction, and neuroinflammation. These findings establish PARP-1 as a key mediator in the systemic pathophysiology of chronic stress and highlight PARP inhibition as a promising therapeutic approach for stress-related disorders with treatment-resistant features.}, }
@article {pmid42094498, year = {2026}, author = {Singh, J and Grant, TD and Gulick, AM}, title = {Structure of a Stand-Alone Homodimeric NRPS Condensation Domain Reveals Occlusion of the Canonical Carrier-Protein Interface.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.24.720670}, pmid = {42094498}, issn = {2692-8205}, support = {R01 GM133998/GM/NIGMS NIH HHS/United States ; R35 GM136235/GM/NIGMS NIH HHS/United States ; R35 GM158053/GM/NIGMS NIH HHS/United States ; }, abstract = {Fatty acid amides (FAAs) produced by gut-resident bacteria act as potent modulators of host G protein-coupled receptor signaling, yet the enzymatic mechanisms underlying their biosynthesis remain poorly understood. In many bacteria from the gut microbiome, including Coprococcus eutactus , FAA production is mediated by a nonribosomal peptide synthetase-like pathway that includes OaaC, a free-standing condensation domain that catalyzes amide bond formation between acyl carrier protein (ACP) tethered fatty acids and small-molecule amine acceptors. Here, we combine structural, biophysical, biochemical, and evolutionary analyses to interrogate the molecular basis of OaaC function. Solution scattering and X-ray crystallography reveal that OaaC adopts an atypical homodimeric architecture that occludes the canonical ACP-binding surface and donor access pathways. Mass photometry demonstrates that this homodimer is stable in the absence of substrates and is insensitive to free fatty acids, free amines, and apo-ACP. In contrast, holo or acyl-loaded OaaACP selectively destabilizes the homodimer forming the OaaC-OaaACP complex population. LC-MS reconstitution assays confirm that OaaC catalyzes fatty acid amide formation in vitro and can utilize acyl donors spanning multiple chain lengths and saturation states. Phylogenetic and sequence analyses place FAA-associated condensation domains in a distinct clade most closely related to starter condensation domains and reveal a conserved noncanonical active site motif that differentiates them from PCP-dependent NRPS condensation domains. Together, these findings support a model in which OaaC activity is regulated through substrate-dependent modulation of oligomeric state, providing a model framework for understanding FAA biosynthesis in gut microbes and expanding the known functional diversity of NRPS condensation domains.}, }
@article {pmid42094537, year = {2026}, author = {Debray, R and Dickson, CC and Webb, SE and Ferretti, P and Meloimet, A and Gilbert, J and Alberts, SC and Blekhman, R and Archie, EA and Tung, J}, title = {Social microbiome transmission predicts microbial specialization and host lifespan in a wild primate.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.29.721577}, pmid = {42094537}, issn = {2692-8205}, abstract = {Social interactions are proposed to provide reliable routes for microbial transmission between animals, facilitating animal-microbiome co-evolution. However, microbiome transmission remains challenging to measure in wild populations. Here we combine behavioral observations of wild baboons with repeated strain-resolved metagenomic profiling to identify individual gut microbial species that follow a dominant mode of social transmission. In an 18-year metagenomic time series from the same population, baboons with higher levels of socially transmitted species lived longer than those with lower levels of socially transmitted species. Socially transmitted species were also more stable and persistent within baboons, yet had narrower host ranges outside of baboons. Thus, social transmission is not only detectable in free-living primates, but may play a special role in both host and microbial fitness.}, }
@article {pmid42094709, year = {2026}, author = {Mallick, S and Pavloudi, C and Chakkalakkal, GJ and Lažetić, V and Saw, J and Eleftherianos, I}, title = {A dataset on microbiome alterations in Drosophila melanogaster infected by entomopathogenic nematodes.}, journal = {Data in brief}, volume = {66}, number = {}, pages = {112794}, pmid = {42094709}, issn = {2352-3409}, abstract = {The fruit fly Drosophila melanogaster is an excellent model for dissecting the molecular processes that regulate host-microbe interactions and the role of the microbiome in host homeostasis. More recently, the fly has also been used as a model for understanding entomopathogenic nematode infection and host response against these parasites. To gain insights into the effect of entomopathogenic nematode infection on the insect microbiome, D. melanogaster larvae were exposed to Heterorhabditis bacteriophora containing their symbiotic bacteria Photorhabdus luminescens (symbiotic worms) and nematodes lacking their bacterial symbionts (axenic worms). Microbiome changes were examined through 16S rRNA sequencing. Data were collected at 24- and 48-hours following infection of D. melanogaster larvae with either type of nematode. The complete set of raw sequencing data generated in this study has been deposited in the European Nucleotide Archive under accession number PRJEB85826.}, }
@article {pmid42094772, year = {2026}, author = {Luo, H and Shen, Z and Jian, Y and Wang, M and Luo, S and Wang, J and Nan, L and Tang, L and Rehman, MU and Carbonero, F}, title = {Editorial: Unravelling the wildlife gut microbiome: the crucial role of gut microbiomes in wildlife conservation strategies.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1838495}, pmid = {42094772}, issn = {1664-302X}, }
@article {pmid42094775, year = {2026}, author = {Nguyen, D and Ovadia, O and Masasa, M and Tarnecki, A and Brennan, NP and Rhody, NR and Main, KL and Guttman, L}, title = {Microbial dynamics along nutrient flow and removal in an integrated multitrophic aquaculture system.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1781931}, pmid = {42094775}, issn = {1664-302X}, abstract = {Microbial community assembly in marine integrated multi-trophic aquaculture (IMTA) systems remains poorly understood, particularly across interconnected extractive compartments spanning spatial and temporal scales. Two-step biofilters that incorporate seaweeds and multi-species biofilms (periphyton) are widely used to remove excess nitrogen and phosphorus from aquaculture effluents while simultaneously generating protein-rich, edible biomass. Variations in nutrient composition along these biofilters suggest that microbial diversity and functionality may be differentially shaped within the system. To address this knowledge gap, in this study, using the 16S rRNA gene amplicon sequencing technique, we examined the assembly and potential functions of aquatic microbial communities along the treatment of marine effluent by Ulva fasciata and periphyton, where species selection may occur spatially through microbial colonization of the different plant substrates or through changes in water-nutrient content. At the same time, we assessed temporal dynamics by the weekly changes over 5 weeks. Community structure and functionality demonstrated that environmental heterogeneity primarily determined dissimilarity among microbial communities across the biofilter's compartments. Microbial beta diversity of periphyton, Ulva thallus, and rearing water was distinct over time. This confirmed the important role of environmental selection despite hydraulic homogeneity caused by the high dispersal rate of running water within the interconnected biofilters. The periphyton microbial community harbored the highest alpha diversity, followed by the water microbiome and Ulva-associated microbiota. In terms of functional potential, nitrogen and sulfur metabolism were generally higher in periphyton than in the water and Ulva assemblies. While nitrate reduction by periphyton is associated with the high prevalence of genes involved in denitrification, the Ulva-microbes interaction benefits the alga through bacterial dissimilatory nitrate reduction to ammonia. Overall, these findings provide novel insights into the spatial and temporal dynamics of microbiomes in integrated culture systems, contribute to optimal IMTA designs and microbial management in holistic mariculture.}, }
@article {pmid42095016, year = {2026}, author = {Li, R and Zhang, S and Liu, Q and Wang, B and Mi, S and Wang, C and Chen, X and He, K and Lv, Y and Gao, X and Fan, Y and Tang, J and Hua, D and Wang, X}, title = {Effects of cotton straw and apple pomace mixed ensilage on growth performance, slaughter performance, meat quality, rumen microbiota and metabolome of Xinjiang Brown cattle.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1796588}, pmid = {42095016}, issn = {2297-1769}, abstract = {This study aimed to investigate the effects of replacing traditional corn silage with cotton straw and apple pomace mixed ensilage feed on the growth performance, slaughter performance, meat quality, rumen microbiota and metabolome of Xinjiang Brown Cattle. Twenty 22-month-old Xinjiang Brown Cattle with similar body conditions were randomly divided into a control group (Con, corn silage) and an experimental group (Tre, cotton straw and apple pomace mixed ensilage). The experiment lasted for 180 days, during which growth performance was evaluated. At the end of the experiment, 6 cattle were randomly selected from each group for slaughter to determine slaughter performance and meat quality. Meanwhile, rumen fluid samples were collected to analyze the rumen microbial community structure using 16S rRNA gene sequencing, and rumen fluid metabolites were analyzed with untargeted metabolomics (LC-MS) technology. The results showed that there were no significant differences in growth performance (average daily gain and final weight) between the two groups. However, compared to the Con group, the carcass weight, dressing percentage and drip loss of the Tre group were significantly decreased (p < 0.05). Rumen fermentation results indicated that the rumen pH value of the Tre group was significantly increased (p < 0.05), while the acetic acid content was significantly decreased (p < 0.05). Microbiome analysis showed that the α-diversity (Shannon and Chao1 indices) of rumen microbiota in the Tre group was significantly higher, and there was a significant difference in β-diversity (p < 0.05); the relative abundance of fiber-degrading bacteria such as Fibrobacter in the Tre group was significantly increased. LC-MS analysis revealed that the contents of beneficial metabolites such as N-Acetyl-L-methionine and Resveratrol were increased in the Tre group. In conclusion, cotton straw and apple pomace mixed ensilage feed can be used as an effective substitute for corn silage, modulating the rumen microbial community structure and altering the metabolite profile, thereby improving meat juiciness. This study provides theoretical support for the resourceful and high-value utilization of agricultural by-products such as cotton straw and fruit pomace in Xinjiang.}, }
@article {pmid42095017, year = {2026}, author = {An, QT and Li, W and Ren, Y and Liu, X and Yao, L and Li, Y and Zhao, X and Zhang, Y and Feng, P and Du, X}, title = {A comparative study of gut microbiota and metabolites in Tibetan sheep during cold and warm seasons.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1768985}, pmid = {42095017}, issn = {2297-1769}, abstract = {Tibetan sheep, a vital livestock species adapted to the extreme hypoxia, low temperatures, and intense radiation of the Qinghai-Tibet Plateau, rely on gastrointestinal microbiota for ecological balance and host nutrition, metabolism, and immunity. However, the possible associations of gut microbiota and metabolites with seasonal phenology remain unclear. Integrating biochemical, metagenomic, and metabolomic analyses, this study investigated seasonal variations in serum indices, microbial communities, and metabolites to inform enhanced breeding strategies. Analysis of forage nutritional composition showed that warm-season forages had significantly higher concentrations of dry matter (DM), crude protein (CP), and ether extract (EE) (p < 0.01), whereas cold-season forages were characterized by significantly greater levels of neutral detergent fiber (NDF) and acid detergent fiber (ADF) (p < 0.01). Correspondingly, serum analysis revealed significantly higher warm-season concentrations of alanine aminotransferase, total cholesterol, creatinine, and urea nitrogen compared with the cold season (p < 0.01). Gut microbiota composition shifted seasonally, with Bacteroides dominating in warm seasons and Bacillus predominating in cold seasons. Functional metagenomics indicated cold-season enrichment in pathways related to carbon metabolism, ABC transporters, aminoacyl-tRNA biosynthesis, pyruvate metabolism, DNA replication, and methane metabolism (p < 0.01). Metabolomics identified elevated warm-season microbial metabolites (His-Met, leucylleucine, luteolin 7-glucoside, ursolic acid; p < 0.05) and higher cold-season compounds (melatonin, glabrol, prostaglandin E2; p < 0.05), with KEGG enrichment linking these to steroid hormone biosynthesis, fatty acid metabolism, bile acid synthesis, and propanoate pathways. These findings suggest possible associations between seasonal extremes and: (1) modulation of nutrient metabolism (e.g., secondary bile acids and short-chain fatty acids); (2) activation of stress-response pathways (e.g., pentose phosphate pathway, ABC transporters, and DNA replication); and (3) immune regulation mediated by bioactive metabolites. Cold-season enrichment in DNA repair and energy-production pathways may be associated with responses to oxidative stress, whereas warm-season shifts in lipid metabolism are consistent with increased nutrient availability. Fluctuations in key metabolites-such as elevated melatonin in cold seasons and elevated ursolic acid in warm seasons-likely reflect adaptations related to thermoregulation and antioxidant defense. This work provides foundational insights into microbiota-host interactions under extreme environmental conditions, supporting the optimization of supplementation, probiotic use, and sustainable husbandry on the Qinghai-Tibet Plateau.}, }
@article {pmid42095188, year = {2026}, author = {Li, J and Yang, Y and Wang, Y and Liu, J and Huang, X and Li, Z and Li, J}, title = {Society and the Microbiome: A Biopsychosocial Window Into Comprehensive Well-Being: A Review.}, journal = {Health science reports}, volume = {9}, number = {5}, pages = {e72162}, pmid = {42095188}, issn = {2398-8835}, abstract = {BACKGROUND AND OBJECTIVES: In addition to biological factors, human social behavior, societal structures, and environmental contexts significantly influence the human microbiome. This review examines how socially relevant factors relate to the microbiome to clarify underlying mechanisms and health impacts, aiming to inform effective preventive and therapeutic strategies.<br><br>METHODS: We synthesized relevant literature from PubMed using a biopsychosocial framework, integrating structural socio-political and contextual factors to elucidate interactions between social behavior and the microbiota.<br><br>RESULTS AND CONCLUSIONS: Social behavior shapes the microbiome through complex biological, psychological, and socio&#x2011;cultural pathways, with health consequences involving immune, mental, and metabolic functions. Future research should clarify the fundamental drivers of this relationship, identify individual differences, and employ longitudinal designs to measure sustained effects.}, }
@article {pmid42095223, year = {2026}, author = {Cheng, Y and Zhang, L and Zhang, M and Yu, J}, title = {Advances in research on the effects of bile acids and their receptors on intestinal function.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1821418}, pmid = {42095223}, issn = {2296-861X}, abstract = {Bile acids (BAs), once regarded primarily as detergents facilitating lipid digestion, are now recognized as pivotal signaling molecules that orchestrate intestinal and systemic physiology through a diverse network of nuclear and membrane receptors, with distinct receptor classes mediating complementary transcriptional and rapid signaling responses, including Farnesoid X Receptor (FXR), Takeda G protein-coupled Receptor 5 (TGR5), Pregnane X Receptor (PXR), Peroxisome Proliferator-Activated Receptor α (PPARα), Vitamin D Receptor (VDR), and Mas-related G protein-coupled Receptor member X4 (MRGPRX4). This review synthesizes recent advances in understanding the molecular architecture of BA signaling, emphasizing receptor structural diversity, spatiotemporal expression patterns along the gastrointestinal tract, ligand specificity shaped by BA chemical modifications, and the emerging roles of microbiota-derived bile acid derivatives and selected non-canonical host targets in intestinal immune and metabolic regulation. Central to this signaling axis is the gut microbiome, which enzymatically reprograms the BAs pool through deconjugation, dehydroxylation, oxidation, and epimerization, as well as emerging reconjugation/amidation pathways, thereby generating classical secondary BAs as well as structurally novel metabolites that modulate host receptor activity and immune-cell programs. In turn, BAs shape microbial composition, establishing a dynamic bidirectional feedback loop critical for maintaining intestinal homeostasis. In addition to classical receptor signaling, selected microbiota-derived BAs metabolites can also influence immune-associated transcriptional regulators, thereby expanding the scope of BAs signaling in mucosal immune homeostasis. Beyond metabolism, BAs-receptor interactions integratively regulate gut barrier integrity via tight junction reinforcement, modulate immune responses through anti-inflammatory pathways and tolerogenic cell induction, and influence gut motility and neuroendocrine signaling. Dysregulation of BAs receptor and metabolite-mediated signaling axes is increasingly implicated in the pathogenesis of inflammatory bowel disease, bile acid malabsorption, diarrhea-predominant irritable bowel syndrome, colorectal cancer-via DNA damage and Wnt/β-catenin pathway activation-and systemic conditions such as obesity, non-alcoholic fatty liver disease, and sepsis-related intestinal injury. Emerging therapeutic strategies aim to restore BAs signaling balance through next-generation receptor modulators, tissue-targeted delivery systems, microbiome-directed interventions, rational use of sequestrants, and synergistic combination therapies, thereby supporting the development of more precise and mechanism-based interventions. Future progress will hinge on interdisciplinary approaches integrating metabolomics, gnotobiotic models, and clinical translation to harness the full therapeutic potential of the BAs signaling network in gastrointestinal and metabolic health.}, }
@article {pmid42095655, year = {2026}, author = {Weis, AM and Matthews, OJ and Bell, R and Pershing, NL and Dankwardt, A and Fleming, BA and Gigic, B and Schneider, M and Hardikar, S and Toriola, AT and Shibata, D and Li, CI and Byrd, DA and Stephens, WZ and Ulrich, CM and Mulvey, MA and Round, JL}, title = {Isolation of a highly virulent colibactin-positive tumor-promoting strain of Escherichia coli from the gut microbiota of an adult.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0021926}, doi = {10.1128/msphere.00219-26}, pmid = {42095655}, issn = {2379-5042}, abstract = {Recent studies have pointed to critical roles for microbes in both exacerbation of and protection from the development of colon cancer. While much has been learned, the field remains understudied, with functional studies available for only a handful of bacteria. To identify novel microbes associated with colorectal cancer (CRC) development, we employed a preclinical chemical carcinogenesis CRC mouse model using germ-free mice that were colonized with human microbiotas. During the course of these studies, we identified a microbiota that exacerbated CRC, from which we isolated an Escherichia coli strain that had disseminated to the mouse kidneys. This strain, which we designated as AW001, was genetically similar to the reference adherent-invasive E. coli (AIEC) strain NC101 and encoded the DNA-damaging toxin colibactin. In relevant animal models, AW001 worsened both colitis and sepsis, making it a colitogenic AIEC-like strain with the capacity to cause invasive systemic infections similar to extraintestinal pathogenic E. coli (ExPEC). This strain will be a relevant tool to study human-associated intestinal E. coli strains capable of causing disease in mice.IMPORTANCEColorectal cancer (CRC) is a significant burden on human health. A growing body of work has pointed to critical roles for microbes in the exacerbation of and protection from the development of CRC. Specific Escherichia coli strains can produce colibactin, a genotoxin that has been implicated in exacerbating CRC. In this study, we tested human microbiotas in a mouse model of CRC and isolated a colibactin-positive Escherichia coli strain that led to tumorigenesis, disseminated from the gut to the mouse kidneys, caused death, and worsened both colitis and sepsis in murine models. Identification of this strain enhances our collective knowledge and adds an important tool for future studies on the role of microbes and CRC tumorigenesis.}, }
@article {pmid42096014, year = {2026}, author = {Ng, WS and Ng, NC and Wong, RS and Goh, BH}, title = {Fermented Durian Tempoyak as a Source of Probiotics for Colorectal Cancer Prevention through Gut Microbiome Modulation.}, journal = {Current gastroenterology reports}, volume = {28}, number = {1}, pages = {}, pmid = {42096014}, issn = {1534-312X}, mesh = {Humans ; *Probiotics/therapeutic use ; *Colorectal Neoplasms/prevention &amp; control/microbiology ; *Gastrointestinal Microbiome ; *Fermented Foods/microbiology ; Dysbiosis/complications ; }, abstract = {PURPOSE OF REVIEW: Colorectal cancer (CRC) remains a major global and Malaysian public health concern, with increasing recognition of gut dysbiosis as a contributor to colorectal tumorigenesis. This review examines fermented durian tempoyak as a culturally relevant, probiotic-rich traditional food with potential application in CRC prevention through gut microbiome modulation.<br><br>RECENT FINDINGS: Dysbiosis may promote CRC through disruption of gut barrier integrity, chronic mucosal inflammation, immune dysregulation, reactive oxygen species (ROS)-mediated DNA damage, and altered microbial metabolism leading to carcinogenic metabolites such as secondary bile acids and hydrogen sulphide. Tempoyak commonly contains lactic acid bacteria, particularly Lactiplantibacillus plantarum, as well as Limosilactobacillus fermentum and Levilactobacillus brevis. Preclinical evidence suggests that related LAB strains can attenuate NF-&#x3ba;B, MAPK, STAT3, IL-17, and COX-2-associated inflammatory pathways, reduce immune-cell infiltration and oxidative stress, restore mucus and tight junction proteins, modulate bile acid metabolism, and reduce tumor burden in CRC or colitis-associated CRC models. Current evidence supports the mechanistic plausibility of tempoyak-associated LABs as microbiome-based agents for CRC chemoprevention. However, direct evidence using tempoyak-derived strains remains limited, and translation is constrained by strain-specific effects, microbial variability, sensory acceptability, safety and standardisation issues, and uncertain LAB viability after cooking. Future studies should prioritise strain characterisation, starter culture standardisation, probiotic stabilisation strategies, CRC-specific preclinical models, and well-designed human trials in high-risk populations.}, }
@article {pmid42096024, year = {2026}, author = {Hu, X and Chen, J and Zhou, Y and Ji, X and Shen, S and Qian, J and Li, T and Xu, F and Zhou, Y and Zhou, D and Zhang, X}, title = {n-3 Polyunsaturated Fatty Acids Improve DSS-Induced Acute Colitis in Mice via Intestinal Barrier Fortification and Gut Microbiome Modulation.}, journal = {Digestive diseases and sciences}, volume = {}, number = {}, pages = {}, pmid = {42096024}, issn = {1573-2568}, support = {82404257//the National Natural Science Foundation of China/ ; 82273621//the National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The increasing global burden of ulcerative colitis (UC) is showing a high incidence in developed countries and a swift rise in developing countries. n-3 polyunsaturated fatty acids (PUFAs), particularly eicosatetraenoic acid (EPA) and docosahexaenoic acid (DHA), have demonstrated anti-inflammatory effects. However, their exact mechanisms in intestinal barrier repair for UC remain incompletely elucidated.<br><br>METHODS: Acute UC was induced using 2% dextran sulfate sodium (DSS) and the therapeutic effects of mesalazine, EPA, DHA, and EPA&#x2009;+&#x2009;DHA were evaluated. The mucus barrier was assessed histologically. RT-qPCR and Western blot were used to quantify the expression of Mucin2, mechanical barrier proteins (Claudin-1/Occludin), and key signaling pathways (PI3K/Akt, TNF-&#x3b1;/NF-&#x3ba;B, GPR120/PKA/CREB). Gut microbiome composition was analyzed via 16S rRNA sequencing.<br><br>RESULTS: EPA&#x2009;+&#x2009;DHA intervention demonstrated optimal efficacy in alleviating colitis, through establishing an anti-inflammatory colonic lipid microenvironment by elevating the EPA/AA and DHA/AA ratios. Inhibiting PI3K/Akt/NHE3, downregulating TNF-&#x3b1;/NF-&#x3ba;B/DRA, activating GPR120/PKA/CREB/AQP) improved the mucosal barrier and restored tight junction to enhance the mechanical barrier. Furthermore, EPA&#x2009;+&#x2009;DHA significantly increased the abundance of beneficial microbiome like Lachnospiraceae and Ruminococcaceae.<br><br>CONCLUSION: EPA&#x2009;+&#x2009;DHA effectively alleviates acute UC in mice by fortifying the colonic mucus-mechanical dual barrier and regulating gut microbiome homeostasis, providing a novel potential strategy for UC adjunctive treatment.}, }
@article {pmid42096120, year = {2026}, author = {Wu, R and Yao, G}, title = {Research advancement on the correlation between gut microbiota and chronic kidney disease.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {6}, pages = {}, pmid = {42096120}, issn = {1572-9699}, support = {010086//the Beijing Major Epidemic Prevention and Control Key Specialty Intensive Care Medicine Construction Project under Grant/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Renal Insufficiency, Chronic/microbiology/therapy ; Dysbiosis/microbiology ; Probiotics ; Animals ; }, abstract = {Chronic kidney disease (CKD) represents a significant global health challenge, with its progression and complications associated with dysbiosis of the gut microbiota. Patients with CKD demonstrate stage-dependent alterations in the composition of gut microbiota and a reduction in diversity, which is characterized by a decline in beneficial bacteria (e.g., Bifidobacterium, Lactobacillus) and an increase in pathogenic species. This dysbiosis disrupts the gut-kidney axis, resulting in a depletion of protective metabolites such as short-chain fatty acids (SCFAs) and secondary bile acids, while facilitating the accumulation of toxic metabolites including trimethylamine N-oxide (TMAO), indoxyl sulfate (IS), and p-cresyl sulfate (pCS). These toxins contribute to the progression of CKD and cardiovascular complications through mechanisms that involve oxidative stress, inflammation (e.g., NF-ĸB/NLRP3 activation), fibrosis (e.g., TGF-β/Smad signaling), and endothelial dysfunction. Therapeutic strategies aimed at modulating the gut microbiota encompass dietary interventions (such as increasing fiber and plant-based protein), microecological agents (including probiotics and prebiotics), fecal microbiota transplantation (FMT), and adsorbents (e.g., targeting uremic toxins). Although these approaches show promise in delaying CKD progression and alleviating complications, they necessitate further validation through large-scale clinical trials to confirm their efficacy, safety, and the development of personalized protocols. Investigating the gut-kidney axis may provide novel biomarkers and therapeutic opportunities for enhancing CKD outcomes.}, }
@article {pmid42096418, year = {2026}, author = {Santini, AT and Cerqueira, AES and Moran, NA and Resende, HC and Santana, WC and de Paula, SO and da Silva, CC}, title = {Gut microbiota of Brazilian Melipona stingless bees: Dominant members and their localization in different gut regions.}, journal = {PloS one}, volume = {21}, number = {5}, pages = {e0326546}, pmid = {42096418}, issn = {1932-6203}, mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Brazil ; Symbiosis ; *Bacteria/genetics/classification/isolation &amp; purification ; Phylogeny ; }, abstract = {The gut microbiome of eusocial corbiculate bees, which include honeybees, bumblebees, and stingless bees, consists of anciently associated, host-specific bacteria that play crucial role in nutrition, pathogen defense and host fitness. While the core microbiota of honeybees and bumblebees is well characterized, the composition, spatial organization, and evolutionary dynamics of the microbiota of stingless bees remain poorly understood. This gap is particularly evident in the diverse genus Melipona, where Snodgrassella and Gilliamella, ubiquitous symbionts of honeybees and bumblebees, appear rare or absent, indicating a shift in microbiota composition in these stingless bees. Here, we address this gap by characterizing the microbiota of multiple Melipona species using 16S rRNA amplicon sequencing of newly collected and previously published data from field-collected samples. We also mapped the spatial localization of the dominant microbiota members within the gut regions of Melipona quadrifasciata anthidioides through targeted dissection. The Melipona microbiota is dominated by members of the genera Bifidobacterium, Lactobacillus, Apilactobacillus, Floricoccus, and Bombella, with striking regional structure. Apilactobacillus and Bombella dominate in the crop, whereas Apilactobacillus and other members of the Lactobacillaceae are most abundant in the ventriculus. The ileum lacks Snodgrassella and Gilliamella but contains a putative new symbiont closely related to Floricoccus, as well as strains of Bifidobacterium, Lactobacillaceae (including Apilactobacillus), and Bombella. The rectum is dominated by Bifidobacterium and Lactobacillus. These findings reveal a distinct microbiota architecture in Melipona that differs from other corniculate bees yet retains compartment-specific specialization, suggesting an alternative symbiotic strategy that may reflect unique dietary ecology and evolutionary history. Understanding these patterns advances our knowledge of host-microbe symbiosis and provides a baseline for microbiome conservation in declining stingless bee populations.}, }
@article {pmid42096491, year = {2026}, author = {Ma, Z and Shi, H and Bai, X and Wang, Z and Cao, J and Dong, Y and Chen, Y}, title = {Host metabolism shapes the intestinal microbiota: a top-down paradigm of environmental selection pressure.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2667735}, doi = {10.1080/19490976.2026.2667735}, pmid = {42096491}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Animals ; Dysbiosis/microbiology/metabolism ; Energy Metabolism ; *Host Microbial Interactions ; Intestinal Mucosa/metabolism/microbiology ; Bacteria/metabolism/genetics/classification ; Homeostasis ; }, abstract = {Intestinal homeostasis is not a stochastic microbial assembly but a deterministic outcome orchestrated by host-mediated metabolic gating. Traditional research has prioritized the microbiota's impact on host physiology. However, the consistent expansion of facultative anaerobes, such as Enterobacteriaceae, observed in pathological states like intestinal inflammation, suggests that dysbiosis is fundamentally a consequence of impaired host regulation. Here, we propose a "top-down" paradigm of host metabolic regulation, framing the host as an "ecological engineer" that actively shapes the microbiome through metabolism. We detail three critical metabolic filters: (1) the maintenance of epithelial hypoxia via mitochondrial β-oxidation to suppress aerobic respiration; (2) the implementation of "nutritional immunity" to restrict glucose and inflammation-derived electron acceptors (nitrate and tetrathionate); and (3) the energy-dependent synthesis of the gel-forming mucin 2 (MUC2) mucus layer and antimicrobial peptides (AMPs). We argue that the breakdown of these filters leads to "niche opening," which acts as the fundamental driver of dysbiosis. Finally, we discuss therapeutic strategies aimed at restoring host bioenergetics-including Peroxisome proliferator-activated receptor gamma (PPAR-γ) agonists, melatonin, and ketogenic diets-to rebuild the host's ecological filtration capacity and fundamentally correct dysbiosis.}, }
@article {pmid42096550, year = {2026}, author = {Xie, M and Xu, C and Xiang, N and Liao, T and Liu, X and Liu, Z and Feng, X and He, Q and Liang, Z and Wang, W and Dai, Y and Yan, L and Pogoreutz, C and Barra, L and Au, SWN and Jiang, L and Voolstra, CR and Luo, H}, title = {Trait-based signatures associated with persistence and thermal benefit in a genomically decayed coral probiotic.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag106}, pmid = {42096550}, issn = {1751-7370}, abstract = {A key bottleneck in microbiome engineering is ensuring long-term host association of introduced microbes. Selecting probiotic candidates based on evolutionary genomic decay signatures of emerging host dependency offers a potential solution. The Ruegeria strain B4 of population MC10, identified by such signatures, showed persistent coral colonization in a companion study. Whether this persistence translates into measurable host benefit compared to other coral-associated Ruegeria strains, and which mechanisms underlie such benefit, remained unknown. Here we directly compare the probiotic efficacy of MC10-B4 against two sympatric Ruegeria strains isolated from the same coral colony and mucus compartment, controlling for host genotype and microenvironment. MC10-B4 inoculation significantly increased heat stress tolerance in the model cnidarian Aiptasia (Exaiptasia diaphana strain H2), outperforming both controls. To understand the mechanistic basis, we characterized the functional profile of MC10-B4 using integrated multi-omics. The MC10 genome is enriched in host-interaction genes, including siderophore-mediated iron acquisition and exopolysaccharide biosynthesis, confirmed phenotypically by iron scavenging and enhanced biofilm formation. Following exposure to coral tissue extract, MC10-B4 underwent a coordinated "motile-to-sessile" proteomic reprogramming, downregulating flagellar motor components whereas upregulating flagellin and biofilm regulators. This response was distinct from sympatric relatives, which instead mounted broad upregulation of nutrient acquisition systems. MC10-B4's functional profile, particularly its oxidative stress sensitivity, contrasts with traits favored in conventional probiotic screens. Our results provide mechanistic insight into traits associated with long-term host association and thermal benefit, validating an evolution-guided approach that prioritizes innate colonization potential over pre-defined laboratory functionalities for rational probiotic design.}, }
@article {pmid42096749, year = {2026}, author = {Kafkoutsou, AL and Stewart, M and Bakali, U and Beaver, CC and O'Connor, G and Kobetz, EN and Caban-Martinez, AJ and Deo, SK and Daunert, S and Schaefer Solle, N}, title = {Vaginal polycyclic aromatic hydrocarbons (PAHs), HPV infection, and vaginal microbiome in firefighters: A cross-sectional study.}, journal = {Journal of hazardous materials}, volume = {511}, number = {}, pages = {142072}, doi = {10.1016/j.jhazmat.2026.142072}, pmid = {42096749}, issn = {1873-3336}, abstract = {Female firefighters are routinely exposed to combustion-derived toxicants, yet the reproductive health implications of this exposure are largely unknown. We investigated whether polycyclic aromatic hydrocarbons (PAHs) are detectable in the vaginal tract of female firefighters and whether these contaminants are linked to high-risk human papillomavirus (HPV) infection and vaginal microbiome alterations. In this cross-sectional study 49 female firefighters and 51 community controls self-collected vaginal swabs for analysis of 16 EPA-priority PAHs, high-risk HPV, and microbial composition. All 16 PAHs were detectable and median total PAHs were 3-fold higher in firefighters than controls (p < .0001). PAH burden increased with firefighting tenure showing a strong positive correlation between high- and low-molecular-weight congeners (r = 0.85). High-risk HPV was detected in 12.2% of firefighters versus 3.9% of controls and was associated with higher PAH levels (p = 0.02). Firefighters exhibited a microbiome shift characterized by increased relative abundance of Gardnerella (r = 0.32 with total PAHs) and reduced Lactobacillus dominance. Detection of vaginal PAHs along with their associations with HPV and dysbiosis, suggests a previously unrecognized pathway by which occupational exposures may elevate cervical cancer risk. Targeted exposure reduction policies and vigilant gynecologic screening should be considered for this underserved workforce.}, }
@article {pmid42096978, year = {2026}, author = {Crespo-García, C and Taaffe, DR and Peddle-McIntyre, CJ and Jeffery, E and Campbell, JP and Thomas, R and Galvao, DA and Newton, RU}, title = {Precision nutrition in breast cancer: Towards patient- and tumour-informed dietary strategies.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {61}, number = {}, pages = {106670}, doi = {10.1016/j.clnu.2026.106670}, pmid = {42096978}, issn = {1532-1983}, abstract = {Dietary strategies are increasingly recognized as important modulators of breast cancer outcomes, acting through effects on metabolic regulation, weight management, hormone signalling, immune function, and the gut microbiome. However, breast cancer heterogeneity and inter-individual variability mean that generic dietary guidelines may not fully capture patient needs. Precision nutrition offers the opportunity to align dietary interventions with tumour subtype, treatment context, and host biology, potentially enhancing therapeutic response and survivorship in patients diagnosed with breast cancer. In this narrative review, we summarize evidence on dietary patterns and prognosis, and explore how targeted interventions, including fasting regimens, ketogenic diets, and caloric restriction, may be informed by and targeted to host factors such as obesity, metabolic dysfunction, genetics and epigenetics, and microbiome composition, as well as tumour and treatment characteristics. We also discuss the emerging role of digital tools and multi-omics approaches to support personalization. While clinical translation is at an early stage, refining dietary recommendations through precision approaches may open new opportunities to improve prognosis and long-term care in breast cancer.}, }
@article {pmid42097107, year = {2026}, author = {Panyakhamlerd, K and Rungruxsirivorn, T and Panichaya, P and Nimitpanya, P and Payungporn, S and Ariyasriwatana, C and Suwan, A and Visedthorn, S and Ruengket, P and Tanprasertkul, C}, title = {The effect of hormone therapy on vaginal microbiota in women with genitourinary syndrome of menopause: A double-blind, randomized, placebo-controlled trial.}, journal = {Maturitas}, volume = {209}, number = {}, pages = {108963}, doi = {10.1016/j.maturitas.2026.108963}, pmid = {42097107}, issn = {1873-4111}, abstract = {This double-blind, randomized, placebo-controlled trial investigated the effects of oral combined menopausal hormone therapy (MHT) on vaginal microbiota and clinical outcomes in postmenopausal women with genitourinary syndrome of menopause (GSM). Thirty-four healthy postmenopausal women aged 40-60 years with moderate to severe GSM were randomized to receive either oral estradiol 1 mg/dydrogesterone 5 mg (Femoston conti®) or placebo daily for 12 weeks. Vaginal microbiota was assessed at baseline and week 12 using 16S rDNA gene sequencing. Clinical outcomes, including the most bothersome symptom (MBS), vaginal atrophy score (VAS), vaginal pH, vaginal health index (VHI) and vaginal maturation value (VMV), were evaluated at baseline, week 6, and week 12. The MHT group demonstrated significant more improvement in all clinical measures compared with placebo: MBS (p = 0.008), VAS (p < 0.001), vaginal pH (p = 0.001), VHI (p < 0.001) and VMV (p < 0.001). However, no significant differences were observed in microbial composition or diversity between groups after treatment. These findings suggest that while systemic hormone therapy provides meaningful symptom relief and improves vaginal tissue health, these clinical benefits can occur without concurrent, statistically significant changes in the vaginal microbiota. This supports the clinical value of early systemic MHT in managing GSM, even in the absence of microbiome restoration.}, }
@article {pmid42097142, year = {2026}, author = {El Mouali, Y and Tawk, C and Huang, KD and Sivapornnukul, P and Mengoni, C and Segata, N and Strowig, T}, title = {Biogeography-associated emergence of enhanced oxygen tolerance in the abundant human gut commensal Segatella copri.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.04.006}, pmid = {42097142}, issn = {1934-6069}, abstract = {In the human gut, oxygen levels decrease with increasing distance from the epithelium, creating a gradient that dictates the spatial distribution of commensal bacteria based on varying oxygen tolerance. However, dietary and lifestyle changes can disrupt this ecosystem. Segatella copri, a prevalent ancestral commensal, typically displays greater oxygen sensitivity than Bacteroides species. Here, we find that the transcriptional regulator PerR controls a genetic network underlying S. copri's oxygen response that is critical for gut colonization. Notably, a subset of S. copri strains have acquired an additional oxygen response regulator, OxyR, likely through horizontal gene transfer from other Bacteroidales, conferring enhanced oxygen tolerance. Interestingly, OxyR-positive strains are more prevalent in industrialized countries yet absent in contemporary humans with traditional lifestyles and in ancient human samples. These findings point to recent evolutionary pressures on Segatella, potentially driven by lifestyle changes, which may impact the spatial distribution of the human gut microbiome.}, }
@article {pmid42097143, year = {2026}, author = {Antunes Fernandes, K and Sanders, F and Cafiero, TR and Huang, C and Reyes, J and Biswas, A and Lim, AI}, title = {Maternal helminths rewire the microbiota to promote offspring antiviral immunity.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.04.009}, pmid = {42097143}, issn = {1934-6069}, abstract = {Maternal environmental exposures can alter microbiome composition and lead to changes in offspring immunity. Industrialization has led to significant shifts in the microbiome, but whether these have transgenerational impacts remains unclear. Here, we discovered that maternal helminths, an evolutionarily conserved mammalian partner lost in industrialized societies, confer broad and lasting protection against respiratory viruses in offspring. This heterologous antiviral immunity is mediated by helminth-induced changes in the maternal microbiota. The tryptophan metabolite indole-3-propionic acid (IPA), derived from helminth-altered microbiota, induces lung epithelial IFN-I responses and is sufficient to protect offspring from respiratory syncytial virus (RSV) and influenza A virus infections. Analysis of chronically helminth-infected human populations reveals gut microbiota enriched for tryptophan metabolic capacity. Additionally, IPA treatment is sufficient to enhance antiviral IFN-I signaling in human bronchial epithelial cells. Collectively, this work uncovers the importance of maternal helminth-driven trans-kingdom crosstalk across generations and highlights microbial metabolites as actionable strategies to strengthen antiviral defense.}, }
@article {pmid42097354, year = {2026}, author = {Kaliappa, GD and Palanisamy, H and Vidyalakshmi, S}, title = {Integrative Machine Learning Models to Unravel Gut Microbial Dysbiosis and Functional Disruption in Polycystic Ovary Syndrome.}, journal = {F&amp;S science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.xfss.2026.04.005}, pmid = {42097354}, issn = {2666-335X}, abstract = {OBJECTIVE: To study gut microbial diversity and metabolic pathway disruptions in women with PolyCystic Ovary Syndrome (PCOS) compared to healthy controls, and to evaluate the diagnostic potential of microbiome-driven machine learning models.<br><br>DESIGN: Case-controlled metagenomic data analysis SUBJECTS: Gut metagenomic data from women diagnosed with PCOS and age-matched healthy female controls EXPOSURE: Presence of PolyCystic Ovary Syndrome (PCOS) MAIN OUTCOME MEASURES: The primary outcome measures will include gut microbial alpha and beta diversity indices, microbial taxon abundance, functional pathway profiles, predicted metabolite levels, microbe-functional pathway-metabolite interaction networks, and the diagnostic accuracy of microbiome-based machine learning models.<br><br>RESULTS: Alpha and beta diversity analyses revealed marked gut microbial dysbiosis in women with PCOS, despite comparable species richness to healthy controls. Differential abundance analysis identified 41 significantly altered microbial species, including enrichment of pro-inflammatory taxa such as Bacteroides vulgatus and Ruminococcus gnavus, and depletion of beneficial commensals including Roseburia hominis and Prevotella copri. These compositional shifts indicate a pro-inflammatory microbial community structure in PCOS. Functional profiling demonstrated the upregulation of pathways involved in nucleotide turnover, lipid and carbohydrate metabolism, and neurotransmitter synthesis, potentially contributing to metabolic and neuroendocrine disruption. Network analysis revealed fragmented and unstable microbial-metabolite associations in PCOS compared with cohesive networks in controls. Microbiome based machine learning models achieved a diagnostic accuracy of 84.25% (AUC 0.93), underscoring their predictive potential.<br><br>CONCLUSION: The gut microbiome in PCOS is characterized by a pro-inflammatory community structure and disrupted metabolic pathways. These findings demonstrate the diagnostic potential of microbiome-based models and underscore the gut microbiome as a promising target for therapeutic interventions in the management of PCOS.}, }
@article {pmid42097383, year = {2026}, author = {Yang, Z and Liang, Z and Cao, L and Li, S and Gao, L and Tian, D and Qiu, Z and Chen, J}, title = {Altitude-Dependent Variations in Environmental Conditions and Human Activities Regulate Microbial Community Assembly and Carbon Metabolism Patterns in Headwater Rivers.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124656}, doi = {10.1016/j.envres.2026.124656}, pmid = {42097383}, issn = {1096-0953}, abstract = {Microorganisms are core drivers of biogeochemical processes in headwater stream ecosystems, yet the response mechanisms of their community composition and carbon metabolic traits to altitudinal gradients and local environmental conditions remain poorly resolved. Elucidating these altitude-dependent patterns is critical for understanding microbiome-mediated ecosystem functioning in vulnerable headwater freshwater habitats. Here, we investigated microbial community structure and carbon substrate utilization in three headwater streams with >1000 m altitudinal span, combining 16S rRNA gene amplicon sequencing, Biolog EcoPlate metabolic phenotyping, and multivariate statistics to characterize microbial taxonomic and functional diversity and their key environmental drivers. Proteobacteria (45.7% average relative abundance) and Bacteroidota (13.6%) dominated all samples, collectively accounting for >60% of the total community. A 1000 m altitude was identified as the ecological threshold, with significant divergences in microbial diversity, community assembly, and carbon utilization patterns across this boundary. Stochastic processes dominated community assembly in steep-gradient streams (68% relative contribution), while deterministic homogeneous selection prevailed in topographically gentle streams (67% contribution); increasing human activity shifted the dominant assembly process from homogeneous selection (67%) to heterogeneous dispersal (52%). Microbial carbon utilization efficiency showed three distinct altitudinal patterns (decreasing, hump-shaped, U-shaped). Variation partitioning analysis revealed that altitude, hydrochemistry, and water physical parameters independently explained 21%, 17%, and 9% of community variation, respectively. Proteobacteria acts as the key phylum governing carbon utilization. This study confirms that altitude is a pivotal driver of headwater microbial diversity and metabolic function, and microbes can adapt to environmental changes by adjusting carbon substrate utilization strategies. Our findings provide new insights into the links between microbial functional traits, ecosystem stability, and nutrient cycling in headwater streams.}, }
@article {pmid42097542, year = {2026}, author = {Habibyan, YB and Sharkey, KA and Nasser, Y}, title = {PROTEASES AND ABDOMINAL PAIN - OLD DOG, NEW (MICROBIAL) TRICKS.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {}, number = {}, pages = {101803}, doi = {10.1016/j.jcmgh.2026.101803}, pmid = {42097542}, issn = {2352-345X}, }
@article {pmid42097543, year = {2026}, author = {Peisl, S and Melum, E}, title = {From Kimchi to PSC: Leuconostoc citreum LB-P8 as a microbiome-based therapeutic approach.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {}, number = {}, pages = {101800}, doi = {10.1016/j.jcmgh.2026.101800}, pmid = {42097543}, issn = {2352-345X}, }
@article {pmid42097977, year = {2026}, author = {Krifors, A and Larsson, T and Wångdahl, A and Stensvold, CR}, title = {Time to rethink Blastocystis in faecal microbiota transplantation.}, journal = {Trends in parasitology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pt.2026.04.005}, pmid = {42097977}, issn = {1471-5007}, abstract = {Blastocystis commonly colonises the human gut, but its presence has traditionally led to the exclusion of faecal microbiota transplantation donors. Emerging evidence links it to greater microbial diversity and favourable metabolic profiles, while no harm is seen in immunocompetent recipients. Routine screening may be unnecessary, except for subtype-specific testing in immunocompromised patients.}, }
@article {pmid42098022, year = {2026}, author = {Baba, Y}, title = {[Esophageal Cancer and Gut Microbiome].}, journal = {Gan to kagaku ryoho. Cancer &amp; chemotherapy}, volume = {53}, number = {3}, pages = {158-161}, pmid = {42098022}, issn = {0385-0684}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Esophageal Neoplasms/microbiology/therapy ; }, abstract = {The gut microbiota has recently garnered considerable attention across the medical field, as its involvement has been reported in a broad spectrum of conditions including cancer, obesity, inflammatory bowel disease, and even neuropsychiatric disorders. The human body is composed of approximately 30 trillion human cells and an almost equal number of bacterial cells, forming a highly integrated symbiotic relationship. While the human genome encodes only about 20,000 genes, the gut microbiota harbors several million to tens of millions of genes, offering an overwhelmingly greater genetic repertoire. The composition of the microbiota is influenced by diet, lifestyle, medications, and aging, thereby shaping unique individual - specific patterns. Regional and temporal variations are also recognized, and functional redundancy among different bacterial taxa, known as"functional mimicry,"further underscores its flexibility. Thus, the gut microbiota should be regarded as a dynamic and modifiable ecosystem rather than a fixed entity, making it a promising target for disease prevention and therapeutic intervention. In the context of esophageal cancer, emerging evidence indicates that alterations in the microbiota may affect carcinogenesis, disease progression, and therapeutic responses. These insights highlight the potential of the microbiota as both a biomarker and a therapeutic target, and suggest that integrating microbiome research into clinical oncology could open new avenues for improving patient outcomes.}, }
@article {pmid42098023, year = {2026}, author = {Shibata, T}, title = {[Microbiome and Colorectal Cancer].}, journal = {Gan to kagaku ryoho. Cancer &amp; chemotherapy}, volume = {53}, number = {3}, pages = {162-167}, pmid = {42098023}, issn = {0385-0684}, mesh = {Humans ; *Colorectal Neoplasms/microbiology/genetics ; *Microbiota ; Mutation ; Peptides ; Polyketides ; }, abstract = {The number of colorectal cancer patients in Japan continues to rise, placing the country among the highest rates globally, surpassing even Western nations. Furthermore, the increase in colorectal cancer among younger individuals(under 50 years old)is a significant concern. This rapid rise in colorectal cancer patients cannot be explained solely by the adoption of Western lifestyles, suggesting the presence of unknown carcinogenic factors. Colibactin toxin, produced by certain gut bacteria (pks+ Escherichia coli), binds to AT-rich DNA and induces characteristic mutation patterns. An international collaborative study compared the differences in these mutation patterns across 981 colorectal cancer samples collected from 11 countries, including Japan. Surprisingly, it revealed that Japanese cases exhibited a significantly higher frequency of the colibactin toxin - induced mutation patterns(SBS88 and ID18)compared to other countries. Furthermore, SBS88 and ID18 were particularly prevalent in younger patients and notably prominent in the right colon, including the rectum. These findings suggest that interventions such as preventing infection with pks+ bacteria, eradicating them, or inhibiting the function of colibactin toxin could potentially reduce the incidence of colorectal cancer, particularly in younger patients. Such prevention is also considered likely to be effective in Japan, where infection is presumed to be highly prevalent.}, }
@article {pmid42098024, year = {2026}, author = {Oya, Y and Tanaka, I}, title = {[Current Status and Future Perspectives of Microbiome Research in Lung Cancer].}, journal = {Gan to kagaku ryoho. Cancer &amp; chemotherapy}, volume = {53}, number = {3}, pages = {168-174}, pmid = {42098024}, issn = {0385-0684}, mesh = {Humans ; *Lung Neoplasms/microbiology/drug therapy/immunology/therapy ; *Microbiota ; *Gastrointestinal Microbiome ; }, abstract = {Recent advances in immune checkpoint inhibitors(ICIs)and molecular targeted therapies have substantially improved outcomes in lung cancer; however, marked inter-individual variability in efficacy and toxicity remains. Accumulating evidence suggests that the gut microbiota, acting through the"gut-lung axis,"is a key modifier of treatment response and tolerance in this setting. High microbial diversity and the abundance of beneficial taxa such as Akkermansia, Bifidobacterium, and Faecalibacterium have been associated with favorable ICI responses, whereas dysbiosis induced by antibiotics, proton pump inhibitors, cytotoxic chemotherapy, or lifestyle factors is linked to reduced efficacy and increased toxicity. Microbial metabolites, including short-chain fatty acids and tryptophan derivatives, shape antitumor immunity by modulating T-cell activation, regulatory T-cell differentiation, and the tumor immune microenvironment. In addition, emerging data indicate that the gut microbiota may influence the pharmacodynamics and adverse event profiles of EGFR tyrosine kinase inhibitors(EGFR- TKIs)and other targeted agents, particularly with respect to gastrointestinal toxicity. Smoking, a central etiological factor in lung carcinogenesis, also alters gut microbial composition, decreasing beneficial anti-inflammatory species and promoting pro-inflammatory taxa, thereby potentially aggravating systemic inflammation and impairing ICI responsiveness. Notably, partial restoration of a healthier microbiome appears possible with smoking cessation and rational supportive care. Interventions aimed at favorably modifying the gut ecosystem-such as high-fiber or plant-forward diets, probiotics, and fecal microbiotatransplantation-have begun to show promise in enhancing ICI efficacy without substantially increasing immune-related adverse events. Prospective trials in lung cancer are now underway to evaluate the clinical utility of microbiome-based biomarkers and interventions. Collectively, these findings position the gut microbiota as both a predictive biomarker and a modifiable therapeutic target, with the potential to refine patient stratification, optimize treatment selection, and advance truly personalized medicine in lung cancer.}, }
@article {pmid42098025, year = {2026}, author = {Fukushima, H and Ishikawa, D and Nagahara, A}, title = {[Gut Microbiota Transplantation for Esophageal and Gastric Cancer].}, journal = {Gan to kagaku ryoho. Cancer &amp; chemotherapy}, volume = {53}, number = {3}, pages = {175-181}, pmid = {42098025}, issn = {0385-0684}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Stomach Neoplasms/therapy/microbiology/immunology ; *Esophageal Neoplasms/therapy/microbiology/immunology ; *Fecal Microbiota Transplantation ; }, abstract = {Immune checkpoint inhibitors(ICIs)have remarkably improved survival with durable response for patients with multiple cancer type. But, the accurate predictors of response and toxicity to immunotherapy are still unclear. In recent years, the human microbiota, specially the gut microbiota, has been attracting attention in various fields, and it is one of the topics in the field of oncology. The gut microbiome, which refers to the microorganisms and their genes, affects the host immunity both locally and systemically. Modulation of the gut microbiota alters the immune systems and affects the efficacy of ICI. Many clinical trials targeting the gut microbiota, such as fecal microbiota transplantation(FMT)and biotics intervention, are currently being conducted. In this review, we consider the evidence on the role of the microbiome in cancer patients and research began the impact of FMT on the efficacy of ICIs in cancer. ln the future, research on carcinogenesis mechanisms and advance cancer treatment focusing on the human microbiota will become in creakingly active.}, }
@article {pmid42098165, year = {2026}, author = {Sharma, MK and Agarwal, N and Stadulis, SE and Dugan, EM and Giovannoni, CB and Glesener, H and Abdollahzadeh, D and Tanveer, H and Gracey, PR and Huang, M and Gibney, PA and Voth-Gaeddert, LE and Tako, E}, title = {Dietary grape pomace mitigates high-NSP-induced inflammation and production loss via microbiome-SCFA-immune mediated pathways.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00996-8}, pmid = {42098165}, issn = {2055-5008}, abstract = {The United States poultry industry is transitioning away from antibiotic growth promoters (AGP) to antibiotic-free programs, which may increase the risk of chronic intestinal inflammation due to exposure to multiple factors. Grape pomace (GP), a polyphenol-rich by-product, might be a promising candidate for mitigating such inflammation. This study investigated the fermented and non-fermented GP as potential substitutes for antibiotic growth promoters in broilers. A total of 126 broilers were divided into six treatment groups: (i) standard diet (STD), (ii) high non-starch polysaccharide diet (NSP), (iii) NSP + zinc bacitracin (AGP), (iv) NSP + 0.5% GP (GP), (v) NSP + 0.5% Lactobacillus casei fermented GP (LAB FGP), and (vi) NSP + 0.5% Saccharomyces cerevisiae fermented GP (YST FGP). NSP-fed birds exhibited reduced growth and increased TNF-α and IL-1β expression, indicating chronic inflammation. GP and FGP suppressed cytokine expression, modulated microbial homeostasis, and increased butyrate production, suggesting functional modulation of the cecal microbiome. Exploratory correlation identified the Lactobacillaceae-butyrate-IL-1β pathway, positively associated with growth, microbiome, and SCFA production, and negatively associated with inflammation. Overall, incorporating 0.5% of GP or FGP into the diet may serve as an effective alternative to AGPs in broiler production, with the added benefits of antioxidants and prebiotics.}, }
@article {pmid42098175, year = {2026}, author = {Niu, Z and Xu, J and Hou, X and Liu, G and Yao, J and Cao, Y and Du, Q and Tong, D and Wu, S}, title = {Multi-omics atlas of the bovine coronavirus-infected calf jejunum: reduction of Phocaeicola coprophilus and deoxycholic acid linked to Th17/Treg imbalance.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00997-7}, pmid = {42098175}, issn = {2055-5008}, support = {32272966//National Natural Science Foundation of China/ ; 32573272//National Natural Science Foundation of China/ ; 2452023072//Chinese Universities Scientific Fund/ ; 2024-KFKT-031//National Center of Technology Innovation for Dairy/ ; 2025JH-ZRKX-0639//General Project of the Natural Science Foundation of Xi'an, Shaanxi Province/ ; }, abstract = {Optimal calf rearing is fundamental for ensuring efficient milk production. Bovine coronavirus (BCoV) poses a significant threat to calf health and leads to substantial economic losses in the dairy industry. However, the mechanisms by which the intestinal mucosal microbiome regulates the host immune response during infection remain unclear. In this study, we constructed a high-resolution map of the jejunal mucosal microenvironment in BCoV-infected calves. Our findings revealed that BCoV infection led to severe microbial dysbiosis, characterized by a marked reduction in Phocaeicola coprophilus (formerly known as Bacteroides coprophilus) and decreased secondary bile acid, especially deoxycholic acid (DCA). Concurrently, enrichment of harmful microbiota correlated with increased arachidonic acid metabolites. At the host level, BCoV infection altered the composition of jejunal mucosal cells and affected metabolic and immune-related pathways. The differentiation of CD4[+] T cells played a central role in the jejunum's response to BCoV infection. By integrating these metabolic alterations with dynamic host cellular responses, we suggested a putative that DCA deficiency might contribute to the pathological polarization of CD4[+] T cells toward a Th17 phenotype while suppressing Treg differentiation. These findings suggest that restoring the Phocaeicola coprophilus-affected bile acid transformation might represent a promising therapeutic strategy for BCoV infection.}, }
@article {pmid42098416, year = {2026}, author = {Albaugh, VL and Devarakonda, SLS}, title = {Surgically reshaping the gut microbiome.}, journal = {Nature metabolism}, volume = {}, number = {}, pages = {}, pmid = {42098416}, issn = {2522-5812}, }
@article {pmid42098417, year = {2026}, author = {Olsson, LM and Borgeraas, H and Chakaroun, RM and Hofsø, D and Hertel, JK and Dwibedi, C and Mitteregger, M and Holst, JJ and Tremaroli, V and Hjelmesæth, J and Bäckhed, F}, title = {Gut microbiota responses to bariatric surgery are associated with metabolic outcomes and type 2 diabetes remission.}, journal = {Nature metabolism}, volume = {}, number = {}, pages = {}, pmid = {42098417}, issn = {2522-5812}, support = {2018-05973//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2022-06725//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2013-07800//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 615362//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; NNF13OC0008163//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; METABASE//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 2017.0026//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; 17CVD01//Fondation Leducq/ ; }, abstract = {Bariatric surgeries, such as Roux-en-Y gastric bypass (RYGB) and sleeve gastrectomy (SG), improve obesity and type 2 diabetes (T2D). Both surgeries affect the gut microbiota, but their contribution to T2D remission remains unclear. In this subanalysis (RYGB, n = 39; SG, n = 38) of the randomized controlled Oseberg trial (NCT01778738), in which participants underwent either RYGB or SG surgery, we profiled the faecal microbiome of individuals with obesity and T2D before and 12 months after surgery. We show that both surgeries altered the microbiome in the same direction, but with larger changes after RYGB. The SG-associated altered microbiome composition correlated positively with circulating glucagon-like peptide 1 levels, beta-cell function and 5 year T2D remission. Remission was also linked to increased gene richness and metabolic potential for fermentation, methanogenesis and butyrate production. Notably, these associations persisted after accounting for the extent of weight loss. Our findings indicate that surgery-specific microbial adaptations influence metabolic improvements and may help to explain heterogeneity in T2D remission after bariatric surgery.}, }
@article {pmid42098439, year = {2026}, author = {Prendergast, PJ and Bishop, HV and Herbold, CW and Verdu, EF and Dobson, RCJ and Day, AS and Ogilvie, OJ}, title = {Comprehensive cross-cohort analysis reveals global gut microbiome signatures of celiac disease.}, journal = {Communications medicine}, volume = {}, number = {}, pages = {}, doi = {10.1038/s43856-026-01627-1}, pmid = {42098439}, issn = {2730-664X}, abstract = {BACKGROUND: Celiac disease affects ~1-2% of people and remains incurable, requiring lifelong dietary restriction. The gut microbiome is thought to contribute to the development and progression of celiac disease. However, findings across previous studies are fragmented, making it difficult to understand exactly how the gut microbiome is involved.<br><br>METHODS: We integrate over 900 samples from global datasets spanning different disease stages (before onset, during active disease, and after treatment), body sites, and research methods. Datasets produced using both 16S rRNA gene sequencing and shotgun metagenomics profile the gut microbiome. Alpha and beta diversity analyses and differential abundance testing identify consistent changes in bacterial communities linked to celiac disease. Machine learning tests how well microbiome data predicts disease status.<br><br>RESULTS: Here, we show that celiac disease is not marked by large changes in gut microbiome diversity. Instead, there are subtle, consistent changes in specific bacteria, including a reduction in beneficial butyrate producers (Faecalibacterium, Prevotella, Agathobacter, Gemmiger), changes in mucin-associated microbes (Akkermansia muciniphila), and an increase in potentially harmful bacteria (Helicobacter, Campylobacter, Haemophilus parainfluenzae). These changes are seen before and during active disease and persist on a gluten-free diet. Microbiome-based disease prediction is moderately accurate for active disease and weaker for prospective performance, likely constrained by training data.<br><br>CONCLUSIONS: Our findings suggest that celiac disease is linked to specific changes in gut bacteria that are not fully resolved by diet alone. Future treatments may need to focus on restoring healthy gut bacteria, not just avoiding gluten, to better manage the disease.}, }
@article {pmid42083348, year = {2026}, author = {Valentini, M and Valentini, GM and Akkawi, I and Zeppa, SD and Bartolacci, A and Pegreffi, F and Zmerly, H}, title = {The Interplay between Osteoarthritis and the Microbiome-joint Axis: A Systemic Perspective on Novel Therapeutic Targets.}, journal = {Current rheumatology reviews}, volume = {}, number = {}, pages = {}, doi = {10.2174/0115733971450825260423042902}, pmid = {42083348}, issn = {1875-6360}, abstract = {Osteoarthritis (OA) is a chronic and progressive joint disease involving the articular cartilage, synovium, subchondral bone, and ligaments, ultimately leading to pain, dysfunction, and, in advanced stages, joint destruction. Several factors contribute to the development and progression of OA, including genetic predisposition, biomechanical stress, metabolic imbalance, and chronic low-grade inflammation. Recently, a novel factor has emerged: the gut microbiome. Gut dysbiosis, defined as an alteration in gut microbiota homeostasis, can disrupt immune, metabolic, and inflammatory pathways, promoting systemic inflammation and accelerating degenerative changes in joint tissues. Conversely, restoration of a balanced gut microbiota may play a protective role and represent a promising avenue for innovative therapeutic strategies. The aim of this review is to analyse the relationship between gut dysbiosis and osteoarthritis, and to discuss potential therapeutic approaches targeting the microbiome to prevent disease progression.}, }
@article {pmid42083431, year = {2026}, author = {Ebersole, JL and Kirakodu, SS and Gonzalez, OA}, title = {Transcriptomic analysis of gingival tissues in resolved experimental periodontal lesions of nonhuman primates.}, journal = {Journal of periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1002/jper.70048}, pmid = {42083431}, issn = {1943-3670}, support = {P20GM103538/NH/NIH HHS/United States ; P40RR03640//Caribbean Primate Research Center/ ; //Microarray Core of the University of Kentucky/ ; }, abstract = {BACKGROUND: This study used a preclinical model of experimental periodontitis in nonhuman primates to evaluate the biological features of resolved periodontal lesions.<br><br>METHODS: Macaca mulatta (rhesus monkeys) were age-stratified into young [&#x2264;3 years (7-10-year-old humans)], adolescent/young adult [3-7 years (12-25-year-old)], adults [12-15 years (40-50-year-old)], and aged [17-23 years (60-80-year-old)]. The samples were also analyzed based on sex or matrilineal derivation. The gingival transcriptome was evaluated using microarray analyses on tissue biopsies from healthy tissues and at resolution (i.e., clinical improvement).<br><br>RESULTS: Resolution sites showed clinical improvement, as well as patterns of increased or decreased gene expression in resolution versus healthy tissues in all age groups. These differences represented a large array of adaptive immune genes that were elevated in resolution, with decreased metabolic, regulatory, structural, and transcription factor gene expression in the resolution samples. Many of these genes were common to all age groups or sex/matriline, thus suggesting some fundamental core profile of affected genes that discriminate healthy from lesion resolution tissues.<br><br>CONCLUSIONS: Irrespective of age, the biology of periodontal lesion resolution tissues is distinct from healthy tissues. Despite a robust inflammatory response to the ligature-induced microbiome changes during experimental periodontitis, younger individuals showed significantly less destructive disease and different transcriptome profiles that could reflect improved lesion resolution. While sex and matriline affected the gene expression patterns, these generally overlapped with the prominent genes identified for resolution versus health across age groups. Highly affected genes could be considered biomarkers for resolved tissues, linking clinical and biological resolution of periodontal lesions.}, }
@article {pmid42083540, year = {2026}, author = {YuXuan, G and Iqbal, MK and Khan, B and Khan, H and Ud Din Shah, SS and Al-Hussain, F and Kiyani, MM and Bashir, S}, title = {The Gut-Brain Connection: Exploring the Connection Between the Gastrointestinal System and Parkinson's Disease.}, journal = {CNS &amp; neurological disorders drug targets}, volume = {}, number = {}, pages = {}, doi = {10.2174/0118715273419693251206130059}, pmid = {42083540}, issn = {1996-3181}, abstract = {Parkinson's disease (PD) is a complex neurodegenerative disorder characterized by motor and non-motor symptoms. Recent studies indicate that the gut-brain axis contributes to both the initiation and progression of PD, a disorder that primarily affects the central nervous system. This article reviews current research on the interaction between the central nervous system and the gastrointestinal tract in PD. The vagus nerve, areas of the enteric nervous system (ENS), systemic inflammation, and the microbiome are all involved in this interaction. For example, recent studies have shown PD-related effects such as abnormal distribution of gut bacteria, increased gut barrier permeability, and α-synuclein transport from the gut to the brain. A comprehensive evaluation of motor and non-motor symptoms was conducted. Additionally, we explored drugs that specifically target the gastrointestinal system, the possible gastrointestinal symptoms of PD, and how these symptoms may serve as early indicators of the disease. Our article also discusses dietary modifications, probiotics, and fecal microbiota transplantation as potential treatments for PD. By reviewing clinical and basic scientific research as well as translational applications, this article highlights the relationship between the central nervous system and the digestive system in PD. A better understanding of this complex connection may lead to improved detection and treatment of this debilitating disease and offer new opportunities for prevention and therapy. Finally, this paper suggests directions for further research in this area.}, }
@article {pmid42083599, year = {2026}, author = {Kozlova, AS and Zgoda, AV and Petushkova, NA and Bolochenkov, NA and Zgoda, VG and Salnitska, MA and Kazakov, DV and Lisitsa, AV}, title = {The Microbiomic Metaproteome of the Taiga Tick Ixodes persulcatus from the Tyumen Region.}, journal = {Acta naturae}, volume = {18}, number = {1}, pages = {55-63}, pmid = {42083599}, issn = {2075-8251}, abstract = {Metagenomic studies have revealed the taxonomic composition of the taiga tick (Ixodes persulca tus) microbiome, whereas metaproteomic data has provided information on the biochemically active fraction of the microbial community residing in the tick. The aim of this study was to characterize the biological pro cesses taking place within the microbiome of the taiga tick I. persulcatus using a metaproteomic approach. To expand the range of identifiable proteins, we used two trypsin concentrations in sample preparation for mass spectrometric analysis. The metaproteomes of unfed female and male ticks were analyzed, which ena bled identification of protein products encoded by 2,100 genes from microorganisms belonging to 203 bacteri al and fungal species. Increased abundance of proteins associated with Ascomycota fungi, particularly abun dant in females, were detected. Proteins from the pathogenic Rickettsia and Borrelia species were identified. These findings enable a transition from a taxonomic metagenomic description to a functional analysis of the microbial consortium role in the physiology of the vector tick, particularly given the identified microbiota differences related to the tick sex.}, }
@article {pmid42083728, year = {2026}, author = {Gaskin, PS and Chami, PS}, title = {Low Weight Loss Response to Incretin Analogs: A Systematic Review.}, journal = {Obesity reviews : an official journal of the International Association for the Study of Obesity}, volume = {}, number = {}, pages = {e70145}, doi = {10.1111/obr.70145}, pmid = {42083728}, issn = {1467-789X}, abstract = {The development of GLP-1 and GIP analogs has been a significant breakthrough in type 2 diabetes and obesity pharmacotherapy. However, individual responses to these medications can vary widely. This systematic review examines factors associated with low or no weight loss response to GLP-1 and GIP analogs. Key predictors of poor response include higher baseline body weight, BMI, HbA1c, and insulin resistance. Genetic factors, such as variants in the GLP1R gene, may also influence treatment outcomes. Metabolic health status, particularly glycemic control and insulin sensitivity, plays a crucial role in determining weight loss efficacy. Adherence to medication regimens is strongly associated with treatment success, with each additional month of treatment linked to greater weight loss. Lifestyle factors, including dietary habits and physical activity, can modulate responses to these medications. Emerging evidence suggests that gut microbiome composition may mediate weight loss outcomes. Demographic factors such as male sex and older age are associated with lower weight loss responses. Understanding these predictors is essential for optimizing treatment strategies, setting realistic expectations, and moving towards a precision medicine approach in obesity care. Further research is needed to validate these findings in diverse populations and develop practical tools for clinical decision-making.}, }
@article {pmid42083785, year = {2026}, author = {Wu, Y and Liu, J and Ren, Y and Zou, C}, title = {Unravelling the Gut-Skin Axis in Chronic Urticaria: Dysbiosis, Metabolites and Immunological Mechanisms.}, journal = {Experimental dermatology}, volume = {35}, number = {5}, pages = {e70261}, doi = {10.1111/exd.70261}, pmid = {42083785}, issn = {1600-0625}, support = {2025C02080//the Key Research and Development Plan of Zhejiang Province/ ; WKJ-ZJ-2409//the National Health Commission Scientific Research Fund/ ; }, mesh = {Humans ; *Dysbiosis/immunology ; *Gastrointestinal Microbiome ; Animals ; *Chronic Urticaria/immunology/microbiology/metabolism ; *Skin/immunology/metabolism ; Mice ; Fatty Acids, Volatile/metabolism ; Mast Cells/immunology ; }, abstract = {Although the core pathophysiological pathways of chronic urticaria (CU) are increasingly understood, the upstream triggers and factors contributing to disease chronicity remain poorly understood. Emerging evidence suggests that gut microbiota dysbiosis represents a potentially modifiable upstream factor, which has been predominantly investigated in patients with chronic spontaneous urticaria (CSU). Multi-omics and Mendelian randomization studies have provided convergent evidence linking gut dysbiosis to systemic inflammation and mast cell instability. This is characterized primarily by the depletion of short-chain fatty acid (SCFA)-producing taxa (e.g., Faecalibacterium, Roseburia and Bifidobacterium) and the relative enrichment of pro-inflammatory Proteobacteria (particularly Enterobacteriaceae). Mechanistically, these alterations may lower the mast cell activation threshold and promote systemic immune dysregulation through specific metabolic shifts, such as the depletion of SCFAs and unsaturated fatty acids, and the translocation of endotoxins (e.g., lipopolysaccharide) due to compromised intestinal barrier function. In this review, we discuss how the use of Mendelian randomization (MR) and germ-free mouse models can advance the gut-urticaria axis (with a primary focus on CSU) from mere correlation to causation, while highlighting the crucial need to account for clinical confounders. Finally, we evaluate the clinical translational potential and associated challenges of microbiome-targeted interventions (e.g., probiotics, faecal microbiota transplantation) as novel adjuvant therapies.}, }
@article {pmid42083883, year = {2026}, author = {Rutigliani, G and Cross, TL and de Jong, E and Glover, ES and Mendoza, ID and Adisa, M and Tomoo, K and Zhou, X and Mattes, RD}, title = {GLP-1 Receptor Agonists and Weight Loss: A Critical Review of Mechanisms.}, journal = {Obesity reviews : an official journal of the International Association for the Study of Obesity}, volume = {}, number = {}, pages = {e70148}, doi = {10.1111/obr.70148}, pmid = {42083883}, issn = {1467-789X}, abstract = {GLP-1 receptor agonist medications have the potential to promote marked weight loss, but maximal and sustained benefit may be compromised by poor compliance and cessation of use. Development of next-generation medications that address current obstacles to effective use and development of effective adjunct treatments will benefit from better characterization of their mechanisms of action. This narrative review critically assesses eight purported mechanisms including modulation of appetite, chemosensory function, cravings/aversions, food noise, gastric emptying, the microbiome, incretin activity, and energy expenditure. Current evidence does not support a single dominant mechanism; a combination of subtle effects may underlie the efficacy of these medications. However, as experience with these medications and methods to assess their effects grows, it should be possible to better determine the relative importance of these and possibly other mechanisms.}, }
@article {pmid42083901, year = {2026}, author = {Gago-Ferrero, P and Boehm, AB and Hsu-Kim, H and Li, XD and Gibson, JM and Vrijheid, M and Wang, B and Zimmerman, J}, title = {The Human Exposome: Integrating the Environment, Human Health, and Society for the Next 60 years.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c03080}, pmid = {42083901}, issn = {1520-5851}, abstract = {The exposome framework promises comprehensive characterization of chemical, physical, and biological exposures shaping human health, yet the measurement capacity now vastly outpaces interpretation and action. Here, we synthesize emerging frontiers that define the translation of exposome science into prevention: moving from "chemical dark matter" in high-resolution mass spectrometry toward functional exposomics; integrating the microbial exposome as both the target and modulator of exposures; deploying AI-enabled causal inference to bridge molecular precision with population-scale patterns; and embedding exposome evidence into proactive interventions, green chemistry, environmental redesign, and environmental justice frameworks. Progress over the next six decades will depend not only on measurement comprehensiveness but also on our capacity to shift from documenting environmental harm to designing healthier environments.}, }
@article {pmid42084201, year = {2026}, author = {Ebihara, S and Kamada, N}, title = {The Oral-Gut Axis: Bidirectional Interactions Between Microbiome and Diseases.}, journal = {Journal of periodontal research}, volume = {}, number = {}, pages = {}, doi = {10.1111/jre.70116}, pmid = {42084201}, issn = {1600-0765}, support = {DK108901/NH/NIH HHS/United States ; DK119219/NH/NIH HHS/United States ; CA288546/NH/NIH HHS/United States ; JP21gm6310023//Japan Agency for Medical Research and Development/ ; JP25gm4010030//Japan Agency for Medical Research and Development/ ; JP23H00404//Japan Society for the Promotion of Science/ ; }, abstract = {Increased colonization of typically oral microorganisms is frequently observed in the gut mucosa or lumen of individuals with gastrointestinal disorders, including patients with inflammatory bowel disease and colorectal cancer. Accumulating clinical and experimental evidence indicates that this phenomenon, known as "gut oralization," plays an important role in the pathogenesis of these diseases. Although several physiological barriers normally restrict the translocation and ectopic colonization of microorganisms from the oral cavity to the gut, certain oral pathobionts-often enriched in individuals with oral diseases such as periodontitis-have evolved specialized strategies to overcome these defenses. This review examines the bidirectional interactions through which bacterial traits, including unique adhesion systems and metabolic adaptations, support colonization and expansion within the gastrointestinal tract, as well as how disease-associated alterations in the gut environment and increased host vulnerability facilitate ectopic colonization by bacteria of oral origin. By integrating clinical and mechanistic evidence, this review highlights the potential of targeting the oral-gut microbial axis as a therapeutic approach for preventing and treating chronic gastrointestinal disorders.}, }
@article {pmid42084382, year = {2026}, author = {Van Beeck, W and Lemos, MLP and Niesen, AM and Finnegan, P and Shih, TM and Ho, A and Rossow, HA and Marco, ML}, title = {Variations in cow milk and teat skin microbiota across the lactation cycle with intramammary cephalosporin use at dry-off.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0231225}, doi = {10.1128/aem.02312-25}, pmid = {42084382}, issn = {1098-5336}, abstract = {Cephalosporins and other broad-spectrum antibiotics are frequently administered prophylactically into the udder when dairy cows end their lactation cycle, termed dry-off, to reduce mastitis risk. However, the use of antibiotics on cows that do not have signs of infection may result in the selection of antibiotic-resistant microorganisms and negatively alter the udder microbiome. In this study, the effects of intramammary cephalosporin therapy with Cephapirin (CB) or Ceftiofur (CH) on milk and teat skin microbiota were examined for three dairies in California. Intramammary injections were given to healthy cows with high somatic cell counts (>200,000 cells/mL), indicative of infection. Samples were collected at dry-off (before treatment), 7 days later, and 55-75 days in milk (DIM) in the next lactation cycle. Dairy (milk: R[2] = 6.22, skin: R[2] = 7.56) and day of sampling (milk: R[2] = 4.74 and skin: R[2] = 3.77) had the highest impact on the milk and skin microbiota. CB or CH use was associated with a small but significant impact on milk microbiota beta-diversity (Bray-Curtis, P =0.003, R[2] = 1.4%), but no effect was observed on the skin. At one dairy (Dairy 3), milk from cows receiving CB and CH had reduced proportions of Staphylococcaceae at 55-75 DIM compared to untreated cows. Overall, antibiotic use did not result in large significant (beneficial or harmful) changes in bacterial diversity in milk or on the teat skin; instead, the microbiota differences were mainly influenced by the time and location of sampling.IMPORTANCEThe use of antibiotics in agriculture is under increasing scrutiny due to the rising spread of antimicrobial-resistant bacteria. Our study showed that common preventative antibiotic intramammary treatment of cows with cephalosporins at the end of their lactation (dry-off) had minimal effects on the milk and teat skin microbiota of asymptomatic cows with high somatic cell counts.}, }
@article {pmid42084394, year = {2026}, author = {Liu, C and Ribeiro, MM and Yang, J and Li, L and Li, J and Chen, X and Wang, Y and Wang, L-L and Wang, B and Zhou, Y and Zhang, J and Jiang, J and Lin, J and Delbaje, E and Xu, J-F and Goldman, GH and Liang, S}, title = {Multi-omics profiling of fungal balls in chronic pulmonary aspergillosis patients reveals microbiome dynamics and metabolic adaptations.}, journal = {mBio}, volume = {}, number = {}, pages = {e0034826}, doi = {10.1128/mbio.00348-26}, pmid = {42084394}, issn = {2150-7511}, abstract = {Fungal balls (aspergillomas) are a debilitating complication of chronic pulmonary aspergillosis, but their functional biology as multi-kingdom ecosystems is poorly understood. Through integrated multi-omics analysis of 61 patient-derived fungal balls, we reveal their complex ecology. While Aspergillus fumigatus dominates the fungal niche (59% of patients), bacterial co-colonization is ubiquitous, primarily by Pseudomonas aeruginosa and Haemophilus influenzae. Metabolomics and metatranscriptomics unveil a structured division of labor and active warfare, including metabolic cross-feeding, competition for iron, and reciprocal antagonism via secondary metabolites, such as fumagillin and fumigaclavine C produced by A. fumigatus. Host metabolomics and transcriptomics revealed a potent but dysregulated human immune response, characterized by neutrophil activation and failed resolution. Our findings redefine aspergilloma not as a mere fungal aggregate, but as a resilient polymicrobial biofilm across kingdoms, in which synergistic and antagonistic inter-kingdom interactions drive pathogenesis and chronicity, suggesting new therapeutic strategies targeting the pathogenic consortium.IMPORTANCEChronic pulmonary aspergillosis (CPA) and its hallmark fungal balls (aspergillomas) represent a debilitating and difficult-to-treat respiratory disease, affecting millions worldwide. Here, we provide the first integrated multi-omics profile of surgically resected fungal balls from 61 CPA patients, revealing these structures not as mere fungal colonies, but as resilient, cross-kingdom biofilms teeming with bacterial co-colonizers, particularly Pseudomonas aeruginosa and Haemophilus influenzae. Our findings uncover a dynamic battlefield where fungi and bacteria engage in metabolic cross-feeding, chemical warfare, and competition for nutrients such as iron. We demonstrate that the host mounts a potent but dysregulated immune response characterized by chronic neutrophilic inflammation and failed resolution, driving tissue damage and disease persistence. Our data provide a foundation for novel therapeutic strategies aimed at disrupting microbial synergy, modulating host inflammation, and breaking the cycle of chronic infection, an approach that could significantly improve outcomes for patients with this refractory disease.}, }
@article {pmid42084439, year = {2026}, author = {Wu, H and Han, Y and Wen, Z and Liu, WV and Tu, N and Yang, W and Li, J and Zha, Y}, title = {Higher Abundance of Genus Desulfovibrio May Underlie Resistance to Antipsychotic-Induced Weight Gain in Schizophrenia.}, journal = {Schizophrenia bulletin}, volume = {52}, number = {3}, pages = {}, pmid = {42084439}, issn = {1745-1701}, support = {JCZRQNB202600163//Natural Science Foundation of Hubei Province/ ; 2022YFC2009900//National Key R&amp;D Program of China/ ; 2022YFC2009905//National Key R&amp;D Program of China/ ; }, mesh = {Humans ; *Schizophrenia/drug therapy/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Antipsychotic Agents/adverse effects/pharmacology ; Male ; Female ; Adult ; *Weight Gain/drug effects ; *Obesity/microbiology/chemically induced ; *Desulfovibrio ; Middle Aged ; Young Adult ; Feces/microbiology ; }, abstract = {BACKGROUND: Obesity is prevalent among schizophrenia (SZ) patients receiving long-term antipsychotic treatment, yet a subset of patients remains lean or maintains a normal weight. While prior studies have linked the gut microbiome to antipsychotic-induced weight gain, its role in maintaining weight stability among non-obese SZ patients remains largely unexplored.<br><br>STUDY DESIGN: We recruited 177 participants for the discovery cohort, including chronically antipsychotic-treated SZ patients with or without obesity, as well as healthy controls (HCs) matched by weight status. Additionally, we enrolled 20 first-episode, drug-na&#xef;ve SZ (FSZ) patients with normal weight to assess their weight changes during one year of antipsychotic treatment. Fecal 16S rRNA sequencing, combined with untargeted metabolomics, was conducted to characterize gut microbiota and metabolite profiles in non-obese SZ patients, and to investigate their association with antipsychotic-induced weight changes.<br><br>STUDY RESULTS: In total, 15 bacterial genera were identified. Among them, the genera Bacteroides, Dialister, and Pseudomonas exhibited the lowest abundance in non-obese SZ patients, whereas the genus Oscillospira showed the highest abundance. Notably, Desulfovibrio was more abundant in non-obese SZ patients and HCs than in their obese counterparts. This microbial profile was accompanied by enhanced tryptophan metabolism. In FSZ patients, higher baseline levels of Desulfovibrio were linked to less weight gain after 1 year of antipsychotic treatment. Moreover, Desulfovibrio abundance correlated positively with fecal indoleacetic acid levels and inversely with serum tryptophan concentrations.<br><br>CONCLUSIONS: These findings suggest a potential protective role of&#xa0;genus Desulfovibrio against antipsychotic-induced weight gain, possibly through modulation of tryptophan metabolism.}, }
@article {pmid42084538, year = {2026}, author = {Jongen, R and Gribben, PE and Erickson, KR and Marzinelli, EM}, title = {Ocean warming indirectly affects seagrass performance through effects on sediment microbial communities.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71195}, pmid = {42084538}, issn = {1469-8137}, support = {DP240100566//Australian Research Council/ ; LP200200220//Australian Research Council/ ; }, abstract = {Belowground microbes are increasingly recognised as mediators of plant responses to stress, but it remains unclear whether the thermal histories of marine plants and their associated belowground microbes influence plant performance under ocean warming. We conducted a common-garden field experiment at a long-term warmed site in Lake Macquarie (NSW, Australia, > 30 yr, 1-3°C warming), to test the effects of sediment origin (ambient vs warm-origin), plant origin (ambient vs warm-origin) and microbial disruption (intact vs disrupted rhizosphere and bulk sediment microbial communities) on seagrass (Zostera muelleri) performance. Both plant origins had lower aboveground biomass in intact warm-origin sediments, but warm-origin plants recovered when bulk sediment microbial communities were disrupted, indicating that warming-altered sediment microbial communities can suppress seagrass performance. Disrupted warm-origin sediments were enriched in sulphide-oxidising bacteria, which likely contributed to enhanced performance. In warm-origin sediments, rhizosphere bacterial communities were similar across plant origins, indicating that sediments shape rhizosphere bacterial assembly. Rhizosphere microbial disruption had no effect on plant performance. We show that ocean warming can shape sediment microbial communities in ways that suppress seagrass performance, suggesting that sediment microbial communities can override plant thermal history and act as hidden constraints on seagrass tolerance to warming.}, }
@article {pmid42084709, year = {2026}, author = {Komal, A and Ilyas, D and Khan, MU and Rehman, MKU and Hassan, T and Ayub, H and Naqi, N and Ullah, N and Ilyas, U}, title = {Multi-modal therapeutic approaches to inflammatory bowel disease: plant-derived compounds, nanoparticle drug delivery systems, and gene-based interventions.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {42084709}, issn = {1573-4978}, mesh = {Humans ; *Inflammatory Bowel Diseases/therapy/genetics/drug therapy ; *Nanoparticle Drug Delivery System/therapeutic use ; *Genetic Therapy/methods ; *Drug Delivery Systems/methods ; Nanoparticles ; Animals ; RNA, Small Interfering ; MicroRNAs/genetics ; }, abstract = {Inflammatory bowel disease (IBD) is a chronic, relapsing inflammatory disorder primarily affecting the gastrointestinal tract. The pathogenesis arises from complex interactions among genetic predisposition, immune dysregulation, and gut microbiota alterations. Recent advances in molecular biology, genomics, and microbiome research have identified novel therapeutic targets, enabling the development of innovative treatment strategies. Natural products derived from plants offer bioactive compounds with anti-inflammatory, antioxidant, and immunomodulatory properties, gaining attention for IBD symptom management. Conventional therapeutic management includes aminosalicylates, immunomodulators, corticosteroids, and biologics; however, 30-50% of patients show inadequate response, and oral drug delivery faces challenges due to gastrointestinal environmental heterogeneity. Recent years have witnessed substantial advances in nanoparticle-based drug delivery systems for IBD, offering improved targeting capabilities, enhanced therapeutic efficacy, and better tolerability through stimuli-responsive platforms (ROS-sensitive, pH-responsive) and active targeting strategies. Nanoparticle-mediated gene therapy, including siRNA, miRNA, and emerging CRISPR-based approaches, represents a paradigm-shifting strategy for modulating aberrant gene expression in IBD. This comprehensive review synthesizes the current understanding of IBD pathophysiology, evaluates both conventional and emerging therapeutic approaches, and provides critical analysis of advanced nanoparticle delivery systems and gene-based therapeutic strategies.}, }
@article {pmid42084747, year = {2026}, author = {Kumar, V and Nautiyal, CS}, title = {Harnessing the plant microbiome: innovation towards sustainable agriculture and ecological resilience.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {6}, pages = {}, pmid = {42084747}, issn = {1572-9699}, mesh = {*Microbiota ; Soil Microbiology ; Climate Change ; *Crops, Agricultural/microbiology/growth &amp; development ; *Agriculture/methods ; *Plants/microbiology ; Biodiversity ; Ecosystem ; Plant Breeding ; }, abstract = {Assimilation of plant-microbiome synergism into contemporary sustainable approaches offers transformational prospective for augmenting crop production, and environment resilience. Efficient microbiome enhances nutrients acquisition, encouraging plant's growth, and mitigate diverse stressors. Synthetic microbial communities could be another strategy to augment crop yield by improving bioinoculants activity, regulating and reinstating microbial diversity. Long-term agricultural output depends on microbiome's intervened activities, such as nutrients acquisition, thereby lowering chemical fertilizers necessity. Microbes also contribute to climate change mitigation by endorsing soil carbon stowage and minimizing release of greenhouse gases via enhanced nutrients use efficacy. Developments in sustainable crop breeding and genomics have facilitated the recognition of plant traits and genetic loci that influence alliances of valuable microbes. Integration of plant-microbiome breeding tactics might lead to optimization of microbiome selection in plant varieties, thus improving yield and stress resilience. Such approaches will conserve biodiversity, restore ecosystem by nurturing functional microbiome population, supporting plant's diversity and soil health. Microbiome are also able to improve degraded soils recovery, plant's establishment, parallelly safeguarding ecosystem restoration. The integration of microbial technology in crops could enhance the nutritional value and safety of food while supporting environmental sustainability and human health. Understanding microbiome-plant-climate change interactions is critical for developing adaptive strategies that enhance resilience to environment and climate variability, ensure sustainable food systems, and promote ecological balance in a changing global environment.}, }
@article {pmid42084764, year = {2026}, author = {Joshi, G and Khannam, KS}, title = {Marine microbiomes and their expanding role in biotechnological potential: a systematic review.}, journal = {Archives of microbiology}, volume = {208}, number = {7}, pages = {}, pmid = {42084764}, issn = {1432-072X}, mesh = {*Microbiota ; *Biotechnology ; *Seawater/microbiology ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Ecosystem ; Biodegradation, Environmental ; }, abstract = {Marine bacteria are present almost everywhere in the ocean environment and are essential to many biogeochemical processes. The perspectives of ecologists and evolutionary biologists on the significance of microbes in ecosystem function are shifting as a result of exploring the marine microbiomes. This is especially true in ocean habitats, where microbes comprise the bulk of the biomass and are responsible for the majority of the planet's key biogeochemical cycles, including those that influence the global climate. Emerging research suggests that many ecosystem services provided by coastal marine environments depend on intricate interactions between groups of microbes and the environment or their hosts. The structure, variety, and functional capability of marine microbial populations have been revealed on a global scale thanks to recent developments in molecular ecology techniques. Over-recent-decades, industrialization and urbanization have led to widespread contamination of oceans. These contaminants accumulate in seawater and sediments, particularly in coastal areas, posing risks to marine ecosystems and human health. Marine microorganisms possess diverse catalytic abilities and extreme environmental tolerance, making them suitable for bioremediation of toxins. Effective-degradation of pollutants often depends on syntrophic-interactions within microbial communities, highlighting the importance of understanding their collaboration and communication for marine resource management. Here, we assess the current level of knowledge about marine microbiome research and highlight key issues within this developing field of study. The review aims to enhance understanding of marine microbiome's roles and potential uses in biogeochemical analysis, biotechnology, and environmental remediation, which could support sustainable and circular business models for future generations.}, }
@article {pmid42084801, year = {2026}, author = {Liu, G and Chen, K and Li, J and Zhang, K and Niu, G and Ding, Y and Lv, Y and Tian, Q and Cao, Z and Wang, H and Jia, J and Zhang, G and An, Y}, title = {Deciphering potential significances of biliary microbiome in cholelithiasis and cholangiocarcinoma.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {6}, pages = {}, pmid = {42084801}, issn = {1572-9699}, support = {No. 25A330005//the Key Scientific Research Projects of Henan Higher Education Institutions/ ; No. 202510475073, 202510475143, 202510475139, XJ2025344, XJ2025363//the Innovation Project for College Students of Henan University/ ; No. 262102311042//the Program for Science and Technology Development in Henan Province/ ; }, mesh = {*Cholangiocarcinoma/microbiology ; *Cholelithiasis/microbiology ; Humans ; *Microbiota ; *Bile Duct Neoplasms/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Computational Biology ; *Biliary Tract/microbiology ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: This study aims to investigate the role of biliary microbiota (defined as the microbial community colonizing the biliary tract, including the gallbladder, intrahepatic and extrahepatic bile ducts) in the pathogenesis of cholelithiasis (CHOL) and cholangiocarcinoma (CCA), with a focus on the associations between microbial communities and these biliary diseases.<br><br>METHODS: We conducted a comprehensive bioinformatics analysis using high-throughput sequencing data obtained from the Sequence Read Archive (SRA) database to characterize the composition of microbial communities in patients with CCA and CHOL. We performed operational taxonomic unit (OTU) clustering, statistical analyses and Mendelian randomization (MR) to elucidate the causal relationships between specific bacterial strains and disease outcomes.<br><br>RESULTS: Our findings revealed differences in the relative abundance of specific microbial taxa among research groups. The CCA&#x2009;+&#x2009;CHOL group exhibited a significant increase in the abundance of Fusobacteria, particularly Fusobacterium, compared to the Control or CCA group. This suggests a potential pathogenic role for these microorganisms in CHOL formation. Additionally, the CCA group demonstrated a higher diversity index, indicating that increased microbial diversity may contribute to the progression of the disease. MR analysis identified nominally significant statistical associations between specific bacterial strains. However, the presence of pleiotropy in some analyses necessitates caution when interpreting causal relationships.<br><br>CONCLUSION: Our study highlights the complex interplay between biliary microbiota and the pathogenesis of CHOL and CCA. Modulating biliary microbiota may represent a promising therapeutic strategy for managing these diseases. Future research should focus on the functional roles of specific taxa in bile metabolism and immune modulation, ultimately improving our understanding of biliary health and disease management.}, }
@article {pmid42084812, year = {2026}, author = {Ma, J and Tong, P and Yang, K and Jia, Y and Liu, Z and Zhao, M and Liu, J and Long, F}, title = {Lactiplantibacillus plantarum Mediated Tryptophan Metabolism to Alleviate Tropomyosin-induced Food Allergy.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {42084812}, issn = {1867-1314}, support = {32472454//National Natural Science Fund/ ; YQK[2023]020//Guizhou Provincial Science and Technology Programme for Outstanding Young Talents in Science and Technology/ ; 2024NC-GJHX-04//Key Research and Development Projects of Shaanxi Province/ ; }, abstract = {Food allergy (FA) has become increasingly prevalent, affecting daily life. Probiotics alleviate FA by modulating immune-microbiome interactions. Nevertheless, the key metabolites and mechanisms by which L. plantarum alleviates FA remain unclear. In this study, L. plantarum demonstrated the ability to improve FA by modulating regulatory T/Th1/Th2 balance, modulating gut microbial composition, and regulating gut metabolites. Tropomyosin sensitization was associated with decreased levels of 5-hydroxyindole-3-acetic acid (5-HIAA) in cecum contents, a phenomenon also observed in the serum of FA mice and patients. In vitro experiments showed that tryptophan (Trp), tryptamine, tryptophol, kynurenine, 5-HIAA, and indole-3-acetamide inhibited RBL-2H3 cell degranulation; however, this inhibitory effect was attenuated by the aryl hydrocarbon receptor (AhR) antagonist CH223191. Moreover, in vivo results indicated that dietary supplementation with 5-HIAA or Trp downregulated IgE and cytokine levels in an AhR-dependent manner. This study provided evidence for the positive role of Trp metabolites in alleviating FA.}, }
@article {pmid42085218, year = {2026}, author = {Wang, LL and Xie, Y and Shen, X and Xu, JF}, title = {Advances in understanding respiratory microbiome are reshaping the management of respiratory diseases.}, journal = {American journal of respiratory and critical care medicine}, volume = {}, number = {}, pages = {}, doi = {10.1093/ajrccm/aamag017}, pmid = {42085218}, issn = {1535-4970}, }
@article {pmid42085254, year = {2026}, author = {Zissler, UM and Koczulla, AR}, title = {Lower Airway Dysbiosis Fuels NETosis in NTM Bronchiectasis: Rethinking the Microbiome-Host Axis.}, journal = {American journal of respiratory and critical care medicine}, volume = {}, number = {}, pages = {}, doi = {10.1093/ajrccm/aamag117}, pmid = {42085254}, issn = {1535-4970}, }
@article {pmid42085326, year = {2026}, author = {Appuhami, IA and Bajracharya, S and Davis, DA and Bruce, TJ}, title = {Effects of probiotic dose on growth performance, health, and gut microbiota of Pacific white shrimp reared in biofloc conditions.}, journal = {Journal of aquatic animal health}, volume = {}, number = {}, pages = {}, doi = {10.1093/jahafs/vsag001}, pmid = {42085326}, issn = {1548-8667}, support = {58-6010-0-007//United States Department of Agriculture-Agricultural Research Service (USDA-ARS)/ ; ALA016-1-19143//USDA National Institute of Food and Agriculture Hatch/ ; ALA016-1-19102//USDA National Institute of Food and Agriculture Hatch/ ; }, abstract = {OBJECTIVE: This study evaluated the effect of commercial Bacillus spp. probiotics on growth performance, immunity, gut microbiota composition, and disease resistance to Vibrio parahaemolyticus in Pacific white shrimp Litopenaeus vannamei that were reared under biofloc conditions.<br><br>METHODS: A 56-d feeding trial was conducted in a static biofloc system with postlarval shrimp (1.00 &#xb1; 0.03&#x2005;g). A total of 1,080 shrimp were randomly assigned to three groups: two treatment levels (recommended dose [PRO &#xd7; 1] and a doubled dose [PRO &#xd7; 2]) of a commercial probiotic blend, PRO4000X, alongside a control group (CTL; no probiotics). At the trial end point, hepatopancreas and gut samples were collected for gene expression. Gut samples were also obtained for gut microbiota analysis via 16S ribosomal RNA sequencing, and hemolymph samples were withdrawn to measure the total hemocyte count.<br><br>RESULTS: Probiotic applications did not significantly affect growth performance, including final biomass, mean weight, survival, and feed conversion ratio under the experimental conditions. The probiotic-treated shrimp exhibited enhanced survival during a V. parahaemolyticus (strain A3) challenge, with significantly lower mortality rates (P < 0.001; 42.5 &#xb1; 4.3% for PRO &#xd7; 1 and 60 &#xb1; 6.5% for PRO &#xd7; 2) relative to the CTL (100 &#xb1; 0.00%). Immune parameters, such as total hemocyte count, did not differ. Interestingly, the expression of the antioxidant gene sod (superoxide dismutase) in the shrimp gut was significantly downregulated in the PRO &#xd7; 1 group relative to the control (P = 0.030), which suggests reduced oxidative stress under probiotic supplementation. The analysis of the gut microbiota revealed differences in alpha diversity, specifically in evenness and Shannon index, which were significantly higher in the PRO &#xd7; 1 group. The analysis of the bacterial composition also revealed minor shifts in the dominant genera. Notably, Lysobacter was more abundant in the PRO &#xd7; 1 group, which potentially reflects positive modulation of gut microbial communities in response to probiotic supplementation.<br><br>CONCLUSIONS: Overall, the application of PRO4000X probiotics significantly reduced the V. parahaemolyticus infection in the shrimp that were reared in biofloc water and supported the regulation of immunity and microbial communities in the gut. These findings indicate that probiotics potentially help to improve shrimp health when shrimp are cultured in biofloc systems.}, }
@article {pmid42085335, year = {2026}, author = {Prentice, AM}, title = {Human Milk Bioactives in Breastfeeding: Understanding the Complex Biology of Mother-Child Interactions.}, journal = {Annals of nutrition &amp; metabolism}, volume = {}, number = {}, pages = {1-3}, doi = {10.1159/000551893}, pmid = {42085335}, issn = {1421-9697}, }
@article {pmid42085336, year = {2026}, author = {Mwaniki, M and Nabwera, HM}, title = {Transition from Breast Milk: When and How?.}, journal = {Annals of nutrition &amp; metabolism}, volume = {}, number = {}, pages = {1-11}, doi = {10.1159/000551169}, pmid = {42085336}, issn = {1421-9697}, abstract = {BACKGROUND: Breastfeeding is the cornerstone of infant and young child nutrition with implications for long-term health and well-being. However, despite having World Health Organization guidance on the transition from exclusive breastfeeding to complementary feeding, in practice it is often fraught with challenges. This review examines the biological and clinical foundations of breastfeeding, addresses the critical questions of when and how to introduce complementary foods and discusses the gaps that hinder optimal infant feeding practices across different geographies. Finally, it highlights the pivotal role of healthcare professionals in guiding safe and responsive feeding transitions.<br><br>SUMMARY: Human breast milk is an essential component of the factors that promote optimal child health, growth and neurodevelopment. Evidence supports exclusive breastfeeding for approximately 6 months. Readiness for complementary feeding should be judged by developmental cues rather than chronological age alone. Complementary feeding introduces new nutritional and immunological demands: texture progression supports oral-motor development, timely exposure to allergens may promote tolerance, and micronutrient status is critical. Global variation in infant feeding practices reflects socioeconomic, cultural, and structural barriers that often limit adherence to guidelines. When exclusive breastfeeding is not feasible despite an optimal healthcare provider and family, partial breastfeeding or formula feeding can support infant growth. However, such decisions ideally require guidance from healthcare providers, which may not be readily accessible to all mothers. Transitioning from exclusive breast milk should be viewed as a gradual layering of foods onto an existing nutritional foundation (often provided by breast milk) rather than abrupt weaning. For maternal and child health practitioners, the priority should be to provide person-centred care that is informed by the individual circumstances of the mother-infant dyad. This includes evidence-informed practical advice that is responsive to their needs, supporting exclusive breastfeeding whenever possible, while ensuring access to safe, nutritionally adequate and sustainable alternatives where needed. Aligning health systems, community support, and policy protections is essential to enable families globally to achieve optimal feeding practices.<br><br>KEY MESSAGES: Exclusive breastfeeding for about 6 months provides significant nutritional, immunological, and developmental benefits, but readiness for complementary feeding should be guided by developmental cues, not chronological age alone. Complementary feeding should emphasise iron-rich, diverse foods introduced with appropriate texture progression, alongside continued breastfeeding for sustained child health and growth. Implementation gaps persist globally largely due to unaddressed maternal challenges of navigating breastfeeding and the transition to complementary feeding. An interdisciplinary approach with mothers at the core is important in translating global guidelines into context-specific, practical guidance for families.}, }
@article {pmid42085795, year = {2026}, author = {Kang, S and Han, X and Gao, J and Zhou, T and Yang, X and Zheng, F}, title = {Distribution patterns and driving mechanisms of antibiotic resistance genes and virulence factor genes under the urbanization gradient.}, journal = {Journal of hazardous materials}, volume = {511}, number = {}, pages = {142270}, doi = {10.1016/j.jhazmat.2026.142270}, pmid = {42085795}, issn = {1873-3336}, abstract = {Antibiotic resistance genes (ARGs), as emerging environmental contaminants, have become a global environmental health concern due to their distribution and dissemination across urbanization gradients. This study systematically investigated the diversity, abundance patterns, and driving mechanisms of 173 ARGs, 30 mobile genetic elements (MGEs), and 120 virulence factor genes (VFGs) along a typical urbanization gradient (urban, suburban, and ecological zones) using soil samples collected from Baoding city center to Baiyangdian Lake periphery. High-throughput sequencing and quantitative PCR analyses revealed that suburban areas exhibited significantly higher total relative abundance of ARGs compared to urban and ecological zones (p < 0.05), particularly for aminoglycoside-, fluoroquinolone-, Macrolide-Lincosamide-Streptogramin B-, and multidrug-resistance genes. Suburban soils also showed elevated levels of VFGs associated with Klebsiella pneumoniae, Salmonella enterica, and Escherichia coli (p < 0.05). Notably, significant associations between ARGs and VFGs were observed, with both demonstrating high loads in suburban areas, suggesting these transitional zones may serve as "incubators" for resistant pathogens. Correlation analyses suggest that both biotic (MGEs, microbial communities) and abiotic factors (urbanization, heavy metals, soil properties) may contribute to ARGs and VFGs dissemination, with MGEs appearing to play a central role. Structural equation modeling indicates that urbanization could influence ARGs and VFGs assembly, potentially by altering soil properties, heavy metals, and microbial communities. MGE-mediated horizontal transfer might facilitate ARGs spread, whereas heavy metals and specific microbial taxa may be associated with VFG distribution patterns. These findings provide critical scientific insights into the transmission dynamics of resistance genes during urbanization and offer strategic guidance for developing targeted environmental management policies to mitigate resistance dissemination.}, }
@article {pmid42085931, year = {2026}, author = {Wang, Z and Wang, Y and Peters, BA and Post, WS and Brown, TT and Palella, FJ and Rinaldo, CR and Witt, MD and Gange, SJ and Kuniholm, MH and Sha, BE and Chichetto, NE and Clish, CB and Gerszten, RE and Hodis, HN and Sharma, A and Anastos, K and Burk, RD and Kaplan, RC and Qi, Q and Hanna, DB}, title = {Multi-omics analysis of the gut microbiome and carotid artery atherosclerosis in men with and without HIV.}, journal = {EBioMedicine}, volume = {127}, number = {}, pages = {106281}, doi = {10.1016/j.ebiom.2026.106281}, pmid = {42085931}, issn = {2352-3964}, abstract = {BACKGROUND: How gut microbiota alterations may contribute to host inflammation and metabolomic profiles affecting atherosclerosis is not fully elucidated, especially in the context of HIV.<br><br>METHODS: We examined associations between gut microbial features (measured by shotgun metagenomics) and subclinical carotid atherosclerosis, as assessed by high-resolution B-mode ultrasound, in 359 men from the MACS/WIHS Combined Cohort Study. We measured 822 plasma metabolites using LC-MS/MS, and up to 2866 circulating proteins by the Olink Explore 3072/384 platform (with a primary focus on 617 proteins related to inflammation and immune function).<br><br>FINDINGS: Carotid artery plaque was detected in 115/359 men (32%). Adlercreutzia equolifaciens and Eubacterium sp3131 were associated with lower odds of plaque (OR [95% CI] = 0.57 [0.43, 0.77], 0.84 [0.76, 0.93], respectively), while Coprococcus sp13142 was associated with higher odds of plaque (OR [95% CI] = 1.14 [1.06, 1.23]). Results were consistent in men both with and without HIV. A. equolifaciens was positively correlated with HDL cholesterol and inversely correlated with systolic blood pressure. These plaque-associated microbial species were also associated with a range of circulating metabolites and inflammatory proteins. For example, A. equolifaciens positively correlated with the metabolites palmitoyl-EA and mesobilirubinogen, and inversely correlated with the pro-inflammatory chemokine CXCL9, the immune regulator CD160, and IL-24.<br><br>INTERPRETATION: We identified gut microbial features associated with carotid artery atherosclerosis, consistent across HIV status; these associations were partially explained by specific microbiota-related metabolites and inflammatory markers. If validated, these findings suggest gut microbiota-related targets for CVD prevention.<br><br>FUNDING: The study was funded by the National Heart, Lung, and Blood Institute (U01HL146204-04S1, K01HL169019).}, }
@article {pmid42086047, year = {2026}, author = {Cai, C and Wang, A and Shao, Q and Zhang, J and Wang, Y and Hu, H and Yuan, K and Li, L and Wang, X and Fang, Q and Ma, Y}, title = {Cryo-EM structures of prevalent gut phage PD491P1 uncover extensive disulfide stabilization and distinct structural adaptations.}, journal = {Structure (London, England : 1993)}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.str.2026.04.005}, pmid = {42086047}, issn = {1878-4186}, abstract = {Bacteriophages play crucial roles in modulating the human gut microbiome, yet structural characterization of prevalent gut phages remains limited. Here, we present high-resolution cryo-EM structures of Parabacteroides phage PD491P1, which is one of the most abundant bacteriophages in the human gut. The structures reveal its mature virion organization, including the capsid, head-to-tail interface, and tail tip regions. Strikingly, PD491P1 exhibits an exceptionally extensive disulfide bond network that covalently stabilizes nearly the entire virion. Unique structural features include an elaborate portal-adaptor-terminator interface and distinctive, upward-pointing and flexible tail fibers with multiple putative host recognition domains. These structural adaptations may enable phage PD491P1 to achieve survival and robust infection in the challenging gut environment. These findings expand our understanding of gut phage structural diversity, reveal mechanistic insights into phage stability and infection, and provide a foundation for future development of phage-based microbiome therapeutics.}, }
@article {pmid42086326, year = {2026}, author = {Azulay, A and Gotesdyner, L and Aharoni-Frutkoff, Y and Focht, G and Talmor, Y and Borenstein, E and Plotkin, L and Orlanski-Meyer, E and Lev-Tzion, R and Ledder, O and Yogev, D and Assa, A and Broide, E and Yerushalmy-Feler, A and Kierkuś, J and Schwerd, T and Wine, E and Turner, D}, title = {Multi-omics-based machine learning model predicts response and guides treatment in Crohn disease: a case study in nutritional therapy.}, journal = {Inflammatory bowel diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/ibd/izag060}, pmid = {42086326}, issn = {1536-4844}, support = {//Leona M. and Harry B. Helmsley Charitable Trust/ ; }, abstract = {BACKGROUND: Biomarkers are needed to predict treatment response and guide therapeutic decisions in Crohn disease (CD). We aimed to develop and validate a multi-omics machine learning (ML) model to predict response to nutritional therapy in pediatric CD.<br><br>METHODS: Treatment-naive children with newly diagnosed CD who were initiating exclusive enteral nutrition (EEN) were prospectively enrolled in this study. Metabolomics and lipidomics were measured in the serum and stool, as well as the fecal microbiome. Following feature selection via minimum redundancy maximum relevance, random-forest models were constructed for single- and multi-omics and performances were evaluated. The models were externally validated in an independent prospective cohort of treatment-naive children and young adults with CD treated with EEN.<br><br>RESULTS: The discovery cohort consisted of 50 children (mean&#x2009;&#xb1;&#x2009;SD age 14.3&#x2009;&#xb1;&#x2009;2.7&#x2009;years), of whom 34 (68%) responded to EEN. Combining complementary signals from host metabolism, gut microbiota, and lipid profiles from serum and stool in a multi-omics ML model yielded a model for predicting treatment response (training accuracy 94%; 95% CI, 82%-100%). Key predictive features included serum metabolites (2-hydroxyglutaric acid, Cer[d18:0/22:0], and HexCer[d18:1/d26:1]), fecal metabolites (3-methyladipic acid, DG[16:0&#x202f;20:0], PC aa C42:2), and microbial taxa (family Bifidobacteriaceae and genus CAG-56). The validation cohort consisted of 21 patients of whom 12 (57%) responded to EEN. The multi-omics model performance achieved an area under the receiver operating characteristic curve (AUROC) of 0.81 (95% CI, 0.6-1.0). Clinical and endoscopic features did not improve the predictive ability of the model.<br><br>CONCLUSION: As a proof-of-concept, we showed that integrated multi-omics ML models can predict EEN response in pediatric CD patients, supporting their potential use in precision nutrition and personalized care strategies.}, }
@article {pmid42086392, year = {2026}, author = {Fan, J and Ye, Y and Xia, W}, title = {Comment on: "Intratumoral microbiome composition and its role in tumor recurrence in primary liver cancer".}, journal = {Journal of the Formosan Medical Association = Taiwan yi zhi}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jfma.2026.04.114}, pmid = {42086392}, issn = {0929-6646}, }
@article {pmid42086396, year = {2026}, author = {Zhang, J and Yang, B and Martin, FM}, title = {Harnessing microbiomes to redefine medicinal plant agriculture.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2026.04.007}, pmid = {42086396}, issn = {1878-4380}, abstract = {Medicinal plants link agriculture, ecosystem health, and human therapeutics, with bioactive compound profiles providing a direct and economically meaningful readout of microbiome function. Although microbial inoculation can enhance pharmacologically relevant metabolites under controlled conditions, these effects are context dependent and rarely reproducible in the field. This efficacy gap reflects three ecological constraints: introduced microbes are excluded by resident communities, environmental variation overrides laboratory-optimised functions, and inoculants fail to persist without mutualistic feedback. Addressing these barriers requires shifting from disposable inputs to microbiome stewardship: rewilding beneficial communities, designing climate-adapted consortia, and managing soil as living infrastructure. Whether such stewardship produces measurably different bioactive profiles and therapeutic outcomes under field conditions remains the empirical question on which its One Health rationale ultimately depends.}, }
@article {pmid42086397, year = {2026}, author = {Cheng, Y and Wang, Y and Luo, T and Guo, L}, title = {Challenges and future directions in AI-driven biomaterials for microbiome-associated oral infectious diseases: A systematic review.}, journal = {Dental materials : official publication of the Academy of Dental Materials}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.dental.2026.04.025}, pmid = {42086397}, issn = {1879-0097}, abstract = {Oral biofilm-induced antimicrobial resistance is the core pathogenic mechanism of microbiome-associated oral infectious diseases (dental caries, periodontitis, peri-implantitis, and endodontic infection). Traditional therapies and biomaterials are limited by poor biofilm penetration, drug resistance induction, single functionality, and inadequate adaptation to dynamic oral microenvironmental changes (e.g., pH fluctuations, salivary rinsing, masticatory stimulation). Artificial intelligence (AI) has transformed the field by integrating materials science, microbiology, and stomatology data. Via machine learning, deep learning, and multi-physics simulation, AI optimizes biomaterial physicochemical properties, decodes microenvironmental signals, constructs precise sensing-response loops, and supports the full chain of material design, performance prediction, and action simulation, advancing treatment from empirical intervention to precision regulation. This systematic review retrieved literature from PubMed, Embase, and Web of Science (January 2016-January 2026) using keywords across three dimensions: AI, biomaterials, and oral microbiome. Following inclusion/exclusion criteria, 99 articles were included. It elaborates on five core mechanisms of AI-driven oral biomaterials (precise oral microbiome analysis, targeted material design/optimization, performance prediction/simulation, targeted delivery/intervention, effect evaluation/dynamic regulation), analyzes their applications in microbiome-targeted biomaterial research and development (R&amp;D) and clinical practice for the four major oral infectious diseases, addresses technical bottlenecks (insufficient targeting specificity and precision of biomaterials, poor stability and durability in complex oral microenvironments, inadequate biofilm disruption capacity, and clinical translation obstacles), and proposes future directions (multimodal design to enhance targeting specificity, structural and component optimization to improve stability/durability, development of multi-mechanism synergistic biofilm disruption strategies, strengthening translational research for clinical application, and deep integration of AI in the full chain of biomaterial R&amp;D). This work provides comprehensive theoretical and practical support for the R&amp;D, optimization, and clinical translation of AI-driven microbiome-targeted oral biomaterials.}, }
@article {pmid42086572, year = {2026}, author = {Gracie, R and Wiedenmann, J and Lam, P and Sweet, M and D'Angelo, C}, title = {Breakdown of microbial networks links nutrient stress and reef coral disease.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42086572}, issn = {2041-1723}, support = {522271101//Leverhulme Trust/ ; INSPIRE DTP//RCUK | Natural Environment Research Council (NERC)/ ; }, mesh = {Animals ; *Coral Reefs ; *Anthozoa/microbiology ; Nitrogen/metabolism/analysis ; *Microbiota/physiology ; Seawater/chemistry/microbiology ; Phosphorus/metabolism/analysis ; Cyanobacteria/isolation &amp; purification/metabolism ; Symbiosis ; Stress, Physiological ; Nutrients/metabolism ; Ecosystem ; }, abstract = {Coral diseases are increasing in prevalence, accelerating the global decline of tropical reefs, which threatens over 25% of marine biodiversity and vital ecosystem services for human societies. While outbreaks are frequently linked to environmental change, including heat stress, sedimentation, and reduced water quality, the mechanisms by which such factors promote disease remain poorly understood. Here we show that nutrient stress, caused by skewed seawater nitrogen-to-phosphorus (N:P) stoichiometry, promotes the onset of Black Band Disease (BBD), a common and easily recognisable syndrome that affects corals around the globe. Using Turbinaria reniformis as a model system, controlled laboratory experiments demonstrate that skewed N:P ratios disrupt the functional integrity of coral-associated microbial networks while favouring opportunists that exploit dysfunctional host-symbiont interactions. Disease lesion-associated microbial mats are dominated by cyanobacteria and include sulphur-metabolising bacteria, hallmarks of natural BBD communities. Strikingly, similar cyanobacterial taxa are also detected in the visually healthy coral tissue ahead of the expanding lesions, suggesting an opportunistic recruitment of disease-associated members from the resident microbiome. Global analyses of BBD outbreaks reveal that over 88% occurred in regions with skewed N:P ratios, compared with only 16% that were linked to prior heat stress. Together, our findings identify nutrient-driven microbiome destabilisation as a key pathway to coral disease, reinforcing nutrient management as a major lever for reef conservation and restoration practice.}, }
@article {pmid42086594, year = {2026}, author = {Wang, K and Li, Y and Li, C and Kahiel, M and Nagaoka, K and Shen, D and Li, C}, title = {Lung microbiota-mediated biotransformation of mogroside preserves pulmonary barrier integrity and attenuates PM2.5-induced inflammation via NF-κB-Th17 modulations.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00992-y}, pmid = {42086594}, issn = {2055-5008}, support = {32372935, 32072781//National Natural Science Foundation of China/ ; KYLH2025004//Fundamental Research Funds for the Central Universities/ ; 2023YFD1300802-4//National Key Research and Development Program of China/ ; }, abstract = {PM2.5-induced lung injury challenges poultry health with limited treatments. Mogroside's unique therapeutic impact on pulmonary inflammation may involve modulating the lung microbiome, which influences immune function and respiratory health. We first demonstrated that mogroside (MG) supplementation improved growth performance and mitigated PM2.5-induced alveolar damage, inflammatory cytokine release, and Th17 differentiation (p < 0.05). MG increased the abundance of beneficial bacteria, particularly Lactobacillus (p < 0.01). Notably, MG IIE accumulated in lung tissues and bronchoalveolar lavage fluid (BALF). To further clarify the role of microbe-metabolite interactions, BALF from MG-treated broilers was transplanted. Only complete BALF containing both MG and microbiota significantly alleviated fibrosis (p < 0.05), reshaped lung microbial composition, and modulated metabolites such as taurine and lactic acid. Microbiome analysis identified Sphingomonas as a key taxon enriched in MG-BALF, strongly correlated with protective metabolites. In vitro assays confirmed that Sphingomonas degraded MG IIE into mogrol via β-glucosidase activity. Finally, a Calu-3-Jurkat T lymphocytes co-culture model revealed that MG IIE, particularly in combination with Sphingomonas metabolites, preserved barrier integrity, suppressed NF-κB phosphorylation, reduced ROS, and inhibited Th17-associated cytokine expression. Collectively, MG IIE and its Sphingomonas-mediated metabolites form a lung microbiota-metabolite-host axis that protects against PM2.5-induced pulmonary injury.}, }
@article {pmid42087172, year = {2026}, author = {Chamberlin, ML and Spears, ML and Cooper, G and Miller, ZJ and Bothner, B and Walk, ST and Yeoman, CJ and Miles, MP}, title = {Impact of the gut microbiome on health impacts of Haskap berries: study protocol for a randomized control trial.}, journal = {Trials}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13063-026-09759-4}, pmid = {42087172}, issn = {1745-6215}, support = {2024-67018-42493//National Institute of Food and Agriculture/ ; }, abstract = {BACKGROUND: Haskap berries have great potential as a superfood due to high polyphenolic content which confers both anti-inflammatory and antioxidant activity. These health impacts are mitigated, at least in part, by the gut microbiome as most ingested polyphenols pass to the large intestine for microbial enzymatic action and conversion to secondary phenolic metabolites. These microbial actions mediate both the bioavailability and the bioefficacy of Haskap-derived phenolics. However, clinical intervention trials characterizing the impact of long-term Haskap consumption on human health and the interaction between Haskap-derived phenolics and the gut microbiome are limited. This study aims to determine the impact of Haskap consumption on gut microbiome composition, gut microbial and serum metabolites, and other health outcome metrics in a cohort of adults with both low and high risk of metabolic syndrome.<br><br>METHODS: This is a four-armed, randomized, triple-blind, placebo-controlled clinical trial conducted in a cohort of adults with both low and high risk of metabolic syndrome. A total of 120 participants (60 metabolically healthy, 60 metabolically unhealthy) will be randomized in a 1:1 ratio to consume a daily dose of either Haskap or placebo juice for 8 weeks. Outcome measures will be collected before and after the intervention period to determine the health impacts of Haskap in both groups. Primary outcome measures include fasting blood markers of glucose and lipid metabolism and inflammation, fat oxidation rates during submaximal exercise, 16S rRNA fecal microbial composition data, and mass spectrometry-acquired fecal and serum metabolomic data. Secondary outcome measures include anthropometric and sleep quality measures as well as acute and habitual dietary intake data.<br><br>DISCUSSION: Investigating how the gut microbiome influences the health benefits of consuming Haskap berries will help elucidate potential mechanisms of Haskap-induced metabolic health benefits and help inform the development of effective strategies to decrease metabolic disease risk through Haskap consumption.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov NCT06546020. Registered on 1 August 2024.}, }
@article {pmid42087225, year = {2026}, author = {Youn, HY and Park, S and Min, H and Ngoc, NB and Kim, YH and Cha, KH and Park, YT and Kwon, HY and Lee, CG and Kim, M}, title = {Micheliolide ameliorates colon cancer cachexia by modulating gut microbiota-immune signaling via Phocaeicola vulgatus enrichment.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02412-x}, pmid = {42087225}, issn = {2049-2618}, support = {26Z0001//Korea Institute of Science and Technology intramural research grant/ ; }, abstract = {BACKGROUND: Cancer cachexia profoundly impacts patient survival and quality of life. Current treatments fail to halt this trajectory, highlighting an urgent clinical need for host-directed therapies capable of uncoupling skeletal muscle wasting from tumor progression. This study investigated the therapeutic potential of micheliolide (MCL) across distinct tumor contexts.<br><br>METHODS: We employed immunocompetent murine models of colon cancer (CT26) and lung cancer (LLC) cachexia, pseudo-germ-free (pseudo-GF) mice, murine C2C12 myotubes, and primary human skeletal muscle cells. We evaluated MCL's impact on muscle wasting, systemic inflammation (splenic CD4[+] T cell phenotypes), gut microbiota composition, and short-chain fatty acid (SCFA) production. The direct effects of Phocaeicola vulgatus (P. vulgatus) administration were also assessed in the CT26 model.<br><br>RESULTS: MCL functions as a potent host-directed therapy, ameliorating muscle wasting in both models-particularly CT26-completely uncoupling muscle preservation from tumor cytotoxicity. In vitro, MCL directly prevented catabolism in both C2C12 and human primary myotubes. In vivo, MCL robustly rescued muscle mass and function. This was associated with the suppression of local muscle NF-&#x3ba;B hyperactivation and a marked reduction in the absolute counts of activated (CD25[+]) and exhaustion marker-expressing (PD-1[+], TIM-3[+]) splenic CD4[+] and CD8[+] T cells, resolving splenomegaly. Crucially, targeted microbiota depletion in pseudo-GF mice entirely abrogated these anti-cachectic benefits, establishing the gut microbiome as an indispensable mediator. MCL selectively enriched the beneficial bacterium P. vulgatus while differentially suppressing potential pathobionts like Enterococcus faecalis in CT26 and Streptococcus acidominimus in LLC. Microbial functional analysis indicated MCL increased the predicted potential for biotin biosynthesis in the CT26 model. Correlation analyses linked P. vulgatus abundance and increased SCFAs to reduced cachexia severity and modulated T cell profiles. Validating its functional significance, oral P. vulgatus administration significantly attenuated muscle wasting, increased cecal butyrate, and beneficially altered specific gut bacterial taxa in the CT26 model.<br><br>CONCLUSION: By therapeutically rewiring the gut-immune-muscle axis, MCL exerts pronounced and context-dependent anti-cachectic efficacy. Through dampening of systemic inflammation via T cell modulation, beneficial remodeling of the gut microbiota, and enhancement of predicted microbial biosynthesis pathways, MCL serves as a highly translational, host-directed intervention to mitigate cancer-induced systemic catabolism independent of tumor growth inhibition. Video Abstract.}, }
@article {pmid42087248, year = {2026}, author = {Duan, Y and Ma, Z and Liu, Y and Jia, Y and Zhang, Z and Yang, C and Gong, X and Mao, Z and Li, C and Ma, F}, title = {MdUGT88F1 enhances plant resistance to Fusarium proliferatum f.sp. malus domestica MR5 via root exudate-mediated assembly of disease-suppressive rhizosphere microbiota.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02416-7}, pmid = {42087248}, issn = {2049-2618}, support = {32302476//National Natural Science Foundation of China/ ; U24A20414//National Natural Science Foundation of China/ ; NO.ts20190923//Taishan Scholar Funded Project/ ; CARS-27//Agriculture Research System of China/ ; 2023B02018//Xinjiang Key Research and Development Project/ ; }, abstract = {BACKGROUND: Apple replant disease (ARD) is a major threat to the sustainable development of China's apple industry. It is primarily caused by the accumulation of phloridzin and the pathogen Fusarium proliferatum f.sp. malus domestica MR5 (Fpmd MR5). MdUGT88F1-mediated phloridzin biosynthesis is known to enhance disease resistance, but its role in shaping the rhizosphere microbiome and conferring resistance against Fpmd MR5 remains unclear. In this study, we used wild-type (WT) and MdUGT88F1 transgenic apple lines to systematically investigate the mechanism by which MdUGT88F1 regulates the rhizosphere microbiome to mitigate ARD.<br><br>RESULTS: Compared with WT and MdUGT88F1-OE plants, MdUGT88F1-RNAi plants exhibited enhanced tolerance to ARD, as indicated by reduced disease severity, decreased abundance of Fpmd MR5 in the rhizosphere soil, and lower phloridzin content. Further greenhouse experiments demonstrated that the rhizosphere bacterial communities were triggered mainly by changes in community composition. Multi-omics joint analysis revealed that members of the family Bacillaceae with multiple plant growth-promoting traits were enriched in the MdUGT88F1-RNAi plant rhizosphere but only upon Fpmd MR5 invasion. MdUGT88F1-RNAi plants exhibited significantly higher exudation of D-tagatose, D-galactose, sucrose, 3-O-methyl-D-glucose, and maltitol. Interestingly, exogenous application of these compounds promoted the proliferation of Bacillus, enhancing plant resistance to Fpmd MR5. In vitro assays demonstrated that the recruited Bacillus significantly inhibited the hyphal growth and fumonisin B1 production of Fpmd MR5 and alleviated plant disease symptoms. We experimentally validated this observation by inoculating a synthetic microbial community (Bacillus velezensis, Bacillus mojavensis, Bacillus subtilis, Bacillus amyloliquefaciens, and Bacillus licheniformis) into replanted soil, which led to a significant reduction in pathogen Fusarium abundance and promoted plant growth.<br><br>CONCLUSION: Overall, these findings highlight that plant disease resistance is a complex trait driven by dynamic interactions among the host genetic background, rhizospheric microbial communities, and pathogens. Targeted modulation of the rhizospheric microbiome represents a potent "prebiotic" strategy. This approach can indirectly enhance plant disease resistance by fostering beneficial microbial activity in the rhizosphere. This study also provides a theoretical basis and practical solutions for the green control of ARD through prebiotics and synthetic microbial communities. Video Abstract.}, }
@article {pmid42087326, year = {2026}, author = {Iida, A and Toyota, Y and Itagaki, T and Yawaka, Y and Hasebe, A}, title = {Oral and Gut Microbiota in Individuals With Autism Spectrum Disorder: A Pilot Case-Control Study.}, journal = {International journal of paediatric dentistry}, volume = {}, number = {}, pages = {}, doi = {10.1111/ipd.70095}, pmid = {42087326}, issn = {1365-263X}, support = {20K18798//Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research (JSPS KAKENHI)/ ; }, abstract = {BACKGROUND: Recent studies suggest that gut microbiota play important roles in individuals with autism spectrum disorder (ASD), potentially influencing the development and severity of the condition. Oral bacteria may be directly or indirectly involved in the biological and symptomatic aspects of ASD through their effect on gut microbiota.<br><br>AIM: This pilot study aimed to characterise compositional alterations in the oral and gut microbiota of individuals with ASD and to identify bacterial taxa in saliva and faeces that may serve as potential microbial indicators of ASD.<br><br>DESIGN: Salivary and faecal samples were collected from 10 individuals with ASD and 10 typically developing controls. The oral and gut microbiota were evaluated using 16S ribosomal RNA marker-gene sequencing.<br><br>RESULTS AND CONCLUSION: Distinct features of the oral and gut microbiota were identified that differed between individuals with ASD and typically developing controls. Based on linear discriminant analysis effect size, the relative abundances of the genera Neisseria were higher in the oral microbiota of the ASD groups, whereas the genera Faecalibacterium were enriched in the gut microbiota. These findings highlight the potential relevance of the oral-gut-brain axis in ASD. Additionally, non-invasive sampling of saliva and faeces may be utilised for early ASD screening.}, }
@article {pmid42087591, year = {2026}, author = {Ebersole, JL and Kirakodu, SS and Zhang, X and Dawson, D and Miller, CS}, title = {Salivary Biological Responses to Nonsurgical Periodontal Treatment in Type 2 Diabetics.}, journal = {JDR clinical and translational research}, volume = {}, number = {}, pages = {23800844261437825}, doi = {10.1177/23800844261437825}, pmid = {42087591}, issn = {2380-0852}, abstract = {BACKGROUND: This investigation evaluated the predictive capacity of the oral microbiome and host salivary biomarkers on treatment outcomes for periodontitis in patients with type 2 diabetes mellitus (T2DM).<br><br>METHODS: Two patient cohorts were enrolled: T2DM without periodontitis (DWoP; n = 32) and T2DM with periodontitis (DWP; n = 29). Whole saliva was collected at baseline and 4 to 7 wk posttreatment (i.e., DWoP, supragingival prophylaxis; DWP, scaling and root planing). The oral microbiome (operational taxonomic units; OTUs) and targeted salivary biomarkers were assessed in pre- and posttreatment saliva.<br><br>RESULTS: Most OTUs (57%-68%) and salivary biomarkers (43%-55%) decreased after treatment in both groups. Supragingival prophylaxis in the DWoP patients altered a limited number of taxa (V. dispar, P. denticola, Rothia, Neisseria), showing substantial increases in the microbiome, whereas predominantly gram-negative OTUs decreased. In the DWP, decreases were observed following therapy for Bacillota, Bacteroidetes, and Proteobacteria, again representing primarily gram-negative taxa. Microbe-host response biomarker correlations increased posttherapy in DWoP and decreased in DWP samples. Importantly, poor response (PR) to therapy was independent of HbA1c levels but associated with higher pretreatment levels of multiple bacterial genera (i.e., Alloprevotella, Campylobacter, Corynebacterium, Fusobacterium, and Leptotrichia) and elevated levels of interleukin (IL)-1b, IL-6, matrix metalloprotease-8 (MMP-8), adiponectin, and resistin. After therapy, PR was characterized by increases in Lachnospiraceae, Prevotella, and a lack of effects on Leptotrichia, Alloprevotella, Porphyromonas, and Stomatobaculum.<br><br>CONCLUSIONS: Poor clinical response to therapy was characterized by (1) less microbiome diversity and elevated levels of specific bacteria and salivary analytes pretherapy and (2) posttherapy elevations in multiple taxa and sustained levels of IL-1b and MMP-8 in both groups of PR patients. These findings support that a panel of salivary features could enhance our prediction and earlier decisions on response to therapy at the biological level, thus opening the door for more precise patient-level management.Knowledge Transfer Statement:These findings contribute to a pathway for understanding oral health using biological measures as a standard for better decisions in oral health care. Specifically, microbiome and host response parameters provided important insights with predictive value and differential biological presentation related to response to therapy. While these measures do not dictate disease causation, they appear to reflect the periodontal environment, hallmarks of disease, and response to therapy.}, }
@article {pmid42087714, year = {2026}, author = {Mautone Gomes, H and Kleber Silveira, A and Santos Froemming, L and Martins Silva, A and Campos Soares, M and Hansen, J and Carazza Kessler, FG and Bastos Mendes, L and da Rosa Paz, AH and Gasparotto, J and Gelain, DP and Fonseca Moreira, JC}, title = {In vivo methylmercury toxicity is exacerbated by polystyrene microplastic exposure, leading to colon barrier disruption, gut dysbiosis, and systemic oxidative imbalance.}, journal = {Journal of toxicology and environmental health. Part A}, volume = {}, number = {}, pages = {1-29}, doi = {10.1080/15287394.2026.2666544}, pmid = {42087714}, issn = {2381-3504}, abstract = {Methylmercury (MeHg) is a well-recognized toxicant, whereas microplastics (MP) are contaminants whose health effects continue to be explored. Evidence suggests that concomitant exposure to MeHg and polystyrene (PS) may enhance adverse outcomes in the gastrointestinal system. The aim of this study was to investigate the combined effects of MeHg and PS-MP on intestinal homeostasis, as well as systemic oxidative and inflammatory responses. A total of 64 rats with 30-days-old (n = 16 per group) were exposed to environmentally relevant doses of 0.5 mg/L MeHg and/or 0.2 mg/L PS-MP of 5 µm during 8 weeks. Co-exposure resulted in colon shortening, mucus depletion, and disruption of tight junction proteins, accompanied by macrophage infiltration and elevated pro-inflammatory cytokines. Structural and inflammatory changes were accompanied by gut dysbiosis, including altered microbial composition and reduced diversity indices. Biochemically, co-exposure amplified oxidative stress in the colon, with loss of free thiols and enhanced lipid peroxidation, while not markedly affecting glutathione-S-transferase activity. Systemically, combined treatment increased serum cytokines and induced genotoxicity. Although compensatory antioxidant responses were detected in blood, oxidative stress was evident in peripheral organs, particularly liver, kidneys, and heart. Taken together, these findings demonstrate that the intestine may be an early and sensitive target following co-exposure to MeHg and PS-MP, driving cytokine release into circulation and contributing to systemic injury. Our study provides novel in vivo evidence that combined PS-MP and MeHg exposure exacerbates some biological outcomes noted with individual contaminant exposure, indicating the importance of considering co-contamination scenarios in risk assessment of emerging pollutants.}, }
@article {pmid42087981, year = {2026}, author = {Wang, Q and Zhou, K and Zhang, M and Dong, Y and Zhao, M}, title = {Association between dentition defects and Alzheimer's disease risk: a systematic review and meta-analysis.}, journal = {Frontiers in dental medicine}, volume = {7}, number = {}, pages = {1783171}, pmid = {42087981}, issn = {2673-4915}, abstract = {BACKGROUND: Alzheimer's Disease (AD) is the most common neurodegenerative disorder among the elderly, with a steadily rising prevalence that poses a significant global public health challenge. Recently, dentition defects (DD), such as tooth loss, have gained attention as potential risk factors influencing neurocognitive health. However, the relationship between DD and AD remains inconclusive, necessitating a systematic analysis to clarify this association.<br><br>METHODS: This systematic review and meta-analysis was conducted in accordance with PRISMA guidelines. We searched PubMed, Embase, Web of Science, and Cochrane Library databases to identify relevant studies published between 1996 and 2022. Eligible studies assessing the relationship between DD and AD were included. A random-effects model was applied to estimate the pooled odds ratios (ORs) with 95% confidence intervals (CIs). Heterogeneity and publication bias were also assessed.<br><br>RESULTS: Fourteen studies were included, with sample sizes ranging from 52 to 156,450 participants. The meta-analysis revealed a significant association between DD and an increased risk of AD (OR=1.38, 95% CI: 1.09-1.74, P&#x2009;<&#x2009;0.05). Heterogeneity among the studies was substantial (I&#xb2;&#x2009;=&#x2009;97%), reflecting considerable variability in study designs, populations, and exposure definitions. Sensitivity analysis and publication bias assessments indicated the reliability of the results despite high heterogeneity. Mechanistic analyses suggested that DD may elevate AD risk through pathways such as chronic inflammation, nutritional deficiencies, alterations in the oral microbiome, and reduced cognitive reserve.<br><br>CONCLUSIONS: DD are significantly associated with an increased risk of AD. Improving oral health may represent a modifiable factor warranting. However, further high-quality prospective studies are needed to validate these findings and explore the underlying mechanisms.}, }
@article {pmid42088008, year = {2026}, author = {Sgarbossa, C and Forth, E and Squires, S and Groth, A and Farid, M and Gallant, K and Desai, D and Redfearn, W and Milev, R}, title = {Neurobiological effects of microbial treatments within psychiatry: a systematic review.}, journal = {Frontiers in psychiatry}, volume = {17}, number = {}, pages = {1745964}, pmid = {42088008}, issn = {1664-0640}, abstract = {OBJECTIVE: Though microbial interventions such as probiotics and fecal microbiota transplantation have had a growing body of evidence suggesting their efficacy in alleviating the symptoms of psychiatric illnesses, their exact mechanisms of action and impacts on the brain are still not fully characterized. The aim of this review is to compile and summarize the current literature regarding neurobiological changes associated with microbial interventions targeting psychiatric symptoms in healthy and psychiatric populations.<br><br>METHODS: A systematic search of four databases was conducted using key terms related to neuroimaging, microbial interventions, and psychiatric illnesses and/or symptoms. All results were then evaluated based on specific eligibility criteria.<br><br>RESULTS: 10 studies met eligibility criteria and were included in this systematic review. Three of the five healthy control studies and all five of the studies conducted within psychiatric populations, observed significant neurobiological changes associated with probiotic intervention either in areas with psychiatric relevance, in the direction of a healthier profile, or correlated with improved psychiatric and/or affective symptoms. The interventions used in these studies consisted of probiotics with bacterial species primarily from the lactobacillus and bifidobacterium genera, at doses ranging from 1-900 billion CFU, taken for durations ranging from 4 weeks to 6 months.<br><br>CONCLUSIONS: The findings from this review suggest that probiotic intervention may be associated with neurobiological changes, and that these changes could play a role in ameliorating psychiatric symptoms. More research is needed to replicate these findings, explore other psychiatric populations and microbial interventions, and fully elucidate the mechanisms driving these promising neurobiological and clinical changes.}, }
@article {pmid42088307, year = {2026}, author = {Wen, S and Jayaweera, DT and Marzouka, GR and Dong, C}, title = {The role of microRNAs in cardiovascular disease associated with the consumption of ultra-processed foods: a comprehensive review.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1790304}, pmid = {42088307}, issn = {2296-861X}, abstract = {Ultra-processed foods (UPFs) now dominate dietary intake in many countries and are consistently associated with higher risks of cardiovascular disease (CVD), including myocardial infarction, stroke, and heart failure. Beyond excess sodium, sugar, and unhealthy fats, UPFs may exert cardiovascular harm through food matrix disruption, processing-generated toxicants, additive exposure, and microbiome perturbation. These upstream insults converge on inflammatory, oxidative, and metabolic signaling pathways that regulate microRNAs (miRNAs), a class of small non-coding RNAs that orchestrate post-transcriptional gene expression across endothelial cells, vascular smooth muscle cells, macrophages, platelets, and metabolic tissues. In this review, we propose a unifying mechanistic framework in which UPF exposure reshapes both intracellular and extracellular vesicle (EV)-associated miRNA networks, thereby linking gut, liver, adipose tissue, and the vascular wall in a feed-forward cardiometabolic signaling loop. We synthesize evidence across epidemiology, experimental models, and human dietary intervention studies, while explicitly distinguishing established, emerging, and speculative mechanisms to avoid over-interpretation. We further discuss translational opportunities, including circulating miRNA/EV-miRNA biomarkers, nutritionally responsive miRNA signatures, and miRNA-targeted therapeutics. Together, this framework positions the UPF-miRNA/EV axis as a plausible molecular bridge between modern dietary exposure and atherosclerotic disease progression, and highlights priority areas for mechanistic validation and clinical translation.}, }
@article {pmid42088314, year = {2026}, author = {Alsanie, SA}, title = {Probiotic-fortified functional foods: integrating nutrient delivery and gut health benefits.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1815558}, pmid = {42088314}, issn = {2296-861X}, abstract = {Foods fortified with probiotics are a fast-emerging field at the crossroads of food technology, nutritional biochemistry and microbiome science. The increased interest in the gut microbiota as a key controller of host metabolism, immunity and overall homeostasis has led to the creation of diets that provide key nutrients with live and beneficial microbes. Compared to the conventional dietary supplementation, there are improved microbe stability, bioavailability, and microbe-nutrient interactions of probiotic fortification of food matrices. This review is a summary of the literature on the impact of probiotics on the host immunological and metabolic signalling pathways, intestinal barrier functioning, and gut microbiota composition. The biological mechanisms of interaction of probiotics with the intestinal microenvironment are specifically focused on the production of short-chain fatty acids, expulsion of pathogens, the regulation of immune cells, and the communication of the gut-brain axis. New information that can be used to correlate the administration of probiotics with the improvement of gastrointestinal health, systemic inflammation, metabolic maintenance and neurobehavioral phenotypes is narratively synthesized based on available preclinical and clinical evidence. The opportunities of probiotic-enriched functional foods have been highlighted in this review as a strategic tool of disease prevention and health promotion in the context of the mechanistic knowledge in combination with translational health outcomes. The complexity in the interactions between microbial delivery systems and host physiology is the clue to the best efficacy, safety and the future innovation in the development of functional foods.}, }
@article {pmid42088498, year = {2026}, author = {Bu, K and Scherzi, T and Cantor, A and Teng, AA and Pablo, JV and Shandling, AD and Randall, AZ and Davis, E and Jackson, C and Looney, RJ and Campo, JJ and Seppo, A and Järvinen, KM and Clemente, JC}, title = {Gut microbial IgA coating in infants with traditional farming lifestyle and urban infants with allergic outcomes.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1793302}, pmid = {42088498}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Infant ; *Immunoglobulin A/immunology ; Female ; Male ; Feces/microbiology ; *Hypersensitivity/immunology/epidemiology/microbiology ; Milk, Human/immunology ; Urban Population ; Agriculture ; Bacteria/immunology ; Life Style ; }, abstract = {BACKGROUND: The sharp increase in prevalence of atopic disease suggests a role for environmental factors, such as the microbiome. Here, we study the impact of immunoglobulin A (IgA) coating of gut bacteria in infancy on allergic outcomes in two distinct populations: (1) an urbanized cohort of Rochester infants (ROC) enriched for allergies (prevalence of 40%) and (2) infants from a traditional, agrarian Old Order Mennonite (OOM) community with a low prevalence of allergies (less than 2%).<br><br>METHODS: We performed immunoglobulin A sequencing (IgA-SEQ) on stool samples collected at an average of 6 months of life to assess gut microbiome IgA coating levels in 9 OOM and 21 ROC infants. Atopic outcomes were diagnosed throughout the first 2 years; 10 of the ROC infants were diagnosed with atopic dermatitis and/or food allergy, while none of the OOM infants were allergic. We also assessed human milk IgA-binding of taxa-derived protein antigens, as well as IgA binding to live bacterial cell cultures.<br><br>RESULTS: Gut microbiome composition was dominated by Bifidobacterium, followed by Ruminococcus, Enterobacteriaceae, and Blautia. Higher IgA coating of P. melaninogenica and Pasteurellaceae were associated with allergic outcomes and higher coating of R. gnavus was observed in non-allergic infants. IgA coating levels of Atopobium, Bifidobacterium, and Coprococcus were positively associated with infant age, and coating levels of Corynebacterium associated negatively with infant age. In non-allergic infants, IgA coating of Clostridium was decreased, while in allergic infants, IgA coating of Corynebacterium was decreased. Furthermore, breastfeeding was associated with higher levels of fecal IgA in infancy, and IgA-binding capacity to B. infantis, a keystone infant commensal, was subsequently assessed using in vitro experiments. Compared to the ROC cohort, milk from OOM mothers exhibited a higher level of IgA response to B. infantis and several other commensals. Surprisingly, IgA-binding to B. infantis was partially mediated by Fab-independent interactions through binding to glycosylated regions of immunoglobulins.<br><br>CONCLUSION: Differential gut microbial IgA coating may play a role in development of allergic diseases in infancy. Human milk from communities with low rates of allergic diseases exhibit higher IgA responses to infant commensals, including B. infantis.}, }
@article {pmid42088528, year = {2026}, author = {Liu, H and Wang, D and Zhu, L and Li, T and Liu, B and Sun, J and Zuo, X and Chen, S and Liu, J and Xian, J and Feng, X and Zhang, C and Yang, W}, title = {Angelicin: A promising tricyclic aromatic agent for ulcerative colitis through cysteine-mediated proliferation of intestinal epithelial cells.}, journal = {Journal of pharmaceutical analysis}, volume = {16}, number = {5}, pages = {101435}, pmid = {42088528}, issn = {2214-0883}, abstract = {Angelicin (Ang), a natural tricyclic aromatic compound and quality marker derived from Fructus Psoraleae, exhibits significant anti-inflammatory efficacy. Fructus Psoraleae has long been utilized clinically for treating ulcerative colitis (UC). However, the specific role of Ang in UC remains poorly characterized. The present study aimed to elucidate the anti-UC effects of Ang and its underlying mechanisms. The anti-UC activity of Ang was evaluated using two UC models induced by dextran sulfate sodium (DSS) and 2,4,6-trinitrobenzenesulfonic acid (TNBS). Results demonstrated that Ang markedly inhibited the progression of UC. Microbial profiling indicated that the Ang-treated microbiome, particularly Lactobacillus murinus, provided protective effects against UC. Mechanistically, Ang facilitated proliferation of normal colonic epithelial cells, thus enhancing the intestinal mucosal barrier (IMB). Cysteine (Cys) played a crucial intermediary role by promoting glutathione (GSH) synthesis, maintaining redox homeostasis, and consequently facilitating cell proliferation. Additionally, increased Cys levels supported ribosomal biogenesis, enhancing protein translation and further stimulating cell proliferation. G-rich RNA sequence-binding factor 1 (GRSF1) was identified as a direct molecular target of Ang during ribosomal biogenesis. These findings indicated that Ang is a promising agent for promoting Cys-mediated cell proliferation, highlighting its role in maintaining redox homeostasis and protein translation. This study provides evidence supporting the future development of Ang as a therapeutic candidate for UC.}, }
@article {pmid42088583, year = {2026}, author = {Zuo, S and Kurumi, H and Ogihara, R and Kanda, T and Isomoto, H}, title = {Gut microbiota-M cell co-culture in inflammatory bowel disease and its therapeutic potential in organoid platforms.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1778142}, pmid = {42088583}, issn = {1663-9812}, abstract = {Dysbiosis of the gut microbiota is a key driver in the onset and persistence of inflammatory bowel disease (IBD). However, the mechanisms by which microbes influence mucosal immunity via specific epithelial routes remain incompletely elucidated. Microfold (M) cells within follicle-associated epithelium serve as a critical "gateway" for luminal antigens and microbes to access the mucosal immune system. While essential for surveillance of commensal microbes, M cells could also be exploited by adherent-invasive strains and adverse environmental factors to amplify inflammation. Recent studies suggest that both in Crohn's disease and ulcerative colitis, M cell abundance and function are aberrantly regulated, linking microbial imbalance with heterogeneous mucosal inflammatory phenotypes. Traditional animal models and two-dimensional culture systems retain limited capacity to selectively manipulate M cells without perturbing systemic immunity, thereby constraining systematic studies of microbiota-M cell co-cultures. Advances in intestinal organoid technology now enable controlled induction of functionally mature M cells within three-dimensional epithelial structures, and have started to shed light on the roles of RANKL signaling, negative regulators, and microbe-associated factors in M cell differentiation and homeostasis. In this review, we focused on key evidence supporting microbiota-M cell interactions in IBD, discussed how M cell-enriched intestinal organoid models could be leveraged to dissect the impact of pathogenic microbes, candidate probiotics, dietary components, and existing therapies on these interactions as well as to evaluate the related potential and limitations for microbiome interventions and drug screening. Integrating gut microbial plasticity with M cell epithelial entry and organoid platforms promises to provide new experimental foundations and theoretical support for individualized microbiome-based therapies and targeted mucosal treatments in IBD.}, }
@article {pmid42088715, year = {2025}, author = {Alfredo, K and Bedard, E and Buse, HY and Cazals, M and Francisco, P and Lee, J and Masters, S and Osann, E and Stillwell, A and Westerhoff, P and Bartrand, TA}, title = {Ten questions concerning water quality in building hot water systems.}, journal = {Building and environment}, volume = {275}, number = {}, pages = {}, pmid = {42088715}, issn = {0360-1323}, support = {EPA999999/ImEPA/Intramural EPA/United States ; }, abstract = {Hot water systems - water heaters and connected downstream plumbing and fixtures - are at the center of the water-energy nexus. They are ubiquitous and deliver an essential service but are subject to water quality degradation and health risks, scalding risks, energy consumption and greenhouse gas production, and water wastage. While the focus of this paper is on water quality, hot water quality is intimately connected to hydraulics, system layout, water conservation, energy conservation, and user outcomes. Despite their importance, hot water systems are less studied than drinking water production and transmission systems. Better knowledge about hot water will help professionals who design, install, and operate the systems; system users to manage competing risks; and researchers to identify opportunities for innovation. The ten questions posed are focused on the United States. The questions were developed during a workshop that brought together experts in all aspects of hot water systems to identify and prioritize research and innovation opportunities for hot water systems. The questions are ordered to first provide a general description of hot water systems and the chemical and microbiological processes that occur within them, then to discuss the state-of-the-art in modeling and informatics (both critical given the wide diversity in hot water systems), next to explore user and usage aspects of systems and the importance of user-focused design, and finally to identify and prioritize hot water system research and innovation opportunities.}, }
@article {pmid42088993, year = {2026}, author = {Ul Malook, S and Chen, X and Olukolu, BA and Occhialini, A and Lenaghan, SC and Neal Stewart, C and Chen, F}, title = {Microbial-type terpene synthases enable enhanced insect and fungal resistance in engineered plants.}, journal = {Biodesign research}, volume = {8}, number = {2}, pages = {100087}, pmid = {42088993}, issn = {2693-1257}, abstract = {A major challenge in crop improvement is enhancing resistance to diverse biotic stresses. Because terpenoids play key roles in chemical defense, an envisioned strategy is to introduce new terpene metabolic pathways into crops through engineering. Microbial-type terpene synthase-like (MTPSL) genes are widespread in nonseed plants but absent in seed plants. Here, we engineered terpene metabolism in Nicotiana benthamiana using MTPSL genes, enabling production of sesquiterpenes absent in flowering plants and enhanced resistance to pest insects and fungal pathogens. Two liverwort MTPSL genes, RlMTPSL3 and RlMTPSL4, which produce sesquiterpenes absent from flowering plants, were selected for metabolic engineering. In N. benthamiana, both genes generated sesquiterpenes consistent with their in vitro activities, and co-expression yielded combined profiles. Co-expression of RlMTPSL3 and RlMTPSL4, individually or together, with 3-hydroxy-3-methylglutaryl-CoA reductase, the rate-limiting enzyme in sesquiterpene pathway, substantially increased sesquiterpene production. Bioassays of engineered tissues with two defoliating herbivores beet armyworm (Spodoptera exigua) and Colorado potato beetle (Leptinotarsa decemlineata) showed growth suppression and up to 30% mortality. The gut microbiome of beet armyworm feeding on engineered tissues showed differences from those feeding on control tissues, suggesting a potential mechanism underlying reduced pest insect performance. Engineered sesquiterpenes were recovered from larval frass, indicating stability through digestion. Transformed leaves emitted elevated sesquiterpenes as volatiles that repelled beet armyworm. In addition, extracts of engineered tissues inhibited the growth of Fusarium oxysporum, a fungal pathogen, by ∼50%. Together, these results demonstrate that MTPSL-based engineering can introduce new sesquiterpenes into flowering plants, providing a promising strategy for broad-spectrum crop protection.}, }
@article {pmid42089012, year = {2026}, author = {Anderson, KE and Copeland, DC and Mott, BM and Kortenkamp, OL and Erickson, RJ and Allen, NO and Maes, PW and Chao, N and Dalenberg, H and Spivak, M}, title = {A propolis-rich hive environment affects redox gene expression and gut microbiota at the individual and social level in honey bees.}, journal = {FEMS microbes}, volume = {7}, number = {}, pages = {xtag019}, pmid = {42089012}, issn = {2633-6685}, abstract = {The microbiome of the honey bee is associated with immunity, oxidative state, and disease susceptibility. Here we investigated the effects of increased colony-level propolis exposure on gut microbiota and host worker immune and redox gene expression. Sampling pre-marked adult worker bees at 9-days post emergence revealed significantly larger populations of core microbiota in worker guts from propolis-rich colonies, but little change in taxonomic composition or relative structure. We found an overall trend towards decreased expression of immune genes in propolis-rich colonies. The expressions of both pro-phenol oxidase and catalase were significantly reduced in the worker fat body suggesting that propolis-rich colonies better support host redox balance in individual workers. Increased propolis levels resulted in greater expression of superoxide dismutase from the worker fat body and social head glands, consistent with tissue-specific expression considered beneficial in model organisms and humans. Our results suggest that propolis-rich conditions and social head gland secretions contribute to total redox activity throughout the niche space of social immunity. Moreover, our results are consistent with a companion paper that sampled the same colonies and age cohorts, reporting drastic increases in beneficial native bacteria and reduced pathogen prevalence on the mouthparts, a primary marker of social immunity.}, }
@article {pmid42089017, year = {2026}, author = {Taketani, RG and Clark, IM and Yau, PTO and Liu, L and Zhang, F and Bak, GR and Thompson, CMA and Bonnin, JM and Stewart, H and Malone, JG and Jones, S and Holden, N and Ryan, MJ and Mauchline, TH}, title = {Host plant selects bacterial rhizosphere microbiome function whereas community structure is determined by soil legacy.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag083}, pmid = {42089017}, issn = {2730-6151}, abstract = {The drivers between host plant, associated rhizosphere microbiome functions, and related plant health implications are complex and a field of continuous development. Furthermore, understanding of the interplay between soil, plant, and microbiome across different plant species and contrasting geographical areas is scarce. The United Kingdom (UK) Crop Microbiome Cryobank project, the world's first open crop/soil microbiome resource can fill this research gap. It utilizes contrasting UK soil types, with comprehensive environmental and agronomic metadata and has generated associated rhizosphere and bulk soil microbiome information for six crops (wheat, barley, oats, fava beans, oilseed rape, and sugar-beet) including a bacterial culture collection and 16S rRNA gene datasets. Here, using functional and taxonomic data from 24 000 bacterial cultures and 315 16S rRNA gene metabarcoded soil libraries, we show that geographical location and soil environment primarily influence the phylogeny of rhizosphere bacterial communities, whereas crop genotype is key in determining the function of associated rhizosphere microbiota. Sugar-beet and oilseed rape predominantly select for drought tolerant microbes, barley for Zn-solubilizing microbes and fava bean has a reduced selection of N-mineralizing microbes. These findings emphasize the need to consider the host plant's developmental requirements and edaphic factors for successful deployment of microbiome facilitated agriculture.}, }
@article {pmid42089091, year = {2025}, author = {Frey, JS and Grogg, MW and Hoisington, AJ and Wong, BA and Mumy, KL and Mauzy, CA}, title = {In vivo lung microbiome alterations from burn pit emissions and/or sand inhalation exposures.}, journal = {Frontiers in public health}, volume = {13}, number = {}, pages = {1693310}, pmid = {42089091}, issn = {2296-2565}, mesh = {Animals ; Rats, Sprague-Dawley ; Rats ; *Microbiota/drug effects ; *Lung/microbiology ; *Inhalation Exposure/adverse effects ; *Sand ; Male ; Bronchoalveolar Lavage Fluid/microbiology ; RNA, Ribosomal, 16S ; Open Waste Burning ; }, abstract = {INTRODUCTION: In-theater inhalation exposure to burn pit emissions (BPEs) and sand has been linked to respiratory issues, prompting a study to identify molecular alterations and potential biomarkers related to exposure and outcomes.<br><br>METHODS: Using a complex in vivo exposure scenario to mimic in-theater inhalation exposures, Sprague-Dawley rats were exposed to clean air (Control), BPEs, Sand, or a combination of BPE&#x202f;+&#x202f;Sand via whole-body exposure chambers. After euthanasia, bronchoalveolar lavage fluid was collected at 4 days and 90 days post-exposure, and bacterial amplicon sequence variants were identified using genomic DNA extraction and 16S rRNA gene sequencing.<br><br>RESULTS: Both BPE and BPE&#x202f;+&#x202f;Sand exposures significantly altered the lung microbiome, demonstrating increased mean alpha diversity and the highest number of unique ASVs. These changes in the lung microbiome began as early as 4&#x202f;days post-exposure and continued throughout 90 days post-exposure. BPE and BPE&#x202f;+&#x202f;Sand groups had increased levels of Bradyrhizobium and Methylobacterium and decreased levels of Pseudomonas compared to the Control and Sand groups. The genera most associated with the differences at 4 days post-exposure between the BPE vs. Control and BPE&#x202f;+&#x202f;Sand vs. Control groups were Corynebacterium, Geobacillus, Sphingomonas, and Streptococcus. Interestingly, the lung microbiome from the Sand or Control groups was not significantly altered based on alpha or beta diversity and shared the most abundant genera.<br><br>DISCUSSION: These data indicate that BPE exposure significantly alter the lung microbiome, whereas sand inhalation exposures alone did not seem to cause significant changes, nor did they provide an additive effect when combined with BPE. While the sub-chronic exposure study design led to more subtle molecular alterations in the lung tissue than expected, BPE exposures resulted in distinct and significant microbiome compositional changes in the lung. The observed population shift provided a signature specific to the type of inhalation exposure. Further efforts could lead to an understanding of the role of individual lung microbiomes in inhalation exposure risks and outcomes.}, }
@article {pmid42089105, year = {2026}, author = {Michalska-Madej, J and Janik-Superson, K and Zając, B and Krupiński, M and Smith, C and Seweryn, M and Ibáñez, A}, title = {Universes within universes: microbiome diversity associated with different body parts of the sand lizard (Lacerta agilis).}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e21061}, pmid = {42089105}, issn = {2167-8359}, mesh = {Animals ; *Lizards/microbiology ; *Microbiota/genetics ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Cloaca/microbiology ; Skin/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; }, abstract = {The bodies of animals host millions of microbial communities collectively known as the microbiome. The microbiome plays a crucial role in various processes related to the host's health and well-being. Although our understanding of the microbiome's importance to host functioning is growing rapidly, many aspects remain poorly understood. One such aspect is the role of the microbiome in chemical communication. To address this question, we used the sand lizard (Lacerta agilis), a reptile with well-developed chemosensory abilities and commonly distributed in Central Europe. Our first goal was to characterize the bacterial microbiome associated with different body parts potentially involved in chemical signalling (e.g., femoral glands, cloaca, and skin). Additionally, we examined sex-related differences in the microbiome that could be connected to intraspecific communication. Over two years, a total of 274 samples were collected. Amplicon sequencing of the 16S rRNA V3-V4 region revealed significant variation in microbial diversity across body parts, with the skin hosting the most diverse and balanced communities. In contrast, the cloaca and femoral glands contained less diverse but more specialised assemblages. No differences in microbial diversity between sexes were observed, but the year of sampling was an important factor, suggesting a highly dynamic microbiome in sand lizards. There was minimal overlap in the number of unique operational taxonomic units (OTUs) between body parts, indicating a small core microbiome (∼1% of shared taxa). Sex differences in tissue-specific bacteria were more pronounced in the cloaca, supporting the idea that the cloacal microbiome is highly specialised. Our findings suggest that microbial communities vary significantly among body parts, with strong tissue specificity, indicating that each region provides a distinct ecological niche. This study offers promising directions for future research into how host-associated microbiomes could influence chemical communication in vertebrates.}, }
@article {pmid42089249, year = {2026}, author = {Barrett, TC and Zheng, Q and ,  and Thompson, A and Di Guglielmo, MD}, title = {Infant fecal microbiome dysbiosis varies by feeding type in setting of severe bronchiolitis.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1002/jpn3.70435}, pmid = {42089249}, issn = {1536-4801}, support = {U54-GM104941 (PI: Hicks) and the State of Delaware//Institutional Development Award (IDeA) from the National Institute of General Medical Sciences (NIGMS) of the National Institutes of Health (NIH)/ ; P20GM103446 (PI: Duncan)//IDeA from the NIH NIGMS/ ; //Nemours Fellowship Research Award/ ; }, }
@article {pmid42089362, year = {2026}, author = {Southward, T and Zhuang, Y and Tam, A and Minsky, H and Ferri, J and Michel, J and Wu, S and Wu, X and Larman, T and Housseau, F and White, JR and Sears, CL and Queen, J}, title = {Enterotoxigenic Bacteroides fragilis induces host genotype-specific colonic epithelial and immune responses in mice.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiag247}, pmid = {42089362}, issn = {1537-6613}, abstract = {BACKGROUND: Colorectal cancer pathogenesis involves complex interactions between multiple risk factors including somatic mutations and microbial dysbiosis. A number of individual microbiota members have been implicated in colorectal cancer, including enterotoxigenic strains of Bacteroides fragilis (ETBF). ETBF promotes inflammation in mouse models, which has been mechanistically linked to colon tumorigenesis. We hypothesized that ETBF would promote distinct patterns of colonic damage and inflammation in mice expressing different oncogenic mutations.<br><br>METHODS: Mice expressing mutations in the Apc tumor suppressor gene or the BRAF or Kras oncogenes were colonized with ETBF to induce acute colitis. Seven days after colonization, tissues and stools were collected to assess for colonization, epithelial damage, and local and systemic immune responses.<br><br>RESULTS: Despite uniform colonization of ETBF across all genotypes and some common features of colitis across groups, Apc, BRAF, and Kras mutations were associated with distinct patterns of colonic epithelial cell injury and goblet cell loss in response to ETBF. RNA sequencing analysis revealed varied transcriptional profiles based on mouse genotype and colon region. Flow cytometry of intra-epithelial leukocytes revealed differential recruitment of myeloid cells based on oncogenic mutation. In particular, mutant BRAF expression was uniquely associated with more systemic inflammation, resistance to goblet cell loss, an interferon-gamma gene signature, and recruitment of a macrophage-like polymorphonuclear myeloid-derived suppressor cell (PMN-MDSC) population in the midproximal colon.<br><br>CONCLUSIONS: ETBF promotes acute colitis in mice expressing different oncogenic mutations, but with distinct patterns of colonic epithelial cell damage and inflammation dependent on host oncogene context.}, }
@article {pmid42089668, year = {2026}, author = {Lee, JH and Jung, GS and Kim, K and Park, H and Park, Y and Lee, I and Lee, MJ and Lee, J-H and Choi, YS and Cho, S}, title = {Microbiome in women with endometriosis and the in vitro effects of Lactobacillus reuteri on human endometrium.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0368925}, doi = {10.1128/spectrum.03689-25}, pmid = {42089668}, issn = {2165-0497}, abstract = {UNLABELLED: Endometriosis (EMS) is a chronic inflammatory disorder affecting ~10% of reproductive-age women, with increasing evidence implicating the microbiome in its pathogenesis through immunomodulation and estrogen metabolism. This study investigated microbiome composition in the vagina, endometrium, and peritoneal fluid (PF) of women with and without EMS and further assessed the effects of Lactobacillus reuteri (L. reuteri) on endometrial (EM) cells in vitro. Samples from 41 patients were analyzed using 16S rRNA gene sequencing, targeting the V3-V4 regions. Western blotting, ELISA, and LC-MS/MS were employed to evaluate protein expression and estrogen metabolism during EM-L. reuteri co-culture with or without estradiol-17-glucuronide (E2G). Microbiome analysis revealed no significant differences in alpha or beta diversity between EMS and controls across all compartments. However, LEfSe analysis identified several taxa with differential abundance, with L. reuteri consistently altered in both vagina and EM. Across the menstrual cycle, EM and vaginal microbiomes were stable, whereas PF microbiota showed phase-dependent variation involving 60 genera and 76 species. In vitro, L. reuteri alone did not alter endometriosis-related proteins, but in the presence of E2G, it reduced BAX/Bcl-2 ratios and increased p-NF-κB, suggesting anti-apoptotic and pro-inflammatory shifts. Progesterone receptor α/β expression decreased, while estrogen receptor levels remained unchanged. L. reuteri increased β-glucuronidase activity but did not enhance E2G-to-estradiol conversion. These findings highlight L. reuteri as a potentially important species in EMS, with in vitro evidence suggesting survival-promoting effects under estrogenic conditions. Further research should explore multi-species interactions and hormonal contexts to clarify microbial contributions to EMS pathogenesis.<br><br>IMPORTANCE: Although Lactobacillus reuteri appeared more abundant in the vagina and endometrium of controls, suggesting a protective role, in vitro findings paradoxically indicated anti-apoptotic and pro-inflammatory effects under estrogenic conditions, underscoring the need for further investigation of multi-species microbial interactions and hormonal contexts in endometriosis pathogenesis.}, }
@article {pmid42089950, year = {2026}, author = {Robinson, JM and Robinson, K and Barrable, A}, title = {Viewing ourselves as nature: Holobiont literacy influences nature connectedness.}, journal = {Ambio}, volume = {}, number = {}, pages = {}, pmid = {42089950}, issn = {1654-7209}, abstract = {The human holobiont concept-humans as symbiotic assemblages of a host and trillions of microbes-offers a compelling lens for understanding human-nature relationships. This study examined whether: (a) prior holobiont knowledge correlates with nature connectedness, (b) exposure to holobiont information influences nature connectedness and (c) people feel more or less connected to microbes than to other natural entities. Using a randomised, blinded online survey (n = 190), participants were assigned to a holobiont treatment group (n = 91) receiving multimedia information or a control group (n = 99) receiving neutral content. Nature connectedness was measured before and after exposure. Results showed that prior holobiont knowledge was associated with higher nature connectedness, and, strikingly, that exposure to holobiont information significantly increased nature connectedness scores. No differences were found across nature types. These findings suggest that framing humans as holobionts may strengthen psychological connections to nature, with implications for environmental psychology, education and well-being.}, }
@article {pmid42090006, year = {2026}, author = {Ray, SS and Goyal, N and Bhattacharyya, M and Arora, S and Bahukhandi, KD and Mahapatra, DM}, title = {Assessing soil microbiome alterations in agricultural land exposed to pesticides through amplicon-based sequencing.}, journal = {Biodegradation}, volume = {37}, number = {3}, pages = {}, pmid = {42090006}, issn = {1572-9729}, support = {SEED Grant-2021//University of Petroleum and Energy Studies/ ; }, mesh = {*Soil Microbiology ; *Pesticides/toxicity ; *Microbiota/drug effects/genetics ; RNA, Ribosomal, 16S/genetics ; Agriculture ; *Soil Pollutants ; *Bacteria/genetics/classification/drug effects ; Soil/chemistry ; Biodegradation, Environmental ; Phylogeny ; India ; }, abstract = {The degradation of soil health due to intensive pesticide application has emerged as a critical global challenge, undermining ecological sustainability and agricultural productivity. In regions of high agronomic activity such as Dehradun, India, unsustainable practices including monocropping and excessive agrochemical inputs have been implicated in the decline of soil fertility and microbial diversity. This study employs 16S rRNA gene (V3-V4) amplicon-based sequencing to characterize shifts in bacterial community structure for agricultural farming and non-farming soils. Complementary physicochemical analyses revealed significant associations between soil health parameters and microbial community dynamics. Taxonomic profiling revealed distinct microbial signatures in pesticide-contaminated soils, with a notable enrichment of the phyla Proteobacteria, Acidobacteria, Firmicutes, and Actinobacteria. Dominant genera such as Bacillus sp., Chungangia sp., and Streptomyces sp. were identified, indicating their potential functional roles in biogeochemical cycling and adaptive resilience under chemical stress. Functional prediction using PICRUSt2 highlighted key microbial pathways associated with amino acid synthesis, fatty acid synthesis, degradation of aromatic compound, and other essential biochemical processes. These findings highlight the ecological significance of microbial communities in maintaining soil functionality and offer insights into the development of sustainable land management strategies in pesticide-impacted agroecosystems.}, }
@article {pmid42090015, year = {2026}, author = {Arora, PK and Ali, M and Singh, AP and Dubey, VK and Srivastava, A and Garg, SK}, title = {Exploring the oral microbiome: from traditional techniques to advanced omics and databases.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {6}, pages = {}, pmid = {42090015}, issn = {1572-9699}, mesh = {*Mouth/microbiology ; Humans ; *Microbiota ; Bacteria/genetics/classification/isolation &amp; purification ; Computational Biology/methods ; RNA, Ribosomal, 16S/genetics ; Proteomics/methods ; }, abstract = {The oral microbiome comprises analysis of microbes within the oral cavity. Omics, molecular, and bioinformatic methods have significant functions in examining the diversity, composition, and function of the oral microbiome. Molecular techniques, especially 16S and 18S rRNA sequencing, have transformed the study of the oral microbiome. Analysis by 16S rRNA gene sequences of the oral sample creates a broad portrait of the species composition of the oral microbiome and both existing and new species of bacteria. It is instrumental in detecting bacterial pathogens at specific levels, specifically those involved with dental caries, periodontal disease, and oral malignancy. Paralleling the above, analysis by 18S rRNA gene sequencing elicits information related to the composition of fungal as well as protist members within the oral microbiome that plays significant roles for oral health. It can detect oral cavity parasitic infections, which may lead to oral health conditions. Omics tools are general terms for the use of high-throughput approaches to study on a large scale a variety of biological molecules. Applying these technologies to the oral microbiome allows researchers to determine the genetic, transcriptomic, proteomic, and metabolomic profiles of microbes in the oral cavity. These tools help to obtain an overall picture of the oral microbiome, such as its composition, function, and interactions. There are several databases offering useful information on the oral microbiome. These databases store curated information regarding microbial communities in the oral cavity, which aid researchers in the exploration of oral microbiome diversity, composition, and functional characteristics. Some of the examples include Human Oral Microbiome Database (HOMD) and Oral Microbiome Database (OMD). In minireview, we have provided an overview of a variety of molecular and omics tools and databases utilized in the exploration of the oral microbiome.}, }
@article {pmid42090122, year = {2026}, author = {Mikkelsen, E and Amabebe, E and Olmos-Ortiz, A and Hamburg-Shields, E and Prewit, EB and Shynlova, O and Gibbons, DL and Mesiano, S and Taggart, MJ}, title = {The Pathophysiology of Spontaneous Preterm Birth: Emerging Mechanisms Reviewed by the Preterm Birth International Collaborative.}, journal = {Reproductive sciences (Thousand Oaks, Calif.)}, volume = {}, number = {}, pages = {}, pmid = {42090122}, issn = {1933-7205}, abstract = {Around 10% of global births are preterm (before 37 weeks of gestation), posing a significant challenge to maternal and neonatal health. Preterm infants face an increased risk of mortality and long-term health complications, impacting their survival and development across all life stages. Despite decades (~ 80 years) of research, effective methods to predict and prevent idiopathic or spontaneous preterm birth remain limited. Therefore, a deeper understanding of the pathophysiology of spontaneous preterm birth is warranted. This review explores some aspects of recent progress in unravelling the complex pathophysiology of both normal and preterm human birth. We present parturition as an inflammatory event, triggered by stressors affecting the uterine reproductive tissues (myometrium, decidua, and cervix), and involving multiple endocrine and paracrine pathways. These pathways, along with signals from fetal membrane senescence and the vaginal microbiome, contribute to labor induction. Proposed perspectives in parturition research include using mathematical modeling and machine learning (artificial intelligence) to map pregnancy trajectories and identify patient phenotypes associated with preterm birth risk. Additionally, incorporating preterm birth history into routine life course medical surveillance for affected individuals and their offspring is recommended. Finally, increased investment and prioritization from national funding bodies, along with greater support for international collaborations, are essential to identify the causes of preterm birth across multiple populations and develop new, effective treatments.}, }
@article {pmid42090226, year = {2026}, author = {Constable, S and Minazadeh, Y and Buchanan, LB and Ssemunywa, H and Galiwango, RM and Kaul, R and Prodger, JL}, title = {Anaerobe-Driven Inflammation and Epithelial Barrier Disruption in Genital HIV Acquisition.}, journal = {American journal of reproductive immunology (New York, N.Y. : 1989)}, volume = {95}, number = {5}, pages = {e70251}, doi = {10.1111/aji.70251}, pmid = {42090226}, issn = {1600-0897}, support = {//Canada Institutes of Health Research/ ; //Ontario Graduate Scholarship/ ; //Engineering Health Equity Fellowship/ ; //Frugal Biomedical Innovations Program at Western University/ ; CRC-2020-00175//Canada Research Chairs Program/ ; //Canada Graduate Scholarship (SC)/ ; }, mesh = {Humans ; *HIV Infections/immunology/microbiology/transmission ; Female ; Male ; *Vagina/microbiology/immunology ; *Bacteria, Anaerobic/immunology ; *Penis/microbiology/immunology ; *Inflammation/immunology/microbiology ; Microbiota/immunology ; *Urethra/microbiology/immunology ; *Dysbiosis/immunology ; *Mucous Membrane/microbiology/immunology ; }, abstract = {BACKGROUND: Genital microbiome dysbiosis is an important risk factor for the sexual acquisition of human immunodeficiency virus (HIV) in both the male and female genital tracts. The vaginal, penile and urethral mucosae are distinct microenvironments with characteristic microbiome compositions. However, all three sites can be colonised by a group of strictly anaerobic bacteria that are strongly associated with mucosal inflammation and HIV risk. Our understanding of the relationship between genital anaerobes and HIV acquisition has largely focused on mucosal target cell density and activation. Yet, genital anaerobes disrupt epithelial barrier integrity, a crucial component of mucosal defence.<br><br>OBJECTIVE: To comprehensively evaluate the influence of genital anaerobes on epithelial barrier integrity in the context of HIV acquisition, across the penile, vaginal, and urethral mucosae.<br><br>RESULTS: Within the vaginal microbiome, anaerobes have been studied extensively in the context of bacterial vaginosis and several mechanisms of mucosal barrier disruption, including mucus degradation, epithelial cell damage and junction protein cleavage, have been identified and linked to HIV risk. The effects of these same bacteria are less defined in the context of the penile and urethral epithelia, despite their prevalence and association with HIV acquisition.<br><br>CONCLUSIONS: Further investigation of genital anaerobe-mediated barrier disruption in both sexes is needed to elucidate shared and site-specific mechanisms influencing HIV transmission. This knowledge is essential to understanding HIV risk and developing effective prevention strategies.}, }
@article {pmid42090264, year = {2026}, author = {Dubinkina, V and Smith, BJ and Zhao, C and Pino, C and Pollard, KS}, title = {Linkage of nucleotide and functional diversity varies across gut bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {19}, pages = {e2521012123}, doi = {10.1073/pnas.2521012123}, pmid = {42090264}, issn = {1091-6490}, support = {R01HL160862//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; //San Simeon fund/ ; //Chan Zuckerberg Biohub/ ; predoctoral fellowship//NSF (NSF)/ ; PHY-2309135//NSF (NSF)/ ; 2919.02//Gordon and Betty Moore Foundation (GBMF)/ ; }, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; Polymorphism, Single Nucleotide ; *Bacteria/genetics/classification ; Genome, Bacterial ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Linkage ; Genetic Variation ; }, abstract = {Understanding the forces shaping genomic diversity within bacterial species is essential for interpreting microbiome evolution, ecology, and host associations. Here, we analyze over one hundred prevalent gut bacterial species using the Unified Human Gut Genome collection to characterize patterns of intraspecific genomic variability. Gene content divergence scales predictably with divergence in core genome single nucleotide polymorphisms (SNPs), though there is substantial variability in evolutionary dynamics across species. Overall, accessory genes exhibit consistently faster linkage decay compared to core SNPs, highlighting the fluidity of functional repertoires within species boundaries. This signal is strongest for mobile genetic elements, which show minimal linkage to core genome SNPs. Together, our findings reveal species-specific recombination regimes in the gut microbiome, underscoring the importance of accounting for horizontal gene transfer and genome plasticity in microbiome-wide association studies and evolutionary models.}, }
@article {pmid42090359, year = {2026}, author = {Cui, S and Zhou, L and Zhu, N and Hu, K and Wang, F and Huang, X and Kong, F and Jin, D and Xiao, H and Liu, Y}, title = {Grass-Livestock-Fruit System Enhances Grape Health and Productivity by Regulating Leaf and Fruit Microbiota.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c17775}, pmid = {42090359}, issn = {1520-5118}, abstract = {The crop-livestock system is a sustainable agricultural model. Plant microbiomes play essential roles in host fitness and functionality. Here, the responses and functional roles of microorganisms in leaves and fruits were systematically investigated. Endophytic communities remained stable and predominantly beneficial, while epiphytic microorganisms responded more strongly to grass planting and sheep grazing. Grass planting increased the alpha diversity of epiphytic bacteria on leaves, while grazing enhanced the alpha diversity of epiphytic fungi, though both treatments reduced epiphytic bacterial richness on fruits. Grazing enriched potentially beneficial taxa, suppressed potential pathogens, and enhanced the bacterial metabolic potential and symbiotic fungal guilds. Correlations between microbial community variation and grape growth, health, and yield were stronger in leaves than in fruits, more pronounced for epiphytic than endophytic, and greater for bacteria than for fungi. Management simplified fruit and endophytic networks while increasing leaf epiphytic complexity. These findings reveal that microbiome-mediated mechanisms underpin the ecological benefits of integrated management.}, }
@article {pmid42090363, year = {2026}, author = {Satterthwaite, EV and Ruiz, TD and Patin, NV and Alksne, MN and Thomas, L and Dinasquet, J and Lampe, RH and Chan, KG and Patrick, NA and Allen, AE and Baumann-Pickering, S and Semmens, BX}, title = {Microbial and small zooplankton communities predict density of baleen whales in the southern California Current Ecosystem.}, journal = {PloS one}, volume = {21}, number = {5}, pages = {e0334209}, doi = {10.1371/journal.pone.0334209}, pmid = {42090363}, issn = {1932-6203}, mesh = {Animals ; California ; *Ecosystem ; *Zooplankton/genetics ; *Balaenoptera/microbiology ; RNA, Ribosomal, 16S/genetics ; Population Density ; *Whales/microbiology ; *Microbiota ; Population Dynamics ; }, abstract = {Understanding the distribution and abundance of marine mammals is important for assessing population dynamics and evaluating the impacts of human activities on these species. Here, we assessed the capability of microbial and small plankton communities to predict the density of Balaenopteridae whales in the Southern California Current Ecosystem in each season from 2014 to 2020 using data from the California Cooperative Oceanic Fisheries Investigations (CalCOFI). Densities of Balaenopteridae whales were estimated from visual line transect surveys for three target species - blue (Balaenoptera musculus), fin (Balaenoptera physalus), and humpback (Megaptera novaeangliae) whales - and microbial and small plankton communities were examined in concurrent water samples via metabarcoding of the 16S and 18S rRNA genes. Planktonic communities specific to each target whale species appeared as strong statistical predictors of whale estimated density, explaining 81-99% of variability and predicting density estimates to within ~1 individual per 1000 km2. Our approach improved out-of-sample root mean square prediction error by up to 65% compared with simple alternative methods. Specific planktonic communities observed indicate that some predictor taxa may be ecologically associated with whales as parasites, as skin and respiratory microbiome species, or through the food chain of whale prey. However, further studies are needed to understand how these organisms function collectively as a community and interact with the "ecological habitat" that supports whales. Our results suggest that using planktonic communities to quantify the potential ecological habitat of larger organisms, like baleen whales, can enhance predictive models and may inform hypotheses about the ecological relationships between whales and the biological communities with which they co-occur.}, }
@article {pmid42090386, year = {2026}, author = {Pelland, ZJ and Zafar, A and Ay, AA and Belanger, KD}, title = {Non-concussive head impacts sustained during American football correlate with changes in gut microbiome diversity and composition.}, journal = {PloS one}, volume = {21}, number = {5}, pages = {e0345651}, doi = {10.1371/journal.pone.0345651}, pmid = {42090386}, issn = {1932-6203}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Football/injuries ; Male ; Young Adult ; *Brain Concussion/microbiology ; Athletes ; Adult ; }, abstract = {Non-concussive head impacts (NHIs) are a significant health concern among at-risk groups, including athletes and military personnel. NHIs are hits to the head or head acceleration events (HAEs) that do not generate clinically detectable symptoms and are unlikely to meet diagnostic criteria for mild traumatic brain injury (mTBI). The composition of the gut microbiota influences many aspects of health and wellness and can be altered by TBIs and by brain-related diseases and disorders; however, microbiome alterations have not previously been linked to NHIs. We investigated whether NHIs in a cohort of American football players correlate with acute and long-term changes in the gut microbiome. This study monitored head impact exposure, gut microbiome composition, and a breadth of clinical and behavioral factors in a cohort of collegiate American football players across a competition season. Both short- and long-term changes in the microbiome were analyzed for correlation with head impact events and mathematical modeling was used to examine the contribution of NHIs and other clinical factors to these changes. We observe that NHI exposure correlates with changes in microbial diversity and composition three days following a head impact event. Furthermore, the athletes' gut microbiomes change significantly across the season, with evidence from mixed-effects modeling indicating that the cumulative effects of NHIs contribute to this change. Our results provide strong evidence for a link between NHIs and changes in the diversity and composition of the gut microbiome. The outcomes of this study emphasize the importance of careful monitoring of head impacts, including those that do not generate clinical symptoms.}, }
@article {pmid42090556, year = {2026}, author = {}, title = {Correction to: Exploring the role of normalization and feature selection in microbiome disease classification pipelines.}, journal = {GigaScience}, volume = {15}, number = {}, pages = {}, doi = {10.1093/gigascience/giag050}, pmid = {42090556}, issn = {2047-217X}, }
@article {pmid41857155, year = {2026}, author = {Wang, Z and Tan, W and Zhang, P and Xiong, H and Zhu, L and Cui, J and Li, L and Guo, C and He, L and Huang, J and Wei, H and Liu, H}, title = {Potential subtype-specific alterations in gut microbiota and branched-chain amino acid metabolism in hydrogen- and methane-predominant small intestinal bacterial overgrowth.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41857155}, issn = {2045-2322}, abstract = {We aimed to investigate the clinical, microbiome, and metabolomic characteristics of hydrogen (H2)- and methane (CH4)-predominant small intestinal bacterial overgrowth (SIBO) subtypes. We retrospectively enrolled adults who underwent standardized lactulose hydrogen–methane breath testing between February 2021 and July 2025. Participants were categorized as Normal, H2–SIBO, CH4–SIBO, or mixed H2/CH4–SIBO. Clinical characteristics were compared using Kruskal–Wallis tests and chi-square tests. Multivariable logistic regression was used to identify factors independently associated with each SIBO subtype. Expiratory gas profiles (AUC, peak, and mean values) were quantified, and correlations with age and body mass index (BMI) were assessed using Spearman analysis. In a subset of participants, stool samples underwent 16S rRNA gene sequencing and untargeted metabolomic profiling, followed by integrative analyses of microbiota composition, diversity, and metabolic signatures across SIBO subtypes. Among 503 participants, higher serum albumin levels were independently associated with H2–SIBO, whereas higher fasting glucose was independently associated with CH4–SIBO. Breath-test profiling indicated that methane parameters, rather than hydrogen, better differentiated SIBO subtypes, and total (H2 + CH4) gas output was modestly correlated with age but not BMI. In the exploratory multi-omics subset, fecal microbiota composition and metabolomic signatures differed by subtype; LEfSe identified Bacteroidaceae as a CH4-SIBO signature and Alcaligenaceae/Acidaminococcaceae as H2–SIBO signatures. Differential metabolites were enriched in pathways related to branched-chain amino acid biosynthesis, lipid metabolism, and mineral absorption. H2- and CH4-predominant SIBO subtypes exhibit distinct clinical correlates and stool microbiome–metabolome profiles. Methane exhalation appears more informative for differentiating subtypes, and age is modestly associated with total expiratory gas volumes. These findings support potential subtype-specific host–microbe metabolic interactions, although the multi-omics results should be interpreted as exploratory.}, }
@article {pmid42078608, year = {2026}, author = {Ullah, T and Khan, AM and Mustafa, A and Fatima, M}, title = {Gut microbiome dysbiosis as a trigger for area postrema syndrome exacerbation in AQP4+ NMOSD with HBV co-exposure.}, journal = {Annals of medicine and surgery (2012)}, volume = {88}, number = {5}, pages = {3002-3003}, pmid = {42078608}, issn = {2049-0801}, }
@article {pmid42078675, year = {2026}, author = {Yang, X and Dong, LL and Jin, XX and Liu, XJ and Gao, M and Fang, J}, title = {Composition and Diversity Characteristics of Gut Microbiota during the Development of Telchinia issoria (Lepidoptera: Nymphalidae).}, journal = {Ecology and evolution}, volume = {16}, number = {}, pages = {e73596}, pmid = {42078675}, issn = {2045-7758}, abstract = {Ramie (Boehmeria nivea) was a traditional economic crop of high commercial value, whose cultivation was threatened by the leaf-feeding pest Telchinia issoria. This study investigated how the gut microbiota of T. issoria shifted across its larval, pupal, and adult stages using 16S rRNA amplicon sequencing. We found that Pseudomonadota and Bacillota dominated across all stages, with stage-specific enrichments of key genera: Burkholderia-Caballeronia-Paraburkholderia in early larvae, Acinetobacter and Culicoidibacter in mid-instars, Serratia in late larvae, Enterococcus in pupae, and Pseudomonas in adults. Alpha diversity exhibited a U-shaped pattern during larval development, decreasing initially before rising again, with the lowest overall diversity observed in the pupal stage. Beta diversity confirmed distinct community structures in pupae and adults. Functionally, as predicted by PICRUSt2 based on 16S rRNA gene sequencing data, carbohydrate metabolism was enriched in pupae, whereas pathways associated with amino acid, cofactor, and vitamin metabolism were significantly decreased relative to other developmental stages. Correlation analysis suggested that elevated temperature may contribute to the decreased diversity observed in this study, which warranted further verification under controlled temperature gradients. This work establishes a foundational understanding of stage-specific microbial symbiosis in T. issoria and offers insights for future research into lepidopteran gut microbial ecology and potential biocontrol applications.}, }
@article {pmid42078837, year = {2026}, author = {Pang, Y and Wang, Y and Deng, Q and Wang, X and Wang, J and Xue, W}, title = {Integrative transcriptomic and microbiome analyses reveal thermal adaptation mechanisms in green and red color morphs of Myzus persicae (Hemiptera: Aphididae).}, journal = {Frontiers in insect science}, volume = {6}, number = {}, pages = {1780864}, pmid = {42078837}, issn = {2673-8600}, abstract = {Under global warming, the frequency and severity of agricultural pest outbreaks have intensified, posing serious threats to agriculture. The green peach aphid (Myzus persicae (Hemiptera: Aphididae)), an important agricultural pest, exhibits green and red color morphs and differentiated thermal tolerance, yet the underlying molecular mechanisms remain unclear. In this study, based on transcriptome and 16S rDNA amplicon sequencing, we analyzed the gene expression patterns and microbial community dynamics of green and red morphs of M. persicae under high-temperature stresses (30 °C and 35 °C) and across different exposure durations, comparing their similarities and differences in heat-response processes. Principal component analysis of transcriptomic data indicated that temperature had a greater influence on the physiological responses of M. persicae than body color, with a more pronounced effect observed at 35 °C. Differential gene expression analysis revealed overlap in temperature-responsive genes but different response patterns between the two morphs, suggesting activation of divergent molecular response mechanisms. Genes encoding heat shock proteins, detoxification-related enzymes, ribosomal protein family and so on were significantly up-regulated under high temperature, with a more pronounced induction in the green morph, indicating morph-specific regulatory strategies in response to thermal stress. Moreover, 16S rDNA sequencing revealed that the primary symbiont Buchnera displayed different relative abundance trends in the green and red morphs, remaining relatively stable in the red morph but declining markedly in the green morph under heat stress, potentially associated with their variation in thermal tolerance. Collectively, this study elucidates the molecular responses and microbe-mediated regulatory mechanisms underlying thermal tolerance in green and red morphs of M. persicae, providing novel insights into the thermal adaptation of aphids and a theoretical basis for developing pest management strategies under global warming.}, }
@article {pmid42078866, year = {2026}, author = {Ghura, S and Jmii, H and Griffith, J and Schaeffer, AJ and Klumpp, DJ}, title = {Gut Microbiome-Driven Microglial Activation Links Dysbiosis to Pain in Interstitial Cystitis/Bladder Pain Syndrome.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-9087060/v1}, pmid = {42078866}, issn = {2693-5015}, abstract = {Background Interstitial cystitis/bladder pain syndrome (IC/BPS) is a debilitating condition of chronic pelvic pain associated with urinary frequency and comorbid anxiety and depression. Recent studies in IC/BPS patients and rodent models implicate fecal dysbiosis and increased systemic exposure to endotoxin. These changes potentially elicit innate immune responses via the activation of microglial cells in the central nervous system, key mediators of pain. Microglial ablation and inactivation have previously been associated with analgesia in preclinical studies, underscoring the role of microglia in IC/BPS pain. Here, we investigated whether IC/BPS-associated fecal microbiota differentially activate microglia and whether activation correlates with patient symptoms. Methods Microbiome-microglia interactions were assessed using three complementary in vitro culture models: BV2 cells, enriched primary microglia (~ 95% microglia), and mixed glial cultures (microglia and astrocytes). Microglial cultures were exposed to heat-killed, stool-derived microbiota, and the pro-inflammatory cytokines tumor necrosis factor-α (TNF-α), RANTES/CCL5, and interleukin-6 (IL-6) were quantified by ELISA. Cytokine levels were evaluated for patients and controls and correlated with patient-reported genitourinary pain index (GUPI) scores. Results In all culture models, microglia exhibited significantly increased proinflammatory responses to fecal microbiota of IC/BPS patients relative to controls. Mixed glial cultures, incorporating astrocyte-microglia interactions, exhibited the most robust cytokine responses. Cytokine levels positively correlated with GUPI pain scores. Conclusions Together, these findings further support a role for gut dysbiosis in IC/BPS symptoms and suggest microglial activation and glial-glial interactions as a contributing mechanism. Understanding gut-brain axis interactions in IC/BPS will thus enable development of novel microbiome-based therapies for treating IC/BPS patients.}, }
@article {pmid42079003, year = {2026}, author = {Comerford, KB}, title = {The impacts of ready-to-eat-cereals and cereal fibers on gut health, body weight, and cardiometabolic health.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1717345}, pmid = {42079003}, issn = {2296-861X}, abstract = {Ready-to-eat breakfast cereals are a major source of dietary fiber, and their intake is associated with better diet quality and reduced incidence of chronic disease. However, dietary fiber intake remains significantly lower than recommended levels, particularly in North America. This fiber gap is one of the most important issues facing public health nutrition and deserves continued attention. This extensive analysis summarizes the body of research from the last decade on whole grain/high-fiber breakfast cereals, cereal fibers, and/or selected fiber sources commonly found in, or added to, breakfast cereals (e.g., wheat bran, psyllium). The primary health outcomes of interest for this review are digestive function, gut microbial effects, satiety signaling, body weight management, cardiovascular disease and blood glucose control. The evidence indicates that the fiber amount, fiber type, processing techniques, and numerous associated nutrients and phytochemicals in ready-to-eat breakfast cereals are all critical factors impacting health outcomes. Therefore, in addition to dietary guidance on total daily intake levels, guidance targeting specific health outcomes should also emphasize the unique mechanisms of action (e.g., gel-forming, digestion slowing, fecal-bulking, laxative, toxin binding, prebiotic) for the predominant types of fibers in ready-to-eat cereals and other fiber-rich foods. In particular, a growing body of research indicates that wheat bran, the predominant source of fiber in the U.S. and Canada, contains a novel array of fibers and phytonutrients that support bowel function and influence gut microbiota composition, and may help lower the risk for cardiometabolic disease. Notably, the research shows that individuals with low-cereal fiber consumption are most likely to benefit from an increase in their daily intake. While there is still much to discover regarding the mechanistic effects of different types of cereal fibers, continued encouragement to increase daily consumption of wheat fiber-rich foods, including ready-to-eat cereals, could help to close the fiber gap and reduce the incidence of multiple diet-related chronic diseases.}, }
@article {pmid42079098, year = {2026}, author = {Wucher, BR and Pardo-De la Hoz, CJ and Stamper, I and Sharma, S and Kaune, D and Bendale, P and Peled, J and Xavier, JB}, title = {Metabiosis underlies a microbiota permissive to Pseudomonadota and increases the risk of gut-borne bloodstream infection.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.20.716137}, pmid = {42079098}, issn = {2692-8205}, abstract = {The gut microbiota contains trillions of bacteria essential to health, but also harbors potential pathogens. The phylum Pseudomonadota, which includes Escherichia coli , Klebsiella pneumoniae , and Pseudomonas aeruginosa , typically composes <1% of the microbiota but causes disproportionate numbers of gut-borne bloodstream infections. Identifying the ecological dependencies that enable Pseudomonadota to cause gut-borne disease is important for human health. Here, we studied microbiota dynamics in patients undergoing allogeneic hematopoietic cell transplantation (allo-HCT) to find that microbiota compositions permissive to Pseudomonadota had, following antibiotic prophylaxis, high levels of Bacteroides- a major reservoir of polysaccharide utilization loci (PULs). We tested the causality of this clinical association in a mouse co-colonization model and discovered that Bacteroides fragilis promotes Pseudomonas gut colonization and survival to ciprofloxacin, a drug commonly used as prophylactic in allo-HCT. In vitro experiments revealed a general mechanism by which diverse Pseudomonadota species depend on Bacteroides polysaccharide breakdown to grow better, form more biofilm, and survive ciprofloxacin treatment under anaerobic conditions, a type of ecological dependency termed metabiosis . Guided by this insight, we used metagenomics to identify the PUL-encoded functions underlying the metabiotic potential of a patient's microbiota and establish a link to gut-derived Gram-negative bacteremia in allo-HCT. Together, our findings translate mechanistically based microbiome ecology into a clinically actionable framework for early risk stratification and intervention.}, }
@article {pmid42079116, year = {2026}, author = {Bar, O and Murthy, M and Cosgrove, K and Saidi, Y and El-Arar, W and Goldenberg, M and Sauvage, G and Bergerat, A and Cooley Demidkina, B and Laliberte, K and Xu, J and Pierson, G and Kwon, DS and Niles, J and Yassour, M and Mitchell, CM}, title = {An Observational Study of the Impact of Systemic B-cell Depletion on Cervicovaginal Mucosal Environment.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.16.718227}, pmid = {42079116}, issn = {2692-8205}, abstract = {IMPORTANCE: Emerging data show that B-cell depleting chemotherapies, which are increasingly used to treat autoimmune disorders and multiple sclerosis, can be associated with mucosal side effects such as inflammatory vaginitis.<br><br>OBJECTIVE: Evaluate the impact of rituximab treatment on vaginal mucosal immune markers, endocervical immune cell populations and vaginal microbiome.<br><br>DESIGN: Cross-sectional observational study conducted between 2022 - 2024.<br><br>SETTING: Academic medical center, Boston Massachusetts.<br><br>PARTICIPANTS: We enrolled women aged >18 years who were either 1) receiving rituximab for autoimmune renal disease or were 2) healthy controls.<br><br>EXPOSURE: Treatment with rituximab, an anti CD20 monoclonal antibody.<br><br>MAIN OUTCOME AND MEASURE: We compared endocervical immune cell populations, vaginal fluid immune markers, vaginal fluid immunoglobulins and vaginal microbiome composition between individuals being treated with rituximab and healthy controls.<br><br>RESULTS: We enrolled 26 women treated with rituximab for autoimmune renal disease and 26 healthy controls. Median circulating and endocervical B-cell and plasma cell proportions were significantly lower in treated participants compared to controls. Median vaginal fluid IgA concentrations were significantly lower in participants treated with rituximab, while ILE, IgM, IgG1, IgG2, IgG3 and IgG4 were not different between groups. Total T cell frequencies were similar between groups, but the proportion of activated T cells (CD4+CD38+HLADR+) was significantly lower in people treated with rituximab. Concentrations of IL10, IL13, IL17, IL21, IL23, IL4, ITAC and TNFa were elevated in vaginal fluid from the rituximab group, while IL-8 was lower. A CST-IV-C, low- Lactobacillus pattern of vaginal microbiota was more common in the rituximab group.<br><br>CONCLUSIONS AND RELEVANCE: Systemic B-cell depletion is associated with reduced vaginal fluid IgA, a more diverse microbiome composition, and increases in many vaginal fluid immune markers compared to healthy controls. The reduction in vaginal fluid IgA may provide opportunities for vaginal bacteria to induce inflammation.<br><br>KEY POINTS: Question: How does circulating B-cell depletion impact the vaginal microenvironment?Findings: In this cross-sectional study of 52 women, B cell and plasma cell proportions were significantly lower in both blood and vaginal mucosa among rituximab-treated participants compared to healthy controls. Vaginal IgA concentrations, but not other immunoglobulins, were significantly lower in rituximab treated participants. In treated participants, vaginal cytokine concentrations were elevated, and microbiome composition shifted toward non- Lactobacillus -dominant communities. In six people with inflammatory vaginitis, both circulating and endocervical B cells were lowest in people with the most severe symptoms. Meaning: Systemic B cell depletion is associated with alterations in vaginal mucosal immune markers and microbiome composition which increase local inflammation.}, }
@article {pmid42079144, year = {2026}, author = {Nkera-Gutabara, C and Olubayo, LAI and Oduaran, OO and Kisiangani, I and Khoza, S and Gama, K and Maritze, M and Mabunda, C and Keya, D and Adetunji, KE and Tollman, S and Micklesfield, LK and Mohamed, SF and Gómez-Olivé, FX and Tluway, F and Ramsay, M and Bhatt, AS and Hazelhurst, S and Maghini, DG and , }, title = {Participant engagement and feedback in microbiome projects: a case of AWI-Gen 2.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.20.718838}, pmid = {42079144}, issn = {2692-8205}, abstract = {UNLABELLED: Returning individualized microbiome results in ways that are ethical, comprehensible, and useful remains under-explored in African settings. We nested a multi-site, mixed-methods study within the AWI-Gen Wave 2 gut microbiome sub-study of 1,801 women aged 42 - 86 years to engage the participants and provide feedback. All (1,001) participants from Agincourt and Soweto (South Africa) and Nairobi (Kenya) were invited to feedback meetings: 496 from Agincourt, 87 from Soweto, and 195 from Nairobi responded. Engagement strategies were tailored by site (small-group and home-based sessions, visual metaphors, Foldscopes, and local-language delivery). Using semi-structured discussions and structured observations analysed thematically in MAXQDA under COREQ, five cross-cutting themes emerged: (1) understanding of microbiome reports, (2) emotional responses to feedback, (3) perceived health relevance, (4) trust in research institutions, and (5) suggestions for improving engagement. Culturally grounded explanations and local-language facilitation enhanced comprehension and perceived relevance; English-heavy sessions were associated with more confusion. Most participants expressed satisfaction and described planned or enacted dietary and lifestyle changes, while frustration centred on long delays between sampling and feedback. Trust increased with transparency and individualized return of results but was often conditional on minimizing burdensome procedures such as repeat blood sampling (phlebotomy) and ensuring timely feedback. Engagement was feasible and low-cost (approximately USD 29-59 per participant) with site-specific resource needs. Limitations included constrained generalizability beyond the three study sites. Returning individualized microbiome findings in community settings in Africa is acceptable, feasible, and can motivate health-promoting behaviours when delivered promptly and in culturally and linguistically appropriate ways.<br><br>IMPORTANCE: Microbiome studies rarely return individualized results in low-resource settings due to concerns about appropriate feedback and associated costs. This gap risks eroding trust and diminishing research impact. In three African communities, tailored feedback on gut microbiome profiles was provided to 778 women. By documenting a costed, multi-site engagement model and the themes influencing acceptance and actionability, this work offers a practical framework for ethically returning complex -omics results at scale in underrepresented populations - advancing scientific equity and strengthening community trust in microbiome research.}, }
@article {pmid42079178, year = {2026}, author = {Zhang, S and Buttimer, C and Trepka, KR and Lam, KN and Hernandez, LAR and Soto-Perez, P and Noecker, C and Canigiula, P and Ortega, EF and Lee, J and Ramirez, L and Partipilo, G and Lawrence, HB and Bottacini, F and Draper, LA and Ross, RP and Coffey, A and Shkoporov, A and Hill, C and Turnbaugh, PJ}, title = {Eggerthella lenta evades bacteriophage through reversible megabase-scale inversions of capsular polysaccharide gene clusters.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.24.720693}, pmid = {42079178}, issn = {2692-8205}, abstract = {Bacteriophages are a promising tool for microbiome editing, yet their development has been constrained by limited insights into bacteriophage-host interactions within their shared mammalian body habitat. We isolated a lytic phage ΦKL11 that efficiently targets a disease-associated member of the human gut microbiota, Eggerthella lenta , during in vitro growth. However, ΦKL11 selects for a pre-existing and reversible bacteriophage-resistant sub-population in mice. Long-read sequencing revealed a massive genomic inversion event, representing >50% of the E. lenta genome, enriched in response to bacteriophage infection. Transcriptomics linked this inversion to the altered expression of three capsular polysaccharide synthesis (CPS) gene clusters and transmission electron microscopy confirmed differential capsule production. Finally, we show that ΦKL11 has a broad host range attributable to CPS and other strain-variable genes. These findings suggest a previously unrecognized strategy for phage evasion in the gut, involving megabase-scale genomic inversions and reversible capsule variation driving phage resistance.}, }
@article {pmid42079212, year = {2026}, author = {Mills, T and Vinzelj, JM and Cook, ER and Mills, E and Rurik, AJ and Dallas, JW and Walker, DM and Stone, PA and Siler, CD and Elshahed, MS and Youssef, NH}, title = {Exploring the diversity and community structure of the Testudines fecal mycobiome.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.22.720109}, pmid = {42079212}, issn = {2692-8205}, abstract = {UNLABELLED: Most gut microbiome studies have focused on bacteria, leaving a knowledge gap regarding gut associated fungi. We assessed fungal diversity in the gastrointestinal tract of the reptilian order Testudines (turtles and tortoises) using samples from 6 families, 19 genera, and 27 species. A highly diverse community affiliated with 17 phyla and 157 orders was encountered, with four phyla (Neocallimastigomycota, Chytridiomycota, Ascomycota, and Basidiomycota) representing 89.13% of the community. Neocallimastigomycota was identified in host families Testudinidae (land tortoises), Chelidae , Chelydridae , Emydidae , Geoemydidae , and Kinosternidae , with higher relative abundances in Testudinidae (40.18±37.97%) compared to all other families combined (2.71±4.04%). Neocallimastigomycota sequences were mostly affiliated with orders Testudinimycetales in the host family Testudinidae and Neocallimastigales in other host families. Chytridiomycota was identified in all host families, but was more ubiquitous and abundant in Kinosternidiae (45.17±34.12%), and exhibited a high level of variability across samples. Dikarya communities were highly diverse, with 108 orders identified, and, similar to Chytridiomoycota, exhibited a highly stochastic distribution pattern. Representatives of multiple yet-uncultured phyla (Candidatus "Algovoracomycota", "Sedimentomastigomycota", "Tartumycota" and "Cantoromastigomycota") were identified, as well as eight novel orders in Chytridiomycota and Rozellomycota. Deterministic selection shaped community assembly in the host family Testudinidae , while the process was more stochastic in other host families. Distinct community structure was driven by differences in abundance and identity of the Neocallimastigomycota when comparing Testudinidae to. Our results describe a diverse and dynamic fungal community, shaped by the co-occurrence of autochthonous (resident) and transient (allochthonous) members of the gut microbiome.<br><br>IMPORTANCE: Fungi are known to inhabit the gastrointestinal tract (GIT) of humans and mammals. However, information on the fungal community in the GIT of reptiles is relatively sparse. We investigated the diversity and community structure of fungi in the reptilian order Testudines. We conducted a culture-independent diversity survey on fecal samples obtained from 27 different host species. We identify representatives of 17 fungal phyla. As well, we demonstrate that the anaerobic gut fungi (phylum Neocallimastigomycota) are not restricted to the family Testudinidae (land tortoises) as previously suggested, but could successfully colonize and inhabit all other testudines families, including those exhibiting a predominantly omnivorous or carnivorous lifestyles. In addition, we expand on the known fungal diversity by identifying additional representatives of multiple recently described yet-uncultured phyla, and describe multiple novel orders and classes within existing phyla. Collectively, this effort adds to the growing body of knowledge of mycobiomes in underexplored animal hosts.}, }
@article {pmid42079297, year = {2026}, author = {Cornman-Homonoff, J and Rajendran, KM and Kolandaivelu, S and Coon, SD and Kupec, JT and Wang, L and Hu, G and Jala, VR and Sandle, GI and Rajendran, VM}, title = {Dietary Sodium Restriction Reprograms Gut Microbial Fermentation and Reduces Host Energy Harvest.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.20.719706}, pmid = {42079297}, issn = {2692-8205}, abstract = {Diet is a major determinant of gut microbiome structure and function, yet the role of dietary electrolytes-particularly sodium-remains poorly defined. Here, we identify dietary sodium availability as a key regulator of gut microbial fermentation and host energy harvest. Using a controlled sodium-sufficient versus sodium-deprived dietary intervention in rats, we integrated shotgun metagenomic sequencing, functional pathway analysis, targeted short-chain fatty acid (SCFA) quantification, and host physiological phenotyping. Sodium deprivation induced a coordinated restructuring of the gut microbiome, characterized by depletion of classical saccharolytic Firmicutes, including multiple Lactobacillus species, and enrichment of stress-tolerant, metabolically flexible taxa. Functional profiling revealed a shift away from growth-associated metabolic programs toward stress-adaptive and nutrient-scavenging pathways. Consistent with these changes, fecal concentrations of key SCFAs-including acetate, butyrate, hexanoate, and valerate-were significantly reduced, indicating impaired microbial fermentative capacity. These microbiome-level alterations translated into measurable host phenotypes, including reduced cecal mass and attenuated weight gain, consistent with decreased microbial energy harvest. Together, these findings establish a functional link between luminal sodium availability, microbial metabolic efficiency, and host energy balance, extending the framework of diet-microbiome interactions beyond macronutrients to include dietary electrolytes. This work identifies sodium as a previously underappreciated ecological constraint shaping gut microbial metabolism and suggests that modulation of dietary sodium intake may influence host metabolic outcomes through microbiome-mediated mechanisms.}, }
@article {pmid42079325, year = {2026}, author = {Akif, A and Munami, JW and Das, R and Shawon, NJ}, title = {Dietary Polyphenols in Non-Communicable Chronic Diseases: Neuro-Enteric Mechanisms, Multi-Omics Biomarkers and Translational Opportunities.}, journal = {Food science &amp; nutrition}, volume = {14}, number = {}, pages = {e71856}, pmid = {42079325}, issn = {2048-7177}, abstract = {Polyphenols from plant foods (tea, cocoa, berries, grapes, and extra-virgin olive oil) modulate oxidative stress, inflammation, vascular function, and the gut microbiome-axes central to non-communicable chronic diseases (NCCDs) that involve the brain and enteric nervous system (ENS). Recent randomized trials and longitudinal studies report modest but reproducible benefits on cognitive domains and vascular/endothelial function with berry/grape extracts, matcha/green tea, and high-polyphenol extra-virgin olive oil; effects appear stronger in older adults or those with metabolic risk. Complementary evidence in irritable bowel syndrome (IBS)-a prototypical gut-brain disorder-suggests polyphenol-based combinations (often with probiotics/fiber) can improve quality of life and inflammatory markers, supporting enteric-central crosstalk. Emerging genetics (Mendelian randomization) and multi-omics readouts strengthen causal inferences for tea polyphenols in neurodegeneration-adjacent outcomes and outline mechanistic mediators (endothelial/BBB function, cytokine tone, microbiome-derived metabolites). Key gaps remain: heterogeneous formulations/doses, limited head-to-head trials, sparse target engagement biomarkers, and uncertain durability after discontinuation. We synthesize clinical and mechanistic advances, propose a standardized biomarker set (neurocognitive, endothelial, immune, and microbiome-metabolome), and outline designs for mechanism-anchored RCTs that integrate ENS endpoints with brain outcomes to translate associative signals into precision nutrition strategies for NCCDs.}, }
@article {pmid42079427, year = {2026}, author = {Xolalpa-Aroche, A and Contreras-Peruyero, H and Delgado-Suárez, EJ and Hernández-Mena, DI and Moguel-Chin, WI and Rivero-Cruz, JF and Velarde, RA and Ortiz-Vázquez, E and Rivero-Cruz, BE and Lovaco-Flores, JA and Rodríguez Orduña, L and Licona-Cassani, C and Barona-Gómez, F and Sélem-Mojica, N}, title = {Genome-resolved metagenomics reveals a phylogenetically cohesive Acetilactobacillus-like species complex dominating stingless bee pot honey.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag063}, pmid = {42079427}, issn = {2730-6151}, abstract = {Pot honey, the honey produced by stingless bees, is valued for its antimicrobial capacity, which may be influenced by its microbial content. While Lactobacillaceae species are commonly associated with honeybees and honey microbiomes, most studies have focused on Apis mellifera, leaving pot honey microbial diversity largely unexplored. We present the first pot honey shotgun metagenomic analysis from bee species Melipona beecheii and Scaptotrigona mexicana. We reconstructed 24 metagenome-assembled genomes (MAGs), 15 of which lacked close matches to any described species, showing [Formula: see text]81% Average Nucleotide Identity (ANI) to available reference genomes. Phylogenetic analyses resolved these MAGs into four well-defined clades (intraclade ANI [Formula: see text], interclade ANI [Formula: see text]), consistent with four novel species within the family Lactobacillaceae. GTDB-Tk classification placed MAG clades 1 and 2 closest to Nicoliella, and clades 3 and 4 closest to Acetilactobacillus. We validated the presence of these lineages in honey by sequencing three isolates that clustered within MAG clade 2. Aminoacid similarity (AAI/cAAI) indicates the presence of two genus-level lineages: one occupying a transitional genomic space near Nicoliella, and a second representing an undescribed genus. The genomic similarity of our MAGs and isolates to those from pot honey or larval food in Malaysia, Brazil, and Australia suggests these taxa are closely associated with stingless bees and may contribute to honey properties. By reducing the genomic underrepresentation of evolutionarily divergent sister clades related to Nicoliella and Acetilactobacillus, our genome-resolved analyses reveal a globally distributed, phylogenetically cohesive Lactobacillaceae species complex dominating pot honey.}, }
@article {pmid42079428, year = {2026}, author = {Griggs, RG and Mills, DA and Bokulich, NA}, title = {Spatial heterogeneity and microbial terroir: balancing dispersal limitation and cultivar as drivers of microbial diversity in viticulture.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag074}, pmid = {42079428}, issn = {2730-6151}, abstract = {The microbial communities inhabiting grapevines and wines exhibit spatiotemporal patterns linked to region, climate, and cultivar. However, the degree of spatial heterogeneity within and between vineyards and its relationship to cultivar-associated biodiversity selection has not been studied previously. We combined high-density sampling of grapevine microbiota (N = 230) with spatial modeling and satellite imagery in two experiments: (i) two monoclonal Chardonnay vineyards to examine spatial heterogeneity in a genetically homogenous population and (ii) three old-vine vineyards interplanted with mixed cultivars to investigate the relative effects of spatial distance and cultivar on the microbiota. Contrary to expectations based on monoclonal vineyards, cultivar effects were not apparent in mixed-cultivar vineyards. Instead, we demonstrate extensive spatial variation in the bacterial and fungal communities inhabiting individual grapevines and vineyards, and that community similarity is correlated with spatial distance within and between vineyards. This suggests that dispersal limitation may play an important role in shaping grapevine microbiota, as well as cumulative diversity within the vineyard ecosystem (gamma diversity), with implications for both plant health and wine quality. Spatial models may identify abnormalities in microbial communities, such as contaminant sources within vineyards, and future studies examining microbiota in agricultural settings should account for spatial variation within the study design, e.g. by sufficiently dense spatial sampling or collection of aggregate samples (e.g. grape musts) to avoid undersampling bias. Overall, this study adds to the complicated story of microbial biogeography associated with winegrowing and wine quality (microbial 'terroir'), highlighting the roles of dispersal and potential microclimate effects in agricultural settings.}, }
@article {pmid42079429, year = {2026}, author = {Christensen, R and Wang, YHD and Arnoldini, M and Cremer, J}, title = {Abundance-weighted pathway mapping demonstrates family-level structure of butyrate and propionate production across the human gut microbiome.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag075}, pmid = {42079429}, issn = {2730-6151}, abstract = {Fermentation products released by bacteria in the large intestine, such as butyrate and propionate, play central roles in host physiology and health. While the metabolic pathways producing these short-chain fatty acids (SCFAs) are well-characterized, less is known about their relative prevalence across hosts and gut conditions. Here, we introduce a genome-resolved, abundance-weighted bioinformatics framework that integrates pathway-based gene identification with extensive literature validation to systematically quantify the potential for butyrate and propionate production across bacterial species and human gut microbiomes. By comparing pathway predictions against over 700 experimentally characterized strains, we demonstrate high concordance with reported metabolic phenotypes, validating our approach beyond prior purely computational studies. Weighted by species abundance across ~18 000 metagenomic samples, we find that dominant gut taxa disproportionately drive SCFA production, with butyrate pathways enriched in Bacillota and propionate pathways in Bacteroidota. This abundance-weighted analysis reveals that pathway presence is well conserved at the family level, highlighting the ecological relevance of dominant taxa for community-level fermentation potential. Our results further show pronounced inter-individual variation and associations with age, birthing method, and inflammatory bowel disease, emphasizing how shifts in microbiota composition influence SCFA availability. By combining pathway-level resolution, abundance-weighted inference, and literature-based validation, our framework provides a robust, scalable approach to link microbial functional potential with host-relevant outcomes.}, }
@article {pmid42079430, year = {2026}, author = {Scott, WT and Nataya, ED and Belzer, C and Schaap, PJ}, title = {Metabolic modeling unveils potential probiotic roles of Flavonifractor plautii in reshaping the Western gut microbiota landscape.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag077}, pmid = {42079430}, issn = {2730-6151}, abstract = {Flavonifractor plautii, a prevalent gut commensal, uniquely combines flavonoid degradation with the capacity to produce health-promoting short-chain fatty acids (SCFAs), notably butyrate and propionate. However, its metabolic pathways, ecological roles, and health impacts remain poorly characterized. To explore its probiotic potential and ecological functions, we developed a genome-scale metabolic model, iFP655, using automated reconstruction, deep-learning-based gap-filling, thermodynamic constraints, and transcriptomics. The iFP655 model substantially improved the predictions of growth rates and SCFA profiles compared to previous models. Simulations identified acetyl-CoA pathways as the preferred route for butyrate production, whereas the energetically costly lysine pathway remained inactive despite robust gene expression. Propionate synthesis occurred primarily via the methylmalonyl-CoA pathway. Community metabolic modeling with representative species of a Western minimal gut microbiota highlighted F. plautii's contributions to enhanced SCFA production, especially butyrate, amino acid metabolism, and syntrophic interactions driven by dietary substrates. Our findings indicate that diet-driven syntrophy significantly shapes microbial community structure and function, underscoring the ecological importance of F. plautii in gut microbial interactions and highlighting its potential as a probiotic candidate to beneficially modulate gut microbiota through dietary interventions.}, }
@article {pmid42079440, year = {2026}, author = {Yang, L and Luo, R and Zhou, W and Yin, P and Feng, Y and Zhang, Y}, title = {Recent advances in noncanonical inhibition mechanisms of anti-CRISPR proteins.}, journal = {mLife}, volume = {5}, number = {2}, pages = {133-147}, pmid = {42079440}, issn = {2770-100X}, abstract = {The CRISPR-Cas system constitutes an adaptive immune mechanism in prokaryotes that defends against mobile genetic elements. Within the perpetual co-evolutionary arms race between bacteria and their viral predators, bacteriophages encode anti-CRISPR (Acr) proteins that use sophisticated molecular strategies to sabotage CRISPR-Cas function. While canonical Acr proteins rely on steric blockade of Cas effectors, recent discoveries reveal unprecedented noncanonical mechanisms spanning CRISPR immunity stages. This review synthesizes recent mechanistic advances in this field since 2023, highlighting the expansion of noncanonical inhibition mechanisms beyond type I to include types II, V, and VI, as well as novel Acr interventions targeting multiple functional stages, such as spacer acquisition, translation-coupled inhibition, complex assembly/disassembly, and R-loop DNA binding. Structural insights demonstrate how Acr proteins achieve substoichiometric inhibition via conformational hijacking, catalytic repurposing, and molecular mimicry. Forged by the intense selective pressure of the phage-host conflict, these molecular innovations represent both remarkable evolutionary adaptations and versatile precision tools. They enable spatiotemporal control of CRISPR technologies, from engineered off-switches to diagnostic reset mechanisms, while posing critical challenges for therapeutic safety and microbiome management.}, }
@article {pmid42079634, year = {2026}, author = {Li, L and Cai, F and Liu, S and Peng, P and Liang, J and Liu, Z and Xu, H and Mo, W and Qin, J and Tang, S and Ruan, H and Zhang, J and Liang, C and Liu, S and Qin, M and Qin, R and Luo, F and Xiong, G and Yang, C and Geng, Y and Zou, J and Huang, J}, title = {Worldwide research trends on the Helicobacter pylori-gut microbiome nexus: a bibliometric analysis.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1794021}, pmid = {42079634}, issn = {1664-3224}, mesh = {Humans ; *Helicobacter pylori/immunology ; *Gastrointestinal Microbiome/immunology ; *Helicobacter Infections/microbiology/immunology ; Bibliometrics ; Dysbiosis/microbiology ; *Biomedical Research/trends ; }, abstract = {INTRODUCTION: The impact of Helicobacter pylori (H. pylori) on the gastrointestinal tract ecosystem has been widely investigated beyond the stomach. Researchers have made considerable progress in understanding the relationship between H. pylori infection, gut microbiome dysbiosis, and systemic effects in recent years. This study aimed to explore the prospects and developing trends in the field of the H. pylori-gut microbiome nexus from a bibliometric perspective.<br><br>METHODS: Articles were collected from the Web of Science Core Collection, Scopus, and PubMed (2000-2025) and analyzed using bibliometrix, VOSviewer, and CiteSpace. Analysis of 1,592 publications reveals a distinct three-phase evolutionary structure in the field.<br><br>RESULTS AND DISCUSSION: Geographically led by China and the USA, the research focus has undergone a paradigm shift: evolving from an initial "infection and eradication" phase, through a transitional "dysbiosis and ecological intervention" phase, to the current "tumor-immunity axis" hotspot. Recent high-strength citation bursts for terms like "Fusobacterium nucleatum" and "immunity" underscore this transformation, indicating that academic attention has moved beyond local gastric pathogen control to understanding H. pylori's systemic role in modulating tumor microenvironments and therapeutic responses. This bibliometric analysis maps the field's rapid growth trajectory, highlighting its value for guiding future precision oncology and microecological strategies.}, }
@article {pmid42079661, year = {2026}, author = {Yu, J and Zhuang, WW and Lei, B and Shan, RY and Wang, XM and Qu, P and Hannig, M and Liu, Y}, title = {The oral-vascular axis: immune mechanisms linking periodontal dysbiosis to systemic vascular pathology.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1793621}, pmid = {42079661}, issn = {1664-3224}, mesh = {Humans ; *Dysbiosis/immunology ; *Periodontitis/immunology/microbiology ; Animals ; *Atherosclerosis/immunology ; *Mouth/immunology/microbiology ; *Cardiovascular Diseases/immunology ; }, abstract = {Periodontitis is among the most prevalent chronic inflammatory diseases worldwide and may affect vascular health beyond the oral cavity. Framed within the concept of an oral-vascular axis, this review synthesizes clinical and mechanistic evidence linking periodontal disease with atherosclerotic cardiovascular disease (ASCVD). Epidemiological studies and meta analyses consistently associate periodontitis with higher risks of coronary heart disease (CHD), stroke, and cardiovascular mortality, with modest but reproducible effect sizes that persist after adjustment for traditional risk factors. However, heterogeneous study designs and residual confounding preclude definitive causal inference. Interventional evidence is currently dominated by surrogate endpoints, and event-level cardiovascular benefit from periodontal therapy remains unproven. Mechanistically, chronic periodontal inflammation may influence endothelial function and atherogenesis through interlocking pathways that can be viewed as a spatiotemporal, dual-regulatory network of immunity and metabolism: local dysbiosis and barrier disruption increase systemic access to microbial ligands and vesicular cargo, while systemic immune activation interacts with metabolic remodeling to shape inflammatory set-points and vascular susceptibility. Microbe-derived and host-microbe co-metabolites may further modulate redox balance, inflammatory tone, and vascular homeostasis within this network. We highlight limitations of existing interventional trials, methodological challenges in microbiome- and genetics-based causal inference, and priorities for translational research. Clinically, the oral-vascular axis motivates interdisciplinary exchange and research-facing collaboration that integrates oral health assessment with immune and vascular phenotyping, while recognizing that cardiovascular benefit from periodontal interventions remains investigational and requires event-driven validation.}, }
@article {pmid42079714, year = {2026}, author = {Guima, SES and Bischain, B and Morais Gama, LC and Faria, AC and Lourenço, T and Bueno, DF and Heller, D and Passos-Bueno, MR and Setubal, JC}, title = {The oral maternal microbiome plays a role in the development of cleft lip and palate condition in children.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e21128}, pmid = {42079714}, issn = {2167-8359}, mesh = {Humans ; *Cleft Lip/microbiology ; *Cleft Palate/microbiology ; Female ; *Microbiota ; Male ; *Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Infant ; Mothers ; Adult ; Case-Control Studies ; }, abstract = {Non-syndromic cleft lip or palate (NS-CL/P) is an oral birth defect with complex aetiology. We compared the microbial diversity and composition of the oral microbiome of mothers of babies with NS-CL/P (CLP group) and mothers of babies without NS-CL/P (control group). Oral microbiome composition was determined by sequencing the V3-V4 regions of the 16S rRNA gene. CLP and control groups had overall similar microbial compositions, but significant differences were observed. The most significant microbial genus related to these differences was Cutibacterium, which was more abundant in the CLP group. Based on the literature, we hypothesize that a member of the Cutibacterium genus present in the oral microbiota may have a role in inflammation processes that could be related to NS-CL/P development. We found additional differences in terms of differential abundance when subsetting the dataset for mothers with a male child; in this case, depletion of Limosilactobacillus and an unknown taxon, in the CLP group, was a significant result. We conclude that the maternal oral microbiome likely plays a role in the development of the NS-CL/P condition.}, }
@article {pmid42079748, year = {2026}, author = {Zheng, L and Jia, T and Li, Y and Zhang, Z and Su, H and Zhang, R}, title = {The interplay between gastrointestinal dysfunction and gut microbiota dynamics in sepsis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1761536}, pmid = {42079748}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Sepsis/microbiology/physiopathology/complications/immunology ; *Dysbiosis/microbiology ; Animals ; *Gastrointestinal Diseases/microbiology ; *Gastrointestinal Tract/microbiology/physiopathology ; Intestinal Mucosa/microbiology ; Multiple Organ Failure ; }, abstract = {Sepsis frequently involves early gastrointestinal dysfunction, in which intestinal barrier breakdown and microbiota dysbiosis amplify systemic inflammation and contribute to multi-organ failure. Emerging evidence indicates that the gut is not merely a bystander in sepsis but an active driver of pathogenic cascades through epithelial injury, mucosal immune dysregulation, ischemia-reperfusion stress, and impaired motility, collectively promoting microbial translocation and immune deviation. In parallel, sepsis is associated with profound remodeling of the gut microbiome, characterized by reduced commensal diversity, expansion of pathobionts, and functional shifts in key microbial metabolites, including short-chain fatty acids, bile acids, and tryptophan-derived products, which further compromise mucosal integrity and host immune tone. This narrative review synthesizes experimental, translational, and clinical findings to elucidate the bidirectional interaction gut barrier-microbiota interplay in sepsis and to summarize mechanistic links across epithelial, immune, and metabolic signaling pathways, including gut-liver and gut-brain axes relevant to sepsis-associated organ dysfunction. dysfunctional microbial community leads to systemic immune deviation, multi-organ dysfunction and sepsis-associated encephalopathy, a common and severe neurological complication of sepsis. We also discuss emerging therapeutic strategies targeting the gut-microbiota axis-such as early enteral nutrition, prebiotics/postbiotics, defined microbial consortia, fecal microbiota transplantation, and metabolite-based supplementation-and evaluate their potential and limitations in septic populations. Finally, we highlight key challenges, including unresolved causality, inter-individual variability, context-dependent responses, and safety concerns, underscoring the need for longitudinal multi-omic profiling, host-microbiome phenotyping, and mechanism-informed interventional trials to enable precision microbiome-based approaches for sepsis.}, }
@article {pmid42079749, year = {2026}, author = {Pi, H and Lin, H and Zhou, J and Liu, H and Liang, S and Zhu, R and Li, D and Lu, X and Yang, M and Chen, H and Li, Y}, title = {Targeted next-generation sequencing analysis of pathogens and microecology in pediatric lower respiratory tract infections identifies risk factors for severe community-acquired pneumonia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1796357}, pmid = {42079749}, issn = {2235-2988}, mesh = {Humans ; *Community-Acquired Infections/microbiology/epidemiology ; Female ; Male ; Retrospective Studies ; Child, Preschool ; Risk Factors ; *High-Throughput Nucleotide Sequencing ; Child ; *Respiratory Tract Infections/microbiology/epidemiology ; Infant ; Severity of Illness Index ; *Bacteria/genetics/classification/isolation &amp; purification ; Microbiota/genetics ; *Pneumonia/microbiology ; Mycoplasma pneumoniae/genetics/isolation &amp; purification ; Haemophilus influenzae/genetics/isolation &amp; purification ; Community-Acquired Pneumonia ; }, abstract = {BACKGROUND: Traditional diagnostic methods have inherent limitations in the comprehensive assessment of the etiological spectrum and microecological characteristics of pediatric lower respiratory tract infections (LRTIs), particularly community-acquired pneumonia (CAP). Against this backdrop, the present study seeks to delineate the pathogen profile of children with LRTIs via targeted next-generation sequencing (tNGS), and further explore the associations between clinical manifestations, upper respiratory microbiome signatures and disease severity in pediatric CAP cases.<br><br>METHODS: A retrospective, single-center study was conducted on 2299 children with suspected lower respiratory tract infections. Throat swab samples from all patients underwent tNGS for pathogen detection. For 1845 CAP patients (293 SCAP, 1552 non-severe CAP [nsCAP]), clinical data and tNGS results were analyzed. Statistical comparisons, correlation analyses, and multivariate logistic regression were performed to identify factors associated with SCAP. Microbial diversity (Shannon/Simpson indices) and relative abundance of detected species were also analyzed.<br><br>RESULTS: Mycoplasma pneumoniae was the dominant atypical pathogen, with an outbreak peaking in July 2024. M. pneumoniae detection rate (35.8% vs. 8.9%, P<0.001) and relative abundance (RA) were significantly higher in SCAP than nsCAP patients and correlated positively with severity markers. Multivariate analysis identified M. pneumoniae positivity, older age, female sex, circulatory and metabolic diseases as independent risk factors for SCAP. In M. pneumoniae-negative patients, pathogens like Streptococcus pneumoniae and Haemophilus influenzae were more common in nsCAP. Upper respiratory microbial diversity was lower in SCAP patients. Increased RA of specific commensals like Schaalia odontolytica was a protective factor, while increased abundance of Stenotrophomonas maltophilia was a risk factor for SCAP. Compared to bronchoalveolar lavage fluid (BALF), throat swab tNGS showed high agreement for M. pneumoniae but higher detection of potential colonizers like H. influenzae.<br><br>CONCLUSIONS: During the study period, M. pneumoniae was a key driver of SCAP in children. Beyond single-pathogen detection, decreased upper respiratory microbial diversity and shifts in colonizing bacteria abundances were associated with pneumonia severity, offering a new ecological perspective. Throat swab tNGS is valuable for pathogen screening. The associations between upper respiratory microbial features and severity highlight a potential ecological dimension of pneumonia pathogenesis.}, }
@article {pmid42080299, year = {2026}, author = {Li, Z and Ren, M and Hu, A and Meng, F and Wang, J}, title = {Depth Stratification Shapes Viral Diversity, Interactions, and Metabolic Potential in a Deep Freshwater Lake.}, journal = {Molecular ecology}, volume = {35}, number = {9}, pages = {e70367}, doi = {10.1111/mec.70367}, pmid = {42080299}, issn = {1365-294X}, support = {U24A20578//National Natural Science Foundation of China/ ; 42507557//National Natural Science Foundation of China/ ; 42372353//National Natural Science Foundation of China/ ; BK20240111//Basic Research Program of Jiangsu Province/ ; }, mesh = {*Lakes/virology/microbiology ; *Viruses/genetics/classification ; Metagenomics ; Fresh Water/virology ; Microbiota/genetics ; Ecosystem ; Geologic Sediments/virology ; Biodiversity ; Metagenome ; }, abstract = {Deep freshwater lakes exhibit distinct microbial community stratification across depth gradients, which plays important roles in biogeochemical cycling and ecosystem stability. As crucial regulators of microbiome composition and function, viruses may play key ecological roles in these stratified systems, yet their distribution patterns and ecological significance in deep-lake surface sediments remain poorly understood. Here, we assessed viral community dynamics and functional potential across the entire water depth gradient (0-155 m) of Fuxian Lake using metagenomics from 44 surface sediment samples. A total of 11,523 viral OTUs were recovered, with only 18% annotated to the family level and approximately 93% classified as putatively lytic. Viral communities showed systematic depth-related shifts across multiple dimensions. Specifically, alpha diversity, community turnover, and stochastic assembly processes increased significantly with water depth, accompanied by enhanced lytic virus dominance and larger genome sizes. Predicted virus-host association networks transitioned from highly connected and generalized at shallow depths to increasingly sparse and specialized at greater depths. Virus-encoded auxiliary metabolic genes showed significantly increasing abundance with water depth, along with functional shifts from host defense to enhanced biosynthesis and energy metabolism, especially regarding carbon fixation and organic matter degradation. Collectively, these results highlight the importance of water depth gradients in structuring viral communities within surface sediments and expand our understanding of viral ecological functions in deep lake ecosystems.}, }
@article {pmid42080579, year = {2026}, author = {Sidi Mabrouk, A and Depelteau, JS and Foini, C and Kempff, A and Jonker, S and Brenzinger, S and Limpens, R and Majrouh, M and Meijer, AH and Briegel, A}, title = {ICP1 bacteriophage treatment antagonizes colonization of the zebrafish larval intestine by Vibrio cholerae.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0356525}, doi = {10.1128/spectrum.03565-25}, pmid = {42080579}, issn = {2165-0497}, abstract = {UNLABELLED: Outbreaks of cholera pose a major threat to human health. Currently, antibiotics are the most effective treatment against the causative agent, the bacterium Vibrio cholerae. However, the use of antibiotics eventually leads to the emergence of resistant strains, which necessitates the need for alternative approaches. The use of bacteriophages to target the infection by antibiotic-resistant bacteria is one promising alternative. While clearance of Vibrio cholerae with the use of phages has been performed on several animal models, none of these models are naturalistic hosts of V. cholerae. Therefore, we set out to investigate the interaction between V. cholerae and bacteriophage ICP1 both in vitro and in vivo in a naturalistic host, the zebrafish model, Danio rerio. To study the interplay between host, bacteria, and phages, we used a combination of light and ultrastructural imaging techniques, including confocal fluorescence microscopy, serial block face scanning electron microscopy (EM) imaging, and cryogenic EM, which allowed us to investigate both the colonization process by V. cholerae and clearance by the ICP1 bacteriophage. In addition, we determined the effects of the microbiome on this treatment by using germ-free, conventionalized, and monoassociated zebrafish larvae as a host. Independent of the presence and composition of microbiomes used here, V. cholerae efficiently colonized the larval intestine. Finally, we demonstrate significant in vivo clearance of V. cholerae N16961-dsRED by ICP1, underscoring the role of phage-bacteria dynamics in shaping pathogen colonization within the zebrafish larval host.<br><br>IMPORTANCE: Cholera remains a life-threatening disease that causes recurring outbreaks and significant mortality, particularly in developing and conflict-affected regions. As antimicrobial resistance continues to rise, there is an urgent need to better understand the ecological and microbial dynamics that govern Vibrio cholerae colonization and persistence. This research investigates how V. cholerae interacts with bacteriophages, the host environment, and the resident microbiota within a natural vertebrate host, offering new insights into the factors that influence pathogen clearance and shaping of the gut ecosystem during infection. The powerful combination of serial block-face scanning and cryogenic electron microscopy, fluorescence microscopy, and traditional colony/plaque counting methods revealed previously unobserved aspects of the interplay between host, pathogen, phages, and selected microsymbionts, highlighting phage-driven clearance of V. cholerae during colonization.}, }
@article {pmid42081026, year = {2026}, author = {Zomorodimanesh, S and Razavi, SH and Zomorodimanesh, P}, title = {Exploring the Role of Probiotics in the Prevention and Treatment of Gastrointestinal Cancer.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {42081026}, issn = {1867-1314}, abstract = {Probiotics, live microorganisms with health-promoting properties, play a vital role in modulating the gut microbiota and enhancing immune responses. Their potential for regulating key signaling pathways, including NF-κB, PI3K/AKT, and Wnt/β-Catenin, suggests promise in cancer prevention as they can mitigate inflammation, strengthen intestinal barriers, and influence cytokine production, offering multiple therapeutic benefits. This review highlights the mechanisms by which probiotics may contribute to gastrointestinal cancer prevention and treatment, discussing their capacity to regulate inflammatory cytokines, enhance epithelial integrity, and balance gut microbiota. Evidence from preclinical and a growing number of clinical studies is summarized. Additionally, challenges such as strain specificity, dose optimization, and safety evaluations are analyzed alongside potential integration into conventional cancer therapies. Current data indicate that probiotics hold potential as complementary agents in oncology, possibly capable of inhibiting tumor growth, enhancing immune surveillance, and improving the efficacy of existing treatments. Future research should prioritize robust, long-term clinical trials and molecular studies to optimize their application in cancer management.}, }
@article {pmid42081130, year = {2026}, author = {Bak, NK and Østergaard, SK and Schacksen, PS and Nielsen, JL and Rohde, PD and Kristensen, TN}, title = {Host genetics and diet jointly shape the microbiome of Drosophila melanogaster but do not predict lifespan or age-related traits.}, journal = {Biogerontology}, volume = {27}, number = {3}, pages = {}, pmid = {42081130}, issn = {1573-6768}, support = {DFF-2032-00205A//Danmarks Frie Forskningsfond/ ; }, mesh = {Animals ; *Drosophila melanogaster/microbiology/genetics/physiology ; *Longevity/genetics ; *Microbiota/genetics ; *Diet ; *Aging/genetics ; Genetic Variation ; Male ; Female ; }, abstract = {The microbiome is a key determinant of organismal health, yet inter-individual variability and heterogeneous responses to environmental conditions complicates the understanding of its effects on hosts. Here, we present a comprehensive analysis using the Drosophila Genetic Reference Panel (DGRP) to investigate how the interplay between host genetic variation and diet influences microbiome composition, and to assess whether microbiome features in young flies can be used to predict lifespan and age-related traits. Our findings show that adult flies reared on a nutritionally rich control diet exhibited higher microbial richness but lower evenness compared to those on a nutritionally poor restricted diet. Principal component analysis (PCA) highlighted substantial diversity among lines reared on the same diet, and this variation was evidenced by high heritability estimates for all measured α-diversity metrics, including Unique OTU counts, Shannon and Simpson indices, as well as the relative abundances of genera and species with relative abundances exceeding 1%. These results underscore the critical roles of both environmental factors and genetic variation in shaping microbiome composition under different dietary conditions. Moreover, we identified widespread genotype-by-diet interactions, suggesting that the genetic regulation of the microbiome is highly complex. Finally, we found that the microbiome features of young flies including diversity indices, taxonomic abundances, or ordination scores cannot predict age-associated phenotypes (lifespan, locomotor activity, dry weight, and heat knockdown time). Our findings offer valuable insights into the genetic architecture that governs microbiome composition, dietary responses, and aging in Drosophila melanogaster.}, }
@article {pmid42081188, year = {2026}, author = {Pollock, J and Liu, R and Rwenji, E and Orobi, E and Udayakumar, S and Huibner, S and Kung'u, M and Kabuti, R and Babu, H and ,  and Irungu, E and Ngurukiri, P and Muthoga, P and Adhiambo, W and Weiss, HA and Seeley, J and Abramsky, T and Kimani, J and Beattie, TS and Kaul, R}, title = {Assessing the Impact of Female Genital Mutilation/Cutting on Genital Inflammation and Microbiota Among Kenyan Female Sex Workers.}, journal = {American journal of reproductive immunology (New York, N.Y. : 1989)}, volume = {95}, number = {5}, pages = {e70250}, pmid = {42081188}, issn = {1600-0897}, support = {MR/R023182/1//Medical Research Council (MRC) and the UK Department of International Development (DFID)/ ; //EDCTP2 supported by the European Union/ ; PJT-156123//Canadian Institute of Health Research (CIHR)/ ; PJT-180629//Canadian Institute of Health Research (CIHR)/ ; }, mesh = {Humans ; Female ; Kenya/epidemiology ; *Sex Workers ; Adult ; *Microbiota/immunology ; *Circumcision, Female/adverse effects ; *HIV Infections/epidemiology/immunology ; *Inflammation/immunology ; Young Adult ; Cytokines/metabolism ; *Vagina/microbiology/immunology ; *Genitalia, Female/microbiology/immunology ; }, abstract = {PROBLEM: Female genital mutilation/cutting (FGM/C) is harmful to physical, mental, and reproductive health, though the effect of this practice on a woman's HIV susceptibility is poorly understood. Despite the known associations of FGM/C with short-term vaginal epithelial damage, neither genital inflammation nor the genital microbiome have been explored in women who have undergone FGM/C. In this study we compare the genital immune milieu and microbiome among female sex workers (FSWs) by FGM/C status, hypothesizing that these biological factors are dysregulated in women who have undergone FGM/C, heightening their risk of HIV acquisition.<br><br>METHOD OF STUDY: 1003 FSWs in Nairobi, Kenya, were enrolled in the Maisha Fiti study and visited a study clinic up to three times from June 2019 to March 2021. Participants self-reported any previous exposure to FGM/C as well as other relevant sociodemographic factors. Levels of proinflammatory cytokines and soluble E-cadherin (sE-cad), a biomarker of epithelial barrier disruption, were measured by multiplex immunoassay using self-collected cervicovaginal secretion samples provided by HIV-uninfected participants. Genital inflammation was defined using a composite score of inflammatory cytokines previously associated with HIV acquisition. The presence of inflammation was compared longitudinally between groups using mixed models to control for potential confounders including age, bacterial vaginosis (BV) status as defined by Nugent score, and others. Vaginal bacterial abundance, Shannon diversity, and total levels of key vaginal bacteria were measured by qPCR and compared by FGM/C status in an exploratory analysis.<br><br>RESULTS: 44 of 1003 (4%) participants had undergone Type I or II FGM/C. These participants were older (p < 0.001) and more likely to test positive for herpes simplex virus-2 (HSV-2; p = 0.04), and less likely to have completed primary education (p = 0.03). Among HIV-uninfected participants, there was no evidence that genital inflammation was associated with FGM/C status after controlling for potential confounders (aOR = 0.70; 95% CI: 0.31-1.59; p = 0.40). There was no evidence of a difference in BV prevalence (p > 0.99), total bacterial abundance (p = 0.96), or Shannon diversity (p = 0.15) by FGM/C status.<br><br>CONCLUSIONS: Type I or II FGM/C was not associated with genital inflammation or microbial dysregulation in the long-term among HIV-negative FSWs in this cohort. This may be due to the duration elapsed since FGM/C occurred or the lowered mucosal immune activation previously observed in FSWs.}, }
@article {pmid42081950, year = {2026}, author = {Garvey, MI and Moran, RA and Wilkinson, MAC and Sanches Ferreira, AD and Gardiner, A and Holden, E and McNally, A}, title = {What grows in the sink splash zone.}, journal = {The Journal of hospital infection}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jhin.2026.04.010}, pmid = {42081950}, issn = {1532-2939}, abstract = {BACKGROUND: The hospital sink drain microbiome can harbour opportunistic pathogens and antimicrobial resistance genes. Patients may be exposed to waterborne pathogens via water outlets and sink drains. We have previously shown water from a clinical hand wash basin can splash up to two metres away from the sink/tap. Here we wanted to identify which organisms could be cultured from environmental sampling within the splash zone.<br><br>METHODS: Queen Elizabeth Hospital Birmingham (QEHB) is a large UK tertiary centre. We placed an SAS Super 180 air sampler within the splash zone at approximately one metre distance of a tap on a clinical hand wash basin in the critical care unit and undertook sampling both with and without the tap running. All Gram-negative organisms were cultured and any carbapenemase producing Enterobacterales (CPE) isolated were sequenced.<br><br>RESULTS: Environmental sampling undertaken when the tap was running yielded a variety of organisms, with Gram-negative isolates including Citrobacter freundii, Enterobacter kobei, Enterobacter cloacae, Enterobacter asburiae, Pseudomonas aeruginosa and Sphingobacterium multivorum. Amongst these, we identified one CPE, C. freundii isolate QE-SINK-CF1, which carried a plasmid bearing the blaKPC-2 gene. Structural variants of this plasmid have been involved in clinical infections at QEHB. Control sampling without the tap running yielded no Gram-negative organisms.<br><br>CONCLUSIONS: Here we show a variety of Gram-negative microorganisms, including CPE, can be cultured from within the 2-metre sink splash zone. This latest work provides further evidence healthcare settings should consider splash zones and waterborne pathogen transmission risk.}, }
@article {pmid42082045, year = {2026}, author = {Zhang, Y and Wang, Y and Yang, Q and Yang, L and Yang, X and Zhao, X and Zhao, S}, title = {Unveiling the interactions of 8:2 fluorotelomer sulfonic acid (8:2 FTSA) with the earthworm-microbe symbiosis in soil.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {400}, number = {}, pages = {128247}, doi = {10.1016/j.envpol.2026.128247}, pmid = {42082045}, issn = {1873-6424}, abstract = {8:2 fluorotelomer sulfonic acid (8:2 FTSA), an important per- and polyfluoroalkyl substance (PFAS) found in aqueous film-forming foams (AFFFs), is frequently detected in soil. However, the interactions of 8:2 FTSA with soil-terrestrial invertebrate systems are poorly understood. This study investigated the biotransformation, toxicity, microbiome shifts, and microbial degradation of 8:2 FTSA in a soil-earthworm system through in